BIS2A SS1 Week 2

what happen to product formation as you increase the initial amount of substrate and hold enzyme concentrations constant?

when holding enzyme concentrations constant, initially you see a large increase in product formations when going from S —> 2S —> 4S and slows down as enzymes become saturated (increasing initial concentration has less effect)

enzymes — velocity

rate at which product formed (aka how fast the enzyme can catalyze reaction)

Vo

initial velocity when mostly substrate

effect of increasing substrate concentration on velocity (Vo)

Vo does not infinitely increase as substrate concentration increases (reaches a maximum aka Vmax)

Vmax

the maximum velocity of an enzyme at which point substrate concentration and rate are independent of each other

Km

at ½ of Vmax
the point at which the enzyme is at the most regulatable state (small changes in substrate concentration affects Vo)

effect of temperature on enzymes

really high temperature —> results in denaturation of protein so rate decreases fast

really low temperature —> rate is slow because reactants don’t collide with enzyme as much

there is an optimal temperature at which an enzyme operates

effect of pH on enzymes

active sites that contain many hydrogen and ionic bonds (acid-base chemistry) will be affected by pH

active site without these chemistries are not affected by pH

allosteric inhibition

activity is regulated (in this case, decreased) by a compound binding to another site (and sometimes the active site)

locks into place the inactive conformation (can be reversible)

allosteric activator

activity increased (active conformation) by binding of a compound to another site (allosteric site) or sometimes the active site

competitive inhibition

blocks activity by binding to the active site and competing with the substrate

functions of the membrane

differentiate between the inside and outside of the cell

semipermeability (regulating what goes inside; more impermeable)

cell-cell recognition

signaling

components of the membrane

phospholipids, integral proteins, peripheral proteins, protein channels, glycoproteins, glycolipids, cholestrol

phospholipids

ester linked glycerol to two fatty acid chains with a phosphate group attached

polar head (glycerol, phosphate group, polar group), 2 nonpolar tails

freely moving/fluid

glycoproteins and glycolipids functions

adhesion, cell-cell recognition

peripheral membrane proteins functions

signaling and cell-cell recognition

integral proteins functions

pumps, channels, carriers (hydrophobic components on outside, hydrophilic inside)

cholestrol function

maintain fluidity at low temps, prevent cell membrane from falling apart at high temps

archael phospholipids

ether linked methylated isoprenoid chains (2) to glycerol + phosphate group, can be bilayer or monolayer

permeability of the phospholipid bilayer

small polar molecules can pass through easily (protonated hexanoic acids)

polar/charged molecules cannot pass through/have a harder time passing through

how can you prevent a molecule from inside the cell from passing through the phospholipid bilayer? what is an example of this?

attached a charged group on it, so it cannot pass through the nonpolar/hydrophobic interior of the membrane

ex. attach phosphate group to glucose to prevent it from leaving + creates a concentration gradient so glucose flows into molecule

uniporter

moves one compound in one direction

symporter

moves two molecules in the same direction

antiporter

moves two compounds in different direction (in and out)

passive transport

transport down the concentration gradient — usually until equilibrium is reached

simple diffusion

diffusing through the membrane without the use of anything

few molecules can do this

facilitated diffusion

diffusion down the concentration gradient that requires a channel (doesn’t use energy)

channel protein

restrictive channel that allows certain molecules to go in (they are specific)

used in facilitated diffusion (based on size, shape, charge, etc.)

interior often has polar/charged R groups with properties that facilitate transport; outside is mostly hydrophobic

carrier protein

channel binds to substrate — high specificity

used in both passive and active transport

active transport

transport that requires the use of ATP (primary active) /electrochemical gradient (secondary active) to move substances across the membranes

uses pumps to move against the concentration gradient

active/energized membrane

all cells need an active/energized membrane that has a charge difference

positive charge on outside and negative charge on inside

charge buildup causes protons and another compound to move inside (more negative)

redox pumps

active transport — protons can bring in compounds alongside it as it moves down the electrochemical gradients

external concentration and the rate of diffusion

greater external concentration increases the rate of diffusion to a certain extent (like an enzyme)

what fibers make up the cytoskeleton?

microfilaments (actin) — smallest

intermediate filaments

microtubules (tubulin) — largest

function of cytoskeleton

cell shape

internal organization

force generation (transporting stuff inside, movement of cell, etc.)

