AP BIO FINAL GUIDE
(⭐ = learning objectives + essential knowledge)
Unit 1
Elements
Four main elements of life: carbon, oxygen, hydrogen, and nitrogen
These elements are essential for the formation of biomolecules such as proteins, nucleic acids, carbohydrates, and lipids.
Also used to form storage compounds and cells for organisms, and energy transfer and structural integrity within living systems
Organic compounds contain mostly carbon since its used in storage compounds and cell formation in all organisms ⭐
Nitrogen is found in protein and nucleic acids ⭐
Trace elements: elements needed in minute quantities
They are iron, iodine, and copper
Subatomic Particles
Atoms: unit of life, building blocks, etc
Protons = positively charged (+)
Neutrons = uncharged, neutral
Electron = negatively charged (-)
Atoms that have same # of protons but dif neutrons in the nucleus, leading to different atomic masses are isotopes
Stable isotopes do not emit radiation
Unstable isotopes emit radiation, which can lead to radioactive decay and the release of energy in the form of alpha, beta, or gamma radiation.
Compounds
Compounds consist of two or more elements that are chemically bonded together, forming a distinct substance with unique properties.
The chemical bonds could be ionic, covalent, or hydrogen
Ionic bonds are formed between two atoms when one atom donates 1 or more electrons to the other, resulting in charged ions that attract each other due to opposite charges
Covalent bonds are formed when electrons are shared between atoms. ⭐
Non-polar covalent bonds: electrons are shared equally
Polar covalent bonds: electrons are shared unequally
Difference: in ionic bonds, one atom donates electrons; in covalent bonds, both atoms exchange electrons
Hydrolysis and Dehydration synthesis used to cleave and form covalent bonds between monomers ⭐
Hydrolysis: The reaction of a chemical compound breaking down in water
Dehydration synthesis: reaction involving loss of water from the reacting molecule/ion
Van Der Waal bonds are the weakest bonds between covalent molecules, bonding gases, liquids and polymers
Van Der Waal forces highlight attraction and repulsion between atoms and molecules
Water
Hydrogen bonds are weak, formed when a hydrogen atom is covalently bonded to another ⭐
Hydrogen bonds that hold water molecules together contribute to: cohesion, adhesion, surface tension, high heat capacity, and expansion on freezing ⭐
Cohesive forces are when water molecules have strong tendency to stick together
Water molecules that stick to OTHER substances are adhesive
Capillary action is the ability for water to rise up the roots, trunks/stems, and branches of plants/trees via cohesion and adhesion working together
Cohesion of water molecules contribute to surface tension (water molecules stick together so light things strive on top of water)
High heat capacity is ability for substance to absorb and keep a certain amount of heat without huge increase in temperature
Attraction of water forms a net of crystals as water freezes since water molecules are attracted to one another
Acids and Bases
Whether a solution is acidic, basic, or neutral affects reactions
Acids: solution contains a lot of hydrogen ions (H+)
Tastes sour
Can conduct electricity
Do not dissolve in water
Colorless when placed in an indicator
Appear red on blue litmus paper
Have a pH <7
Bases: contain hydroxide ions (OH-)
Taste bitter
Appear pink when placed in an indicator
Appear blue on red litmus paper
Have a pH >7
Can conduct electricity
Do not dissolve in water
pH at 7 is considered the midpoint or neutral pH
Organic Molecules
Molecules with carbon are organic, molecules w/o carbon are inorganic compounds ⭐
Carbon is a versatile atom: has the ability to bind with other carbons and with other elements like nitrogen, oxygen and hydrogen
Polymers are chains of building blocks in macromolecules
Monomers are individual building blocks of a polymer
Structure of polymers derives from the way monomers are assembled ⭐
Polymers are formed through dehydration synthesis (or condensation) reactions. A water molecule is lost in the reaction and a larger compound is formed.
Hydrolysis is when polymers can also be broken down into monomers
Water breaks bond between monomers
Four classes of organic compounds on Earth: ⭐
Carbohydrates
Proteins
Lipids
Nucleic Acids
Carbohydrates
Organic compounds that contain carbon, hydrogen, oxygen. Ratio is 1:2:1
comprise linear chains of sugar monomers connected by covalent bonds ⭐
Most carbs are categorised as either monosaccharides, disaccharides, or polysaccharides
Saccharide means “sugar” ⭐
Monosaccharides
Energy source for cells
Two most common sugars are glucose and fructose; chem formula is C6H12O6 ⭐
Glucose: important part of food we eat, product of photosynthesis in plants
Disaccharides
Joining two monosaccharides results in a disaccharide sugar (bond is called a glycosidic linkage)
Add water to break disaccharide into two monosaccharides
Polysaccharides
Made up of many repeated units of monosaccharides
Consist of branched or unbranched chains of monosaccharides: starch, cellulose, and glycogen ⭐
Glycogen and starch are sugar storage molecules. Glycogen stores sugar in animals and starch stores sugar in plants ⭐
Cellulose is made of d-glucose and is major part of cell wall, functions to lend structural support ⭐
Chitin: polymer of d-glucose molecules, structural molecule in fungal walls and arthropod exoskeletons ⭐
Proteins
important for structure, function and regulation of tissues and organs
Amino acids are building blocks of proteins. Contain carbon, oxygen, hydrogen, and nitrogen atoms. There are 20 different amino acids. ⭐
Amino acids have directionality, an amino terminus and a carboxyl terminus ⭐
Proteins have 4 important parts around central carbon:
1 amino group, a carboxyl group, a hydrogen, and an R-group ⭐
Amino acids differ only in R-group or the “side-chain” ⭐
Side chain polarity affects whether amino acids is hydrophobic or hydrophilic ⭐
Hydrophobic: repelled by water, non-polar and uncharged, more likely to be found on interior of proteins
Hydrophilic: attracted to water, polar and uncharged, found on exterior of proteins
Ionic: polar and charged
Of common amino acids:
Two donate a proton so they’re negatively charged (glutamic and aspartic)
Two accept a proton so they’re positively charged (lysine and arginine)
Polypeptides
When two amino acids join = dipeptide
Peptide bond: bond between two amino acids
If a group of aminos acids is joined by a “string”, that organic compound is a polypeptide
Proteins are made up of polypeptide chains
Specific order of amino acids in polypeptide determines shape of protein ⭐
Linear sequence of amino acids is primary structure of a protein ⭐
When polypeptides twist, they form a coil (alpha helix) or a zigzag pattern (beta-pleated sheets). These are the secondary structures ⭐
DNA is also arranged in this helix, contain adenine + thymine nucleotides (connected with two hydrogen bonds) and cytosine + guanine nucleotides (connected by three hydrogen bonds) ⭐
When secondary structure reshapes polypeptide, amino acids far from primary structure now interact: tertiary structure ⭐
Quaternary structure: when different polypeptide chains interact with each other. Haemoglobin is a molecule in the blood that distributes oxygen to bodily tissues, formed by four separate polypeptide chains, is a quaternary structure ⭐
Lipids
consists of carbon, hydrogen, oxygen (some contain phosphorus ⭐)
most common lipids are triglycerides, phospholipids, and steroids
Lipids are important due to their non-polar structures, they function as structural components of cell membranes, sources of insulation, signalling molecules, and a means of energy storage ⭐
Humans store fat in tissue, adipose (made of adipocytes cells, which are filled with lipids called triglycerides)
Triglyceride made of glycerol molecule with 3 fatty acid chains
Fatty acids can be saturated with hydrogens along its carbon chain or it can’t be unsaturated. Unsaturated fatty acids have double bonds.
