AP Biology Review

has units 1-3 basically

Cohesion

Water sticks to itself through H-bonds

Adhesion

Sticking to other types of molecules through polarity

Capillary action

uses cohestion AND adhesion, goes against gravity, water goes up xylem

How does carbon allow for molecular diversity?

variations in carbon skeletons, can form macromolecules, and crucial for 4 types of macromolecules/polymers: carbohydrates, lipids, nucleic acids, proteins

What does Nitrogen and carbon make up?

proteins and nucleic acids

What does phosphorous and carbon make up?

nucleic acids and some lipids

functional groups

Hydroxyl group, carbonyl group, carnoxyl group, amino group, sulfhydryl group, methyl group, phosphate group

Hydroxyl group

Polar

carbonyl group

polar

carboxyl group

polar

amino group

polar

sulfhydryl group

polar

methyl group

nonpolar

phosphate group

polar (H’s may be absent & replaced by -)

dehydration synthesis

bonds 2 monomers with the loss of H2O

Hydrolysis

breaks the bonds in a polymer by adding H2O

Storage polysaccharides

glucose monomers: starch for plants, glycogen for animals

Structural polysaccharides

Cellulose: tough substance that forms plant cell walls

Chitin: forms exoskeleton of arthropods

Forming peptide bonds

dehydration synthesis, CARBOXYL group (C-terminus) of one AA must be positioned next to the free AMINO group (N- terminus) of the other AA

molecules in proteins

CHONS

types of secondary protein folding structure

Beta pleated sheet- hydrogen bonds between peptide chains lying side by side(messy)

Alpha helix- hydrogen bonding between every 4th AA(organized)

triglyceride molecular structure

glycerol and 3 fatty acids via ESTER LINKAGE

What makes up fats?

glycerol (w hydroxyl group) and fatty acids (w carboxyl group)

ester linkage

bonds fats

saturated vs unsaturated fatty acid

saturated- full of H, no double bonds or kinks

unsaturated- some double bonds because not full of H, not straight, has kinks

phospholipid structure

Head: glycerol and phosphate group

tails: one saturated fatty acid and one unsaturated

what are steroids?

lipids with 4 fused rings w/ groups attached that determines steroid type

ex: testosterone & cholesterol

purines v pyrimidines

purines = 2 rings (pur As Gold)

pyrimidines = 1 ring, (CUT the py)

deoxyribose vs ribose

both 5 carbon sugars (pentose)

ribose less stable, extra OH, RNA

Nucleoside

nucleotide half without the phosphate group/backbone (aka sugar and nucleic acid)

What bond links nucleotides?

phoshodiester linkage

elements that make up nearly all living matter

CHON (95%) (PS both also important)

smooth ER function

Synthesizes lipids

Metabolizes carbs(does chemical reactions with carbs)

Detoxifies the cell

golgi complex structure

Contains flattened membranous sacs called CISTERNAE

Each cisternae is not connected

directionality:

• CIS face: faces Rough ER

• Function: receives vesicles from Rough ER

• TRANS face: faecs membrane

• Function: sends vesicles back out into the cytosol to other locations or to the plasma membrane to be secreted

golgi complex function

Receives transport vehicles with materials from Rough ER

Modifies the materials(makes sure that new proteins are folded/modified correctly)

Sorts the materials

Adds molecular tags

Packages materials into new transport vesicles that EXIT the membrane via EXOCYTOSIS

Lysosome function

contains hydrolytic enzymes (breaks things down w hydrolysis)

digests things inside cell

involved in endocytosis

peroxisome function

some oxidative reactions and catalyzing

protects cell from H2O2

produces some energy?

metabolizes lipids maybe?

