1.2: Elements essential to life

• 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

1.3: Intro to Biomacromolecules

• 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

1.4: Nucleic Acids

• 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)

1.5: Properties of Bio-Macromolecules

• 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)

1.6: Biomacromolecules - Structure and Function

• 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)

2.3: Cell Structure and Function

• 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

2.4: Cell Compartments and Membranes

• 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)

2.5: Cell Transport

• 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)

3.1: DNA/RNA Structure

• 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)

3.3: Transcription & RNA Processing

• 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

4.1: Cell Communication and Signal Transduction

• 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

4.2: Cell Signaling

• 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

4.3: Homeostasis and Feedback

• 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

5.1: Meiosis Part 1

• 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

5.1: Meiosis Part 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

5.3: Complex Inheritance

• 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

Protein Synthesis: Review Day

• 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

5.4: Gene Expression & Regulation

• 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

5.5: Mutations

• 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

6.1: Standard deviation/Standard error:

• 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

6.3: Enzymes

• 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(E_A)

    • 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 E_A 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

6.4: Cellular Respiration

• 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

7.1: Evidence for Evolution

• 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

7.2: Hardy-Weinberg

• 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

7.3: Speciation

• Link

  • https://aisdblend.instructure.com/courses/452152/pages/7-dot-3-speciation?module_item_id=49703249

• 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

7.4: Population in Ecology

• 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

7.5: Communities and Trophic Levels

• 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