Lipid Saturation: extent of saturation in a lipid can affect its structure and function. the more double bonds, the more unsaturated it is ⭐
Phospholipids
contain two fatty acid “tails” and one negatively charged phosphate “head”
important cuz some unique properties they have concerning water: the tails are hydrophobic since they’re non-polar, the “head” is hydrophilic since it carries a negative charge, drawing to positively charged water
Phospholipids have both hydrophilic and hydrophobic region - it’s an amphipathic molecule ⭐
Cholesterol
four-ringed molecule found in membranes
generally increases membrane fluidity, except at very high temperatures. also important for making some hormones and making vitamin D
Nucleic Acids
contain carbon, hydrogen, oxygen, and nitrogen and phosphorus ⭐
are molecules made up of single units called nucleotides
biological info encoded in these sequences of nucleotide monomers ⭐
Nucleotides arranged in linear sequence with ends of 3’ hydroxyl and 5’ phosphate of nucleotide’s sugar, during DNA/RNA synthesis, nucleotides are added to the 3’ end - results in formation of covalent bond between nucleotides ⭐
DNA contains heredity “blueprints” or life, RNA is essential for protein synthesis ⭐
DNA and RNA structure: ⭐
both have sugar, phosphate group and nitrogen base that form nucleotides
DNA contains deoxyribose; RNA contains ribose
RNA contains uracil; DNA contains thymine
DNA = double stranded; RNA = single stranded
DNA is antiparallel in directionality (orientation)
Class Notes:
know proteins very well (primary, secondary, tertiary structures)
best to study gene expression instead of nucleic acids
water: adhesion, cohesion, capillary action
how does water travel from soil to plant?
how does transpiration work?
know macromolecules: monomers, polymers
know what AREN’T polymers (lipids)
carbon (all organic compounds contain carbon)
reason why is cuz it can form up to four bonds
functional groups: hydroxide, phosphate group, aiming groups
Unit 2
Living Things
Life’s basic unit of structure and function is a cell
As cell’s volume increases, the surface area-to-volume ratio decreases, and exchange of materials = less efficient.
Surface area-to-volume ratio concept can be applied to organisms: as organism size increases, ratio will decrease and this can affect properties like heat exchange between organism and surroundings. Smaller organisms lose heat at much higher rates than larger organisms as a result of efficient heat exchange ⭐
Types of cells and organelles
Light microscope: used to study stained or living cells, can magnify the size of an organism x1000
Electron microscope: used to study detailed structures of a cell that cannot be easily seen or observed by light microscopes
Transmission EM: used to view thin interiors of cells (uses transmitted electrons passing through the sample) to create image
Scanning EM: used to scan surface of object using beam of electrons
Two distinct types of cells: prokaryotic and eukaryotic
Prokaryotic Cells
much smaller and simpler than a eukaryotic cell ⭐
examples of prokaryotes are bacteria and archaea
inside of cell is filled with cytoplasm
genetic material in a prokaryote is one continuous, circular DNA molecule that is found free in the cell’s nucleoid
most prokaryotes have a cell wall made up of peptidoglycans that surround a lipid layer called plasma membrane
Prokaryotes have small ribosomes
some bacteria have one or more flagella (used for motility) and might have thick capsule outside cell wall for extra protection
do have a cell wall
do not have any membrane-bound organelles. their only membrane is the plasma membrane ⭐
Eukaryotic Cells
fungi, protists, plants and animals are eukaryotes
eukaryotic cells have many organelles, some are same structures as in prokaryotic cells but most are not ⭐
eukaryotes evolved from prokaryotes via endosymbiosis ⭐
Plasma Membrane
outer envelope of the cell, made mostly of phospholipids and proteins ⭐
regulates movement of substances in and out of the cell, it is semipermeable (allows certain molecules to cross) ⭐
proteins loosely associated with the lipid bilayer are peripheral proteins, located temporarily on either the inner of outer surface of the membrane, functions in support, communication, enzyme, molecule movement, and sending cells signals in and out of cell ⭐
Integral proteins: amphipathic proteins that are firmly bound to plasma membrane, critical for movement of molecules across membrane
type of integral protein that extend all the way through membrane is transmembrane protein
arrangement of phospholipids and proteins known as fluid-mosaic model
adhesion proteins form junctions between adjacent cells
Receptor proteins like hormones are docking sites for arrivals at cell
membrane contains chlorophyll pigments and electron transport proteins (comprise photosystems)⭐
transport proteins form pumps the use ATP for active transport of molecules across membrane
passive transport is movement without use of ATP like diffusion and osmosis ⭐
channel proteins form channels that selectively allow ions or molecules to pass through
cell surface markers (ex. glycoproteins and some lipid (glycolipids)) are exposed on extracellular surface, play a role in cell recognition and adhesion
carbohydrate side chains found on outer surface of plasma membrane
Nucleus
usually largest organelle in cell
directs what’s happening in cell, allows cell to reproduce, home of DNA organized in chromosomes
visible structure of nucleus is nucleolus, where rRNA is made and ribosomes assemble
RIbosomes
found in all forms of life (both prokaryotes and eukaryotes) ⭐
sites of protein synthesis: manufacture proteins needed for cell of secreted by cell ⭐
round structures composed of two subunits (large and small)
structure made of rRNA and proteins ⭐
can be either free floating or attached to the endoplasmic reticulum
Endoplasmic Reticulum (ER)
a continuous channel extending throughout cytoplasm and provides mechanical support and transportation ⭐
Rough ER compartmentalizes cell ⭐
region of ER that lacks ribosomes is Smooth ER: makes lipids, hormones, and steroids and breaks down toxic chemicals ⭐
Golgi Complex
membrane-bound structure made of membrane sacs ⭐
After ribosomes on rough ER have synthesized proteins, golgi complex modify, process, and sort products ⭐
packaging and distribution centers for materials being sent out of cell, package in vesicles, which carry products to plasma membrane ⭐
Mitochondria
power stations that convert energy from organic molecules into ATP usable for the cell
consists of inner and outer portions (double membrane) ⭐
