Biology Comprehensive Guide
Electrons can be anywhere in the electron cloud at any given point
Can only see snapshots and can only predict the possibility of where it would be
To get out of the electron cloud, it absorbs energy to go to another orbital
Carbon, nitrogen, hydrogen, and oxygen are the elements of life because…
Oxygen has a higher electronegativity
These elements are lighter than their groups
Bonds between oxygen and hydrogen are stronger because sulfur has more shielding
Essentials of H2O
Polarity (polar neutral)
Charge poles on individual elements in an atom
Cohesive/adhesive properties
Has the ability to influence other water molecules
Cohesion is where water molecules are attracted to each other due to hydrogen bonding
Adhesion is where water molecules are attracted to other molecules
Structure gives rise to function
How the molecule is shaped affects how they interact with other molecules
The bonds can flex and break but still maintain their shape
Carbon
Hydrocarbons are only made up of hydrogens and carbons
Many molecules have a backbone of this(DNA, lipids)
Lipids have hydrophobic tails and hydrophilic heads
The base is a hydrocarbon
Hydrocarbons’ orientation relates to the function that the organism will have
The bonds that atoms make limit the amount of rotation
Unsaturated fats cause bends in hydrocarbon chains
Better than saturated because straight chains will only build upon each other while the bent chains are more likely to move around and not block arteries/veins
Hydrolysis uses water to break bonds and release energy through enzymatic reactions
Dehydration is the formation of new bonds through energy input and water release
Carbohydrates(1:2:1)
Two monosaccharides bonded together are linked by glycosidic bonds(alpha carbon 1-carbon 4)
Monosaccharides(deoxyribose, ribose) - > 5 carbon sugars
Disaccharides(sugars)
Polysaccharides(starch, cellulose for peristalsis)
Uses of carbs
Energy for cell and structure support
Helps to regulate glucose consumption and removes excess cholesterol
Nucleotides
A nitrogenous base, phosphate group, sugar
Nitrogenous bases
Know how {cytosine, thymine, uracil} - pyrimidines, {adenine, and guanine} - purines look like
Pentose sugars(deoxyribose, ribose)
Deoxyribose has H at Carbon 4 and ribose has OH at Carbon 4
DNA
Right-handed helix(directionality of folding of helix)
Anti-parallel
5’ to 3’
Major groove vs. minor groove
It helps to tell the location of DNA
Major grooves have a higher distance between turns
RNA
U for T
Translation of genetic info to proteins
Multiple functions
mRNA, tRNA, rRNA
Can have intramolecular bonding(not always stranded cause they are in motion constantly)
Lipids
Fats and oils, waxes, phospholipids, steroids
Saturated fats are surrounded by hydrogen bonds and are all single bonds while unsaturated are not saturated by hydrogen bonds, causing double bonds
Can have cis and trans unsaturated fats
Cis is where the hydrogens are on the same side, and it is also called the z-formation
Trans is where hydrogen bonds are on the opposite side of the bonds
Phospholipids
Phosphate connected to glycerol and glycerol are connected to two separate fatty acid chains(one saturated and another unsaturated, causing a bend)
Form outer membranes
Micelles can be used to target drug delivery
Are introduced into hydrophilic or hydrophobic environments, causing them to open or close at the location site after they encapsulate with the drug and act as a transport mechanism(bio-encapsulation)
Steroids
Cholesterol is part of steroids and they have a ring structure that doesn’t resemble other liquids
The ring structure is important for certain types of hormones and ring transductors
Rings are interconnected and they can rotate throughout the structure(resonance)
Proteins
Amino acids are monomers for proteins
4 structural formations
An umbrella term for various biomacromolecules
Undergoes folding and denaturations(breaks down tertiary and quaternary structure)
Amino acid base structure consists of an r-group, an amino group, and a carboxyl group
R-group is specifically for carbon-based chains and R is the specific structure that interchanges with functional groups(have to specify what R is on a test)
Carboxyl group can be an acid depending on if it is protonated
Amino acid R groups
Positive charge or negative charge, polar or nonpolar, hydrophobic or hydrophilic (have to remember this for AP)
Nonpolar R groups are generally hydrocarbons, hydrogens, or carbons
Structures
The primary structure is the sequence of a chain of amino acids(A-I-G) - linearized amino acid sequence
Secondary structure is the local folding of polypeptide chains into helices or sheets
Alpha helix(DNA), beta helix, beta pleated sheets(wave, folded sheets), alpha sheets
Tertiary structure is a 3D folding pattern of a protein due to side chain interactions(intramolecular reactions)
The beta-pleated sheet can turn into a helix
Beta pleated and helix together are tertiary
Quaternary
A protein consisting of more than one amino acid chain(multiple tertiaries combine to form a full molecule)
Types of proteins that are biomacromolecules
Enzymes, hormones, toxins
Protein folding
Structure gives rise to function(e.g. Denatured proteins)
The cell is the smallest unit, all living things are made of cells and all cells come from pre-existing cells
Prokaryotes are bacteria and archaea
Plants, animals, fungi, and protists are eukaryotes
Prokaryotes have no nucleus and no membrane-bound organelles
The plasma membrane is semi-permeable, meaning that only certain substances can go in and out, regulating homeostasis
Cytoskeleton support organelles in cytoplasm
Ribosomes are not membrane-bound organelles and make protein(free or attached)
The nucleus holds genetic material and controls cell activities(nucleolus where ribosomes are produced)
ER transports molecules with vesicles and produces proteins(rough ER) while smooth ER does detoxification(reason why liver cells have a lot of smooth ER)
Golgi is the ultimate packaging center(enzymes, packaging, transporting)
Mitochondria powers all the above processes by making ATP through cellular respiration and using glucose
Animal vs plant
Plants have mitochondria and chloroplasts which make glucose through photosynthesis (chlorophyll captures light energy)
Vacuoles for both where the plant has one and the animal has several
Plants have a cell wall unlike animal cells
Eukaryotic cells
All cells have a cell membrane, cytoplasm, and DNA
Chromatin is found in the nuclear membrane and DNA turns into chromosomes
After ribosomes leave the nucleolus, they make proteins
ER transports proteins synthesized by ribosomes
Proteins emerge from ER in small vesicles (bubbles that leave the organelle membrane as bubbles of transport)
Golgi body receives them and they are customized to fold proteins into usable shapes or add lipids or carbs to them
Vacuoles store things like the central vacuole stores water
Lysosomes are garbage collectors and are filled with enzymes that are filled with cellular debris
The cytoskeleton has microfilaments made of proteins and microtubules that are thin, hollow tubes
Some autotrophic plants have chloroplasts and the cell wall covers the cell membrane
Other unique structures
Cilia, which are hair-like projections that trap particles in the air and expel them when you cough
Flagella, which is on bacteria and is like the sperm cells’ tails
Mitochondria is double membraned and has compartments for different metabolic reactions like Kreb’s cycle, electron transport chain, and ATP synthesis
Lysosomes contain a large number of hydrolytic enzymes that, when released from the lysosomes, can come into contact with cytosolic targets and contribute to apoptotic cell death
Exocytosis - the ability of something to exit the cell
Plant cells
Thylakoids are organized in stacks called grana
Stroma is fluid within the inner chloroplast membrane and outside of thylakoids
Grana is where light-dependent photosynthesis occurs
Carbon fixation reactions of photosynthesis occur in the stroma or the Benson cycle
Plasma/cell membrane
Fluid mosaic model, meaning the membrane is not a straight line and not a perfect circle
Freedom of oscillation, or the capability to move and change
Interstitial protein/carbs are bound within the membrane and are also able to move within the lipid bilayer
Typically stay within a certain environment
Trans vs. cis membrane proteins
Proteins that span both inside and outside of the plasma membrane(trans) vs. carbs that or only present on the outside of the plasma membrane
Endosymbiosis
Endo means within another and symbiosis means a mutually beneficial relationship
The cell theory says that some of the organelles of eukaryotes were once prokaryotic microbes that were phagocytized
Evidence
Some organelles have double membranes(the outer membrane may be vesicular in origin)
Antibiotics - susceptible to antibiotics (organelles may have bacterial origins
Division - reproduction occurs via a fission-like process
DNA - has its DNA which is naked and circular (like prokaryotic DNA)
Ribosomes - have ribosomes which are 70S in size (identical to prokaryotic ribosomes)
Compartmentalization
Different parts of the cell have different functions
Cells work similarly in compartmentalizing to stop random molecules from disrupting processes
Short processing/transfer times(increase surface area by folds, thus increasing production)
Specialized functions
Keep external systems out of necessary internal parts
Membrane permeability
Cell walls = boundaries and selectively permeable barriers for keeping cell material internalized
Allows for things to flow or transport in and out of the cell but only for certain things
Depends on polar vs. nonpolar, hydrophobic/hydrophilic, or if a molecule moves freely or assisted across the membrane(passive/active)
HIV tends to hide by C4 protein(undetected by the immune system and it can lay dormant for a few years or show symptoms immediately)
Passive Transport: Net movement of molecules from high concentration to low concentration without the direct input of metabolic energy
Active Transport: Requires the direct input of energy to move molecules from regions of low concentration to regions of high concentration
Types of passive transport
Diffusion
The passage only relies on the concentration gradient
Facilitated diffusion
Materials move across the membrane with the help of carrier proteins
Feedback inhibition tells when there is too much of a certain substance passing through the ion channels (passage)
Membrane proteins are required for diffusion of large, polar molecules through a membrane
Large quantities of water pass through aquaporins
Small nonpolar molecules pass through easily unlike water molecules, so aquaporins help with passage
Charged ions like sodium and potassium require channel proteins
Membranes may become polarized by movement of ions across the membrane
Types of active transport
Electrochemical gradient
Ion pumps(sodium-potassium ion pumps)
Actively push ions in or out of the cell
ATP dependant carrier proteins
Glucose transporter protein
Other transports
Endocytosis: the process of capturing a substance or particle from outside of the cell by engulfing it with the cell membrane
Exocytosis: the process of vesicles fusing with the plasma membrane and releasing their contents to the outside of the cell
Since it’s a fluid mosaic model, vesicles can just remove obstacles out of the way and go into the membrane
Tonicity/Osmosis
Osmosis is the movement of water molecules
Hypotonic: water enters and causes the cell to swell
Hypertonic: Water leaves the cell and causes it to shrivel
Isotonic: nearly perfect
Water potential
The potential of water to move across a membrane by osmosis from areas of high water potential/low osmolarity/low solute concentration to areas of low water potential/high osmolarity/high solute concentration
Psi(Ѱ) = water potential in megapascals
Ѱp = pressure potential
Ѱs = solute potential
Formula: Ѱ = Ѱp + Ѱs
Ѱs = -iCRT defines solute potential
I = ionization constant(1 for sucrose because sucrose does not ionize in water) - it is the number of ions produced/in production
C = molar concentration
R = pressure constant ( R=.0831 liter bars/mole K)
T = temperature in Kelvin (℃ + 273) - assuming standard temperature and pressure of 273.15 K unless specified
A negative sign in front of I means moving from a high water potential to a low water potential(moves from the cell into the solution)
Nucleotide
The phosphate group is negative, so DNA has a negative charge because phosphate groups are facing outward
DNA vs. RNA
The 5-sugar ring on DNA has hydrogen on the carbon 2 and RNA has a hydroxide on carbon 2(identifying factor on tests)
Naming of carbon sugars
Start from oxygen and go clockwise
Write carbon anywhere there is a bend or an end
Identifying direction
5’ phosphate and 3’ hydroxide
Counting carbon numbers
Central Dogma
DNA to RNA is transcription and RNA to protein is translation
Genetic information
DNA is the primary source and RNA is a secondary source
Plasmids - small, extrachromosomal, double-stranded circular DNA molecules(primarily in prokaryotes but can be in eukaryotes)
Sequence of RNA bases and structure of RNA molecule determines RNA function
tRNA and rRNA are structural molecules while mRNA are functional
rRNA
Functional building blocks for ribosomes
Ensures proper alignment of mRNA and ribosome
Also has enzymatic activity
Peptidoglycan transferase - catalyzes the formation of the peptide bonds between two aligned amino acids
Formation(similar to mRNA)
RNA polymerase 1(in nucleolus) is a nuclear substructure that is responsible for transcribing, processing, and assembling rRNA into ribosomes
Also has a pre-rRNA step where it is cleaved and processed before becoming mature rRNA
Different from mRNA because it gets transported to another location out of the nucleus
RNA polymerase
The enzyme responsible for copying a DNA sequence into an RNA sequence during transcription
Uses a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecule
3 stages of RNApol
Initiation - RNApol wraps around the promoter region of DNA, which is a sequence that guides RNApol on where to bind. Eukaryotes need help to bind unlike prokaryotes using transcription factors.