cytoskeleton must be strong/rigid and dynamic

microfilament characteristics

is directional — has a + and - end (not charged; just the direction)

• can either go + to - or - to +

helical

made of actin

found on the periphery to give strength, structure, and movement

monomer incorporation and ATP hydrolysis are closely related

microfilament functions

cell shape

movement of entire cell/parts of cell (like in pseudopods/amoeba)

intermediate filaments characteristics and functions

not directional

actin and myosin can create muscle movements

used for almost exclusively structure (typically permanent)

microtubules characterstics

made of tubulin

directional (+ and - end)

growth and shortening of the tubulin depends on GTP hydrolysis

largest + start in center and move outward

microtubules functions

rigid internal skeleton for some cells

framework for movement of motor proteins so cargo can be moved

DNA segregation

endocytosis

movement of materials inside the cell; mediates via actin

phagocytosis

cell “eating”; movement of a molecule into the cell

pinocytosis

cell “drinking”; movement of fluid/liquid into the cell

receptor mediated endocytosis

receptor proteins on cell surface capture a specific substance

flip over to see images of the types of endocytosis

motor proteins

used to move cargo (vesicles) + binds to microtubules

dynein and kinesin

dynein

go from the + to - end of microtubule with vesicle (periphery to center)

kinesin

go from the - to + end of microtubule with ATP hydrolysis (center to periphery)

energy

the ability to do work

entropy (S)

the disorder of a system

favorable reactions increase entropy (entropy is unusable energy)

free energy (G)

the usable energy that can be manipulated to do work

∆G equation + what is ∆G

∆G = G_products - G_reactants
∆G is the usable energy released by a reaction; not all the energy released from a reaction is usable however…

first law of thermodynamics

energy is conserved in a reaction — it can be transformed but not created or destroyed

∆E = 0 in reaction

do you always get 100% usable energy out a reaction?

NO! in chemical reaction, you can have lots of potential free energy, but you cannot harvest all of it out of a reaction

Second Law of Thermodynamics

in a closed system, free energy decreases and the amount of unusable energy (aka entropy) increases

what is a way that organisms can harness unusable energy/waste?

when an organism gives off waste/unusable energy, another organism can use it for its own needs

ex. after respiration, we release carbon dioxide, which can be used by plants for their own energy

at what temperature is water most dense? why is that important

most dense at 4 celsius

important bc ice floats above water and cold water sinks (preserves life)

in the reaction A —> B, what happens to the change in energy? ∆S?

∆E = 0 — first law of thermodynamics

∆S > 0 (positive) — second law of thermodynamics

endothermic

a reaction that requires an input of heat energy

exothermic

a reaction that releases heat energy to its surroundings

enthalpy (H)

the total energy in a system

what does it mean when ∆H > 0? ∆H < 0?

∆H > 0 —> reaction absorbs heat, endothermic

∆H < 0 —> reaction releases heat, exothermic

temperature

indicates the direction in which energy flows as heat —> higher to lower temperatures while objects are in thermal contact

interpret ∆H = ∆G + T∆S in words

change in total energy (∆H) = change in usable energy (∆G) + change in unusable energy (T∆S)

how can the free energy be harnessed?

in chemical reactions that break down things (catabolic), energy is released and we can try to harness that (ex. creating ATP)

the energy can be captured and used

exergonic

a reaction that has a negative ∆G + is thermodynamically favorable (spontaneous)

catabolic reaction

a reaction in which a larger molecule is broken down into smaller molecules; often releases energy (exergonic)

endergonic

a reaction that has a positive ∆G and requires addition of energy (thermodynamically unfavorable/not spontaneous)

free energy of the system increases

chemical equilibrium

the state in which forward and backward reaction rates are the same and there is no net change in the concentrations of reactants or products

this is because chemical reactions can run in both directions

Keq

the equilibrium constant

Keq = products/reactants

when is Keq > 1? Keq < 1?

Keq > 1 when the reaction is exergonic/spontaneous

Keq < 1 when the reaction in endergonic/not spontaneous

what is ∆G at equilibrium?