inner mitochondrial membrane forms folds (cristae) and separates mitochondrial matrix (where Krebs cycle happens) from inner-membrane space ⭐
inner membrane also where electron transport and ATP synthesis occur ⭐
folds allow more surface area which allows for more ATP synthesis ⭐
outer membrane separates inner-membrane from cytoplasm
also one of organelles that possess their own DNA
Lysosomes
have sacs that carry digestive enzymes, breaking down old organelles, debris, and large ingested particles ⭐
made when vesicles containing specific enzymes from trans Golgi fuse with vesicles made during endocytosis
essential during apoptosis: programmed cell death ⭐
Vacuoles
fluid-filled sacs that store water, food, wastes, salts and pigments ⭐
serve multiple functions in plant cells like balance water intake ⭐
Peroxisomes
organelles that detoxify substances and produce hydrogen peroxide (H2O2) as byproduct
have enzymes that break down H2O2 into oxygen and water
Cytoskeleton
shape of cell is determined by network of protein fibers called the cytoskeleton
most important fibers are microtubules and microfilaments
Microtubules: made up of tubulin protein, participate in cell division and movement
Microfilaments: assist in movement, thin rod-like structures composed of actin protein, actin monomers join and break apart to let microfilaments grow/shrink
Cilia and Flagella
have locomotive properties in single-celled organisms
beating motion of cilia and flagella allow it to move
Plant Versus Animal Cell
Plant cells have cell wall (made of cellulose) that animals don’t
cell wall: rigid layer outside plasma membrane providing support for cell
Plant cells have chloroplasts with double outer membranes ⭐
Chloroplasts contain chlorophyll, giving plants green color, and their own set of DNA
Chloroplasts contain thylakoids organized in stacks called grana as well as stroma ⭐
Stroma: fluid within inner chloroplast membrane and outside thylakoid, also where carbon fixation (Calvin-Benson cycle) reactions occur ⭐
Light dependent and independent reactions occur in chloroplast
light dependent reactions of photosynthesis occur in grana
Cytoplasm in plant cell has large vacuole called the central vacuole
Plant Cells don’t have centrioles like animal cells do
Transport Across Membrane
ability of molecules to move across cell membrane depends on:
semipermeability of plasma membrane ⭐
size/charge of particles wanting to get through
small substances can easily cross membrane since “like dissolves like”, lipid bilayer has hydrophilic outside and hydrophobic inside so hydrophobic things only can enter central zone ⭐
Cell walls (composed of carbs) act as structural boundary and permeability barrier for substances ⭐
if a hydrophilic substance wants to enter central zone, assistance is needed called facilitated transport
aquaporins are water-specific channels ⭐
glucose ions (like Na+ or K+) transported across membrane via membrane proteins that may become polarized as ions move across them ⭐
Passive Transport: Diffusion
substances diffuse from areas of high concentration to low concentration, moving down a concentration gradient: this is diffusion ⭐
when molecule that is diffusing is hydrophobic, diffusion is called simple diffusion cuz non-polar molecule can drift through membrane w/o trouble
When diffusion requires help of a channel protein, it’s facilitated diffusion ⭐
anytime substance is diffusing, it’s passive transport since no outside energy is required ⭐
Osmosis
only difference from diffusion is that in diffusion the membrane is usually permeable to solute; in osmosis it isn’t
in plants, cell wall protects osmotic changes, while membrane can shrink from wall (plasmolysis) if it loses water and can expand and squeeze against wall if it takes in water
tonicity describes osmotic gradients
if environment is isotonic to cell, solute concentration is same inside and out of cell
hypertonic solution has more total dissolved solutes than cell, while hypotonic solution has less
if the cell is in: ⭐
Hypertonic solution then water will leave cell, cell shrinks
Hypotonic solution then water will enter cell, cell expands
Isotonic solution then there’s no net water movement
water potential is measure of potential energy in water and describes the eagerness of water to flow from area of high water potential to low ⭐
water potential is affected by: pressure potential and solute potential
osmoregulation maintains water balance
growth and homeostasis are maintained by constant molecular movement ⭐
Active Transport
movement against natural flow is active transport
some proteins in membrane are powered by ATP ⭐
active transport requires membrane proteins ⭐
example of active transport: sodium-potassium pump
pump ushers three sodium ions (Na+) and brings in two potassium ions (K+) across cell membrane
pump depends on ATP to get ions across that would otherwise be forced to stay in regions of higher concentration
Primary active transport occurs when ATP is directly utilized for transport
Secondary active transport occurs when something transports using energy captured from movement of other substance across concentration gradient
Endocytosis
when particles that want to enter cell are too large, part of cell membrane engulfs substance, forming pocket to pinch in and eventually form a vacuole or vesicle: this is endocytosis ⭐
3 types:
Pinocytosis: cell ingests liquids
Phagocytosis: cell ingests solids
Receptor-mediated endocytosis: cell surface receptors work with endocytic pits lined with clathrin protein; when particle/ligand binds to receptor, brought to folding in of cell membrane (invagination); a vesicle forms around ligand and carries it into interior of cell
Ligand: a molecule that binds another molecule, sometimes delivering a signal
Bulk Flow
one-way movement of fluids brought by pressure (ex. movement of blood through blood vessel, movement of fluids in xylem/phloem of plants)
Dialysis
diffusion of solutes across a selectively permeable membrane
Kidney dialysis is specialized process where blood is filtered using machines and concentration gradients
Exocytosis
cell ejects waste products or secretion products like hormones via fusion of vesicle with plasma membrane, expelling contents to extracellular space (aka reverse endocytosis) ⭐
Class Notes:
30%+ test on cell (STUDY)
structure + function of membrane
how do things pass through it
Unit 3
Bioenergetics
study of how cells transform energy is bioenergetics
Thermodynamics
zero law: if two bodies are at equilibrium with third body, then they’re at equilibrium with each other
first law: cells cannot take energy out of thin air, must harvest it from somewhere; energy cannot be created or destroyed, only transferred