Elongation - unwinds double-stranded DNA into two single strands
Termination - when RNApol sees a terminator sequence, it stops adding complementary nucleotides to the RNA strand
Transcription
DNA strand acting as the template strand is also referred to as the noncoding strand/minus strand/antisense strand
The determined noncoding strand is dependent on the gene being transcribed
RNApol synthesizes mRNA molecules in the 5’ to 3’ direction by reading the template DNA strand in the 3’ to 5’ direction
Reads DNA backwards
Cell-to-cell communication is important for the function and survival of cells and organism
Responsible for the growth and development of multicellular organisms
Communicate through chemical signals
An example is the fight or flight response - epinephrine
Cell communication
Signaling cells release small volatile or soluble molecules called a ligand
Ligands get sent out to the system as a signal(like a substrate)
They bind to the receptor portion on the target cell(like an enzyme)
The final relay of the message is called a cellular response
The whole point of cell communication is to initiate a cellular response
Three ways to communicate
Direct contact
Cell going up to another cell and relaying the message
Form extracellular components like transmembrane proteins
Blocking cell communication prevents cells from knowing what to do(could target cancer cells)
Local signaling
Short-distance signaling - within the same organ system/tissue
Long-distance signaling
For example when your toe is hurt and sent to your brain
Another example is an upset stomach
Between different systems or nerves
Signaling
Autocrine
Cell targets itself
Signaling across gap junctions
Paracrine
Short-distance signaling where a cell targets a nearby cell
Endocrine
A cell targets a distant cell through the bloodstream(kind of like glucose levels)
Direct contact
Signaling substances and other material dissolved in cytoplasm can pass freely between adjacent cells
Animal cells have gap junctions while plant cells have plasmodesmata
White blood cell
On the T-cell we have antigens and when a signal is released that produces the substrate, causing an alarm to be produced, activating the immune system
Also called antigen-presenting cells
Local regulators
A secreting cell will release chemical messages(ligands) that travel a short distance through the extracellular fluid
Chemical messages will cause a response in a target cell
Nerve disorders due to uncontrolled chemical messages
Examples
Paracrine signaling
Secretory cells release local regulators via exocytosis to an adjacent cell to make sure the target cell receives ligands
Synaptic signaling
In animal nervous systems
Neurotransmitters are secreted by the axon and are uptaken by the synaptic system(target cells)
Through diffusion
The synaptic cleft is the distance neurotransmitters have to travel to get to target cells
Can be long-distance depending on the length of the neuron(for the sake of AP Bio we consider it as short-distance)
Long-distance signaling
Insulin counts cause it is only produced in one specific area: the pancreas
Animals and plants use hormones for long-distance signaling
Plants release hormones that travel in the plant vascular tissue(xylem and phloem) or through the air to reach the target tissue
Animals use endocrine signaling
Specialized cells release hormones into the circulatory system where they reach target cells
Example
Insulin is released into the pancreas into the bloodstream where it circulates in the bloodstream
Cell processing
Cells process signals when the substrate binds to the active site, causing a molecule to be released and interact with other molecules until it finally reaches the nucleus and other places
Cell signaling overview
Reception
The detection and receiving of a ligand by a receptor in the target cell
Receptor: macromolecules that bind to signal molecules(ligands)
All receptors have an area that interacts with the ligand and an area that transmits a signal to another protein
The binding between ligand and receptor is highly specific
When a ligand binds to the receptor, the receptor activates through a conformational change
Conformational change can change another part of the receptor, initializing reactions sometimes
Can be intracellular or in the plasma membrane
Transduction
Signal is converted
Is the conversion of an extracellular signal to an intracellular signal that will bring about a cellular response
Signal transduction pathway - a series of steps by which a signal on a cell’s surface is converted into a specific cellular response
Regulates protein activity through phosphorylation by the enzyme protein kinase(adds phosphates)
Relays signal inside the cell
Dephosphorylation by the enzyme protein phosphatases(removes a phosphate)
Shut off pathways
Change in shape means change in function
Amplifies signal(multiple responses)
Second messengers: small, non-protein molecules and ions help relay the message and amplify the response
Cyclic AMP is a common second messenger
Response
Cell process is altered
The final molecules in the signaling pathway convert the signal to a response that will alter a cellular process
Examples
Protein that can alter membrane permeability
Enzymes that will change a metabolic process
Protein that turns genes on or off
Signal transduction pathways
Can influence how a cell responds to its environment
Results in changes in gene expression and cell function
Mutations to receptor proteins or any component of the signaling pathway will result in a change to the transduction of the signal
Important receptors
In eukaryotic cells
G protein-coupled receptors(GPCRs)
An entire molecule is called a 7-fold double-spanning system(spans cell membrane 7 times)
Has an extracellular and intracellular portion
Largest category of cell surface receptors because there are multiple binding sites
Important in animal sensory systems
Binds to a G protein that can bind to GTP, which is an energy molecule like ATP
Is an enzyme and the protein is inactive until the ligand binds to GPCR on the extracellular side
Inactive GPCR - ligand binds - conformational change occurs - activates GPCR - activates G protein - becomes energy
Allows phosphorylation of GTP to GDP
The amplified signal leaves a cellular response(stays active until dephosphorylated)
Ion channels
Ligand-gated ion channels
Typically closed until a response makes it open
Located on plasma membranes and are very important for the nervous system
When a ligand binds to the receptor, the gate opens/closes allowing the diffusion of specific ions
Initiates a series of events that lead to a cellular response
Most water-soluble signal molecules bind to specific sites on receptor proteins that span the plasma membrane
3 main types
G protein-coupled receptors, receptor tyrosines, ion channels
Can internally signal by passing through ion channels or externally signal through the g protein
Receptor tyrosine kinase
Are membrane receptors that attach phosphate to tyrosines
Can trigger multiple signal transduction pathways at once
Abnormal function is associated with many types of cancers
Part of an ATP pathway and do it through the conformational change of two tyrosines after the ligand binds to them
Become active and can phosphorylate 6 at a time
Ion channel
When a signal molecule binds as a ligand to the receptor, the gate allows specific ions such as sodium and calcium through a channel in the receptor
Intracellular receptors
Are found in the cytosol or nucleus of target cells; only cells with proper receptors respond
Small or hydrophobic chemical messengers can cross the membrane and activate receptors that are inside
Steroids, thyroid hormones
An activated hormone-receptor complex can act as a transcription factor, turning on specific genes
Protein kinases transfer phosphates from ATP to protein
Phosphatases remove the phosphates from proteins
Second messengers
Ligand to receptor (first messenger)
Smaller molecule, non-protein (small messenger)
Amplification
Camps
Adenylyl cyclase(an enzyme in the plasma membrane) converts ATP to cAMP in response to an extracellular signal
Signal molecules trigger the formation of cAMPs
Usually activates protein kinase A
G-protein inhibits adenylyl cyclase
Calcium ions and inositol triphosphate
Calcium ions also act as second messengers
Important because cells can regulate their concentration
A signal relayed can trigger an increase in cytosolic calcium
Pathways leading to the release of calcium involve inositol triphosphate (IP3) and diacylglycerol (DAG) as additional second messengers
Signal response
This leads to the regulation of transcription or cytoplasmic activities
Response to an extracellular signal is called output response
The signal transduction pathway leads to multiple responses in the cytoplasm or nucleus
Other pathways regulate the activity of enzymes rather than their synthesis
Fine-tuning of response
Amplification of signal
Specificity of response
Efficiency of response(enhanced by scaffolding proteins)
Scaffolding proteins are large relay proteins to which other relay proteins are attached, which helps to increase signal transduction efficiency by grouping proteins in the same pathway
Scaffolding proteins can also help to activate relay proteins
Termination of signal
Inactive mechanisms are important for signaling
If ligand concentration falls, fewer receptors will be bound
Unbound receptors go back to the inactive state
The body must be able to monitor its internal conditions at all times
Set points: values for various physiological conditions that the body tries to maintain
Has a normal range for which it can fluctuate
For instance, body temperature
Set point: 98.6 degrees Fahrenheit
Normal range: 97 degrees to 99 degrees
Homeostasis: the state of relatively stable internal conditions
Organisms detect and respond to a stimulus
The body maintains homeostasis through feedback loops
Feedback loops
Negative and positive
The most common is negative feedback
Reduces the effect of the stimulus
Examples
sweat(we need to start cooling down)
Blood sugar(don’t want high/low amount of insulin)
Breathing rate(oxygen lowered)
Body temperature
Stimulus: Heat -> Receptor: temperature receptors or skin -> Effector: sweat glands -> Response: sweat
Stimulus: Cold -> Receptor: temperature receptors or skin -> Effector: muscles -> Response: shivering
Positive feedback is where you have to respond more, saying that you need more of a certain stimulus
Increases effect of a stimulus
Examples
Childbirth
Stimulus: baby pushes on cervix -> Receptor: nerve cells in cervix send a signal to the brain -> Effector: pituitary gland releases oxytocin -> Response: oxytocin stimulates contractions
Blood clotting
Fruit ripening
Stimulus: a variable that will cause a response(kind of like a ligand)
Receptor/sensor: this information is sent to the control center
Effector: muscle or gland that will respond
Response: changes the effect of the stimulus(increase/decrease)
Homeostatic imbalances
Diabetes or hormone imbalances
Genetic disorders
Drug or alcohol abuse
Linked to a genetic disorder
The chance of becoming a drug abuser is increased if you have a drug addict in your lineage
Intolerable conditions(extreme heat or cold)
Can’t stay outside for long periods
Diseases: When the body is unable to maintain homeostasis
Cancer: The body can’t regulate cell growth
Diabetes: The body cannot regulate glucose levels
Cell signaling
Cells in an organism must communicate to maintain homeostasis
Communication occurs in signal transduction pathways
Genes
Units of heredity; made up of segments of DNA
Passed to the next generation through gametes
Each gene has a specific location on a chromosome called a locus
Most DNA is packaged into chromosomes
Somatic cells are any cell other than sex cells/gametes
23 pairs of chromosomes
Karyotype: ordered display of chromosomes from a cell
Human games have one set of 23 chromosomes
Autosomes: normal chromosomes that do not determine sex
Sex chromosomes: determine sex and are X and Y
Females have two XXs and males have XY
2 chromosomes in each pair in somatic cells are called homologous chromosomes
Same length and shape and similar gene characteristics
Each pair of chromosomes has one from each parent
23 from mother and 23 from father
Diploid: cell with two sets of chromosomes(2n = 46)
Haploid: cell with one set of chromosomes(n = 23)
Sister chromatids
DNA synthesis allows two chromosomes to form
Each replicated chromosome has two identical sister chromatids
Meiosis
Preceded by replication of chromosomes
Two divisions: Meiosis 1 and 2
Results in 4 genetically unique daughter cells
Each daughter cell has half as many chromosomes as the parent cell
Stages
Chromosome duplication in S-phase
Meiosis 1
Before meiosis, chromosomes are replicated to form identical sister chromatids, joined by a centromere
Single centrosome replicates, forming two centrosomes
Reductional division
Homologs pair up and separate, resulting in two haploid daughter cells with replicated chromosomes
Phases
Prophase 1
Duplicated chromosomes pair and exchange segments
Crossing over:
Synopsis: homologous chromosomes loosely pair, aligned gene by gene
Non-sister chromatids exchange DNA segments
Each pair of chromosomes forms a tetrad
Each tetrad has one or more chiasmata(X-shaped regions where crossing over occurs, which increases genetic diversity)
Metaphase 1
Chromosomes line up by homologous pairs
Anaphase 1
Homologous chromosomes separate
Telophase 1 & Cytokinesis
Two haploid cells form; each chromosome still consists of two sister chromatids
Meiosis 2
Equational division
Sister chromatids separate in similar phases to mitosis
Forms 4 haploids
Sister chromatid cohesion
Allows sister chromatids of a single chromosome to stay together during meiosis 1
Done through protein complexes called cohesins
Mitosis, cohesins are cleaved at the end of metaphase
Meiosis, cohesins are cleaved along chromosome arms in anaphase 1 and at centromeres at anaphase 2
Genetic variation
Source of genetic diversity
Mutations create different versions of genes called alleles
Can shuffle the alleles through
Crossing over
Produces recombinant chromosomes that combine DNA inherited from each parent
Beings early in prophase 1
Homologous portions of two non-sister chromatids trade places
Contributes to genetic variation by combining DNA from two parents into a single chromosome
Independent assortment
Homologs orient randomly in metaphase 1
Each pair of chromosomes sorts maternal and paternal homologs into daughter cells independently of other pairs
The number of combinations possible is 2^n, where n is the haploid number
For humans(n=23) that means that there are more than 8 million possible combinations
Random fertilization
This adds to genetic variation because any sperm can fuse with any ovum(unfertilized)
The fusion of two gametes produces a zygote with 70 trillion diploid combinations
Particulate hypothesis
Reappearance of traits after several generations
Documented by Mendel
Mendel studied pea plants
Many varieties with distinct heritable features and characteristics called traits
Mating can be controlled
Chose to track characters that occurred in two distinct forms
Used varieties that were true-breeding(plants that produce offspring of the same variety when they self-pollinate)
Mated two contrasting varieties, a process called hybridization
P generation: true-breeding parents
F1 generation: hybrid offspring of the P generation
F2 generation: product of a cross between F1 generation
Easier to domesticate because it is less wild
A heritable factor is called a gene
Hypothesis to explain 3:1 ratio inheritance
Model
Alternative versions of genes account for variation in inherited characteristics
Alleles are alternative versions of genes
Each gene resides at a specific locus on a specific chromosome
For each character, an organism inherits two alleles, one from each parent
If two alleles at a locus differ, then the dominant allele determines the organism’s appearance, and the recessive allele has no noticeable effect
Law of segregation
Two alleles for a heritable character separate during gamete formation and end up in different gametes
An egg or a sperm gets only one of the two alleles that are present in the organism
Corresponds to the distribution of homologous chromosomes to different gametes in meiosis
Complex inheritance patterns
Heritable characters are not determined by only 2 alleles
independent assortment and segregation still apply
Degrees of dominance
Complete dominance
When phenotypes of the heterozygote and dominant homozygote are identical
Example is Mendel’s peas(green rough, green smooth, white smooth)
Incomplete dominance
The phenotype of F1 hybrids is somewhere between the phenotypes of the two parental varieties
Example is the snapdragon flower color(mix of red and white dominant genes where they are expressed partially)
No distinct white or red until F2 generation
Codominance
Two dominant alleles affect the phenotype in separate distinguishable ways
Examples are human blood type and dalmatians
One person can have AB and the other can have AB and after breeding, they can have children with blood types AB, AB, AA, and BB
For any character, dominance/recessiveness relationships of alleles depend on the level that we examine the phenotype
Tay-sachs disease - a dysfunctional enzyme causes an accumulation of lipids in the brain
At the organism level(as people), the allele is recessive
At the biochemical level, the phenotype(the enzyme activity level) is incompletely dominant
At the molecular level, the alleles are codominant
Dominant alleles are not more common than recessive; it’s just a matter of who expresses it
One baby out of 400 in the US is born with extra fingers or toes(polydactyl), but it’s a dominant allele rather than a recessive allele
Humans have multiple blood types(A, B, AB, O)
Pleiotropy
Genes exhibit multiple phenotypic effects
Cystic fibrosis, sickle cell anemia
The SRY(sex-determining region Y-gene) gene produces a protein that is a transcription factor which begins the development of testis in male individuals(what causes a fetus to become a male)
The testis then secretes testosterone and leads to the development of a male phenotype
Yellow coated mice who are homozygous for the dominant yellow coat gene do not survive(dominant lethal)
The gene is pleiotropic because it impacts the color and survival of the mice
Epistasis
A gene at one locus alters the phenotypic expression of a gene at a second locus
In labrador retrievers and many others mammals, coat color depends on two genes
One gene determines the pigment colors(B=black; b=brown) and the other determines whether the pigment will be deposited(E=color; e=no-color)
Interacting genes
Two genes are responsible for one effect(2 separate alleles that are expressed together unlike codominance where it is expressed on the same allele)
You can’t have one without the other
In a wild-type cobra, one gene is for orange and one gene is for black
Wild-type is the most common snake
Polygenic inheritance
Quantitative characters
Vary in the population along a continuum
Usually indicates polygenic inheritance, an additive effect of two or more genes on a single phenotype
Can do skin color and height in humans
Environmental impact
Phenotype depends on environment
Norms of reaction: the phenotypic range of a genotype influenced by the environment
Most common ones are hydrangeas(flowers) of the same genotype that range from blue-violet to pink, depending on soil acidity
Mitochondrial DNA
mtDNA does not follow Mendelian rules
It is inherited with mitochondria, which are randomly assorted into gametes and daughter cells
In animals, mtDNA is transmitted by the egg and not the sperm, causing mtDNA to be maternally inherited
Makes mtDNA useful for studying population and migration patterns
Designer babies are done through taking mitochondria from one, egg from another, and sperm from donor father
Maternal mitochondria is useful for studying migrations
Humans are not good subjects for genetic research because generation times are too long, parents produce few offspring, and breeding experiments are unacceptable
Pedigree
A family tree that describes the interrelationships of parents and children actress generations
Inheritance patterns of particular traits can be traced and described using pedigrees
Recessively-inherited disorders show up in homozygous offspring
Carriers
Heterozygous people who carry the recessive allele but are phenotypically normal
Autosomal pedigrees are used for following the traits to see the expression throughout the generations
Squares are males and circles are females
X-linked pedigrees
X-linked recessive(skips every generation): more males than females show the phenotype
None of the offspring of an affected male are affected but all daughters are carriers and half of the other daughters’ sons are affected
Hemophilia, duchenne muscular dystrophy, testicular feminization syndrome
X-linked dominant(occurs every generation): affected males pass the condition on to all daughters but no sons and affected females are mostly heterozygous and pass condition to half of their offspring
Dominant lethal
An individual inheriting two copies of the allele leads to death, making achondroplasia lethal
Huntington’s disease
Degenerative disease of the nervous system
CAG trinucleotide repeats
Condition is irreversible
Multifactorial disorders
Many diseases like heart disease, diabetes, alcoholism, mental illnesses have both genetic and environmental components(multifactorial)
Little is understood about why they occur genetically
Information content of DNA is in the form of specific sequences of nucleotides
