intro to cell/molec bio test 3

catalyst

substance that speeds up chemical rxn without permanently being changed or consumed; provides alternative pathway; catalyzes both forward and reverse rxn

enzyme and ribozyme

protein catalyst and rna catalyst

activation energy

initial input of energy to start chemical reaction; allows molecules to reach transition state

affinity

affects enzyme function; degree of attraction btwn enzyme and sub; high affinity means enzymes bind to substrate when conc low and low affinity means enzymes only bind when conc high

Vmax

maximal rate of velocity; rate of rxn increases until it plateaus at Vmax

Km (michaelis constant)

substrate conc when reaction is half of Vmax, low Km is high affinity and high Km is low affinity

competitive inhibitor

binds noncovalenty to active sites of enzyme; Km increases

noncompetitive inhibitor

binds noncovalenty to allosteric site on enzyme; lowers Vmax for rxn

irreversible inhibitors

binds covalenty to amino acid at active site of enzyme

prosthetic groups

small molecules permanently attached to surface of enzyme and help with function

cofactors

inorganic ions temporarily bound to surface of enzyme and promote chemical rxn

coenzymes

organic molecules temporarily bound to enzyme and help carry out rxn

catabolic rxns

breakdown larger molecules into smaller ones; recycle organic building blocks and breakdown organic molecules for energy

redox rxn

oxidation is loss of electrons and reduction is gain of electrons

nadh

nad+ reduced to nadh; oxidation of nadh is exergonic and used to make atp; nadh donates electrons to energize them

gene regulation

turn off and on genes that code for enzymes, depending on needed function

cell signaling pathways regulation

cells integrate signals from environment and adjust metabolic pathways to adapt to signals

biochemical regulation

binding of molecule to enzyme

negative feedback

reverses a change to bring a system back to normal state, responding to smth

positive feedback

amplifies a change and makes it stronger to reach a particular outcome, responding to smth

feedforward regulation

signal from early step tells a later step to slow or stop, plans ahead

proteases

cleave bonds between amino acids in proteins; in eukaryotes/archaea proteins broken down in proteasome

ubiquitins

1. enzymes that attach them to target protein can recognize wrongly folded proteins and degrade nonfunctional ones

2. when rapid degredation of proteins, ubiquitin targeting can direct it to proteasome

3. amino acids released from proteasome are recycles and used to make new proteins

cellular respiration

metabolic process that cells use to turn food into usable energy; goal is make atp

aerobic respiration

o2 is used and co2 is released

four metabolic pathways

glycolysis, pyruvate oxidation, citric acid cycle, oxidative phosphorylation,

glycolysis

metabolism of glucose into 2 molecules of pyruvate, 10 steps catalyzed by different enzyme, 3 phases

phase 1 glycolysis

energy investment phase, steps 1-3, phosphates from 2 atp molecules are attached to glucose and converted to fructose-1,6-bisphosphate; raises free energy of glucose and allows later rxn to be exergonic

phase 2 glycolysis

cleavage phase, steps 4-5, breaks fructose-1,6-bisphosphate into 2 molecules of glyceraldehyde-3-phosphate; raises free energy of glucose allowing later rxns to be exergonic

phase 3 glycolysis

energy liberation phase, steps 6-10, products are formed

total yield of products per glucose molecules

2 net atp, 2 nadh, 2 pyruvate

rate of glycolysis regulated by

availability of substrates and feedback inhibition

breakdown of pyruvate

pyruvate transported to mitochondria, broken down by pyruvate dehydrogenase, co2 removed from pyruvate, remaning acetyl group attaches to coenzyme A and makes acetyl CoA; 2 e- from pyruvate and h+ given to nad+

glycolysis input

2 atp, one glucose

pyruvate oxidation input

2 pyruvate, 2 coenzyme A, 2 NAD+

pyruvate oxidation output

2 acetyal CoA, 2 CO2, 2 NADH

citric acid cycle

acetyl group removed from acetyal CoA and attached to oxaloacetate making citric acid (6 carbons)

total net yield of products only from citric acid cycle per glucose molecule

6 NADH, 2 ATP, 2 FADH2, 4 CO2 - this is from two cycles but one glucose molecule

net yield of products from glycolysis, pyruvate oxidation, and tca

10 NADH, 2 FADH2, 4 ATP, 6 CO2

oxidative phosphorylation

nadh and fadh2 oxidized to make more atp by phosphorylating adp; two events oxidative phosphorylation and chemiosmosis