second law: energy transfer leads to less organization, energy input must exceed loss to maintain order during cellular processes; entropy constantly increases in closed systems ⭐
third law: entropy of a system approaches a constant value as temp approaches absolute zero
Types of Reactions
Exergonic reactions: products have less energy than reactants (energy exits)
Endergonic reactions: require input of energy; products have more energy than reactants
Enzymes
a catalyst is smth that speeds up reactions
enzymes are biological catalysts, speeding up reactions by lowering activation energy and helping formation of transition state ⭐
enzymes do NOT change energy of starting or ending points in reactions
Enzyme Specificity
each enzyme catalyzes one kind of reaction: called enzyme specificity
enzymes are usually named after molecules they target, aka substrates
Enzyme-Substrate Complex
during reactions, enzyme’s job is to bring transition state about by helping substrates get into position, accomplishes this through region on enzyme called active site ⭐
enzyme temporarily binds one or more substrates to its active site and forms an enzyme-substrate complex ⭐
Enzymes DO: increase rate of reaction by lowering activation energy; enzyme-substrate complexes aren’t affected by reaction
Enzymes DON’T: change reaction, make it occur otherwise or not at all
Induced-fit
enzymes and substrates don’t fit seamlessly together; enzymes have to change shape to accommodate substrate: induced-fit ⭐
because fit must be perfect, enzymes only operate under strict biological conditions
Enzymes Don’t Always Work Alone
enzymes sometimes need help catalyzing reaction, so cofactors (either organic coenzymes or inorganic molecules/ions) assist
vitamins are examples of organic coenzymes
Temperature
rate of reaction increases with temp increase ⭐
increase temp increases frequency of molecule collisions; too much heat can dmg enzyme and it becomes denatured ⭐
enzyme denaturation is reversible if optimal env are restored ⭐
pH
enzymes function best at particular pH ⭐
at incorrect pH, hydrogen bonds can be disrupted and enzyme structure can be altered ⭐
Relative Concentration of Substrates and Products
can also effect rate of enzyme-catalysed reactions ⭐
increase in substrate concentration will initially speed up reaction but once all of enzyme is bound to substrate, reaction no longer speeds up
concentration of substrate where all enzyme is bound is called saturation point, no more increase of reaction speed ⭐
Enzyme Regulation
cell can control enzymatic activity by regulation conditions that influence enzyme shape
enzymes can be turned on or off by things that bind to them; sometimes these things bond to active site, sometimes bind to other allosteric sites
if substance has shape that fits active site, it can compete with substrate and block substrate from getting active site: competitive inhibition ⭐
can identify competitive inhibitor based on what happens when lot of substrate floods system
if inhibitor binds to allosteric site, its an allosteric inhibitor aka noncompetitive; generally distorts enzyme shape so it cannot function; substrate can bind to active site but enzyme can’t catalyze reaction ⭐
Reaction coupling and ATP
cell gets its energy through ATP
ATP consists of molecule of adenosine bonded to 3 phosphates, energy packed into phosphate bonds
when cell needs energy, it takes ATP, splits off 3 phosphates, forming ADP and a loose phosphate while releasing energy ⭐
organisms can use exergonic processes that increase energy, like breaking down ATP, to power endergonic reactions, like building organic molecules ⭐
Sources of ATP
ATP comes from cellular respiration: the process of breaking down sugar and making ATP
in autotrophs, sugar is made during photosynthesis
in heterotrophs, glucose comes from the food we eat
Photosynthesis
the process by which light energy is converted to chemical energy ⭐
6CO2 = 6H2O C6H12O6 +6O2
aka carbon dioxide and water are raw materials used to manufacture simple sugar, oxygen is a product of photosynthesis
strong evidence that prokaryotic photosynthesis contributed to oxygen in atmosphere and laid evolution for eukaryotic photosynthesis to develop ⭐
two stages of photosynthesis: light(-dependent) reactions and dark (light independent) reactions
process begins with photons (energy units) of sunlight striking leaf and activating chlorophyll, exciting electrons ⭐
activated chlorophyll molecule passes electrons to electron carriers producing ATP and NADPH ⭐
both products, along with carbon dioxide, then used in dark reactions to make carbs
along the way water is split and oxygen is released
Chloroplast Structure
leaves of plants contain chloroplasts, which are primary sites of photosynthesis
chloroplasts have fluid filled regions called stroma, inside stroma are stacked structures called grana
disk-like structures making up grana are thylakoids containing chlorophyll, a light absorbing pigment, and enzymes involved ⭐
very inside of thylakoid is called thylakoid lumen
chlorophyll a and b and carotenoids participate in photosynthesis, they’re clustered in thylakoid membrane into antenna complexes
all pigments gather lights but not exciting electrons, antenna pigments gather light and bounce energy to reaction center
two types of reaction centers:
photosystem I and photosystem II
main difference is each photosystem has specific chlorophyll (a) that absorbs a particular light wavelength ⭐
autotrophs are using light and ADP and phosphates (phosphorylation) to produce ATP; absorption spectrum shows how well certain pigment absorbs electromagnetic radiation
carotenoids absorb light on blue-green end of spectrum but not on other end
Light Reactions
when a leaf captures sunlight, energy is sent to P680, reaction center for photosystem II ⭐
activated electrons are trapped by the photosystem and passed to a molecule called the primary acceptor, then passed down to carriers in the electron transport chain ⭐
to replenish electrons in thylakoid, water is split into oxygen, hydrogen ions and electrons: photolysis
electrons from photolysis replace missing electrons in photosystem II; as energized electrons from photosystem II travel down ETC, they pump hydrogen ions into the thylakoid lumen; proton gradient is established; as hydrogen ions move into stroma through ATP synthase, ATP is produced ⭐
after electrons leave photosystem II, they go through photosystem I; electrons passed through second ETC until they reach final electron acceptor NADP+ to make NADPH; photosystems numbered based on discovery, not order
Light-Independent Reactions
dark reactions use products of light reactions (ATP and NADPH) to make sugar (glucose) ⭐