Transcription: synthesis of RNA under the direction of DNA, producing mRNA
Translation: RNA to protein
Primary transcript: the initial RNA transcript from any gene prior to processing
Eukaryotes
Nuclear envelope separates transcription from translation
RNA transcripts are modified through RNA processing to yield finished mRNA
Codons
Flow of information is dependant on codons, which are a series of nonoverlapping, 3-nucleotide words
Codons are transcribed into complementary words of mRNA
These are words are then translated into a chain of amino acids, resulting in a polypeptide
Are read in the 5’ to 3’ direction
Each codon specifies one amino acid(20 total) to be placed at the relevant position of the polypeptide
Of these 64 triplets, 61 code for amino acids while 3 are stop signals to end translation (UAG, UGA, UAA)
The genetic code is redundant(more than one codon may specify a particular amino acid) but not ambiguous - no codon specifies more than one amino acid
Codons must be read in the correct reading frame in order for the specific polypeptide to be produced
Codons and amino acids are linked by tRNA
Need to know what the abbreviations on codon chart stand for
Genetic code is universal
Shared by the simplest bacteria to the most complex animal
Genes can be transcribed and translated after being transplanted from one species to another
Example is luciferase where they move this to another organisms, making them glow
Transcription
RNA synthesis is catalyzed RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides
Follows the same base pairing as DNA
DNA sequence where RNA polymerase attaches is called the promoter region
In bacteria these sequence signaling the end of transcription is called the terminator region
The stretch of DNA is called the transcription unit
RNA polymerase binds to promoter regions, beginning transcription
Transcription factors mediate the binding of RNA polymerase
Transcription initiation complex: after RNA polymerase binds
A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes
Elongation
As RNA polymerase moves along the DNA, it unwinds the double helix 10-20 base pairs at a time
Transcription progresses at a rate of 40 nucleotides per second in eukaryotes
A gene can be transcribed simultaneously by several RNA polymerases
Nucleotides are added to the 3’ end of the growing RNA molecule
There can be different promoter regions on DNA, having RNA polymerases at once in different places
Termination
In eukaryotes
RNA polymerase II transcribes the polyadenylation signal(AAUAAA); the RNA transcript is cut free by proteins about 10-35 nucleotides past this signal
In bacteria:
The polymerase stops transcription at the end of the terminator region, which is why they don’t need modifications
mRNA alteration
5’ cap, 3’ poly-A tail, intron splicing
Functions
Facilitate the export of mRNA
Protect mRNA from hydrolytic enzymes
Help ribosomes attach to the 5’ end
Spliceosomes
Do the cutting of the mRNA(RNA splicing(
Consist of a variety of proteins and several small nuclear ribonucleoproteins(snRNPs) that recognize these splicing sites
Ribozymes
Catalytic ribosomes/RNA molecules
This was the first time that scientists were able to say that not all biological catalysts are proteins
Properties of RNA as an enzyme
It can form a 3D structure because of its ability to base pair with itself
Some bases in RNA contain functional groups that may participate in catalysis (*function as a catalyst)
RNA may hydrogen bond with other nucleic acid molecules
tRNAs
Each one has a different anticodon, so they are not identical
Accurate translation
A correct match between a tRNA and an amino acid must be needed
A correct match between the tRNA anticodon and an mRNA codon must be needed
Flexible pairing at the third base of a codon is called wobble and allows some tRNA’s to bind to more than one codon
rRNA
Large and small subunit
Ribosome has three binding sites for tRNA
P site: holds the tRNA that carries the growing polypeptide chain
A site: holds the tRNA that carries the next amino acid to be added to the chain
E site: the exit site where discharged tRNAs leave the ribosome
Amino acid
Instead of 5’ and 3’, we use terminus
The N-terminus(5’) and the C-terminus(3’) are on two ends of the polypeptide
Is a subset of amino acids on the ends of your protein
Could be 3, 4, 5, or more amino acids that are at the beginning, and it depends on the protein
Modifications
During and after synthesis, a polypeptide chain spontaneously coils and folds into its 3D shape(folds there because of the chemical environment its in)
Proteins may also require post translational modifications before doing their job
Some polypeptides are activated by enzymes that cleave them
Others come together to form the subunits of a larger protein
Transcription regulation
Prokaryotes and eukaryotes can alter gene expression in response to their changing environment
In multicellular eukaryotes, gene expression regulates development and causes differences in cell types
RNA molecules play many roles in regulating gene expression
Bacterial regulation
Natural selection has favored bacteria that produce only the products needed by the cell
A cell can regulate the production of enzymes by feedback inhibition or by gene regulation
Gene expression in bacteria is controlled by the operon
Operons are a cluster of functionally related genes can be under coordinated control by a singleton-off switch(only in prokaryotes)
The switch is a segment of DNA called the operator, which is within the promoter
Operon: the entire stretch of DNA that includes the operator, promoter and controlled genes
Lac operon
Negative control: Regulatory proteins inhibit gene production by binding to dNA and blocking transcription
Repressor: Can switch off the operon by binding to the operatory and blocking RNA polymerase, and it is produced by a regulatory gene and interacts with regulatory proteins and sequences
Positive control: Stimulation of gene expression by binding to DNA and stimulation transcription, or binding to repressors to inactivate them
Activator: A protein that binds to DNA and stimulates transcription
Inducer: A small molecule that inactivates the repressor
Eukaryotic expression
Almost all cells are genetically identical
Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome
Abnormalities in gene expression can lead to cancer
Gene expression is regulated at many stages
Some genes like ribosomal genes are always turn on
Genes in packed heterochromatin are not usually expressed
Histone acetylation: Acetyl groups are attached to positively charged lysines in histone tails
Loosens chromatin structure, promoting transcription
DNA methylation
The addition of methyl groups to certain bases in DNA, which can reduce transcription
Can cause long-term inactivation of genes
In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development
Epigenetic inheritance
Chromatin modifications just discussed don’t alter DNA sequences, but can be passed to future generations of cells
It is the inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
There are multiple control elements in eukaryotic genes, which are segments of noncoding DNA that serve as binding sites for transcription factors
Transcription factors
Eukaryotic RNA polymerase needs transcription factor proteins
Proximal control elements are located close to the promoter while distal control elements/enhancers are far away or in an intron
Activators
A protein that binds to an enhancer and stimulates transcription of a gene
Enhancer: A segment of DNA containing control elements located far away from the gene
Activators have two domains, one that binds DNA and the other activates transcription
Bound activators facilitate a sequence of protein to protein interactions
A significant amount of the genome may be transcribed into noncoding RNAs
miRNAs: Small single-stranded RNA molecules that can bind to mRNA
Can degrade mRNA or block its translation
Chromosomal disorders
Large-scale alterations lead to spontaneous abortions/developmental disorders
Plants tolerate these genetic changes better than animals do
Nondisjunction: pairs of homologous chromosomes do not separate normally during meiosis
One gamete receives two of the same type of chromosome, and another gamete receives no copy
Chromosome number changes
Aneuploidy: results from the fertilization of gametes in which nondisjunction occurred
Offspring with this condition have an abnormal number of a particular chromosome
Monosomic: only one copy of a chromosome
Trisomic: three copies of a chromosome
Polyploidy: a condition in which an organism has more than two complete sets of chromosomes
Triploidy: three sets of chromosomes
Tetraploidy: four sets of chromosomes
Common in plants, not animals and are more normal in appearance compared to aneuploidy
Alterations of chromosome structure
Deletion: removes a chromosomal segment
Duplication: repeats a segment
Inversion: reverses orientation of a segment within a chromosome
Translocation: moves a segment from one chromosome to another
Human disorders
Alterations of chromosome number and structure are associated with some serious disorders
Some types of aneuploidy appear to upset the genetic balance less than others, resulting in individuals surviving beyond birth
These surviving individuals have a set of symptoms/syndrome, characteristic of the type of aneuploidy
Down syndrome
An aneuploid condition that results from three copies of chromosome 21
Affects about one out of every 700 children born in the U.S.
Frequency increases with the age of the mother
Aneuploidy of sex chromosomes
Nondisjunction of sex chromosomes produces a variety of aneuploid conditions
Klinefelter syndrome: result of an extra chromosome in a male, producing XXY individuals
Monosomy X/Turner Syndrome: produces X0 females who are sterile
Jacob’s syndrome: an extra Y chromosome in a male, producing XYY individuals
Structurally altered chromosomes
Cri du chat: results from a specific deletion in chromosome 5
Child with this condition is mentally retarded and has a catlike cry; individuals usually die in infancy or early childhood
Chronic myelogenous leukemia: caused by translocations of chromosomes
Genomic imprinting
Phenotype depends on which parent passed along the alleles for those traits
Involves the silencing of certain genes that are stamped with an imprint during gamete production
Is the result of methylation(addition of CH3) of cysteine nucleotides
Only affects a small number of mammalian genes
Critical for embryonic development
Inheritance of organelle genes
Extranuclear genes are found in organelles in the cytoplasm
Mitochondria, chloroplasts, and other plant plastids carry small circular DNA molecules
Inherited maternally because cytoplasm comes from the egg
Evidence came from studies on inheritance of yellow or white patches on leaves of an otherwise green plant
Some defects in mtDNA prevent cells from making enough ATP and result in diseases that affect the muscular and nervous systems
Ex: mitochondrial myopathy, Leber’s hereditary optic neuropathy
Nucleotide mutation
Changes in the genetic material
Point mutations: Chemical changes in just one base pair of a gene
A single nucleotide change in a DNA template strand can lead to the production of an abnormal protein
Divided into two general categories
Nucleotide pair substitutions
Transition
Transversion
One or more nucleotide pair insertions/deletions
Silent mutations
Have no effect on the amino acid produced by a codon because of redundancy in the genetic code
Missense mutations
Still code for an amino acid, but not the correct amino acid
Nonsense mutation
Change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein
Frameshift mutations(all of above mutations)
Insertions and deletions are additions or losses of nucleotide pairs in a gene
Have a disastrous effect on the resulting protein more often than substitutions do
insertion/deletion of nucleotides may alter the reading frame
Types of mutants
Some mutations cause a gain of function while others cause a loss of function
Loss of function
Dominant mutations are haplo-insufficient, meaning that one ene dosage is insufficient to exhibit the normal phenotype
Recessive mutations are either null(no gene activity) or hypomorph(meaning little gene activity)
Gain of function
Usually dominant and can be either hypermorph(increased activity) or neomorph(new)
Mutagens
Spontaneous mutations can occur during DNA replication, recombination, or repair
Are physical/chemical agents that can cause mutations like carcinogens
Typically collect data on a sample of a population to infer what is happening to a general population
Shows normal distribution of bell curve
Central tendencies
Descriptive statistics that allow for researchers to describe and quantify differences between data sets
Mean, median, mode are centers of distribution
Act as catalysts
Speed up the reaction without being consumed by the reaction
An enzyme is a catalytic protein
Activation energy barrier
All chemical reactions between molecules involve bonds breaking and forming
The initial energy to start a reaction is called the activation energy(EA)
Often supplied in the form of thermal energy(adds KE but too much heat will cause protein to denature) that the reactant molecules absorb from the surroundings
In the transition state, we want to lower it to speed up the activation energy
Enzymes catalyze reactions by lowering the activation energy
Enzymes do not affect the change in free energy, but they fasten reactions
Substrate specificity
Enzyme binds to its substrate, forming an enzyme-substrate complex
Skeleton-key model(one enzyme works on multiple substrate)
Lock and key model(one enzyme to one substrate)
Induced fit(substrate brings groups of the active site into positions that enhance their ability to catalyze the reaction)
Basically forces enzyme into position
The active site can lower the EA barrier by
Orienting substrates correctly
Straining substrate bonds
Providing a favorable microenvironment
Covalently bonding to the substrate
Enzymes can make permanent bonds(not really biological enzymes)
Effects on enzyme activity
Temperature
Want to keep it about 35-75 degrees Celsius
pH
Range is broader than temperature
Concentration of enzyme/substrate
Cofactors
Non-protein enzyme helpers
Can help increase absorption rate
May be inorganic like a metal in ionic form or organic
Organic cofactors are called coenzymes
Include vitamins
Coenzyme Q10 is a cofactor that acts as an electron carrier during the electron transport chain in cellular respiration
Enzyme inhibitors
Competitive inhibitors
Binds to the active site of an enzyme, competing with the substrate
Example
Carbon monoxide(binds before oxygen can)
Noncompetitive inhibitor
Binds to another part of an enzyme(allosteric site), causing the enzyme to change shape and making the active site less effective
Enzyme activity regulation
Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated
A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes
Can increase the production of a non-competitive inhibitor
Allosteric regulation
May either inhibit or stimulate enzyme activity
Each enzyme has active and inactive forms
The binding of an activator stabilizes the active form of the enzyme
The binding of an inhibitor stabilize the inactive form of the enzyme
Cooperativity
Form of allosteric regulation that can amplify enzyme activity
Allosteric regulators
Attractive drug candidates for enzyme regulation because of their specificity
Inhibition of proteolytic enzymes called caspases may help inflammatory responses
Increase in inflammation means a lot of caspases so we need to inhibit them
Feedback inhibition
The end product of a metabolic pathway shuts down the pathway
Prevents a cell from wasting chemical resources by synthesizing extra products
Tells the cell that you can stop producing stuff
Locations
Act as structural components of membranes
Some enzymes reside in specific organelles
Enzymes for cellular respiration are in the mitochondria
Energy flow
Heat energy <- ATP <- cellular respiration in mitochondria <- 6CO2 + 6H2O <- photosynthesis <- organic matter + O2
Catabolic pathways
Aerobic respiration consumes organic molecules and oxygen to yield ATP
anaerobic respiration is similar to aerobic respiration, but consumes compounds other than oxygen
Breakdown of organic molecules is exergonic
Fermentation is a partial degradation of sugars that occurs without oxygen
Cellular respiration includes both aerobic and anaerobic respiration, but is often used to refer to aerobic respiration
Redox reactions
Transfer of electrons during chemical reactions that releases energy stored in organic molecules
Releases energy to use in ATP synthesis
Chemical reactions that transfer electrons between reactants are called oxidation-reduction reactions
In oxidation, a substance loses electrons
In reduction, a substance gains electrons
Have to be able to identify which one is the oxidizing reagent and reduction reagent
Typically oxygen is reduced in O2 to H2O
ETC
Glucose and oxygen are broken down
Electrons from organic compounds are usually first transferred to NAD+, a coenzyme
Each NADH represents stored energy that is tapped to synthesize ATP
NADH passes the electrons to the ETC
Unlike and uncontrolled reaction, the ETC passes electrons in a series of steps
O2 pulls electrons down the chain to generate ATP
Reduction of NAD+ to NADH is due to dehydrogenase
Different by the N+
Stages of Cellular Respiration
Glycolysis
Breakdown of glucose into two molecules of pyruvate
Small amount formed here and in the Krebs cycle by substrate level phosphorylation
For each molecule of glucose degraded, the cell makes up to 32 molecules of ATP
Major phases
Energy investment
Need some sort of investment of energy to get ATP
Energy payoff
Occurs whether or not O2 is present so it is anaerobic/aerobic
Uses 2 ATP, makes 2 ATP and 2 NADH and it repeats the process to make 4 ATP and 4 NADH
Citric acid cycle/Krebs cycle
Completes the breakdown of pyruvate to CO2
Pyruvate is oxidized by being converted to acetyl CoA before going into the Krebs cycle (happens twice for each pyruvate)
Makes 2 NADH, Acetyl CoA, and CO2
Oxidizes organic fuel derived from pyruvate, generating 1 ATP B (technically GTP), a NADH, and 1 FADH2 per cycle
Does 2 cycles
Occurs in the matrix
ATP synthesis through substrate level phosphorylation
Contrasts with oxidative phosphorylation where an inorganic phosphate is added to ADP
Coenzymes capture electrons
Has eight steps(don’t need to know all 7 seven steps but the general information)
Acetyl CoA joins the cycle by combining with oxaloacetate to form citrate
The next seven steps decompose the citrate back to oxaloacetate
NADH and FADH2 produce by by the cycle relay electrons extracted from food to ETC
Oxidative phosphorylation
Accounts for most of the ATP synthesis(90%) and is powered by redox reactions
Chemiosmosis
After this point, we have the greatest amount of ATP
NADH and FADH2 account for most of the energy to transform into ATP
These two electron carriers donate electrons to the ETC that powers ATP synthesis through oxidative phosphorylation
Happens in the inner mitochondrial membrane(cristae)
Most of the chain’s components are proteins that exist as multiprotein complexes
Alternate reduced and oxidized states as they accept and donate electrons
Electrons drop in free energy as they go down the chain and are finally passed to O2(terminal electron acceptor), forming H2O
Electron transport
Transferred from NADH or FADH2 to ETC
Passed through a number of proteins like cytochromes to O2
Chemiosmosis
ETC causes proteins to pump H+ from the matrix to the intermembrane space
H+ then moves back across the membrane through the protein, ATP synthase
Uses the exergonic flow of H” to drive phosphorylation of ATP
Example of chemiosmosis, the use of energy in a H+ gradient to drive cellular work
H+ gradient is referred to proton-motive force, emphasizing its capacity to do work
ATP Production
About 34% of energy in a glucose is transferred to ATP to make 32 ATP molecules
Fermentation
Without oxygen, glycolysis couples with fermentation to produce ATP
Anaerobic respiration uses an ETC with a final electron acceptor other that O2 like sulfate
Fermentation uses substrate-level phosphorylation instead of an ETC to make ATP
Types of fermentation
Alcohol fermentation
Pyruvate is converted to ethanol
Used by yeast
Lactic acid fermentation
Pyruvate is reduced to NADH
Makes cheese and yogurt
Human muscle cells can use lactic acid fermentation to make ATP
Anaerobes
Obligate
Carry out fermentation and cannot survive with O2
Facultative
Can survive using either fermentation or cellular respiration
Pyruvate can be used in two alternative catabolic routes
Metabolic pathways
Glycolysis accepts a wide range of carbohydrates
Usually first converted to glucose but we can use a lot of them
Proteins must be digested to amino acids
Must then by deaminated before oxidation
Fats are digested to glycerol for glycolysis and fatty acids to make acetyl CoA
An oxidized gram of fat produces more ATP than an oxidized gram of carbohydrate
Cellular respiration feedback
If ATP concentration begins to drop, respiration speed up
If ATP concentration is high, respiration slows down
Control of catabolism is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway
Natural selection
Does not create new traits, but edits or selects for traits already present in the population
The local environment determines which traits are beneficial (ex. Peppered moths)
Examples
Staphylococcus aureus is commonly found on people (MRSA)
Became resistant to penicillin in 1945 and to methicillin in 1961 (bacteria continue to evolve!)