electron transport chain

group of protein complexes and small organic molecules in inner mitochondrial matrix; high energy e- taken from nadh and fadh2 passed down protein chain, energy used to pump h+ protons and through atp synthase to make atp

chemiosmosis

atp synthase uses energy stored in h+ gradient fro synthesis of atp via chemiosmosis, h+ travels and energy released synthesizes atp from adp and p

atp synthase structure

mechanical rotation of portion of atp synthase caused by movement of h+ ions from intermembrane space to inside matrix; bind loosely, change shape by squeezing tightly, loosen and release atp

anaerobic respiration

cells metabolize organic molecules without oxygen, have terminal electron acceptor as not oxygen, commonly sulfur iron or nitrate

fermentation

when o2 can be the only e- acceptor, so uses only glycolysis

fermentation in muscle cells

pyruvate reduced to lactate, nadh oxidized to nad+

fermentation in yeast cells

pyruvate broken into co2 and acetaldehyde, acetaldyhyde reduced to ethanol and nadh oxidized to nad+

autotroph

fixes carbon directly from environmental co2

heterotroph

gets carbon from organic molecules by eating

chemotroph

gets energy from breaking down or oxidizing chemical bonds

phototrophs

get energy from sunlight

organotroph

get electrons from organic compounds

lithotrophs

get electrons from inorganic materials like rock/minerals (luca was this)

obligate aerobes

organisms requires o2 to survive, most eukaryotes and prokaryotes

obligates anaerobes

organisms poisoned by o2

aerotolerant anaerobes

organisms dont use o2 but are not poisoned by it, use anaerobic respiration or fermentation

facultative anaerobes

can use o2 in aerobic respiration or can do anaerobic respiration/fermentation depending on whats available

nitrogen fixation

cyanobacteria use nitrogenase to convert n2 from atmosphere to ammonia so plants and algae can use it

photosynthesis

light energy captured, synthesize organic molecules; co2+ 2h2o + light → ch2o + o2 + h2o ; times by six for glucose

reducing and oxidizing agent for photosynthesis equation

h2o is reducing agent (and is oxidized) co2 is oxidizing agent (and is reduced)

two stages of photosynthesis

light reaction: in thylakoid makes atp nadph and o2 calvin cycle: in stroma makes glucose and g3p and uses atp and nadph

laws of thermodynamics

0th: def of temp, two bodies interact with third and nothing changes then bodies equal temp. 1st: energy not created or destroyed only transferred. 2nd: entropy(randomness) only increases in closed system 3rd: there is lowest possible temp where no movement of particles happens anymore and entropy stops

wavelength

distance between peaks

electromagnetic spectrum

all possible wavelengths of electromagnetic radiation; visible light is what humans can detect

light energy

as energy increases, wavelength decreases and vice versa

photons

particles that make up light and travel in wavelike pattern moving at speed of light, each photon as specific amount of energy

transmission, reflection, absorption

when light passes through an object, when object changes the light’s path, when object absorbs light

pigment

molecule that can absorb light energy, light strikes pigment and some wavelengths absorbed and some reflected

object absorbing light energy

valence electrons get excited and jump to higher energy level

excited electron becoming stable again

four options: electron goes back down energy level and releases heat, electron releases energy as light(fluorescence), electron transfers extra energy to nearby electron in other molecule (resonance transfer), electron is removed and moved to stable molecule (photoionization)

absorption spectrum

shows wavelengths of EMR that are absorbed by a pigment

action spectrum

plots rate of photosynthesis as a function of wavelength

photosystem 2

light excites electrons in light harvesting complex, energy transferred to pigment molecule P680, let go from there and travels to other electron carriers, ps2 oxidizes water and generates o2 and h+

photosystem 1

light strikes ps1, energy transferred to reaction center where high energy electron(og from plastocyanin) removed from pigment molecule P700, then transferred to primary electron acceptor, ferredoxin passes electrons to NADP+ reductase, NADP+ accepts e- and h+ to become NADPH

atp synthesis

driven by flow of h+ from lumen to stroma, water split and h+ in lumen, movement of electrons along etc pumps h+ into lumen, forming NADPH consumes h+ in stroma

cyclic electron flow

alternative to light dependant if too much nadph, generates only atp, light excites ps1, electron goes to fd, transfers electron back to ps1, the pumping of h+ along loop drives atp synthesis