carbon source is CO2; carbon fixation means that CO2 from air is converted to carbs
this occurs in the stroma and is called the Calvin Cycle ⭐
plants that live in hot climate have evolved in two ways:
CAM plants temporarily separate carbon fixation and Calvin cycle
they open their stomata at night and incorporate CO2 into organic acids
during the day, stomata are closed and release CO2 from organic acids while light reactions run
C4 plants have different leaf anatomy that allows them to perform CO2 fixation in different part of leaf than Calvin cycle, preventing photorespiration
C4 plants produce four-carbon molecule as first product of carbon fixation and perform cyclic electron flow in light reactions
Cellular Respiration
can break cellular respiration down into two approaches:
aerobic respiration: when ATP is made in presence of oxygen
anaerobic respiration: when oxygen isn’t present
Introduction to Aerobic Respiration
consists of four stages of coupled reactions that establish an electrochemical gradient across membrane: ⭐
Glycolysis
Formation of acetyl-CoA
the Krebs cycle (citric acid cycle)
oxidative phosphorylation (ETC + chemiosmosis)
Stage 1: Glycolysis
the splitting of glucose
glucose is six-carbon molecule that is broken into two three carbon molecules called pyruvates
this results in net production of 2 ATP and 2 NADH ⭐
Glucose + 2 ATP + 2 NAD+ = 2 pyruvate + 4 ATP + 2 NADH
Glycolysis also creates 2 NADH which results from transfer of electrons to carrier NAD+ which becomes NADH ⭐
NAD+ and NADH are constantly being turned into each other as electrons are carried and unloaded
Four important things:
Glycolysis occurs in cytoplasm
net of 2 ATP
2 pyruvate formed
2 NADH formed
Stage 2: Formation of Acetyl-CoA
pyruvate is transported to mitochondria ⭐
each pyruvate is converted to acetyl coenzyme
A (two carbon molecule, acetyl-CoA) and Co2 are released
2 pyruvate + 2 Coenzyme A + 2 NAD+ = 2 Acetyl-CoA +2CO2 + 2NADH
extra carbon leave cell as CO2, once again 2 molecules of NADH are produced
process of turning pyruvate into acetyl-CoA is catalyzed by an enzyme complex called pyruvate dehydrogenase complex
Stage 3: Krebs Cycle
also known as citric acid cycle
begins with each acetyl-CoA produced from stage 2 combining with oxaloacetate (four carbon molecule) to form citric acid
in mitochondria, pyruvate is turned into acetyl-CoA and 1 NADH is made; double this if counting per glucose
Krebs cycle occurs in mitochondrial matrix
ends with oxaloacetate, 1 ATP, 3 NADH, and 1 FADH2; double if per glucose ⭐
citric acid gets turned into several things (cycle begins with 4 carbon molecule and eventually gets turned back into it to maintain cycle)
With each turn of the cycle:
1 ATP
3 NADH
1 FADH2
Stage 4: Oxidative Phosphorylation
Electron Transport Chain
as electrons are removed from glucose molecule, they carry energy that was originally stored in their chemical bonds ⭐
these electrons transferred to readied hydrogen carrier molecules; in case of cellular respiration, these carriers are coenzymes NADH and FADH2 ⭐
We now have:
2 NADH molecules from glycolysis
2 NADH from production of acetyl-CoA
6 NADH from Krebs cycle
2 FADH2 from Krebs cycle
total of 12 electron/energy carriers
these carriers “shuttle” electrons to ETC, the resulting NAD+ and FADH can be recycled to be used again as carriers and hydrogen atoms are split into hydrogen ions and electrons ⭐
high energy electrons are passed down series of protein carrier molecules that are embedded in cristae; thus called ETC
some carrier molecules in ETC are NADH dehydrogenase and cytochrome C
each carrier molecule hands down electrons to next in chain ⭐
electrons travel down ETC till they reach the final electron acceptor, oxygen; oxygen combines these electrons to form water ⭐
Chemiosmosis
energy released from the ETC is used to pump hydrogen ions across inner mitochondrial membrane from the matrix
pumping of hydrogen ions into inter-membrane space creates pH or proton gradient ⭐
hydrogen ions want to diffuse back into matrix; the potential energy established in this gradient is responsible for ATP production
pumping of ions and diffusion of ions to create ATP is chemiosmosis ⭐
overall, the process is called oxidative phosphorylation cuz when electrons are given up it’s called oxidation and then ADP is “phosphorylated” to make ATP ⭐
Know two things:
every NADH from glycolysis yields 1.5 ATP and all other NADH molecules yield 2.5 ATP
every FADH2 yields 1.5 ATP
Photosynthesis vs. Cell Respiration
in both cases, ATP production is driven by proton gradient which is created by an ETC
in respiration: protons pumped from mitochondrial matrix to intermembrane space and back to matrix through ATP synthase down concentration gradient
in photosynthesis: protons pumped from stroma to thylakoids and then return to stroma through ATP synthase down concentration gradient
Krebs cycle seeks to oxidize carbs to CO2 while Calvin cycle seeks to reduce CO2 to carbs
Anaerobic Respiration
when oxygen isn’t available, anaerobic respiration occurs
ETC stops working, electron carriers have nowhere to drop electrons
mitochondrial production of acetyl-CoA and Krebs cycle don’t work either
Glycolysis is only system that still runs, meaning glucose is broken down to give 2 ATP instead of 30 ⭐
Glycolysis also gives 2 pyruvate and 2 NADH; pyruvate helps NADH get recycled back to NAD+ and takes its electrons
pyruvate turns into either lactic acid (in muscles) or ethanol (in yeast) ⭐
since these things are toxic at high concentrations, this process is called fermentation and is only done in emergencies
Yeast cells, some bacteria go through fermentation to make ethanol and CO2, other bacteria produce lactic acid
Muscle Cells Can Ferment
a cramp might be consequence of anaerobic respiration
during exercise, muscles require lots of energy ⭐
to get energy, muscles convert huge amts of glucose to ATP
as exercise continues, body can’t get enough oxygen creating oxygen debt ⭐
muscles switch to anaerobic respiration
pyruvic acid produced from glycolysis is converted to lactic acid
Unit 4
Cell Communication
unicellular organisms detect and respond to environmental signals
Taxis is movement of organism in response to stimulus; can be pos (toward stimulus) or neg (away from stimulus)
Taxes are innate behavioral responses/instincts; chemotaxis is movement in response to chemicals
Signal Transduction & Changes in Pathways
cells of multi-celled organisms must communicate with one another to coordinate activities of organism as a whole
cells communicate through contact or cell signaling; signaling can be short range (only nearby cells) or long range (cells throughout organism) ⭐