Food vacuole

Forms via PHAGOCYTOSIS(cell eating) and then digested by lysosomes

contractile vacuole

not in humans

controls amount of water in cell

central vacuole

found in plants

important for turgor pressure

mitochondrial structure

outer membrane

intermembrane space

inner membrane (has folds called cristae that increase surface area)

enclosed in inner membrane is mitochondrial matrix, site of KREBS CYCLE

chloroplast structure

• Thylakoids

  • Membranous sacs that can organize into stacks called GRANA

  • Light dependent reactions happen here

  • Contains the green pigment chlorophyll

  • inside thylakoid is lumen

• Stroma

  • Fluid around the thylakoids

  • Location for the Calvin cycle/light Independent reactions

  • Contains:

    • Ribosomes

    • Chloroplast DNA

    • Enzymes

SA:V ratio

higher is more efficient for diffusion

fluidity of double membrane and temperature

Temperature affects fluidity

Unsaturated hydrocarbon tails help maintain fluidity at low temperatures

• Kinked tails prevent tight packing which allows more things through

Cholesterol: helps maintain fluidity at high and low temperatures

• High temp: reduces movement

• Low temp: reduces tight packing of phospholipids

integral vs peripheral proteins

integral aka transmembrane proteins embedded

peripheral loosely bonded to membrane surface

amphipathic

part hydrophilic part hydrophobic

membrane carbohydrates

Important for cell to cell recognition

Glycolipids

• Carbs bonded to lipids

Glycoproteins

• Carbs bonded

• Most abundant

transport proteins

channel and carrier proteins that are specific for substances that it facilitates movement for

channel proteins

• Channel for ions and molecules to move through

• Hydrophilic

• Many are gated channels which means that they only allow molecules to pass when there is a stimulus

aquaporin

channel protein specific to water

carrier proteins

Undergo conformational changes for substances to pass through

Membrane potential

unequal concentration of ions across the membrane results in an electrical charge(electrochemical gradient)

Sodium-potassium pump

electrogenic pump

uses ATP and conformational changes

• Animal cells will regulate their relative concentrations of Na+ and K+

• 3 Na+ goes OUT of the cell

• 2K+ goes INTO the cell

• Results in a net +1 charge to the extracellular fluid

electrogenic pump

Proteins that generate voltage across membranes, which can be used later as an energy source for cellular processes

proton pump

Integral membrane protein that builds up a proton gradient across the cell

Used by plants, fungi and bacteria

Pumps H+ out of the cell

cotransport

• The coupling of a favorable movement of one substance with an unfavorable movement of another substance

• Uses the energy stored in electrochemical gradients(generated by the pumps) to move substances against their concentration gradient

• Favorable movement: downhill diffusion

• Unfavorable movement: uphill diffusion

• Plants use cotransport for sugar and amino acids

Sucrose-H+ cotransporter

• Sucrose goes into the the plant cell AGAINST its concentration gradient only if it is coupled with an H+ ion that is diffusing down its electrochemical gradient

exocytosis

the secretion of molecules via vesicles that fuse to the plasma membrane

endocytosis

the uptake of molecules from vesicles fused from the plasma membrane

phagocytosis, pinocytosis, receptor-mediated

phagocytosis

endocytosis, larger food particles

• when a cell engulfs particles to be later digested by lysosomes

• Cell surrounds particles with pseudopodia

• Packages particles into a food vacuole

• Food vacuole fuses with a lysosome to be digested

pinocytosis

endocytosis, larger liquid molecules

• nonspecific uptake of extracellular fluid containing dissolved molecules

• Cell take in dissolved molecules in a protein coated vesicle

• Protein coat helps to mediate the transport of molecules

receptor-mediated endocytosis

specific uptake of molecules via solute binding to receptors on the  plasma membrane

• Allows the cell to take up large quantities of a specific instance

• When solutes bind to the receptors they cluster in a coated vesicle to be taken into the cell

isotonic solution

• no net movement of water

• The concentration of nonpenetrating solutes inside the cell=to that outside the cell

plasmolysis

plants

vacuole shrinks and the plasma membrane pulls away from the cell wall

hypertonic solution

if solution is hypertonic to the cell

then: solution has a higher solute concentration, lower free water concentration

so: water leaves cell to balance concentrations, leaves cell shriveled/plasmolyzed

hypotonic solution

if solution is hypotonic to the cell

then: solution has a lower solute concentration, higher free water concentration

so: water enters cell to balance concentrations, cell swells/bursts aka lyses

turgor pressure/turgidity

plants

the force within the cell that pushes the plasma membrane against the cell wall

water potential relationships (formula on ref sheet)

Water will flow from:

