Exam 2 Bio

adherens junctions

connect adjacent cells via cadherins, binds to actin filaments in band-like structure

adherens junctions function

cell stability

desmosomes junctions

connects to adjacent cells via cadherins, spot like structure anchoring to intermediate filaments

desmosome function

provides mechanical strength

hemidesmosomes

connects cells to ECM via integrins, anchors to intermediate filaments inside cells

hemidesmosomes function

aids in anchoring cells

focal adhesions

connects cells to ECM via integrins, anchors to actin filaments

focal adhesions function

links cytoskeleton to ECM

tight junction

seals gap between adjacent cells, claudins and occludins link to actin

tight junction function

prevents leakage of molecules between cells

gap junctions

animal cells, connexins create channels, coordinates cells to elicit group response

plasmodesmata

plant cells, signals to pass freely between cells for communication and coordination, plasma membrane and smooth ER between two cells is continous

kinetic energy

energy associated with movement, ex: heat

potential energy

energy associated with potential to do work

first law thermodynamics

conservation of energy, energy cannot be created or destroyed, only transformed

second law thermodynamics

total entropy of a system will increase over time

Breakdown of ATP

hydrolysis releases energy, exergonic, can be coupled to fuel endergonic reaction

Gibbs free energy equation

H(total energy) = G(usable energy) + TS(unusable energy)

Exergonic

G value less than 0, release energy, spontaneous

Endergonic

G value more than 0, not spontaneous

Enzyme reaction

lower activation energy but G doesn’t change

Low km value

enzymes have high affinity

km value

the substrate concentration at which an enzyme-catalyzed reaction proceeds at half of its maximum velocity

two main ways substrates bind to active site

lock and key binding, induced fit

how enzymes lower activation energy

1. arrange substrate in optimal position for reacting 2. strain bonds in reactants 3. change local chemical environment

pH impact enzyme activity

impacts folding of proteins

temperature impact enzyme activity

higher temperature increases reaction rate, if temperature increases too much protein denatures

cofactors

molecule besides substrate whose presence is essential enzyme function

prosthetic groups

like cofactor, permanently bound to enzyme, ex: vitamins, metal ions, lipids, heme

coenzymes

cofactors that play role in reaction but remain unchanged

anabolic pathways

endergonic, building things up

catabolic pathways

exergonic, breaking things down

regulation metabolic pathways

1. turn on or off genes 2. cell-signaling pathways 3. biochemical regulation

competitive inhibitors

bind to active site, increase km, prevents reaction from going forward

noncompetitive inhibitors

bind to enzyme, lowers vmax, lowers catalytic availability of the enzyme

Oxidation

loss of electrons, often removal hydrogens

reduction

addition of electrons, often adds hydrogens

C6H12O6 + 6O2

6CO2 + 6H2O

what is oxidized in cellular respiration

glucose

cellular respiration free energy

-686 kcal/mol

4 metabolic pathways cellular respiration

1. glycolysis 2. pyruvate processing 3. citric acid cycle 4. oxidative phosphorylation

