Midterm 2 (10-19) - BIS 2A

How long did it take for O2 to build up in the atmosphere and oceans?

About a billion years to get to 10% of today's levels

methanogens

Archaea that release methane, prospered on anoxic Earth

Why was oxygen considered toxic waste?

O2 is a powerful oxidant, would immediately oxidize susceptible metals

What else happened to the O2 generated by cyanobacteria, besides reacting with iron?

Reacted a lot with methane, might have caused "snowball Earth"

Why did CO2 levels go down?

A lot of available electrons for photosynthesis, so CO2 used up

What else happened when O2 accumulated in Earth's atmosphere and oceans?

Once 0.0002 of present levels reached, started creating a UV-protective ozone layer

A consequence of ozone layer:

UV-driven reaction of O2 with methane slowed, = increased rate of O2 and ozone accumulation

Another consequence of ozone layer:

UV-induced water splitting (to O2 and H2) slowed, preventing escape of H2 (= oceans) to outer space

Yet another consequence of ozone layer is:

life could move onto land.

enzymes

- catalysts for living things
- made of protein and other things (prosthetic groups and cofactors)

Some proteins are:

structural, pumps, machines, carriers - not always catalysts

Why does life use a catalyst for every reaction?
a) To make it go faster
b) To emphasize rate useful reactions and avoid toxic alternatives
c) To optimize rates for current conditions
d) To allow one species to complete

All of the above

The active site of enzymes:

fit their substrates

What are proteins made of?

Several units of amino acids attached in chains which are folded up

What holds proteins together?

Hydrogen, disulfide, ionic, hydrophobic, peptide bonds

How do the various levels of organization affect protein structure?

The levels allow different shapes and different types/places of bonding - each contributes to different function

How does the cell generate very specific 3D shapes?

Sometimes linear forms fold themselves up into their desired shape spontaneously (2', 3', 4') - the code is in the linear sequence of amino acids. (1')

primary structure

- precise series of individual amino acids linked with peptide bonds
- long, flexible chain

peptide linkage

bond between amino group and carboxyl group in amino acids

N-C-C backbone

makes up amino acids

The R group is:

used to represent one of 20 possible side chains, each for a different amino acid.

protein size

can vary from a dozen amino acids to a few thousand

protein

a specific polymer of amino acids

The protein backbone:

helps the protein fold into secondary structures.

secondary structure

- flat planes = beta sheets
- rigid rods = alpha helices

The secondary structure is stabilized by:

several hydrogen bonds between N-H and C=O (from backbone).

beta barrel

- created from beta pleated sheets
- forms a pore through bacterial outer membrane, allowing larger molecules to pass through

rhodopsin

- transmembrane protein that carries retinal molecule at core
- made of alpha helices

The likelihood of folding up into an alpha helix or beta sheet is determined by:

the sequence of R groups.

Glycine's R group is too entropic:

the backbone can form too many shapes.

Proline's R group is too rigid, so:

the N-C bond can't rotate.

Amino acids with positively charged R groups:

Arginine, Histidine, Lysine

Amino acids with negatively charged R groups:

Aspartic Acid, Glutamic Acid

Amino acids with polar, uncharged side chains

Serine, Threonine, Asparagine, Glutamine

Special case amino acid R groups:

Cysteine, Glycine, Proline

Amino acids with hydrophobic side chains:

Alanine, Valine, Isoleucine, Leucine, Methionine, Phenylalanine, Tyrosine, Tryptophan

hydrophobic R groups

- oily
- tend to interact only with other oily R groups or membranes and exclude water and charger or polar R groups

Tertiary and quaternary structures stabilized by:

a variety of weak interactions - ionic bonds, hydrogen bonds, hydrophobic bonds.

Denaturing agents disrupt:

the tertiary and secondary structure of proteins.

denatured proteins

unfolded proteins, often won't fold correctly again

Denatured proteins can be caused by:

heat, high salt, etc.

Very stable proteins are generally:

small and stabilized by disulfide bonds.

Cysteine R-groups covalently pair up to form Cystine, which is more stable because:

the covalent bond 'tacks' them together, giving fewer options.

quaternary structure

multiple subunits - different proteins working together as one complex

An example of the influence of local environment on reduction potential of a cofactor:

What is the difference between a cofactor and a substrate or product?

Cofactors come out of a reaction unchanged, substrates are used up.

Why might binding a regulatory molecule change the accessibility or functionality of the active site?

allostery, in terms of protein structure

as regulatory molecules bind, change protein shape - active site is more or less available (activator protein or inhibitor)

An example of logical regulation of an enzyme by a molecule that is neither a substrate or product:

Aside from enzymes, proteins also:

act as motors, act transporters or pores, define cell shape, regulate processes (gene expression), and determine cell-cell interactions.

3D structure and pattern of charges and/or hydrophobic patches allows the enzyme to:

bind the correct substrate(s) and cofactor group(s) in the right orientation.

metal-binding cofactors

iron-sulfur clusters, heme, chlorophyll...

non-metallic cofactors

NAD, FAD, coA, ... (coenzymes)

Substrates are:

used up in the reaction.

Cofactors are:

regenerated and part of catalysis.