MRSA
Methicillin works by inhibiting a protein used by bacteria in their cell walls
MRSA bacteria use a different protein in their cell walls
Their strains are now resistant to many antibiotics
Homology
Similarity resulting from common ancestry
Homologous structures
Anatomical resemblances that represent variations on a structural theme present in a common ancestor
Produced through divergent evolution or the splitting of an ancestral species to produce two or more related descendant species
Examples
Human arm, cat arm, whale fin, bat wing
Embryonic homology
Comparative embryology reveals anatomical homologies not visile in adult organisms
Ontogeny recapitulates phylogeny
An organism's development will take it through each of the adult stages of its evolutionary history, or its phylogeny
Vestigial structures
Remnants of features that served important functions in the organism’s ancestors
Examples
Human tailbone
Whale pelvis
Evolutionary trees
Are hypotheses about the relationships among different groups
Homologies form nested patterns in evolutionary trees
Convergent evolution
Evolution of similar features in distantly related groups
Produces analogous traits
Similar traits that arise when groups independently adapt to similar environments in similar ways
Do not provide information about ancestry
Fossil record provides evidence of the extinction of species, the origin of new groups, and changes within groups over time
Can document important transitions
Example: the transition from land to sea in the ancestors of cetaceans
Dating
Determining approximate ages of fossils helps provide evidence for evolution
Biogeography
Provides evidence of evolution
Earth’s continents were formerly united in a single large continent called Pangaea, but have separated by continental drift
Can use this drift to predict where different groups evolved
Plate tectonics
At three points in time, the land masses of Earth have formed a supercontinent 1.1 billion years ago, 600 million years ago, and 250 million years ago
Earth’s crust is composed of plates floating on Earth’s mantle
Organisms do not evolve during their lifetimes
Natural selection acts on individuals so only population evolve
Genetic variation provides the diverse gene pool necessary for a species to persist in a diverse environment
Populations
A localized group of individuals capable of interbreeding and producing fertile offspring
A gene pool consists of all the alleles for all loci in a population
A locus is fixed if all individuals in a population are homozygous for the same allele
Genetic variation
Variation in heritable traits is a prerequisite for evolution
Among individuals, it is caused by differences in genes or other DNA segments
Natural selection can only act on variation with a genetic component
Modern synthesis
Importance of populations
Mechanism of natural selection
Gradualism
Hardy-Weinberg equilibrium
Describes a hypothetical population that is not evolving
Shuffling of alleles does not impact the gene pool
In real population, allele and genotype frequencies do change over time when one of the 5 conditions is not met:
No mutations - Mutations
Random mating - Non-Random Mating
No natural selection - Natural Selection
Large population size - Genetic Drift(apparent in small populations)
No gene flow - Gene Flow
Only natural selection produces adaptive radiation
Microevolution
A change in allele frequency in a population over generations
Allele frequency can change by natural selection, genetic drift, or gene flow
States that frequencies of alleles and genotypes in a population remain constant from generation to generation
Gametes contribute to the next generation randomly, leading to no change in allele frequency
Mendelian inheritance preserves genetic variation in a population
Example
We can assume the locus that causes phenylketonuria (PKU) is in Hardy-Weinberg equilibrium since:
1. The PKU gene mutation rate is low
2. Mate selection is random with respect to whether or not an individual is a carrier for the PKU allele
3. Natural selection can only act on rare homozygous individuals who do not follow dietary restrictions
4. The human population is large
5. Migration has no effect as many other populations have similar allele frequencies
Link
Speciation
The origin of new species
Microevolution
Allele frequency changes in a population
Macroevolution
Broad patterns of evolutionary change
Ex: color change
Reproductive isolation
Existence of biological factors(barriers) that inhibit two species from producing viable(live well), fertile offspring
Can be viable but sterile like mules
Prezygotic barriers(block fertilization from ever occurring)
Habitat isolation
Occupy different locations or blocked from meeting by mountains or rivers
Temporal isolation
Species that breed at different times
Behavioral isolation
Have different behaviors that are unique to a species
Ex: Penguins bring gifts to others while blue-footed bobbies dance
Postzygotic barriers(prevent a hybrid zygote from developing)
Reduced hybrid viability
Genes of the different parent species may interact and impair the hybrid’s development
Offspring doesn’t develop the organs correctly
Reduced hybrid fertility
Even if hybrids are vigorous, they are sterile like mules
Hybrid breakdown
When a first-generation hybrid is fertile, but they mate with another species, the next generation offspring are infertile
Species Definitions
The morphological species concept defines a species by structural features
It applies to sexual and asexual species but relies on subjective criteria
The ecological species concept views a species in terms of its ecological niche
It applies to sexual and asexual species and emphasizes the role of disruptive selection
The phylogenetic species concept defines a species as the smallest group of individuals on a phylogenetic tree
It applies to sexual and asexual species, but it can be difficult to determine the degree of difference required for separate species
Speciation
Allopatric
Population is divided by geographical separation
Sympatric
Speciation takes place in geographically overlapping populations(not likely)
Can result in the appearance of new ecological niches
Sexual selection can drive this speciation
Color morphology
Performance
Hybrid zones
A region in which members of different species mate and produce hybrids
Overtime, there is a possibility of an overlapping fusion where the species meet
Three possibilities
Reinforcement
Fusion
Stability
Continental drifts
Tectonic plates shift
Cause changes in species
Mass extinction
Handful of species are able to survive and adapt so those are the ones that continue to live on
Adaptive radiation
Evolution of diversely adapted species from a common ancestor due to mass extinctions, evolution of novel characteristics, or colonization of new regions
Ex: Alligators came from dinos
Endemic species
Species not found anywhere else in the world
Typically on islands and are closely related to species on the nearest mainland or island
Most common one is Darwin’s islands like finches
Ecology
The scientific study of the interactions between organisms and the environment
Global climate patterns
Solar energy
Planetary movement
Seasons
Air currents
Water currents
Climate and terrestrial biomes
Climate affects the latitudinal patterns of terrestrial biomes
Biomes
Major life zones characterized by vegetation type (terrestrial) or physical environment (aquatic)
Climate is very important in determining why terrestrial biomes are found in certain areas
Are affected not just by average temperature and precipitation, but also by the pattern of temperature and precipitation through the year
Similar characteristics can arise in distant biomes through convergent evolution
Disturbance
Is an event such as a storm, fire, or human activity that changes a community
Frequent fires can kill woody plant and maintain the characteristic vegetation of a savanna
Fires and outbreaks of pests create gaps in forests that allow different species to grow
Fire suppression has changed the vegetation of the Great Plains
Microclimate
Is determined by fine-scale differences in the environment that affect light and wind patterns
Every environment is characterized by:
Abiotic factors: non-living attributes such as temperature, light, water, and nutrients
Factors that affect the distribution of organisms include:
Temperature
Water
Sunlight
Wind
Rocks & soil
Most factors vary in space and time
Biotic factors: other organisms that are part of an individual’s environment
Factors that affect distribution of organisms may include:
Predation
Herbivory
For example sea urchins can limit the distribution of seaweeds
Competition
Competitive exclusion
Principle states that two species competing for the same resources cannot coexist
Water and oxygen
Water availability in habitats is another important factor in species distribution
Desert organisms exhibit adaptations for water conservations
Oxygen diffuses slowly in water
Oxygen concentrations can be low in deep communities
Dissolved oxygen (DO) in aquatic communities partially determines metabolic rates and is dependent on temperature (lower temp = more DO), photosynthesis rate, etc
Population
Group of individuals of a single species lying in the same general area
Populations are described by their boundaries and size
Size can be estimated by the mark and recapture method
Density is the number of individuals per unit area of volume
Dispersion is the pattern of spacing among individuals within boundaries of the population
Clumped, uniform, random
Calculations
Population density
Divide the population by the size of the area
Population dynamics
Births and immigration add individuals to a population
Deaths and emigration remove individuals from a population
Survivorship curves
A graphic way of representing data in a life table
Population growth
Useful to study population growth in an idealized situation
The per capita birth rate (b) is the number of offspring produced per unit time
The per capita death rate (d) is the number of individuals that die per unit time (mortality = death rate)
Exponential growth
Is a population increase under idealized conditions
J-shaped curve
Under these conditions, the rate of increase is at the maximum (r-max)
Logistical model
Carrying capacity (K): the maximum population size the environment can support
Vary with the abundance of limiting resources
In the logistic population growth model, the per capita rate of increase declines as carrying capacity is reached
Reduces per capita rate of increase as N approaches K
S-shaped curve
Some populations overshoot K before settling down to a relatively stable density
Some populations fluctuate greatly
Some populations show an allee effect, in which individuals have a more difficult time surviving or reproducing if the population size is too small
K-selected species
Density-dependent selection; selects for life history traits that are sensitive to population density
In density-dependent populations, birth rates fall and death rates rise as population density increases
Competition for resources, territoriality, disease, predation, toxic wastes, and intrinsic factors
R-selected species
Density-independent selection; selects for life history traits that maximize reproduction
In density-independent populations, birth and death rate do not change with population density
Population cycles
Some populations undergo regular boom-and-bust cycles
Lynx populations follow the 10-year boom-and-bust cycle of hare populations
Predators and sunspot activity regulate hare populations
Global human population
The human population increased relatively slowly until about 1650 and then began to grow exponentially
Patterns of population change
To maintain population stability, a regional human population can exist in one of two configurations:
0 population growth = high birth rate - high death rate
0 population growth = low birth rate - low death rate
The demographic transition is the move from the first state to the second state
Age structure
One important demographic factor in present and future growth trends is a country’s age structure
Age structure is the relative number of individuals at each age
Trophic structure
Trophic structure
the feeding relationships between organisms in a community
It is a key factor in community dynamics
Food chains link trophic levels from producers to top carnivores
Autotrophs
Build molecules using photosynthesis or chemosynthesis as an energy source
Change in the producers in an ecosystem impacts other trophic levels; changes in energy in an ecosystem can disrupt the ecosystem and change population sizes
Heterotrophs
Depend on the biosynthetic output of other organisms
Energy and nutrients pass from primary producers (autotrophs) to primary consumers (herbivores) to secondary consumers (carnivores) to tertiary consumers (carnivores that feed on other carnivores)
Detritivores and decomposers
Detritivores and decomposers are consumers that derive their energy from detritus, non-living organic matter
Prokaryotes and fungi are important detritivores
Decomposition connects all trophic levels!
Food webs
A food web is a branching food chain with complex trophic interactions
Decomposers can be depicted in food webs!
In food chains, they would be at each trophic level
Limits on food chain length
Each food chain in a food web is usually only a few links long
Two hypotheses attempt to explain food chain length: the energetic hypothesis and the dynamic stability hypothesis
The energetic hypothesis suggests that length is limited by inefficient energy transfer
For example, a producer level consisting of 100 kg of plant material can support about 10 kg of herbivore biomass
More data supports it
The dynamic stability hypothesis proposes that long food chains are less stable than short ones
Energy flows through ecosystems, whereas matter cycles within them
Conservation of Energy
The first law of thermodynamics states that energy cannot be created or destroyed, only transformed
Energy enters an ecosystem as solar radiation, is conserved, and is lost from organisms as heat
The second law of thermodynamics states that every exchange of energy increases the entropy of the universe
In an ecosystem, energy conversions are not completely efficient, and some energy is always lost as heat
Conservation of mass
The law of conservation of mass states that matter cannot be created or destroyed
Chemical elements are continually recycled within ecosystems
In a forest ecosystem, most nutrients enter as dust or solutes in rain and are carried away in water
Ecosystems are open systems, absorbing energy and mass and releasing heat and waste products
Ecosystem energy budgets
In most ecosystems, primary production is the amount of light energy converted to chemical energy by autotrophs/chemoautotrophs during a given time period
The extent of photosynthetic production sets the spending limit for an ecosystem’s energy budget
The amount of solar radiation reaching Earth’s surface limits the photosynthetic output of ecosystems
Only a small fraction of solar energy actually strikes photosynthetic organisms, and even less is of a usable wavelength
Gross and net production
Total primary production is known as the ecosystem’s gross primary production (GPP)
The conversion of chemical energy from photosynthesis, per unit time
Net primary production (NPP) is GPP minus energy used by primary producers for respiration
NPP is the amount of new biomass* added in a given time period
Only NPP is available to consumers
NPP is expressed as
Energy per unit area, per unit time (J/m2yr)
Biomass added per unit area, per unit time (g/m2yr)
Energy transfer
Secondary production of an ecosystem is the amount of chemical energy in food converted to new biomass during a given period of time
Excess energy obtained than required for survival results in storage of the energy or growth of the organism
Excess energy obtained than required for survival results in storage of the energy or growth of the organism
Production efficiency
When a caterpillar feeds on a leaf, only about one-sixth of the leaf’s energy is used for secondary production
An organism’s production efficiency is the fraction of energy stored in food that is not used for respiration
Birds and mammals have efficiencies in the range of 13% because of the high cost of endothermy
Fish have production efficiencies of around 10%
Insects and microorganisms have efficiencies of 40% or more
Trophic efficiency
The percentage of production transferred from one trophic level to the next
It is usually about 10%, with a range of 5% to 20%
A pyramid of net production represents the loss of energy with each transfer in a food chain
Aquatic limiting nutrients
Depth of light penetration affects primary production in the photic zone
Nutrients limit primary production in oceans and lakes
A limiting nutrient is the element that must be added for production to increase in an area
Nitrogen and phosphorous most often limit marine life
Nutrient sources
Upwelling of nutrient-rich waters in parts of the oceans contributes to regions of high primary production
In some areas, sewage runoff has caused eutrophication of lakes, which can lead to loss of most fish species
In lakes, phosphorus limits cyanobacterial growth more often than nitrogen
Terrestrial primary production
In terrestrial ecosystems, temperature and moisture affect primary production
Primary production increases with moisture
Various adaptations help plants access limiting nutrients from soil
Some plants form mutualisms with nitrogen-fixing bacteria
Many plants form mutualisms with mycorrhizal fungi
Roots have root hairs that increase surface area
Many plants release enzymes that increase the availability of limiting nutrients
Nutrient recycling
Life depends on recycling chemical elements between organic and inorganic reservoirs
Nutrient cycles in ecosystems involve biotic and abiotic components and are often called biogeochemical cycles
Water cycles
Liquid water is the primary physical
97% oceans, 2% ice, 1% liquid freshwater
Moves by evaporation, transpiration, condensation, precipitation, and movement through surface and groundwater
Carbon cycles
Carbon-based organic molecules are essential to all organisms!