glycolysis stages

1. energy investment 2. cleavage 3. energy liberation

glycolysis input

2 ATP

glycolysis output

4 ATP, 2 NADH, 2 pyruvate

steps ATP production glycolysis

substrate level phosphorylation

pyruvate processing input

pyruvate, NAD+, coenzyme A

pyruvate processing output

1 CO2, 1 acetyl group, 1 NADH

pyruvate processing enzyme

pyruvate dehydrogenase

citric acid cycle input

acetyl CoA

citric acid cycle output

2 CO2, 1 ATP, 3 NADH, 1 FADH2

two carbons enter cycle location

citrate, enter via acetyl-coA

two carbons lost as CO2

after isocitrate, after alpha-ketoglutarate

first ATP formed

after succinyl CoA

regeneration oxaloacetate

fumarate-oxaloacetate

feedback inhibition high ATP

blocks citrate formation, blocks sucinyl CoA formation

feedback inhibition high NADH

blocks a-ketoglutarate formation

Electron transport chain input

10 NADH, 2 FADH2

electron transport chain and oxidative phosphorylation output

30-34 ATP, water

proton gradient formation ETC

uses NADH and FADH2

ATP synthase

does oxidative phosphorylation to make ATP via chemiosmosis

complex 1 ETC

NADH dumps electrons onto, 4 protons/electron

complex II ETC

FADH dumps electrons onto

Q and protein cytochrome C

transfer electrons between complexes, Q carries protons across the membrane

Racker and Stoeckenius

confirmed that ATP synthase uses an H+ electrochemical gradient, bacteriorhopsodin pumps protons across membrane in the presence of light

hans kreb

co-winner nobel prize 1953 for “discovery citric acid cycle”

organisms never use fermentation if

appropriate electron acceptor available cellular respiration (no O2)

consequence shutting down citric acid cycle and ETC

need to regenerate NAD+

regenerating NAD+ solution

add NADH electrons to organic final electron acceptor

6 CO2 + 12 H2O + light energy

C6H12O6 + 6 O2 + 6 H2O

molecule reduced photosynthesis

CO2

molecule oxidized photosynthesis

H2O

photosynthesis free energy

+685, endergonic

chloroplast membranes

outer, inner, thylakoid that contains pigment (chlorophyll)

granum

stack of thylakoids

stroma

fluid filled region between thylakoid membrane and inner membrane

light reaction photosynthesis

located in thylakoid membranes, produces ATP, NADPH, O2

calvin cycle photosynthesis

stroma, uses ATP and NADPH to incorporate CO2 into organic molecules

light reaction input

light, H2O from thylakoid lumen, ADP and Pi from stroma, NADP+ from stroma

photosystem II captures light energy steps

1. light hits light harvesting complex 2. resonance energy transfer transfers energy to P680 3. P680’s excited electron gets transferred to Pp 4. electrons from H2O are used to replace P680’s electron

PSII functions

makes ATP, ETC makes H+ gradient to make ATP

PSI

addition H+ NADP contributes to H+ electrochemical gradient

Z scheme

potential energy of E- electron, forms Z

energy electron highest

excited PSI pigment

energy electron lowest

non-excited pigment molecule PSII

calvin cycle input

CO2 from outside, ATP from lumen, NADPH from lumen, RuBP regenerated

calvin cycle output

G3P, ADP+ Pi, NADP+, RuBP

phases carbon cycle

1. Carbon fixation 2. reduction and carbohydrate production 3. regeneration RuBP

carbon fixation

CO2 incorporated into RuBP via rubisco, 6 carbon intermediate splits into 2 3PG

reduction and carbohydrate production

ATP used to convert 3PG into 1,2 biphosphoglycerate, NADPH electrons reduced to G3P

regeneration RuBP

2 G3P used to make glucose and sugars, remaining 10 used to regenerate using ATP and enzymes

Cyclic flow

makes extra ATP during light reactions, e- from PS1 cycled back through cytochrome complex, no new NADPH made because never reaches NADP+ but protons still pumped into lumen increasing ATP production

Rubisco

most abundant protein on earth, enzyme responsible for fixing CO2

C3 plant

no separation CO2 fixation and calvin cycle, stomata open in day, best adapted to cool and wet environments

C4 plants

separation CO2 fixation and calvin cycle between besophyll and bundle-sheath cells, stomata open in day, best adapted to hot sunny environments

CAM

separation CO2 and calvin cycle between night and day, stomata open in night, best adapted to very hot dry environments

oxaloacetate

product carbon fixation C4 and CAM

PEP carboxylase

only CO2, 0 affinity for O2

mesophyll cells

form protective layer so plants not exposed to high CO2

final electron acceptor cellular respiration

oxygen

final electron acceptor photosynthesis

NADP+