• HIGH water potential->LOW water potential

• LOW solute concentration->HIGH solute concentration

• HIGH pressure-> LOW pressure

catabolic pathways

break down, release energy

anabolic pathways

building, using up energy

exergonic

releases energy

endergonic

absorbs energy

1st law of thermodynamics

Energy CANNOT be created or destroyed

Energy CAN ONLY be transformed or transferred  

2nd law of thermodynamics

Energy transformation increase the ENTROPY (disorder) of the universe 

During energy transfers/transformations, some energy is unusable and often lost as heat

phosphorylation

ATP sends its terminal phosphate group to bind to something to give it energy for something like a conformational change, becomes ADP

cofactors

inorganic, help enzymes

coenzymes

organic, helps enzymes

allosteric site

not active site

photosynthesis redox reaction

Electrons are transferred with H+ (from split H2O) to CO2 reducing it to sugar (glucose) 

stomata

pores in the leaves that allows CO2 in and O2 out

photosynthetic pigments

• Chlorophyll a

  • Primary Pigment 

  • Involved in light reactions  

  • Blue/green pigment

• Chlorophyll b  

  • Accessory pigment

• Carotenoids

  • Broaden the spectrum of colors that drive photosynthesis 

  • Photoprotection: carotenoids absorb and dissipate excess light energy that could damage chlorophyll or interact with oxygen

Photosystems

Thylakoid membrane has 2 photosystems, system 2 comes first

• reaction center and light capturing complexes (group of proteins stuck together to form a task)

  • Reaction center: a complex of proteins associated with chlorophyll a and an electron acceptor

  • Light capturing complexes: pigments associated with proteins

electron transport chain path/photosynthesis light dependent rxn

NADP+/NADPH electron carriers

PS2 gets energy from sun, excites an electron. Photolysis: H2O donates H+, O2 released as byproduct.

Electrons move through ETC and cytochrome, pumping H+ into lumen to create a gradient

PS1 takes energy from sun again, excites electron, and also uses past electrons, which reduces NADP+ to NADPH which goes onto calvin cycle

ATP Synthase makes ATP when protons passively diffuse through it. ADP + Pi → (powered by proton gradient/proton motive force) ATP

diffusion direction: lumen (High H+) → stroma (low H+)

calvin cycle general

light independent

powers turning CO2 (inorganic) into usable organic C3 molecule glucose

3 stages: carbon fixation, reduction, RuBP regeneration

uses ATP and NADPH, REDUCES CO2

to net synthesize 1 G3P molecule, must take place 3 times bc need 3 CO2 per G3P but CO2 really goes in only one at a time

what is photolysis

using photon sun energy to break apart H2O

why is rubisco important

its an enzyme responsible for carbon fixation in calvin cycle

most abundant enzyme on the planet

what products of the light reactions are used in the calvin cycle

ATP & NADPH

final electron acceptor in photosynthesis

NADP+

what products of the calvin cycle are used in the light reactions

ADP, NADP+

what substrate uses rubisco enzyme to fix carbon dioxide?

RuBP

photosynthesis electron donor

water/H20

final electron acceptor

O2

carbon fixation (phase 1 calvin cycle)

CO2 combines w RuBP

rubisco enzyme catalyzes rxn

reduction (phase 2 calvin cycle)

energy inputs from ATP & NADPH lead to G3P formation

regeneration of RuBP (phase 3 calvin cycle)

3C compounds reorganize and combine to produce RuBP, uses some ATP

regenerates RuBP which helps to restart cycle

how does the concentrations of CO2, O2, and RuBP change as photosynthesis goes on and on and on

CO2 decreases, O2 increases, RuBP fluctuates

guard cells

near stomata

osmotic pressure changes shape causing them to swell. can create an opening for gas exchange or close to prevent water loss

photorespiration

when rubisco mistakenly binds to O2 instead of CO2, no sugar is produced and wastes energy

bad and can happen more when plants close stomata on hot days to prevent water loss because [O2] increases and [CO2] decreases

C3 plants

nothing special, 85% of plants

fixes CO2 directly from air

less efficient in hot and dry regions

photorespiration reduces photosynthesis by 25%

C4 Plants

minimizes photorespiration

separates calvin cycle and CO2 fixation into different cell types

bandle sheath cells

plants like sugarcane and corn

CAM Plants

minimizes photorespiration

fixates carbon at night and does the rest of carbon cycle during the day

can keep stomata closed during the day, preventing water loss due to heat, while opening them at night to decrease oxygen concentration

plants like pineapples and succulents