Photosynthetic organisms convert CO2 to organic molecules (fixation)
Carbon reservoirs include fossil fuels, soils and sediments, solutes in oceans, plant and animal biomass, the atmosphere, and sedimentary rocks
photosynthesis/respiration
Nitrogen cycles
Nitrogen is a component of amino acids, proteins, and nucleic acids
The main reservoir of nitrogen is the atmosphere (N2), though this nitrogen must be converted to NH4+ or NO3– for uptake by plants, via nitrogen fixation by bacteria
Nitrogen fixation, ammonification, nitrification, denitrification
Phosphorus cycles
Phosphorus is a major constituent of nucleic acids, phospholipids, and ATP
Phosphate (PO43–) is the most important inorganic form of phosphorus
The largest reservoirs are sedimentary rocks of marine origin, the oceans, and organisms
Cycles slowly
Decomposition and nutrient cycling
Decomposers/detritivore play a key role in the general pattern of chemical cycling
Rates at which nutrients cycle in different ecosystems vary greatly, mostly as a result of differing rates of decomposition
The rate of decomposition is controlled by temperature, moisture, and nutrient availability
Electrons can be anywhere in the electron cloud at any given point
Can only see snapshots and can only predict the possibility of where it would be
To get out of the electron cloud, it absorbs energy to go to another orbital
Carbon, nitrogen, hydrogen, and oxygen are the elements of life because…
Oxygen has a higher electronegativity
These elements are lighter than their groups
Bonds between oxygen and hydrogen are stronger because sulfur has more shielding
Essentials of H2O
Polarity (polar neutral)
Charge poles on individual elements in an atom
Cohesive/adhesive properties
Has the ability to influence other water molecules
Cohesion is where water molecules are attracted to each other due to hydrogen bonding
Adhesion is where water molecules are attracted to other molecules
Structure gives rise to function
How the molecule is shaped affects how they interact with other molecules
The bonds can flex and break but still maintain their shape
Carbon
Hydrocarbons are only made up of hydrogens and carbons
Many molecules have a backbone of this(DNA, lipids)
Lipids have hydrophobic tails and hydrophilic heads
The base is a hydrocarbon
Hydrocarbons’ orientation relates to the function that the organism will have
The bonds that atoms make limit the amount of rotation
Unsaturated fats cause bends in hydrocarbon chains
Better than saturated because straight chains will only build upon each other while the bent chains are more likely to move around and not block arteries/veins
Hydrolysis uses water to break bonds and release energy through enzymatic reactions
Dehydration is the formation of new bonds through energy input and water release
Carbohydrates(1:2:1)
Two monosaccharides bonded together are linked by glycosidic bonds(alpha carbon 1-carbon 4)
Monosaccharides(deoxyribose, ribose) - > 5 carbon sugars
Disaccharides(sugars)
Polysaccharides(starch, cellulose for peristalsis)
Uses of carbs
Energy for cell and structure support
Helps to regulate glucose consumption and removes excess cholesterol
Nucleotides
A nitrogenous base, phosphate group, sugar
Nitrogenous bases
Know how {cytosine, thymine, uracil} - pyrimidines, {adenine, and guanine} - purines look like
Pentose sugars(deoxyribose, ribose)
Deoxyribose has H at Carbon 4 and ribose has OH at Carbon 4
DNA
Right-handed helix(directionality of folding of helix)
Anti-parallel
5’ to 3’
Major groove vs. minor groove
It helps to tell the location of DNA
Major grooves have a higher distance between turns
RNA
U for T
Translation of genetic info to proteins
Multiple functions
mRNA, tRNA, rRNA
Can have intramolecular bonding(not always stranded cause they are in motion constantly)
Lipids
Fats and oils, waxes, phospholipids, steroids
Saturated fats are surrounded by hydrogen bonds and are all single bonds while unsaturated are not saturated by hydrogen bonds, causing double bonds
Can have cis and trans unsaturated fats
Cis is where the hydrogens are on the same side, and it is also called the z-formation
Trans is where hydrogen bonds are on the opposite side of the bonds
Phospholipids
Phosphate connected to glycerol and glycerol are connected to two separate fatty acid chains(one saturated and another unsaturated, causing a bend)
Form outer membranes
Micelles can be used to target drug delivery
Are introduced into hydrophilic or hydrophobic environments, causing them to open or close at the location site after they encapsulate with the drug and act as a transport mechanism(bio-encapsulation)
Steroids
Cholesterol is part of steroids and they have a ring structure that doesn’t resemble other liquids
The ring structure is important for certain types of hormones and ring transductors
Rings are interconnected and they can rotate throughout the structure(resonance)
Proteins
Amino acids are monomers for proteins
4 structural formations
An umbrella term for various biomacromolecules
Undergoes folding and denaturations(breaks down tertiary and quaternary structure)
Amino acid base structure consists of an r-group, an amino group, and a carboxyl group
R-group is specifically for carbon-based chains and R is the specific structure that interchanges with functional groups(have to specify what R is on a test)
Carboxyl group can be an acid depending on if it is protonated
Amino acid R groups
Positive charge or negative charge, polar or nonpolar, hydrophobic or hydrophilic (have to remember this for AP)
Nonpolar R groups are generally hydrocarbons, hydrogens, or carbons
Structures
The primary structure is the sequence of a chain of amino acids(A-I-G) - linearized amino acid sequence
Secondary structure is the local folding of polypeptide chains into helices or sheets
Alpha helix(DNA), beta helix, beta pleated sheets(wave, folded sheets), alpha sheets
Tertiary structure is a 3D folding pattern of a protein due to side chain interactions(intramolecular reactions)
The beta-pleated sheet can turn into a helix
Beta pleated and helix together are tertiary
Quaternary
A protein consisting of more than one amino acid chain(multiple tertiaries combine to form a full molecule)
Types of proteins that are biomacromolecules
Enzymes, hormones, toxins
Protein folding
Structure gives rise to function(e.g. Denatured proteins)
The cell is the smallest unit, all living things are made of cells and all cells come from pre-existing cells
Prokaryotes are bacteria and archaea
Plants, animals, fungi, and protists are eukaryotes
Prokaryotes have no nucleus and no membrane-bound organelles
The plasma membrane is semi-permeable, meaning that only certain substances can go in and out, regulating homeostasis
Cytoskeleton support organelles in cytoplasm
Ribosomes are not membrane-bound organelles and make protein(free or attached)
The nucleus holds genetic material and controls cell activities(nucleolus where ribosomes are produced)
ER transports molecules with vesicles and produces proteins(rough ER) while smooth ER does detoxification(reason why liver cells have a lot of smooth ER)
Golgi is the ultimate packaging center(enzymes, packaging, transporting)
Mitochondria powers all the above processes by making ATP through cellular respiration and using glucose
Animal vs plant
Plants have mitochondria and chloroplasts which make glucose through photosynthesis (chlorophyll captures light energy)
Vacuoles for both where the plant has one and the animal has several
Plants have a cell wall unlike animal cells
Eukaryotic cells
All cells have a cell membrane, cytoplasm, and DNA
Chromatin is found in the nuclear membrane and DNA turns into chromosomes
After ribosomes leave the nucleolus, they make proteins
ER transports proteins synthesized by ribosomes
Proteins emerge from ER in small vesicles (bubbles that leave the organelle membrane as bubbles of transport)
Golgi body receives them and they are customized to fold proteins into usable shapes or add lipids or carbs to them
Vacuoles store things like the central vacuole stores water
Lysosomes are garbage collectors and are filled with enzymes that are filled with cellular debris
The cytoskeleton has microfilaments made of proteins and microtubules that are thin, hollow tubes
Some autotrophic plants have chloroplasts and the cell wall covers the cell membrane
Other unique structures
Cilia, which are hair-like projections that trap particles in the air and expel them when you cough
Flagella, which is on bacteria and is like the sperm cells’ tails
Mitochondria is double membraned and has compartments for different metabolic reactions like Kreb’s cycle, electron transport chain, and ATP synthesis
Lysosomes contain a large number of hydrolytic enzymes that, when released from the lysosomes, can come into contact with cytosolic targets and contribute to apoptotic cell death
Exocytosis - the ability of something to exit the cell
Plant cells
Thylakoids are organized in stacks called grana
Stroma is fluid within the inner chloroplast membrane and outside of thylakoids
Grana is where light-dependent photosynthesis occurs
Carbon fixation reactions of photosynthesis occur in the stroma or the Benson cycle
Plasma/cell membrane
Fluid mosaic model, meaning the membrane is not a straight line and not a perfect circle
Freedom of oscillation, or the capability to move and change
Interstitial protein/carbs are bound within the membrane and are also able to move within the lipid bilayer
Typically stay within a certain environment
Trans vs. cis membrane proteins
Proteins that span both inside and outside of the plasma membrane(trans) vs. carbs that or only present on the outside of the plasma membrane
Endosymbiosis
Endo means within another and symbiosis means a mutually beneficial relationship
The cell theory says that some of the organelles of eukaryotes were once prokaryotic microbes that were phagocytized
Evidence
Some organelles have double membranes(the outer membrane may be vesicular in origin)
Antibiotics - susceptible to antibiotics (organelles may have bacterial origins
Division - reproduction occurs via a fission-like process
DNA - has its DNA which is naked and circular (like prokaryotic DNA)
Ribosomes - have ribosomes which are 70S in size (identical to prokaryotic ribosomes)
Compartmentalization
Different parts of the cell have different functions
Cells work similarly in compartmentalizing to stop random molecules from disrupting processes
Short processing/transfer times(increase surface area by folds, thus increasing production)
Specialized functions
Keep external systems out of necessary internal parts
Membrane permeability
Cell walls = boundaries and selectively permeable barriers for keeping cell material internalized
Allows for things to flow or transport in and out of the cell but only for certain things
Depends on polar vs. nonpolar, hydrophobic/hydrophilic, or if a molecule moves freely or assisted across the membrane(passive/active)
HIV tends to hide by C4 protein(undetected by the immune system and it can lay dormant for a few years or show symptoms immediately)
Passive Transport: Net movement of molecules from high concentration to low concentration without the direct input of metabolic energy
Active Transport: Requires the direct input of energy to move molecules from regions of low concentration to regions of high concentration
Types of passive transport
Diffusion
The passage only relies on the concentration gradient
Facilitated diffusion
Materials move across the membrane with the help of carrier proteins
Feedback inhibition tells when there is too much of a certain substance passing through the ion channels (passage)
Membrane proteins are required for diffusion of large, polar molecules through a membrane
Large quantities of water pass through aquaporins
Small nonpolar molecules pass through easily unlike water molecules, so aquaporins help with passage
Charged ions like sodium and potassium require channel proteins
Membranes may become polarized by movement of ions across the membrane
Types of active transport
Electrochemical gradient
Ion pumps(sodium-potassium ion pumps)
Actively push ions in or out of the cell
ATP dependant carrier proteins
Glucose transporter protein
Other transports
Endocytosis: the process of capturing a substance or particle from outside of the cell by engulfing it with the cell membrane
Exocytosis: the process of vesicles fusing with the plasma membrane and releasing their contents to the outside of the cell
Since it’s a fluid mosaic model, vesicles can just remove obstacles out of the way and go into the membrane
Tonicity/Osmosis
Osmosis is the movement of water molecules
Hypotonic: water enters and causes the cell to swell
Hypertonic: Water leaves the cell and causes it to shrivel
Isotonic: nearly perfect
Water potential
The potential of water to move across a membrane by osmosis from areas of high water potential/low osmolarity/low solute concentration to areas of low water potential/high osmolarity/high solute concentration
Psi(Ѱ) = water potential in megapascals
Ѱp = pressure potential
Ѱs = solute potential
Formula: Ѱ = Ѱp + Ѱs
Ѱs = -iCRT defines solute potential
I = ionization constant(1 for sucrose because sucrose does not ionize in water) - it is the number of ions produced/in production
C = molar concentration
R = pressure constant ( R=.0831 liter bars/mole K)
T = temperature in Kelvin (℃ + 273) - assuming standard temperature and pressure of 273.15 K unless specified
A negative sign in front of I means moving from a high water potential to a low water potential(moves from the cell into the solution)
Nucleotide
The phosphate group is negative, so DNA has a negative charge because phosphate groups are facing outward
DNA vs. RNA
The 5-sugar ring on DNA has hydrogen on the carbon 2 and RNA has a hydroxide on carbon 2(identifying factor on tests)
Naming of carbon sugars
Start from oxygen and go clockwise
Write carbon anywhere there is a bend or an end
Identifying direction
5’ phosphate and 3’ hydroxide
Counting carbon numbers
Central Dogma
DNA to RNA is transcription and RNA to protein is translation
Genetic information
DNA is the primary source and RNA is a secondary source
Plasmids - small, extrachromosomal, double-stranded circular DNA molecules(primarily in prokaryotes but can be in eukaryotes)
Sequence of RNA bases and structure of RNA molecule determines RNA function
tRNA and rRNA are structural molecules while mRNA are functional
rRNA
Functional building blocks for ribosomes
Ensures proper alignment of mRNA and ribosome
Also has enzymatic activity
Peptidoglycan transferase - catalyzes the formation of the peptide bonds between two aligned amino acids
Formation(similar to mRNA)
RNA polymerase 1(in nucleolus) is a nuclear substructure that is responsible for transcribing, processing, and assembling rRNA into ribosomes
Also has a pre-rRNA step where it is cleaved and processed before becoming mature rRNA
Different from mRNA because it gets transported to another location out of the nucleus
RNA polymerase
The enzyme responsible for copying a DNA sequence into an RNA sequence during transcription
Uses a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecule
3 stages of RNApol
Initiation - RNApol wraps around the promoter region of DNA, which is a sequence that guides RNApol on where to bind. Eukaryotes need help to bind unlike prokaryotes using transcription factors.