0

because forward and backward rxns running at same rate

how can we keep the forward reaction moving?

keeping product concentrations low or keeping reactant concentrations high, since reactions want to reach equilibrium

cells naturally keep product concentrations low (intermediates)

what happens if you remove products/add reactants?

the rate of the forward reaction would increase/the forward reaction would be more favored, to get the system to equilibrium
vice versa applies to removing reactants/adding products

the importance of speed to reactions

even though breakdown is thermodynamically favorable/spontaneous, it still takes time

not all reactions happen at the same rate

ex. decomposition of wood

activation energy

the minimum amount of energy needed to start a reaction (aka energy barrier)

catalysts

substance that speeds up a reaction without being consumed

properties of catalysts

not consumed in the reaction

no catalyst can make a reaction occur that doesn’t already happen

they lower the activation barrier but don’t change ∆G

enzymes (proteins) and ribozymes (RNA) serve as catalysts in biological processes

reaction coupling

when you couple an exergonic reaction (ex. breakdown of ATP) with an endergonic reaction to make the overall process spontaneous

usually use this to drive anabolic processes in a cell

ATP

the acidic anhydrous bonds between the 3rd and the 2nd and the 2nd and the 1st phosphate group hold energy

hydrolyzing these bonds release energy that can be used in reaction coupling (exergonic)

why do cells rely on ATP?

for the capture and transfer of the free energy needed for chemical work

reduction potential (E₀’)

tendency of compound to gain electrons and be reduced (intrinsic to each compound)
more positive reduction potential = greater affinity to be reduced/gain electrons

standard reduction potential reaction

2H+ + 2e- = H₂, E₀’=0.00V at standard conditions

at physiological conditions, has a E₀’ = -0.44 (H₂ wants to be oxidized)

how to determine if a compound is more inert

more O = more inert

how to determine if a compound has more energy

more H = more energy

reduction

gaining electrons

oxidants/oxidizing agents are reduced

oxidation

losing electrons

reductants/reducing agents are oxidized

in the reaction AH + B+ —> BH + A+, which is the oxidant? reductant?

oxidant: B+

reductant: AH

how to read electron tower/table from top to bottom

if close to the top (more negative reduction potential), will want to lose electrons (an energy source like glucose)

if closer to the bottom (more positive reduction potential), will want to gain electrons (electron acceptors like O2)

calculating ∆E₀’ + what sign should it be

∆E₀’ = ∆E_oxidant - ∆E_reductant

this should be positive for it to be spontaneous!!!

relationship between ∆G and ∆E₀’

∆G = -nF∆E₀’

the sign of ∆G and ∆E₀’ should be opposite of each other (inversely related)

how do cells convert food/energy source to energy?

redox reactions! transfer of electrons from a reduced compounds (like glucose) to one that is not

substrate level phosphorylation (SLP)

removing a high energy phosphate from one compound (look for anhydride bond) and putting it on another compound (like ATP)

the newly phosphorylated compound can be used as an energy source!

exergonic (bc creates ATP, which captures free energy)

where does the energy for SLP come from?

from food!

in this case, food is the original source of electrons (which generate energy) and for that high energy phosphate group

glycolysis

10 step process that converts glucose (6 carbon sugar) to 2 pyruvate (3 carbon sugar)
generates 2 net ATP and 2 NADH per glucose

what happens in the first half of glycolysis (aka energy investment phase)?

glucose 6-phosphate is converted into 2 molecules of glyceraldehyde 3-phosphate (G3P)

uses 2 ATP to phosphorylate twice

what happens in the second half of glycolysis (aka energy payoff phase)?

2 G3P are converted into 3 pyruvate molecules

generates 2 ATP and 1 NADH per G3P

key reactions: G3P —> 1,3 bisphosphoglycerate

1,3 bisphosphoglycerate —> 3 phosphoglycerate

what happens in G3P to 1,3-bisphosphoglycerate? what key molecule is generated from this process? what type of reaction is this?

G3P (reductant) is converted to 1,3-bisphosphoglycerate (releases electrons)

this process generates 1 NADH molecule (reduced from NAD+ to NADH) and 1 phosphate is added to G3P

this is a redox reaction

dehydrogenase

an enzyme that is involved in redox reactions; found in G3P to 1,3-bisphosphoglycerate

1,3-bisphosphoglycerate to 3-phosphoglycerate

high energy phosphate (that stored energy from G3P reaction) is transferred from 1,3-bisphospho. onto ADP to create 1 ATP