can be done by cell junctions or signaling molecules called ligands that bind to receptors and trigger a response by changing shape of receptor protein ⭐
Signal transduction is process where an external signal is transmitted to inside of cell; involves these steps: ⭐
a signaling molecule binds to specific receptor ⭐
activation of a signal transduction pathway ⭐
production of a cellular response ⭐
signaling molecules that cannot enter cell, a plasma membrane receptor is required
plasma membrane receptors form an important class of integral membrane proteins that transmit signals from the extracellular space into the cytoplasm; each receptor binds a particular molecule in a highly specific way
Three Classes of Membrane Receptors
Ligand-gated ion channels in plasma membrane open or close an ion channel upon binding a particular ligand. This channel opens in response to acetylcholine and a massive influx of sodium depolarises the muscle cell and causes it to contract ⭐
Catalytic (enzyme-linked) receptors have an enzymatic active site on the cytoplasmic side of the membrane. Enzymatic activity is initiated by ligand binding at the extracellular surface
A G-protein-linked receptor does not act as an enzyme, but instead will bind a different version of a G-protein (often GTP or GDP) on the intracellular side when a ligand is bound extracellularly. This causes activation of secondary messengers within the cell. One important second messenger is cyclic AMP (cAMP) ⭐
signal transduction cascades are helpful to amplify a signal ⭐
Feedback
the set of conditions under which living things can successfully survive is homeostasis ⭐
blood glucose levels are regulated by insulin and glucagon, two hormones released from your pancreas
many of these responses are controlled by negative or positive feedback pathways
a negative feedback pathway (feedback inhibition) works by turning itself off using the end product of the pathway. End product inhibits the process from beginning, thus shutting down the pathway ⭐
Positive feedback pathway also involves an end product playing a role, but instead of inhibiting the pathway, it further stimulates it ⭐
Cell Cycle
every cell has life cycle—the period from beginning of one division to beginning of the next ⭐
cell’s life cycle is known as cell cycle
cell cycle divided into interphase and mitosis ⭐
Interphase: growing phase
Three stages of Interphase: G1, S, G2 ⭐
most important is S phase where cell replicates genetic material
during interphase, every chromosome in nucleus is duplicated
identical strands of DNA are now sister chromatids
chromatids held together by centromere
each chromatids remain attached so not called chromosome; to be called chromosome, each needs its own centromere
once chromatids separate, they become chromosomes
Cell Cycle Regulation
G1 and G2- cell performs metabolic reactions and produces organelles, proteins, and enzymes ⭐
G stands for “gap” but also growth
these three phases are highly regulated by checkpoints and special proteins called cyclin and cyclin-dependent kinases (CDKs) ⭐
Cell cycle checkpoints are control mechanisms that make sure cell division is happening properly in eukaryotic cells
in eukaryotes, checkpoint pathways function mainly at phase boundaries (like G1/S transition)
when damaged DNA is found, checkpoints are activated and cell cycle progression stops. Cell uses the extra time to repair damage in DNA. If DNA damage is so extensive it cannot be repaired, the cell can undergo apoptosis, or programmed cell death
Cell cycle checkpoints control cell cycle progression by regulating two families of proteins:
cyclin-dependent kinases
cyclins
to induce cell cycle progression, an inactive CDK binds a regulatory cyclin. once together the complex is activated, can affect many proteins in the cell, and cause cell cycle to continue
to inhibit cell cycle progression, CDKs and cyclins are kept separate; they were first studied in yeast, unicellular eukaryotic fungi
Cancer
cancer occurs when normal cells start behaving and growing very abnormally and spread to other parts of the body ⭐
mutated genes that induce cancer are called oncogenes
they are genes that can convert normal cells into cancerous cell healthy version is called a proto-oncogene
tumour suppressor genes produce proteins that prevent the conversion of normal cells into cancer cells. they can detect damage to the cell and work with CDK complexes to stop cell growth until the damage can be repaired
they can also trigger apoptosis if the damage is too severe to be repaired ⭐
Mitosis
Mitosis, or cell division, occurs in five steps
prophase, prometaphase, metaphase, anaphase, and telophase ⭐
during prophase, cell structures break down, chromosomes condense, mitotic spindle forms and nucleolus disappears
prometaphase: spindle captures and organizes chromosomes, chromosomes continue to condense and nuclear envelope breaks down
metaphase: chromosomes align at metaphase plate, also where spindle checkpoint occurs
anaphase: sister chromatids separate and pulled to opposite sides of cell
telophase re-establishes cell structures, cytokinesis starts, chromosomes decondense, two new nuclei for
cytokinesis which starts in telophase, ends mitosis as cytoplasm and plasma membrane pinch to form two distinct daughter cells
in plants, cell wall forms, in animals, cell is pinched at cleavage furrow
new daughter cells re-enter interphase and process starts over
Purpose of Mitosis
mitosis achieves two things:
production of daughter cells that are identical copies of parent maintaining proper number of chromosomes through generations
impetus to divide occurs because an organism needs to grow, a tissue needs repair or asexual reproduction takes place
Unit 5
Haploids vs Diploids
cell that has two sets of chromosomes is a diploid (chromosome # is 2n)
if cell has only one set of chromosomes, it’s a haploid (n)
duplicate versions of each chromosome are homologous chromosomes
homo chromosomes that make each pair or similar in size and shape and contain same genes in same locations
Gametes
sex cells are haploid
parent will contribute a gamete with one set that will be paired with set from other parent to produce a new diploid aka a zygote
Gregor Mendel: Father of Genetics
genetics was discovered by a monk named Gregor Mendel
DNA and RNA are carriers of genetic information ⭐
ribosomes found in all forms of life ⭐
traits are influenced by one or more genes
position of gene on a chromosome is a locus
diploid organisms usually have two copies of each gene (homologous chromosomes)
humans have 23 pairs of homo chromosomes
homo chromosomes have same size, shape and have same genes but contain different alleles (versions of genes) and different genetic sequences