Elongation - unwinds double-stranded DNA into two single strands
Termination - when RNApol sees a terminator sequence, it stops adding complementary nucleotides to the RNA strand
Transcription
DNA strand acting as the template strand is also referred to as the noncoding strand/minus strand/antisense strand
The determined noncoding strand is dependent on the gene being transcribed
RNApol synthesizes mRNA molecules in the 5’ to 3’ direction by reading the template DNA strand in the 3’ to 5’ direction
Reads DNA backwards
Cell-to-cell communication is important for the function and survival of cells and organism
Responsible for the growth and development of multicellular organisms
Communicate through chemical signals
An example is the fight or flight response - epinephrine
Cell communication
Signaling cells release small volatile or soluble molecules called a ligand
Ligands get sent out to the system as a signal(like a substrate)
They bind to the receptor portion on the target cell(like an enzyme)
The final relay of the message is called a cellular response
The whole point of cell communication is to initiate a cellular response
Three ways to communicate
Direct contact
Cell going up to another cell and relaying the message
Form extracellular components like transmembrane proteins
Blocking cell communication prevents cells from knowing what to do(could target cancer cells)
Local signaling
Short-distance signaling - within the same organ system/tissue
Long-distance signaling
For example when your toe is hurt and sent to your brain
Another example is an upset stomach
Between different systems or nerves
Signaling
Autocrine
Cell targets itself
Signaling across gap junctions
Paracrine
Short-distance signaling where a cell targets a nearby cell
Endocrine
A cell targets a distant cell through the bloodstream(kind of like glucose levels)
Direct contact
Signaling substances and other material dissolved in cytoplasm can pass freely between adjacent cells
Animal cells have gap junctions while plant cells have plasmodesmata
White blood cell
On the T-cell we have antigens and when a signal is released that produces the substrate, causing an alarm to be produced, activating the immune system
Also called antigen-presenting cells
Local regulators
A secreting cell will release chemical messages(ligands) that travel a short distance through the extracellular fluid
Chemical messages will cause a response in a target cell
Nerve disorders due to uncontrolled chemical messages
Examples
Paracrine signaling
Secretory cells release local regulators via exocytosis to an adjacent cell to make sure the target cell receives ligands
Synaptic signaling
In animal nervous systems
Neurotransmitters are secreted by the axon and are uptaken by the synaptic system(target cells)
Through diffusion
The synaptic cleft is the distance neurotransmitters have to travel to get to target cells
Can be long-distance depending on the length of the neuron(for the sake of AP Bio we consider it as short-distance)
Long-distance signaling
Insulin counts cause it is only produced in one specific area: the pancreas
Animals and plants use hormones for long-distance signaling
Plants release hormones that travel in the plant vascular tissue(xylem and phloem) or through the air to reach the target tissue
Animals use endocrine signaling
Specialized cells release hormones into the circulatory system where they reach target cells
Example
Insulin is released into the pancreas into the bloodstream where it circulates in the bloodstream
Cell processing
Cells process signals when the substrate binds to the active site, causing a molecule to be released and interact with other molecules until it finally reaches the nucleus and other places
Cell signaling overview
Reception
The detection and receiving of a ligand by a receptor in the target cell
Receptor: macromolecules that bind to signal molecules(ligands)
All receptors have an area that interacts with the ligand and an area that transmits a signal to another protein
The binding between ligand and receptor is highly specific
When a ligand binds to the receptor, the receptor activates through a conformational change
Conformational change can change another part of the receptor, initializing reactions sometimes
Can be intracellular or in the plasma membrane
Transduction
Signal is converted
Is the conversion of an extracellular signal to an intracellular signal that will bring about a cellular response
Signal transduction pathway - a series of steps by which a signal on a cell’s surface is converted into a specific cellular response
Regulates protein activity through phosphorylation by the enzyme protein kinase(adds phosphates)
Relays signal inside the cell
Dephosphorylation by the enzyme protein phosphatases(removes a phosphate)
Shut off pathways
Change in shape means change in function
Amplifies signal(multiple responses)
Second messengers: small, non-protein molecules and ions help relay the message and amplify the response
Cyclic AMP is a common second messenger
Response
Cell process is altered
The final molecules in the signaling pathway convert the signal to a response that will alter a cellular process
Examples
Protein that can alter membrane permeability
Enzymes that will change a metabolic process
Protein that turns genes on or off
Signal transduction pathways
Can influence how a cell responds to its environment
Results in changes in gene expression and cell function
Mutations to receptor proteins or any component of the signaling pathway will result in a change to the transduction of the signal
Important receptors
In eukaryotic cells
G protein-coupled receptors(GPCRs)
An entire molecule is called a 7-fold double-spanning system(spans cell membrane 7 times)
Has an extracellular and intracellular portion
Largest category of cell surface receptors because there are multiple binding sites
Important in animal sensory systems
Binds to a G protein that can bind to GTP, which is an energy molecule like ATP
Is an enzyme and the protein is inactive until the ligand binds to GPCR on the extracellular side
Inactive GPCR - ligand binds - conformational change occurs - activates GPCR - activates G protein - becomes energy
Allows phosphorylation of GTP to GDP
The amplified signal leaves a cellular response(stays active until dephosphorylated)
Ion channels
Ligand-gated ion channels
Typically closed until a response makes it open
Located on plasma membranes and are very important for the nervous system
When a ligand binds to the receptor, the gate opens/closes allowing the diffusion of specific ions
Initiates a series of events that lead to a cellular response
Most water-soluble signal molecules bind to specific sites on receptor proteins that span the plasma membrane
3 main types
G protein-coupled receptors, receptor tyrosines, ion channels
Can internally signal by passing through ion channels or externally signal through the g protein
Receptor tyrosine kinase
Are membrane receptors that attach phosphate to tyrosines
Can trigger multiple signal transduction pathways at once
Abnormal function is associated with many types of cancers
Part of an ATP pathway and do it through the conformational change of two tyrosines after the ligand binds to them
Become active and can phosphorylate 6 at a time
Ion channel
When a signal molecule binds as a ligand to the receptor, the gate allows specific ions such as sodium and calcium through a channel in the receptor
Intracellular receptors
Are found in the cytosol or nucleus of target cells; only cells with proper receptors respond
Small or hydrophobic chemical messengers can cross the membrane and activate receptors that are inside
Steroids, thyroid hormones
An activated hormone-receptor complex can act as a transcription factor, turning on specific genes
Protein kinases transfer phosphates from ATP to protein
Phosphatases remove the phosphates from proteins
Second messengers
Ligand to receptor (first messenger)
Smaller molecule, non-protein (small messenger)
Amplification
Camps
Adenylyl cyclase(an enzyme in the plasma membrane) converts ATP to cAMP in response to an extracellular signal
Signal molecules trigger the formation of cAMPs
Usually activates protein kinase A
G-protein inhibits adenylyl cyclase
Calcium ions and inositol triphosphate
Calcium ions also act as second messengers
Important because cells can regulate their concentration
A signal relayed can trigger an increase in cytosolic calcium
Pathways leading to the release of calcium involve inositol triphosphate (IP3) and diacylglycerol (DAG) as additional second messengers
Signal response
This leads to the regulation of transcription or cytoplasmic activities
Response to an extracellular signal is called output response
The signal transduction pathway leads to multiple responses in the cytoplasm or nucleus
Other pathways regulate the activity of enzymes rather than their synthesis
Fine-tuning of response
Amplification of signal
Specificity of response
Efficiency of response(enhanced by scaffolding proteins)
Scaffolding proteins are large relay proteins to which other relay proteins are attached, which helps to increase signal transduction efficiency by grouping proteins in the same pathway
Scaffolding proteins can also help to activate relay proteins
Termination of signal
Inactive mechanisms are important for signaling
If ligand concentration falls, fewer receptors will be bound
Unbound receptors go back to the inactive state
The body must be able to monitor its internal conditions at all times
Set points: values for various physiological conditions that the body tries to maintain
Has a normal range for which it can fluctuate
For instance, body temperature
Set point: 98.6 degrees Fahrenheit
Normal range: 97 degrees to 99 degrees
Homeostasis: the state of relatively stable internal conditions
Organisms detect and respond to a stimulus
The body maintains homeostasis through feedback loops
Feedback loops
Negative and positive
The most common is negative feedback
Reduces the effect of the stimulus
Examples
sweat(we need to start cooling down)
Blood sugar(don’t want high/low amount of insulin)
Breathing rate(oxygen lowered)
Body temperature
Stimulus: Heat -> Receptor: temperature receptors or skin -> Effector: sweat glands -> Response: sweat
Stimulus: Cold -> Receptor: temperature receptors or skin -> Effector: muscles -> Response: shivering
Positive feedback is where you have to respond more, saying that you need more of a certain stimulus
Increases effect of a stimulus
Examples
Childbirth
Stimulus: baby pushes on cervix -> Receptor: nerve cells in cervix send a signal to the brain -> Effector: pituitary gland releases oxytocin -> Response: oxytocin stimulates contractions
Blood clotting
Fruit ripening
Stimulus: a variable that will cause a response(kind of like a ligand)
Receptor/sensor: this information is sent to the control center
Effector: muscle or gland that will respond
Response: changes the effect of the stimulus(increase/decrease)
Homeostatic imbalances
Diabetes or hormone imbalances
Genetic disorders
Drug or alcohol abuse
Linked to a genetic disorder
The chance of becoming a drug abuser is increased if you have a drug addict in your lineage
Intolerable conditions(extreme heat or cold)
Can’t stay outside for long periods
Diseases: When the body is unable to maintain homeostasis
Cancer: The body can’t regulate cell growth
Diabetes: The body cannot regulate glucose levels
Cell signaling
Cells in an organism must communicate to maintain homeostasis
Communication occurs in signal transduction pathways
Genes
Units of heredity; made up of segments of DNA
Passed to the next generation through gametes
Each gene has a specific location on a chromosome called a locus
Most DNA is packaged into chromosomes
Somatic cells are any cell other than sex cells/gametes
23 pairs of chromosomes
Karyotype: ordered display of chromosomes from a cell
Human games have one set of 23 chromosomes
Autosomes: normal chromosomes that do not determine sex
Sex chromosomes: determine sex and are X and Y
Females have two XXs and males have XY
2 chromosomes in each pair in somatic cells are called homologous chromosomes
Same length and shape and similar gene characteristics
Each pair of chromosomes has one from each parent
23 from mother and 23 from father
Diploid: cell with two sets of chromosomes(2n = 46)
Haploid: cell with one set of chromosomes(n = 23)
Sister chromatids
DNA synthesis allows two chromosomes to form
Each replicated chromosome has two identical sister chromatids
Meiosis
Preceded by replication of chromosomes
Two divisions: Meiosis 1 and 2
Results in 4 genetically unique daughter cells
Each daughter cell has half as many chromosomes as the parent cell
Stages
Chromosome duplication in S-phase
Meiosis 1
Before meiosis, chromosomes are replicated to form identical sister chromatids, joined by a centromere
Single centrosome replicates, forming two centrosomes
Reductional division
Homologs pair up and separate, resulting in two haploid daughter cells with replicated chromosomes
Phases
Prophase 1
Duplicated chromosomes pair and exchange segments
Crossing over:
Synopsis: homologous chromosomes loosely pair, aligned gene by gene
Non-sister chromatids exchange DNA segments
Each pair of chromosomes forms a tetrad
Each tetrad has one or more chiasmata(X-shaped regions where crossing over occurs, which increases genetic diversity)
Metaphase 1
Chromosomes line up by homologous pairs
Anaphase 1
Homologous chromosomes separate
Telophase 1 & Cytokinesis
Two haploid cells form; each chromosome still consists of two sister chromatids
Meiosis 2
Equational division
Sister chromatids separate in similar phases to mitosis
Forms 4 haploids
Sister chromatid cohesion
Allows sister chromatids of a single chromosome to stay together during meiosis 1
Done through protein complexes called cohesins
Mitosis, cohesins are cleaved at the end of metaphase
Meiosis, cohesins are cleaved along chromosome arms in anaphase 1 and at centromeres at anaphase 2
Genetic variation
Source of genetic diversity
Mutations create different versions of genes called alleles
Can shuffle the alleles through
Crossing over
Produces recombinant chromosomes that combine DNA inherited from each parent
Beings early in prophase 1
Homologous portions of two non-sister chromatids trade places
Contributes to genetic variation by combining DNA from two parents into a single chromosome
Independent assortment
Homologs orient randomly in metaphase 1
Each pair of chromosomes sorts maternal and paternal homologs into daughter cells independently of other pairs
The number of combinations possible is 2^n, where n is the haploid number
For humans(n=23) that means that there are more than 8 million possible combinations
Random fertilization
This adds to genetic variation because any sperm can fuse with any ovum(unfertilized)
The fusion of two gametes produces a zygote with 70 trillion diploid combinations
Particulate hypothesis
Reappearance of traits after several generations
Documented by Mendel
Mendel studied pea plants
Many varieties with distinct heritable features and characteristics called traits
Mating can be controlled
Chose to track characters that occurred in two distinct forms
Used varieties that were true-breeding(plants that produce offspring of the same variety when they self-pollinate)
Mated two contrasting varieties, a process called hybridization
P generation: true-breeding parents
F1 generation: hybrid offspring of the P generation
F2 generation: product of a cross between F1 generation
Easier to domesticate because it is less wild
A heritable factor is called a gene
Hypothesis to explain 3:1 ratio inheritance
Model
Alternative versions of genes account for variation in inherited characteristics
Alleles are alternative versions of genes
Each gene resides at a specific locus on a specific chromosome
For each character, an organism inherits two alleles, one from each parent
If two alleles at a locus differ, then the dominant allele determines the organism’s appearance, and the recessive allele has no noticeable effect
Law of segregation
Two alleles for a heritable character separate during gamete formation and end up in different gametes
An egg or a sperm gets only one of the two alleles that are present in the organism
Corresponds to the distribution of homologous chromosomes to different gametes in meiosis
Complex inheritance patterns
Heritable characters are not determined by only 2 alleles
independent assortment and segregation still apply
Degrees of dominance
Complete dominance
When phenotypes of the heterozygote and dominant homozygote are identical
Example is Mendel’s peas(green rough, green smooth, white smooth)
Incomplete dominance
The phenotype of F1 hybrids is somewhere between the phenotypes of the two parental varieties
Example is the snapdragon flower color(mix of red and white dominant genes where they are expressed partially)
No distinct white or red until F2 generation
Codominance
Two dominant alleles affect the phenotype in separate distinguishable ways
Examples are human blood type and dalmatians
One person can have AB and the other can have AB and after breeding, they can have children with blood types AB, AB, AA, and BB
For any character, dominance/recessiveness relationships of alleles depend on the level that we examine the phenotype
Tay-sachs disease - a dysfunctional enzyme causes an accumulation of lipids in the brain
At the organism level(as people), the allele is recessive
At the biochemical level, the phenotype(the enzyme activity level) is incompletely dominant
At the molecular level, the alleles are codominant
Dominant alleles are not more common than recessive; it’s just a matter of who expresses it
One baby out of 400 in the US is born with extra fingers or toes(polydactyl), but it’s a dominant allele rather than a recessive allele
Humans have multiple blood types(A, B, AB, O)
Pleiotropy
Genes exhibit multiple phenotypic effects
Cystic fibrosis, sickle cell anemia
The SRY(sex-determining region Y-gene) gene produces a protein that is a transcription factor which begins the development of testis in male individuals(what causes a fetus to become a male)
The testis then secretes testosterone and leads to the development of a male phenotype
Yellow coated mice who are homozygous for the dominant yellow coat gene do not survive(dominant lethal)
The gene is pleiotropic because it impacts the color and survival of the mice
Epistasis
A gene at one locus alters the phenotypic expression of a gene at a second locus
In labrador retrievers and many others mammals, coat color depends on two genes
One gene determines the pigment colors(B=black; b=brown) and the other determines whether the pigment will be deposited(E=color; e=no-color)
Interacting genes
Two genes are responsible for one effect(2 separate alleles that are expressed together unlike codominance where it is expressed on the same allele)
You can’t have one without the other
In a wild-type cobra, one gene is for orange and one gene is for black
Wild-type is the most common snake
Polygenic inheritance
Quantitative characters
Vary in the population along a continuum
Usually indicates polygenic inheritance, an additive effect of two or more genes on a single phenotype
Can do skin color and height in humans
Environmental impact
Phenotype depends on environment
Norms of reaction: the phenotypic range of a genotype influenced by the environment
Most common ones are hydrangeas(flowers) of the same genotype that range from blue-violet to pink, depending on soil acidity
Mitochondrial DNA
mtDNA does not follow Mendelian rules
It is inherited with mitochondria, which are randomly assorted into gametes and daughter cells
In animals, mtDNA is transmitted by the egg and not the sperm, causing mtDNA to be maternally inherited
Makes mtDNA useful for studying population and migration patterns
Designer babies are done through taking mitochondria from one, egg from another, and sperm from donor father
Maternal mitochondria is useful for studying migrations
Humans are not good subjects for genetic research because generation times are too long, parents produce few offspring, and breeding experiments are unacceptable
Pedigree
A family tree that describes the interrelationships of parents and children actress generations
Inheritance patterns of particular traits can be traced and described using pedigrees
Recessively-inherited disorders show up in homozygous offspring
Carriers
Heterozygous people who carry the recessive allele but are phenotypically normal
Autosomal pedigrees are used for following the traits to see the expression throughout the generations
Squares are males and circles are females
X-linked pedigrees
X-linked recessive(skips every generation): more males than females show the phenotype
None of the offspring of an affected male are affected but all daughters are carriers and half of the other daughters’ sons are affected
Hemophilia, duchenne muscular dystrophy, testicular feminization syndrome
X-linked dominant(occurs every generation): affected males pass the condition on to all daughters but no sons and affected females are mostly heterozygous and pass condition to half of their offspring
Dominant lethal
An individual inheriting two copies of the allele leads to death, making achondroplasia lethal
Huntington’s disease
Degenerative disease of the nervous system
CAG trinucleotide repeats
Condition is irreversible
Multifactorial disorders
Many diseases like heart disease, diabetes, alcoholism, mental illnesses have both genetic and environmental components(multifactorial)
Little is understood about why they occur genetically
Information content of DNA is in the form of specific sequences of nucleotides
