cell bio unit 2

enzymes

mostly protein, catalyze rxns leading to bond formation

active site

region where substrate binds

substrate

molecule involved in rxn that binds to an enzyme

product

resulting molecules from rxn

factors affecting enzymes

pH, temperature, cofactors

cofactors

moleuces/ions needed by proteins in its structure to get ideal shape

increase in temp

charged bonds start breaking, protein denatures

decrease temp

protein loses flexibility, can’t hold substrate easily, molecule movement in soln decrease, makes it harder to reach enzyme by chance

increase pH

less H+ to help maintian shape

decrease pH

H+ interaction disrupts H-bonds and ionic bonds

inhibitors

stop enzyme from working

competitive inhibitors

bind to active site of enzyme, stopping access to normal substrate, shape resembles normal substrate

non-competitive inhibitors

bind allosterically, shape of enzyme changes so substrate cannot bond

energy molecules

ATP, GTP, NADH, FADH2

3 ways to make ATP

substrate-level phosphorylation, oxidative phosphorylation, photophosphorylation

substrate-level phosphorylation

uses enzyme to transfer PO4 from one molecule to ADP to make ATP

oxidative phosphorylation

addition of PO4 to ADP, powered by oxidation of NADH/FADH2

cellular respiration

glycolysis, pyruvate conversion, KREBS/citric acid/ tricarboxylic acid cycle, oxidative phosphorylation

glycolysis

splits glucose into 2 pyruvates, takes place in cytoplasm, make 2 net ATP, 2 NADH

pyruvate conversion

converts pyruvates into acetyl groups, takes place in mitochondria, 0 ATP, 2 NADH, 2 CO2

KREBS/citric acid/ tricarboxylic acid cycle

release E from acetyl group in a cycle, takes place in mitochondria, 2 ATP, 6 NADH, 2 FADH2, 4 CO2

oxidative phosphorylation

further energy production, strong ATP production, takes place in mitochondria, 34 ATP, -10 NADH, -2 FADH2

glycolysis steps

glucose —> ATP —> ADP

glucose 6-phosphate —>

fructose 6-phosphate —> ATP —> ADP

fructose 1,6-biphosphate —>

(2) glyceraldehyde 3-phosphate

(1) glyceraldehyde 3-phosphate —> NAD+ —> NADH + Pi

1,3 biphosphoglycerate —> ADP —> ATP

3 phosphoglycerate —>

2 phosphoglycerate —>

phosphoenol pyruvate —> ADP —> ATP

pyruvate

Pyruvate conversion steps

pyruvate —> NAD+ —> NADH, -CO2

acetyl —> + Co enzyme A

acetyl coenzyme A (Acetyl CoA)

Citric Acid/ KREBS/ Tricarboxylic acid cycle

drops of acetyl group —>

citrate —> NAD+ —> NADH, -CO2

5 carbon —> NAD+ —>NADH, - CO2

4 carbon —>

GTP —> GDP , ADP —> ATP

FADH—> FADH2

NAD+ —> NADH

oxaloacetate (OAA)

—> citrate/citric acid

when O2 run low/cannot be acceptor

ETC backs up, electrons filling each ETC protein, cannot produce NAD+ from NADH since it is backed up, prevents anything past glycolysis from forming, only uses 2 ATP instead of making 38

chemiosmosis

process of H+ entering membrane resulting in ATP production

human solution to no O2

reduce pyruvate using NADH

pyruvate —> NADH —> NAD+

lactate

yeast cell solution to no O2

reduce pyruvate, produces ethanol

pyruvate —> NADH —> NAD+

acetaldehyde —>

ethanol

photosynthesis eqtn

6 CO2 + 6 H2O + light E —> 6 O2 + C6H12O6

stroma

space inside chloroplast

thylakoid membrane

outer layer of thylakoid

thylakoid space

area inside thylakoid

reflection

light hits and object and reflects off, object does not get energy

transmission

light goes through an object, object does not get energy

absorbed

light absorbed by object, object gets energy

pigments

contains molecules that capture light well, when the energy is absorbed an electron in the blank becomes excited

light harvesting compound

protein with pigments embedded with chlorophyll in the middle forming the reaction center, important during photosynthesis

reaction center

2 chlorophylls, ultimate receiver of the light energy

photosystem

larger protein complex w light harvesting on top of it

Light dependent reactions steps

1. chemiosmosis produces ATP via H+ gradient across thylakoid membrane, H+ ions go through ATP synthase producing ATP by forming bond b/w ADP and Pi

2. Maintaining Gradient via light capture

   A) light wave hits PS 2 which excites its electrons, electrons transfer continues until rx center, excited chlorophyll electrons enter ETC, use energy to move H+ against the gradient

   B) light wave also hits LHC of PS 1, high energy electrons from chlorophyll enter 2nd ETC end up at the enzymatic protein, NADP reductase, NADP + H —> NADPH

   C) Account for electrons, electrons from PS 1 now in NADPH, PS1 grabs electrons from PS 2, PS 2 grabs electrons from water, forms O2 to provide electrons to recuperate from the electron loss

NADP reductase

enzyme catalyzes reaction of NADP+ H to NADPH

photophosphorylation

uses light energy to drive ATP formation

non-cyclic photophosphorylation

electrons do not cycle, make ATP and NADPH

cyclic-photophosphorylation

electrons cycle, make ATP

light independent reactions

takes place in stroma of chloroplast, uses electrons form light reaction (ATP and NADPH) to join CO2s together to make glucose

calvin cycle

key pathway of Dark reactions

photorespiration

occurs when O2 binds instead of CO2 with rubisco, new product is made that does not enter calvin cycle, CO2 lost w new pathway

carbon fixation

takes gaseous CO2 and makes it fully organic

normal conditions in C3 leaf

O2 flows outs (low conc outside), CO2 flows in (low conc inside)

dry conditions in C3 leaf

plant closes stomatal pore to prevent water loss, continues to fix CO2 so CO2 levels decrease, plant keeps splitting H2O so O2 levels increase, O2 binds to rubisco, photorespiration

stomatal pore

spaces where gases flow through in/out of leaf

guard cells

surround stomata, when expanded close stomatal pore

C3 plant

rubisco fixes CO2 and RuBP for calvin cycle

C4 plant

split into bundle sheaths and mesophyll cells, pepsco fixes CO2 and PEP 3C forms oxaloacetate, converted to malate (4C), malate travels from mesophyll cell to bundle sheath cells then converts into CO2 and pyruvate, pyruvate (3C) then converts PEP 3C

phosphoenol pyruvate carboxylase (PEPSCO)

enzyme found in C4 and CAM plants, better at preferentially binding with CO2 over O2

bundle sheath cells

cells in C4 plants, deeper in cell tissues, not directly exposed to gases

mesophyll cells

cells in C4 plants, exposed to gases

CAM plant

uses pesco enzyme to fix CO2 and PEP 3C to make oxaloacetate (4C), then converts to malate (4C), then converted to CO2 and pyruvate (3C), pyruvate then converts to PEP 3C, fixation happens mostly during night