when an organism has two identical alleles for given trait it’s homologous
when an organism has two different alleles for given trait it’s heterozygous
when discussing organisms physical appearance, that’s its phenotype
the genotype concerns the alleles the organism possesses
a dominant alleles receives a capital letter and a recessive allele receives a lowercase of the same letter
First gen is called the parent (P) generation
offspring of P generation is called the filial (F1) generation; next generation is F2 generation
Three principles of genetics: Law of Dominance, Law of Segregation, Law of Independent Assortment
Law of Dominance
Mendel crossed 2 true-breeding pea plants: tall and short
when he mated them, characteristics didn’t blend to produce average height plants, instead all were tall
a monohybrid cross occurs when two individuals are crossed and one gene is being studied, simple way to represent monohybrid cross is a punnett square
Law of Segregation
mendel then took offspring and self pollinated them
ratio of phenotypes was 3:1 (tall:short), ratio of genotypes was 1:2:1 (1 TT: 2 Tt: 1 tt)
Law of Independent Assortment
when studying two traits at the same time each allele of the two traits will get segregated into 2 gametes but how one trait gets split has no bearing on how other does
Dihybrid Cross
different genes assort independently into gametes, dihybrid cross studies two genes
Rules of Probability
a better method for predicting the likelihood of certain results from dihybrid cross is applying Rules of Probability ⭐
to determine probability that two or more independent events occur simultaneously, one calculates product of probability of each independently: product rule
to determine likelihood that EITHER event occurs, not both, use Sum rule
Product Rule: If A and B are independent, then: P(A and B) = P(A) times P(B)
Sum Rule: If A and B are mutually exclusive, then P(A or B) = P(A) + P(B)
Summary of Mendel’s Laws
Law of Dominance: One trait masks the other traits effects
Law of Segregation: Each gamete gets only one of the copies of each gene ⭐
Law of Independent Assortment: Each pair of homologous chromosomes splits independently so alleles of different genes can mix and match ⭐
Non-Mendelian Genetics: Sex-Linked Traits
Linked Genes
sometimes genes on same chromosome stay together during assortment
this group of genes is considered linked and tends to be inherited together (ex. the genes for flower color and pollen shape are linked on same chromosome and show up together) ⭐
since linked genes are found on same chromosome, they cannot segregate independently, violating Law of Independent Assortment
offspring formed from recombination events are called recombinants
percentage of recombination (recombination frequency) can be determined by adding up recombinants and dividing by total number
The frequency of crossing-over between any two linked alleles is proportional to the distance between them. This finding led to recombination mapping— mapping of linkage groups with each map unit being equal to 1 percent recombination.
For example, if two linked genes, A and B, recombine with a frequency of 15 percent, and B and C recombine with a frequency of 9 percent, and A and C recombine with a frequency of 24 percent, what is the sequence and the distance between them?
A-B is 15 units
B-C is 9 units
Total 24 units
Sex-linked traits
Humans contain 23 pairs of chromosomes. Twenty- two of the pairs of chromosomes are called autosomes; they code for many different traits.
The other pair contains the sex chromosomes. This pair determines the sex of an individual.
A female has two X chromosomes. A male has one X and one Y chromosome.
Some traits, such as color blindness and hemophilia, are carried on sex chromosomes.These are called sex-linked traits ⭐
Most sex- linked traits are found on the X chromosome and are more properly referred to as “X-linked.”
Since males have one X and one Y chromosome, what happens if a male has an X-chromosome with the color blindness allele? he’ll express the sex-linked trait, even if it is recessive
However, if a female has only one color blind-X chromosome, she won’t express a recessive sex-linked trait. For her to express the trait, she has to inherit two color blind-X chromosomes.
A female with one color blind-X is called a carrier. Although she does not exhibit the trait, she can still pass it on to her children.
You can also use the Punnett square to figure out the results of sex-linked traits.
Barr Bodies
A look at the cell nucleus of normal females will reveal a dark-staining body known as a Barr body
A Barr body is an X chromosome that is condensed and visible. In every female cell, one X chromosome is activated and the other X chromosome is deactivated during embryonic development.
The X chromosome destined to be inactivated is randomly chosen in each cell.
Therefore, in every tissue in the adult female, one X chromosome remains condensed and inactive. However, this X chromosome is replicated and passed on to a daughter cell.
X-inactivation is the reason it is okay that females have two X chromosomes and males have only one. After X-inactivation, it is like everyone has one copy.
Other Inheritance Patterns
Incomplete dominance (**blending inheritance): In some cases, the traits will blend. For example, if you cross a white snapdragon plant (genotype WW) with a red snapdragon plant (RR), the resulting progeny will be pink (RW). In other words, neither color is dominant over the other.
Codominance: Sometimes you’ll see an equal expression of both alleles. For example, an individual can have an AB blood type. In this case, each allele is equally expressed.
Polygenic inheritance: In some cases, a trait results from the interaction of many genes. Each gene will have a small effect on a particular trait.
Non-nuclear inheritance: Apart from the genetic material held in the nucleus, there is also genetic material in the mitochondria. The mitochondria are always provided by the egg during sexual reproduction, so mitochondrial inheritance is always through the maternal line, not the male line. In plants the mitochondria are provided by the ovule and are maternally inherited. ⭐
Pedigrees
One way to study genetic inheritance is by looking at a special family tree called a pedigree. ⭐
A pedigree shows which family members have a particular trait and it can help determine if a trait is recessive or dominant and if it is sex-linked.
Traits that skip generations are usually recessive.
Traits that appear more in one sex than the other are usually sex-linked.
In a pedigree chart, the males are squares and the females are circles.