Transcription: synthesis of RNA under the direction of DNA, producing mRNA
Translation: RNA to protein
Primary transcript: the initial RNA transcript from any gene prior to processing
Eukaryotes
Nuclear envelope separates transcription from translation
RNA transcripts are modified through RNA processing to yield finished mRNA
Codons
Flow of information is dependant on codons, which are a series of nonoverlapping, 3-nucleotide words
Codons are transcribed into complementary words of mRNA
These are words are then translated into a chain of amino acids, resulting in a polypeptide
Are read in the 5’ to 3’ direction
Each codon specifies one amino acid(20 total) to be placed at the relevant position of the polypeptide
Of these 64 triplets, 61 code for amino acids while 3 are stop signals to end translation (UAG, UGA, UAA)
The genetic code is redundant(more than one codon may specify a particular amino acid) but not ambiguous - no codon specifies more than one amino acid
Codons must be read in the correct reading frame in order for the specific polypeptide to be produced
Codons and amino acids are linked by tRNA
Need to know what the abbreviations on codon chart stand for
Genetic code is universal
Shared by the simplest bacteria to the most complex animal
Genes can be transcribed and translated after being transplanted from one species to another
Example is luciferase where they move this to another organisms, making them glow
Transcription
RNA synthesis is catalyzed RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides
Follows the same base pairing as DNA
DNA sequence where RNA polymerase attaches is called the promoter region
In bacteria these sequence signaling the end of transcription is called the terminator region
The stretch of DNA is called the transcription unit
RNA polymerase binds to promoter regions, beginning transcription
Transcription factors mediate the binding of RNA polymerase
Transcription initiation complex: after RNA polymerase binds
A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes
Elongation
As RNA polymerase moves along the DNA, it unwinds the double helix 10-20 base pairs at a time
Transcription progresses at a rate of 40 nucleotides per second in eukaryotes
A gene can be transcribed simultaneously by several RNA polymerases
Nucleotides are added to the 3’ end of the growing RNA molecule
There can be different promoter regions on DNA, having RNA polymerases at once in different places
Termination
In eukaryotes
RNA polymerase II transcribes the polyadenylation signal(AAUAAA); the RNA transcript is cut free by proteins about 10-35 nucleotides past this signal
In bacteria:
The polymerase stops transcription at the end of the terminator region, which is why they don’t need modifications
mRNA alteration
5’ cap, 3’ poly-A tail, intron splicing
Functions
Facilitate the export of mRNA
Protect mRNA from hydrolytic enzymes
Help ribosomes attach to the 5’ end
Spliceosomes
Do the cutting of the mRNA(RNA splicing(
Consist of a variety of proteins and several small nuclear ribonucleoproteins(snRNPs) that recognize these splicing sites
Ribozymes
Catalytic ribosomes/RNA molecules
This was the first time that scientists were able to say that not all biological catalysts are proteins
Properties of RNA as an enzyme
It can form a 3D structure because of its ability to base pair with itself
Some bases in RNA contain functional groups that may participate in catalysis (*function as a catalyst)
RNA may hydrogen bond with other nucleic acid molecules
tRNAs
Each one has a different anticodon, so they are not identical
Accurate translation
A correct match between a tRNA and an amino acid must be needed
A correct match between the tRNA anticodon and an mRNA codon must be needed
Flexible pairing at the third base of a codon is called wobble and allows some tRNA’s to bind to more than one codon
rRNA
Large and small subunit
Ribosome has three binding sites for tRNA
P site: holds the tRNA that carries the growing polypeptide chain
A site: holds the tRNA that carries the next amino acid to be added to the chain
E site: the exit site where discharged tRNAs leave the ribosome
Amino acid
Instead of 5’ and 3’, we use terminus
The N-terminus(5’) and the C-terminus(3’) are on two ends of the polypeptide
Is a subset of amino acids on the ends of your protein
Could be 3, 4, 5, or more amino acids that are at the beginning, and it depends on the protein
Modifications
During and after synthesis, a polypeptide chain spontaneously coils and folds into its 3D shape(folds there because of the chemical environment its in)
Proteins may also require post translational modifications before doing their job
Some polypeptides are activated by enzymes that cleave them
Others come together to form the subunits of a larger protein
Transcription regulation
Prokaryotes and eukaryotes can alter gene expression in response to their changing environment
In multicellular eukaryotes, gene expression regulates development and causes differences in cell types
RNA molecules play many roles in regulating gene expression
Bacterial regulation
Natural selection has favored bacteria that produce only the products needed by the cell
A cell can regulate the production of enzymes by feedback inhibition or by gene regulation
Gene expression in bacteria is controlled by the operon
Operons are a cluster of functionally related genes can be under coordinated control by a singleton-off switch(only in prokaryotes)
The switch is a segment of DNA called the operator, which is within the promoter
Operon: the entire stretch of DNA that includes the operator, promoter and controlled genes
Lac operon
Negative control: Regulatory proteins inhibit gene production by binding to dNA and blocking transcription
Repressor: Can switch off the operon by binding to the operatory and blocking RNA polymerase, and it is produced by a regulatory gene and interacts with regulatory proteins and sequences
Positive control: Stimulation of gene expression by binding to DNA and stimulation transcription, or binding to repressors to inactivate them
Activator: A protein that binds to DNA and stimulates transcription
Inducer: A small molecule that inactivates the repressor
Eukaryotic expression
Almost all cells are genetically identical
Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome
Abnormalities in gene expression can lead to cancer
Gene expression is regulated at many stages
Some genes like ribosomal genes are always turn on
Genes in packed heterochromatin are not usually expressed
Histone acetylation: Acetyl groups are attached to positively charged lysines in histone tails
Loosens chromatin structure, promoting transcription
DNA methylation
The addition of methyl groups to certain bases in DNA, which can reduce transcription
Can cause long-term inactivation of genes
In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development
Epigenetic inheritance
Chromatin modifications just discussed don’t alter DNA sequences, but can be passed to future generations of cells
It is the inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
There are multiple control elements in eukaryotic genes, which are segments of noncoding DNA that serve as binding sites for transcription factors
Transcription factors
Eukaryotic RNA polymerase needs transcription factor proteins
Proximal control elements are located close to the promoter while distal control elements/enhancers are far away or in an intron
Activators
A protein that binds to an enhancer and stimulates transcription of a gene
Enhancer: A segment of DNA containing control elements located far away from the gene
Activators have two domains, one that binds DNA and the other activates transcription
Bound activators facilitate a sequence of protein to protein interactions
A significant amount of the genome may be transcribed into noncoding RNAs
miRNAs: Small single-stranded RNA molecules that can bind to mRNA
Can degrade mRNA or block its translation
Chromosomal disorders
Large-scale alterations lead to spontaneous abortions/developmental disorders
Plants tolerate these genetic changes better than animals do
Nondisjunction: pairs of homologous chromosomes do not separate normally during meiosis
One gamete receives two of the same type of chromosome, and another gamete receives no copy
Chromosome number changes
Aneuploidy: results from the fertilization of gametes in which nondisjunction occurred
Offspring with this condition have an abnormal number of a particular chromosome
Monosomic: only one copy of a chromosome
Trisomic: three copies of a chromosome
Polyploidy: a condition in which an organism has more than two complete sets of chromosomes
Triploidy: three sets of chromosomes
Tetraploidy: four sets of chromosomes
Common in plants, not animals and are more normal in appearance compared to aneuploidy
Alterations of chromosome structure
Deletion: removes a chromosomal segment
Duplication: repeats a segment
Inversion: reverses orientation of a segment within a chromosome
Translocation: moves a segment from one chromosome to another
Human disorders
Alterations of chromosome number and structure are associated with some serious disorders
Some types of aneuploidy appear to upset the genetic balance less than others, resulting in individuals surviving beyond birth
These surviving individuals have a set of symptoms/syndrome, characteristic of the type of aneuploidy
Down syndrome
An aneuploid condition that results from three copies of chromosome 21
Affects about one out of every 700 children born in the U.S.
Frequency increases with the age of the mother
Aneuploidy of sex chromosomes
Nondisjunction of sex chromosomes produces a variety of aneuploid conditions
Klinefelter syndrome: result of an extra chromosome in a male, producing XXY individuals
Monosomy X/Turner Syndrome: produces X0 females who are sterile
Jacob’s syndrome: an extra Y chromosome in a male, producing XYY individuals
Structurally altered chromosomes
Cri du chat: results from a specific deletion in chromosome 5
Child with this condition is mentally retarded and has a catlike cry; individuals usually die in infancy or early childhood
Chronic myelogenous leukemia: caused by translocations of chromosomes
Genomic imprinting
Phenotype depends on which parent passed along the alleles for those traits
Involves the silencing of certain genes that are stamped with an imprint during gamete production
Is the result of methylation(addition of CH3) of cysteine nucleotides
Only affects a small number of mammalian genes
Critical for embryonic development
Inheritance of organelle genes
Extranuclear genes are found in organelles in the cytoplasm
Mitochondria, chloroplasts, and other plant plastids carry small circular DNA molecules
Inherited maternally because cytoplasm comes from the egg
Evidence came from studies on inheritance of yellow or white patches on leaves of an otherwise green plant
Some defects in mtDNA prevent cells from making enough ATP and result in diseases that affect the muscular and nervous systems
Ex: mitochondrial myopathy, Leber’s hereditary optic neuropathy
Nucleotide mutation
Changes in the genetic material
Point mutations: Chemical changes in just one base pair of a gene
A single nucleotide change in a DNA template strand can lead to the production of an abnormal protein
Divided into two general categories
Nucleotide pair substitutions
Transition
Transversion
One or more nucleotide pair insertions/deletions
Silent mutations
Have no effect on the amino acid produced by a codon because of redundancy in the genetic code
Missense mutations
Still code for an amino acid, but not the correct amino acid
Nonsense mutation
Change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein
Frameshift mutations(all of above mutations)
Insertions and deletions are additions or losses of nucleotide pairs in a gene
Have a disastrous effect on the resulting protein more often than substitutions do
insertion/deletion of nucleotides may alter the reading frame
Types of mutants
Some mutations cause a gain of function while others cause a loss of function
Loss of function
Dominant mutations are haplo-insufficient, meaning that one ene dosage is insufficient to exhibit the normal phenotype
Recessive mutations are either null(no gene activity) or hypomorph(meaning little gene activity)
Gain of function
Usually dominant and can be either hypermorph(increased activity) or neomorph(new)
Mutagens
Spontaneous mutations can occur during DNA replication, recombination, or repair
Are physical/chemical agents that can cause mutations like carcinogens
Typically collect data on a sample of a population to infer what is happening to a general population
Shows normal distribution of bell curve
Central tendencies
Descriptive statistics that allow for researchers to describe and quantify differences between data sets
Mean, median, mode are centers of distribution
Act as catalysts
Speed up the reaction without being consumed by the reaction
An enzyme is a catalytic protein
Activation energy barrier
All chemical reactions between molecules involve bonds breaking and forming
The initial energy to start a reaction is called the activation energy(EA)
Often supplied in the form of thermal energy(adds KE but too much heat will cause protein to denature) that the reactant molecules absorb from the surroundings
In the transition state, we want to lower it to speed up the activation energy
Enzymes catalyze reactions by lowering the activation energy
Enzymes do not affect the change in free energy, but they fasten reactions
Substrate specificity
Enzyme binds to its substrate, forming an enzyme-substrate complex
Skeleton-key model(one enzyme works on multiple substrate)
Lock and key model(one enzyme to one substrate)
Induced fit(substrate brings groups of the active site into positions that enhance their ability to catalyze the reaction)
Basically forces enzyme into position
The active site can lower the EA barrier by
Orienting substrates correctly
Straining substrate bonds
Providing a favorable microenvironment
Covalently bonding to the substrate
Enzymes can make permanent bonds(not really biological enzymes)
Effects on enzyme activity
Temperature
Want to keep it about 35-75 degrees Celsius
pH
Range is broader than temperature
Concentration of enzyme/substrate
Cofactors
Non-protein enzyme helpers
Can help increase absorption rate
May be inorganic like a metal in ionic form or organic
Organic cofactors are called coenzymes
Include vitamins
Coenzyme Q10 is a cofactor that acts as an electron carrier during the electron transport chain in cellular respiration
Enzyme inhibitors
Competitive inhibitors
Binds to the active site of an enzyme, competing with the substrate
Example
Carbon monoxide(binds before oxygen can)
Noncompetitive inhibitor
Binds to another part of an enzyme(allosteric site), causing the enzyme to change shape and making the active site less effective
Enzyme activity regulation
Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated
A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes
Can increase the production of a non-competitive inhibitor
Allosteric regulation
May either inhibit or stimulate enzyme activity
Each enzyme has active and inactive forms
The binding of an activator stabilizes the active form of the enzyme
The binding of an inhibitor stabilize the inactive form of the enzyme
Cooperativity
Form of allosteric regulation that can amplify enzyme activity
Allosteric regulators
Attractive drug candidates for enzyme regulation because of their specificity
Inhibition of proteolytic enzymes called caspases may help inflammatory responses
Increase in inflammation means a lot of caspases so we need to inhibit them
Feedback inhibition
The end product of a metabolic pathway shuts down the pathway
Prevents a cell from wasting chemical resources by synthesizing extra products
Tells the cell that you can stop producing stuff
Locations
Act as structural components of membranes
Some enzymes reside in specific organelles
Enzymes for cellular respiration are in the mitochondria
Energy flow
Heat energy <- ATP <- cellular respiration in mitochondria <- 6CO2 + 6H2O <- photosynthesis <- organic matter + O2
Catabolic pathways
Aerobic respiration consumes organic molecules and oxygen to yield ATP
anaerobic respiration is similar to aerobic respiration, but consumes compounds other than oxygen
Breakdown of organic molecules is exergonic
Fermentation is a partial degradation of sugars that occurs without oxygen
Cellular respiration includes both aerobic and anaerobic respiration, but is often used to refer to aerobic respiration
Redox reactions
Transfer of electrons during chemical reactions that releases energy stored in organic molecules
Releases energy to use in ATP synthesis
Chemical reactions that transfer electrons between reactants are called oxidation-reduction reactions
In oxidation, a substance loses electrons
In reduction, a substance gains electrons
Have to be able to identify which one is the oxidizing reagent and reduction reagent
Typically oxygen is reduced in O2 to H2O
ETC
Glucose and oxygen are broken down
Electrons from organic compounds are usually first transferred to NAD+, a coenzyme
Each NADH represents stored energy that is tapped to synthesize ATP
NADH passes the electrons to the ETC
Unlike and uncontrolled reaction, the ETC passes electrons in a series of steps
O2 pulls electrons down the chain to generate ATP
Reduction of NAD+ to NADH is due to dehydrogenase
Different by the N+
Stages of Cellular Respiration
Glycolysis
Breakdown of glucose into two molecules of pyruvate
Small amount formed here and in the Krebs cycle by substrate level phosphorylation
For each molecule of glucose degraded, the cell makes up to 32 molecules of ATP
Major phases
Energy investment
Need some sort of investment of energy to get ATP
Energy payoff
Occurs whether or not O2 is present so it is anaerobic/aerobic
Uses 2 ATP, makes 2 ATP and 2 NADH and it repeats the process to make 4 ATP and 4 NADH
Citric acid cycle/Krebs cycle
Completes the breakdown of pyruvate to CO2
Pyruvate is oxidized by being converted to acetyl CoA before going into the Krebs cycle (happens twice for each pyruvate)
Makes 2 NADH, Acetyl CoA, and CO2
Oxidizes organic fuel derived from pyruvate, generating 1 ATP B (technically GTP), a NADH, and 1 FADH2 per cycle
Does 2 cycles
Occurs in the matrix
ATP synthesis through substrate level phosphorylation
Contrasts with oxidative phosphorylation where an inorganic phosphate is added to ADP
Coenzymes capture electrons
Has eight steps(don’t need to know all 7 seven steps but the general information)
Acetyl CoA joins the cycle by combining with oxaloacetate to form citrate
The next seven steps decompose the citrate back to oxaloacetate
NADH and FADH2 produce by by the cycle relay electrons extracted from food to ETC
Oxidative phosphorylation
Accounts for most of the ATP synthesis(90%) and is powered by redox reactions
Chemiosmosis
After this point, we have the greatest amount of ATP
NADH and FADH2 account for most of the energy to transform into ATP
These two electron carriers donate electrons to the ETC that powers ATP synthesis through oxidative phosphorylation
Happens in the inner mitochondrial membrane(cristae)
Most of the chain’s components are proteins that exist as multiprotein complexes
Alternate reduced and oxidized states as they accept and donate electrons
Electrons drop in free energy as they go down the chain and are finally passed to O2(terminal electron acceptor), forming H2O
Electron transport
Transferred from NADH or FADH2 to ETC
Passed through a number of proteins like cytochromes to O2
Chemiosmosis
ETC causes proteins to pump H+ from the matrix to the intermembrane space
H+ then moves back across the membrane through the protein, ATP synthase
Uses the exergonic flow of H” to drive phosphorylation of ATP
Example of chemiosmosis, the use of energy in a H+ gradient to drive cellular work
H+ gradient is referred to proton-motive force, emphasizing its capacity to do work
ATP Production
About 34% of energy in a glucose is transferred to ATP to make 32 ATP molecules
Fermentation
Without oxygen, glycolysis couples with fermentation to produce ATP
Anaerobic respiration uses an ETC with a final electron acceptor other that O2 like sulfate
Fermentation uses substrate-level phosphorylation instead of an ETC to make ATP
Types of fermentation
Alcohol fermentation
Pyruvate is converted to ethanol
Used by yeast
Lactic acid fermentation
Pyruvate is reduced to NADH
Makes cheese and yogurt
Human muscle cells can use lactic acid fermentation to make ATP
Anaerobes
Obligate
Carry out fermentation and cannot survive with O2
Facultative
Can survive using either fermentation or cellular respiration
Pyruvate can be used in two alternative catabolic routes
Metabolic pathways
Glycolysis accepts a wide range of carbohydrates
Usually first converted to glucose but we can use a lot of them
Proteins must be digested to amino acids
Must then by deaminated before oxidation
Fats are digested to glycerol for glycolysis and fatty acids to make acetyl CoA
An oxidized gram of fat produces more ATP than an oxidized gram of carbohydrate
Cellular respiration feedback
If ATP concentration begins to drop, respiration speed up
If ATP concentration is high, respiration slows down
Control of catabolism is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway
Natural selection
Does not create new traits, but edits or selects for traits already present in the population
The local environment determines which traits are beneficial (ex. Peppered moths)
Examples
Staphylococcus aureus is commonly found on people (MRSA)
Became resistant to penicillin in 1945 and to methicillin in 1961 (bacteria continue to evolve!)