This diagram of Complex II (succinate dehydrogenase) of the respiratory chain includes many non-protein factors. Which is not a cofactor?
a) FAD
b) Succinate
c) Fe-S
d) Heme

b) Succinate

This heme from hemoglobin is not covalently bound to methionine. Why?

It cannot have another covalent bond, the space is left for oxygen, since it's a oxygen carrier.

How might local environment of active site affect electronics of an e- donor? (1)

Negative charges near a potential donor would encourage loss of en electron (smaller reduction potential = stronger electron donor/weaker electron acceptor).

How might local environment of active site affect electronics of an e- donor? (2)

Water or polar R groups might rearrange to partially neutralize the affects of nearby charges.

Not all enzymes require cofactors, instead enzymes: (1)

' R-groups can participate in chemical reactions with the substrate.

Not all enzymes require cofactors, instead enzymes: (2)

can simply orient/bend substrates.

Not all enzymes require cofactors, instead enzymes: (3)

can provide local changes in environmental conditions (concentration/pH), affecting only their trapped substrate(s).

Many minerals and cofactors critical to catalysis may be clues to how biological catalysis arose:

some may have been adapters, enhancing or restricting catalytic activity.

What early life nucleotide based?

Amino acids (... proteins) could be newer developments that further enhanced specificity for particular substrates.

What is the difference between FAD/FADH2 acting as a cofactor and FADH2 being a product of a reaction?

When the FAD/FADH2 is cyclic and covalently bound/permanently embedded to the protein, it's likely a cofactor

The intermediates and products of metabolism are:

maintained at ideal levels and shared between a variety of pathways.

How does an enzyme stay informed?

feedback inhibition

product of a long pathway inhibits the enzyme that catalyzes the first dedicated step of the pathway

Why make enzymes that shut down unnecessary pathways?

Making more of something that isn't needed is wasteful

Why not just allow mass action (accumulation of product) shut down the pathway?

Mass action isn't reliable, sometimes can require massive amounts - over constrained

How can an enzyme perceive conditions in the cell?

Through allosteric interactions

When the enzyme is in inactive form:

it cannot accept substrate.

Phosphofructokinase catalyzes the first dedicated step in glycolysis (F6P to FBP) and is regulated allosterically by high concentrations of ADP. Does high [ADP] switch the enzyme on or off?

It switches it on - the point of glycolysis is to make ATP, high [ADP] is low [ATP]

Would high [PEP] inhibit or activate phosphofructokinase?

competitive inhibitor

races against substrate to active site, more substrate can reverse it

noncompetitive inhibitor

binds allosterically to a regulatory site to disable active site, more substrate won't help

Penicillin G is a noncompetitive inhibitor - it binds to bacterial enzyme required for cell wall synthesis, this:

irreversibly modifies active site.

irreversible inhibition

inhibitor covalently (or otherwise permanently) binds to or modifies the allosteric or active site

signal metabolites

can switch protein on or off by allosterically affecting its affinity for its substrate

Controlling the concentration of an active catalyst will:

control the reaction rate.

Allosteric regulation of enzyme activity is faster than:

turning on synthesis of a protein.

What kind of reaction joins two amino acids?

A condensation reaction

What two functional groups react in a condensation reaction of two amino acids?

The amino group and the carboxyl group

What is a cell?

A high organized compartment with thin, flexible membrane, concentrated chemicals (aq) - capable of metabolism and autonomous replication

simplest cell

cell lacking nucleus and often other membrane bound organelles

Bacteria and archaea have a _____ cell type.

simple (prokaryotic)

How can cells keep functional molecules from floating away?

Developing a selectively permeable membrane, using lipids

phospholipids

charged, phosphate-containing head + glycerol + two fatty acid tails

Self-ordered shapes of phospholipids result from:

water maximizing hydrogen bonding with other polar molecules - mostly water, plus the polar head groups of lipids.

diffusion

different solutes on opposite sides of lipid bilayer, molecules of each diffuse freely across until equilibrium established - solutes continue to move but now at equal rates

What can diffuse across a membrane?

Non polar molecules (gases, alcohol, benzene...) - small polar molecules can but slowly and large polar molecules rarely can

Which chemical is a million-fold more likely than Na+ to cross a lipid bilayer?
a) Cl-
b) Glucose
c) Glycerol
d) Indole

c) Glycerol

Double bonds in fatty acids cause:

kinks in phospholipid tails, meaning more permeability - kinked = unsaturated.

saturated fatty acid

has as many Hs as possible - many or all saturated fatty acids cause lower permeability

How do lipids move in a membrane?

They can spin and exchange places but cannot flip

Membrane permeability and fluidity are related to: (1)

percentage of unsaturated fatty acid tails - more saturated, more viscous.

Membrane permeability and fluidity are related to: (2)

the length of fatty acid tails - longer tails = thicker membrane = less permeable.

Cold-adapted organism have:

more kinks, preventing the membrane from solidifying.

osmotic issues in the membrane

if a cell has a higher concentration than its environment, water will leak into cell - can potentially blow up cell

How is osmotic pressure prevented in the cell?

A cell wall limits the amount of water that can be taken up