Environmental Effect on Traits
Changes in genotypes can result in changes in phenotype, but environmental factors also influence many traits, directly and indirectly. ⭐
Furthermore, an organism’s adaptation to the local environment reflects a flexible response of its genome
Phenotypic plasticity occurs if two individuals with the same genotype have different phenotypes since they are in different environments. ⭐
An Overview of Meiosis
Meiosis is the production of gametes. ⭐
Meiosis is limited to sex cells in special sex organs called gonads.
In males, the gonads are the testes, while in females they are the ovaries.
The special cells in these organs—also known as germ cells—produce haploid cells (n), and they combine to restore the diploid (2n) number during fertilization. female gamete (n) + male gamete (n) = zygote (2n)
Meiosis is likely to produce sorts of variations than is mitosis, which therefore confers selective advantage on sexually reproducing organisms.
A Closer Look at Meiosis
Meiosis actually involves two rounds of cell division: meiosis I and meiosis II. ⭐
Before meiosis begins, the diploid cell goes through interphase. Just as in mitosis, double-stranded chromosomes are formed during S phase. ⭐
Meiosis I
Meiosis I consists of four stages: prophase I, metaphase I, anaphase I, and telophase I.
Meiosis I ensures that each gamete receives a haploid (1n) set of chromosomes. ⭐
Prophase I
As in mitosis, the nuclear membrane disappears, the chromosomes become visible, and the centrioles move to opposite poles of the nucleus.
The major difference involves the movement of the chromosomes. In meiosis, the chromosomes line up side-by-side with their counterparts (homologs). This event is known as synapsis.
Synapsis involves two sets of chromosomes that come together to form a tetrad (a bivalent). A tetrad consists of four chromatids. Synapsis is followed by crossing-over, the exchange of segments between homologous chromosomes. ⭐
What’s unique in prophase I is that pieces of chromosomes are exchanged between homologous partners. This is one of the ways organisms produce genetic variation. ⭐
Metaphase I
As in mitosis, the chromosome pairs—now called tetrads—line up at the metaphase plate.
By contrast, you’ll recall that in regular metaphase, the chromosomes line up individually.
One important concept to note is that the alignment during metaphase is random, so the copy of each chromosome that ends up in a daughter cell is random.
Anaphase I
During anaphase I, each pair of chromatids within a tetrad moves to opposite poles. The homologs will separate with their centromeres intact.
The chromosomes now move to their respective poles.
Telophase I
During telophase I, the nuclear membrane forms around each set of chromosomes.
Finally, the cells undergo cytokinesis, leaving us with two daughter cells. ⭐
Meiosis II
The purpose of the second meiotic division is to separate sister chromatids
During prophase II, chromosomes once again condense and become visible.
In metaphase II, chromosomes move toward the metaphase plate. This time they line up single file, not as pairs.
During anaphase II, chromatids of each chromosome split at the centromere, and each chromatid is pulled to opposite ends of the cell.
At telophase II, a nuclear membrane forms around each set of chromosomes and a total of four haploid cells are produced.
Gametogenesis
Meiosis is also known as gametogenesis.
If sperm cells are produced, then meiosis is called spermatogenesis.
During spermatogenesis, four sperm cells are produced for each diploid cell.
If an egg cell or an ovum is produced, this process is called oogenesis.
Oogenesis produces only one ovum, not four. The other three cells, called polar bodies, get only a tiny amount of cytoplasm and eventually degenerate since the female wants to conserve as much cytoplasm as possible for the surviving gamete, the ovum.
Meiotic Errors
Nondisjunction—chromosomes failed to separate properly during meiosis.
This error, which produces the wrong number of chromosomes in a cell, usually results in miscarriage or significant genetic defects. ⭐
Individuals with Down syndrome have three—instead of two—copies of the 21st chromosome.
Nondisjunction can occur in **anaphase I (**meaning chromosomes don’t separate when they should), or in anaphase II (meaning chromatids don’t separate).
Either one can lead to aneuploidy, or the presence of an abnormal number of chromosomes.
Unit 6
DNA
made up of repeated subunits of nucleotides
nucleotide includes: five-carbon sugar, phosphate, nitrogenous base
sugar named deoxyribose and is liked to a phosphate and nitrogenous base
types of nitrogenous bases:
adenine (purine)
guanine (purine)
cytosine (pyrimidine)
thymine (pyrimidine)
prokaryotes and eukaryotes can contain plasmids (double-stranded, circular DNA molecules)
long chain of nucleotides is a strand of DNA
nucleotides linked by phosphate bonds between sugar and phosphate: called sugar-phosphate backbone of DNA, serves as a scaffold for the bases
Two DNA Strands
each DNA molecule has two strands wrapped in double helix
double helix deduced by Watson and Crick using Franklins work (1953)
Adenine + thymine (A-T) by forming 2 hydrogen bonds
Cytosine + guanine (C-G) by formed 3 hydrogen bonds
this is called base pairing, each two strands are complementary
5’ end has phosphate group, 3’ end has hydroxyl group (OH)
5’ end of one strand and 3’ end of other strand are opposites aka antiparallel
DNA strands are linked by hydrogen bonds
Genome Structure
all DNA for species is its genome
separate chunks of DNA in a genome are chromosomes
DNA is wrapped in proteins called histones
histones bunched in groups called nucleosome
when genetic material is loose in nucleus: euchromatin and genes are active or available for transcription
when genetic material is condensed in coils: heterochromatin and genes are generally inactive
DNA Replication
copying of DNA is DNA replication
1st step: unwind double helix by breaking hydrogen bonds, done by the enzyme helicase
exposed DNA strands form replication fork
each strand is now template for synthesizing a new strand
DNA replication starts at origins of replication
DNA helix twists and rotates so DNA topoisomerase cuts and rejoins helix to prevent tangling
DNA polymerase adds nucleotides to freshly build new strand
can only add nucleotides to 3’ end of existing strand
RNA primase starts replication, adding short strand of RNA nucleotides called RNA primer
after replication, primer is degraded by enzymes and replaced with DNA
from two strands made by replication fork, one is leading strand (made continuously) and one is lagging strand (made discontinuously)
leading strand: nucleotides steadily added in 5’ to 3’ direction by DNA polymerase
lagging strand: made in pieces called okazaki fragments
nucleotides added only in 5’ to 3’ direction since nucleotides can only be added to 3’ end
double helix is unzipped: one strand going opposite way (lagging), so DNA polymerase builds onto it in fragments
DNA ligase connects fragments into continuous strand