MRSA
Methicillin works by inhibiting a protein used by bacteria in their cell walls
MRSA bacteria use a different protein in their cell walls
Their strains are now resistant to many antibiotics
Homology
Similarity resulting from common ancestry
Homologous structures
Anatomical resemblances that represent variations on a structural theme present in a common ancestor
Produced through divergent evolution or the splitting of an ancestral species to produce two or more related descendant species
Examples
Human arm, cat arm, whale fin, bat wing
Embryonic homology
Comparative embryology reveals anatomical homologies not visile in adult organisms
Ontogeny recapitulates phylogeny
An organism's development will take it through each of the adult stages of its evolutionary history, or its phylogeny
Vestigial structures
Remnants of features that served important functions in the organism’s ancestors
Examples
Human tailbone
Whale pelvis
Evolutionary trees
Are hypotheses about the relationships among different groups
Homologies form nested patterns in evolutionary trees
Convergent evolution
Evolution of similar features in distantly related groups
Produces analogous traits
Similar traits that arise when groups independently adapt to similar environments in similar ways
Do not provide information about ancestry
Fossil record provides evidence of the extinction of species, the origin of new groups, and changes within groups over time
Can document important transitions
Example: the transition from land to sea in the ancestors of cetaceans
Dating
Determining approximate ages of fossils helps provide evidence for evolution
Biogeography
Provides evidence of evolution
Earth’s continents were formerly united in a single large continent called Pangaea, but have separated by continental drift
Can use this drift to predict where different groups evolved
Plate tectonics
At three points in time, the land masses of Earth have formed a supercontinent 1.1 billion years ago, 600 million years ago, and 250 million years ago
Earth’s crust is composed of plates floating on Earth’s mantle
Organisms do not evolve during their lifetimes
Natural selection acts on individuals so only population evolve
Genetic variation provides the diverse gene pool necessary for a species to persist in a diverse environment
Populations
A localized group of individuals capable of interbreeding and producing fertile offspring
A gene pool consists of all the alleles for all loci in a population
A locus is fixed if all individuals in a population are homozygous for the same allele
Genetic variation
Variation in heritable traits is a prerequisite for evolution
Among individuals, it is caused by differences in genes or other DNA segments
Natural selection can only act on variation with a genetic component
Modern synthesis
Importance of populations
Mechanism of natural selection
Gradualism
Hardy-Weinberg equilibrium
Describes a hypothetical population that is not evolving
Shuffling of alleles does not impact the gene pool
In real population, allele and genotype frequencies do change over time when one of the 5 conditions is not met:
No mutations - Mutations
Random mating - Non-Random Mating
No natural selection - Natural Selection
Large population size - Genetic Drift(apparent in small populations)
No gene flow - Gene Flow
Only natural selection produces adaptive radiation
Microevolution
A change in allele frequency in a population over generations
Allele frequency can change by natural selection, genetic drift, or gene flow
States that frequencies of alleles and genotypes in a population remain constant from generation to generation
Gametes contribute to the next generation randomly, leading to no change in allele frequency
Mendelian inheritance preserves genetic variation in a population
Example
We can assume the locus that causes phenylketonuria (PKU) is in Hardy-Weinberg equilibrium since:
1. The PKU gene mutation rate is low
2. Mate selection is random with respect to whether or not an individual is a carrier for the PKU allele
3. Natural selection can only act on rare homozygous individuals who do not follow dietary restrictions
4. The human population is large
5. Migration has no effect as many other populations have similar allele frequencies
Link
Speciation
The origin of new species
Microevolution
Allele frequency changes in a population
Macroevolution
Broad patterns of evolutionary change
Ex: color change
Reproductive isolation
Existence of biological factors(barriers) that inhibit two species from producing viable(live well), fertile offspring
Can be viable but sterile like mules
Prezygotic barriers(block fertilization from ever occurring)
Habitat isolation
Occupy different locations or blocked from meeting by mountains or rivers
Temporal isolation
Species that breed at different times
Behavioral isolation
Have different behaviors that are unique to a species
Ex: Penguins bring gifts to others while blue-footed bobbies dance
Postzygotic barriers(prevent a hybrid zygote from developing)
Reduced hybrid viability
Genes of the different parent species may interact and impair the hybrid’s development
Offspring doesn’t develop the organs correctly
Reduced hybrid fertility
Even if hybrids are vigorous, they are sterile like mules
Hybrid breakdown
When a first-generation hybrid is fertile, but they mate with another species, the next generation offspring are infertile
Species Definitions
The morphological species concept defines a species by structural features
It applies to sexual and asexual species but relies on subjective criteria
The ecological species concept views a species in terms of its ecological niche
It applies to sexual and asexual species and emphasizes the role of disruptive selection
The phylogenetic species concept defines a species as the smallest group of individuals on a phylogenetic tree
It applies to sexual and asexual species, but it can be difficult to determine the degree of difference required for separate species
Speciation
Allopatric
Population is divided by geographical separation
Sympatric
Speciation takes place in geographically overlapping populations(not likely)
Can result in the appearance of new ecological niches
Sexual selection can drive this speciation
Color morphology
Performance
Hybrid zones
A region in which members of different species mate and produce hybrids
Overtime, there is a possibility of an overlapping fusion where the species meet
Three possibilities
Reinforcement
Fusion
Stability
Continental drifts
Tectonic plates shift
Cause changes in species
Mass extinction
Handful of species are able to survive and adapt so those are the ones that continue to live on
Adaptive radiation
Evolution of diversely adapted species from a common ancestor due to mass extinctions, evolution of novel characteristics, or colonization of new regions
Ex: Alligators came from dinos
Endemic species
Species not found anywhere else in the world
Typically on islands and are closely related to species on the nearest mainland or island
Most common one is Darwin’s islands like finches
Ecology
The scientific study of the interactions between organisms and the environment
Global climate patterns
Solar energy
Planetary movement
Seasons
Air currents
Water currents
Climate and terrestrial biomes
Climate affects the latitudinal patterns of terrestrial biomes
Biomes
Major life zones characterized by vegetation type (terrestrial) or physical environment (aquatic)
Climate is very important in determining why terrestrial biomes are found in certain areas
Are affected not just by average temperature and precipitation, but also by the pattern of temperature and precipitation through the year
Similar characteristics can arise in distant biomes through convergent evolution
Disturbance
Is an event such as a storm, fire, or human activity that changes a community
Frequent fires can kill woody plant and maintain the characteristic vegetation of a savanna
Fires and outbreaks of pests create gaps in forests that allow different species to grow
Fire suppression has changed the vegetation of the Great Plains
Microclimate
Is determined by fine-scale differences in the environment that affect light and wind patterns
Every environment is characterized by:
Abiotic factors: non-living attributes such as temperature, light, water, and nutrients
Factors that affect the distribution of organisms include:
Temperature
Water
Sunlight
Wind
Rocks & soil
Most factors vary in space and time
Biotic factors: other organisms that are part of an individual’s environment
Factors that affect distribution of organisms may include:
Predation
Herbivory
For example sea urchins can limit the distribution of seaweeds
Competition
Competitive exclusion
Principle states that two species competing for the same resources cannot coexist
Water and oxygen
Water availability in habitats is another important factor in species distribution
Desert organisms exhibit adaptations for water conservations
Oxygen diffuses slowly in water
Oxygen concentrations can be low in deep communities
Dissolved oxygen (DO) in aquatic communities partially determines metabolic rates and is dependent on temperature (lower temp = more DO), photosynthesis rate, etc
Population
Group of individuals of a single species lying in the same general area
Populations are described by their boundaries and size
Size can be estimated by the mark and recapture method
Density is the number of individuals per unit area of volume
Dispersion is the pattern of spacing among individuals within boundaries of the population
Clumped, uniform, random
Calculations
Population density
Divide the population by the size of the area
Population dynamics
Births and immigration add individuals to a population
Deaths and emigration remove individuals from a population
Survivorship curves
A graphic way of representing data in a life table
Population growth
Useful to study population growth in an idealized situation
The per capita birth rate (b) is the number of offspring produced per unit time
The per capita death rate (d) is the number of individuals that die per unit time (mortality = death rate)
Exponential growth
Is a population increase under idealized conditions
J-shaped curve
Under these conditions, the rate of increase is at the maximum (r-max)
Logistical model
Carrying capacity (K): the maximum population size the environment can support
Vary with the abundance of limiting resources
In the logistic population growth model, the per capita rate of increase declines as carrying capacity is reached
Reduces per capita rate of increase as N approaches K
S-shaped curve
Some populations overshoot K before settling down to a relatively stable density
Some populations fluctuate greatly
Some populations show an allee effect, in which individuals have a more difficult time surviving or reproducing if the population size is too small
K-selected species
Density-dependent selection; selects for life history traits that are sensitive to population density
In density-dependent populations, birth rates fall and death rates rise as population density increases
Competition for resources, territoriality, disease, predation, toxic wastes, and intrinsic factors
R-selected species
Density-independent selection; selects for life history traits that maximize reproduction
In density-independent populations, birth and death rate do not change with population density
Population cycles
Some populations undergo regular boom-and-bust cycles
Lynx populations follow the 10-year boom-and-bust cycle of hare populations
Predators and sunspot activity regulate hare populations
Global human population
The human population increased relatively slowly until about 1650 and then began to grow exponentially
Patterns of population change
To maintain population stability, a regional human population can exist in one of two configurations:
0 population growth = high birth rate - high death rate
0 population growth = low birth rate - low death rate
The demographic transition is the move from the first state to the second state
Age structure
One important demographic factor in present and future growth trends is a country’s age structure
Age structure is the relative number of individuals at each age
Trophic structure
Trophic structure
the feeding relationships between organisms in a community
It is a key factor in community dynamics
Food chains link trophic levels from producers to top carnivores
Autotrophs
Build molecules using photosynthesis or chemosynthesis as an energy source
Change in the producers in an ecosystem impacts other trophic levels; changes in energy in an ecosystem can disrupt the ecosystem and change population sizes
Heterotrophs
Depend on the biosynthetic output of other organisms
Energy and nutrients pass from primary producers (autotrophs) to primary consumers (herbivores) to secondary consumers (carnivores) to tertiary consumers (carnivores that feed on other carnivores)
Detritivores and decomposers
Detritivores and decomposers are consumers that derive their energy from detritus, non-living organic matter
Prokaryotes and fungi are important detritivores
Decomposition connects all trophic levels!
Food webs
A food web is a branching food chain with complex trophic interactions
Decomposers can be depicted in food webs!
In food chains, they would be at each trophic level
Limits on food chain length
Each food chain in a food web is usually only a few links long
Two hypotheses attempt to explain food chain length: the energetic hypothesis and the dynamic stability hypothesis
The energetic hypothesis suggests that length is limited by inefficient energy transfer
For example, a producer level consisting of 100 kg of plant material can support about 10 kg of herbivore biomass
More data supports it
The dynamic stability hypothesis proposes that long food chains are less stable than short ones
Energy flows through ecosystems, whereas matter cycles within them
Conservation of Energy
The first law of thermodynamics states that energy cannot be created or destroyed, only transformed
Energy enters an ecosystem as solar radiation, is conserved, and is lost from organisms as heat
The second law of thermodynamics states that every exchange of energy increases the entropy of the universe
In an ecosystem, energy conversions are not completely efficient, and some energy is always lost as heat
Conservation of mass
The law of conservation of mass states that matter cannot be created or destroyed
Chemical elements are continually recycled within ecosystems
In a forest ecosystem, most nutrients enter as dust or solutes in rain and are carried away in water
Ecosystems are open systems, absorbing energy and mass and releasing heat and waste products
Ecosystem energy budgets
In most ecosystems, primary production is the amount of light energy converted to chemical energy by autotrophs/chemoautotrophs during a given time period
The extent of photosynthetic production sets the spending limit for an ecosystem’s energy budget
The amount of solar radiation reaching Earth’s surface limits the photosynthetic output of ecosystems
Only a small fraction of solar energy actually strikes photosynthetic organisms, and even less is of a usable wavelength
Gross and net production
Total primary production is known as the ecosystem’s gross primary production (GPP)
The conversion of chemical energy from photosynthesis, per unit time
Net primary production (NPP) is GPP minus energy used by primary producers for respiration
NPP is the amount of new biomass* added in a given time period
Only NPP is available to consumers
NPP is expressed as
Energy per unit area, per unit time (J/m2yr)
Biomass added per unit area, per unit time (g/m2yr)
Energy transfer
Secondary production of an ecosystem is the amount of chemical energy in food converted to new biomass during a given period of time
Excess energy obtained than required for survival results in storage of the energy or growth of the organism
Excess energy obtained than required for survival results in storage of the energy or growth of the organism
Production efficiency
When a caterpillar feeds on a leaf, only about one-sixth of the leaf’s energy is used for secondary production
An organism’s production efficiency is the fraction of energy stored in food that is not used for respiration
Birds and mammals have efficiencies in the range of 13% because of the high cost of endothermy
Fish have production efficiencies of around 10%
Insects and microorganisms have efficiencies of 40% or more
Trophic efficiency
The percentage of production transferred from one trophic level to the next
It is usually about 10%, with a range of 5% to 20%
A pyramid of net production represents the loss of energy with each transfer in a food chain
Aquatic limiting nutrients
Depth of light penetration affects primary production in the photic zone
Nutrients limit primary production in oceans and lakes
A limiting nutrient is the element that must be added for production to increase in an area
Nitrogen and phosphorous most often limit marine life
Nutrient sources
Upwelling of nutrient-rich waters in parts of the oceans contributes to regions of high primary production
In some areas, sewage runoff has caused eutrophication of lakes, which can lead to loss of most fish species
In lakes, phosphorus limits cyanobacterial growth more often than nitrogen
Terrestrial primary production
In terrestrial ecosystems, temperature and moisture affect primary production
Primary production increases with moisture
Various adaptations help plants access limiting nutrients from soil
Some plants form mutualisms with nitrogen-fixing bacteria
Many plants form mutualisms with mycorrhizal fungi
Roots have root hairs that increase surface area
Many plants release enzymes that increase the availability of limiting nutrients
Nutrient recycling
Life depends on recycling chemical elements between organic and inorganic reservoirs
Nutrient cycles in ecosystems involve biotic and abiotic components and are often called biogeochemical cycles
Water cycles
Liquid water is the primary physical
97% oceans, 2% ice, 1% liquid freshwater
Moves by evaporation, transpiration, condensation, precipitation, and movement through surface and groundwater
Carbon cycles
Carbon-based organic molecules are essential to all organisms!
Photosynthetic organisms convert CO2 to organic molecules (fixation)
Carbon reservoirs include fossil fuels, soils and sediments, solutes in oceans, plant and animal biomass, the atmosphere, and sedimentary rocks
photosynthesis/respiration
Nitrogen cycles
Nitrogen is a component of amino acids, proteins, and nucleic acids
The main reservoir of nitrogen is the atmosphere (N2), though this nitrogen must be converted to NH4+ or NO3– for uptake by plants, via nitrogen fixation by bacteria
Nitrogen fixation, ammonification, nitrification, denitrification
Phosphorus cycles
Phosphorus is a major constituent of nucleic acids, phospholipids, and ATP
Phosphate (PO43–) is the most important inorganic form of phosphorus
The largest reservoirs are sedimentary rocks of marine origin, the oceans, and organisms
Cycles slowly
Decomposition and nutrient cycling
Decomposers/detritivore play a key role in the general pattern of chemical cycling
Rates at which nutrients cycle in different ecosystems vary greatly, mostly as a result of differing rates of decomposition
The rate of decomposition is controlled by temperature, moisture, and nutrient availability
