chem 153a final :(((((

rip me

Kw=

[H3O+][OH-]=1×10^-14 M²

Keq=

[products]/[reactants]

What occurs at the horizontal region of a titration curve?

This is the buffer region, where pH = pKa, and [base] = 0.5[acid]

What occurs at the vertical region of a titration curve?

This is the equivalence point, where [base]=[acid]

Henderson-Hasselbalch equation

pH = pKa + log([A-]/[HA])

How to find pI:

find 2 pKas around neutral pH, and average them

Hydrogen bond requirements

donor X-H: X is O, N, F

acceptor A: is O, N, F, or anion

salt bridge

ionic interaction + hydrogen bond

forms when acidic and basic side chains interact

Gibbs free energy equation (using enthalpy and entropy)

G = H - TS

Gibbs free energy equation (using standard G) (there are 2)

G = G0 + RTln(Q)

or

G0 = -RTln(K)

rates and disorder of equilibrium

forward and reverse rates are equal

environment and system equally disordered

rates and disorder of steady state

input = output

system more ordered than environment

phi bond

rotation between N and alpha C

psi bond

rotation between alpha C and C

Why don’t we consider bond between C and N?

resonance from carbonyl causes it to be a non-rotational bond

Anfinsen’s theorem

the information determining the tertiary structure of a protein is present in its primary sequence

What does urea do to proteins?

creates preferential H-bonding to amides in the peptide backbone

What does 2-mercaptoethanol do to proteins?

reduces (breaks) disulfide bonds

hydrophobic collapse, what forms and why

the rapid burying of hydrophobic residues in the center of the protein to form molten globule, entropically favorable for the water

chain conformational entropy

the entropy decrease due to formation of ordered polypeptide

non-covalent interactions which contribute to protein folding

H-bonding, LDF, electrostatic forces between charged R groups, hydrophobic effect

Hydrogen bonds form between which atoms in alpha-helices?

carbonyl of n-th residue and amine of (n+4)-th residue

disulfide bonds require ___ environments to form

oxidizing

water soluble protein:

water insoluble protein:

globule

fibrous

Why is silk enriched with glycine and alanine?

they are small and hydrophobic

What repeating pattern does collagen have and why?

Gly-X-Y (X or Y often proline) causes kinks in structure

What kind of interaction to ligands use to bind biomolecules?

non-covalent

Kd =

[P][L] / [PL]

What is Ka in relation to Kd?

Ka = 1 / Kd

[Ptotal] =

[P] + [PL]

What does Y represent?

the fraction of binding sites occupied

2 equations for Y

[PL] / ([P] + [PL])

[L] / (Kd + [L])

At Kd, Y =

0.5

lower Kd means ___ protein-ligand interaction

stronger

How many O2 can myoglobin bind?

1

How many subunits does myoglobin have?

1

How many O2 can hemoglobin bind?

4 O2

What subunits make up hemoglobin?

2 alpha-globin subunits and 2 beta-globin subunits

What do conjugated proteins have?

a non-protein component called a prosthetic group

2 parts of heme

proto-porphyrin + heme

What is at heme prosthetic group coordination sites?

4 occupied by N of pyrrole rings

1 occupied by proximal His

1 for O2

What is the role of the distal His?

stabilizes O2 binding

acts as gate for ligand entry

What structure would form if heme were on its own and why?

a peroxide ridge: heme will bind oxygen and then another heme will bind it

Why is the distal histidine important?

Without it, carbon monoxide can bind linearly, which is very favorable. With it, the sp-hybridized carbon monoxide must bind at an angle, which the sp2 oxygen doesn’t mind, so carbon monoxide’s favorability decreases

Y equation using partial pressure

Y = pO2 / (pO2 + p50)

Y equation using Hill coefficient

Yn = [L]^n / (Kd + [L]^n)

What does O2 do to promote T —> R?

binds with Fe, decreases Fe’s radius, shifts the subunits to R

allosteric regulation

homotropic: substrate also regulates function

heterotrophic: a different molecule than the substrate regulates function

positive: increases activity/binding

negative: decreases activity/binding

2,3-BPG

negatively charged

binds to central cavity of Hb

stabilizes T state

shifts curve right

BPG and fetal hemoglobin

fetal Hb has Ser instead of His

it has more stable R state

necessary to receive O2 from parental Hb

Bohr effect

pH: His and Asp form salt bridge at low pKa, Lys and C terminus also form salt bridge

CO2 forms carbamate on subunits which forms salt bridges

overall —> T state stabilization

glyceraldehyde stereoisomers

-OH on the bottom chiral center points right: D

-OH on the bottom chiral center points left: L

types of D-sugars

alpha - OH is trans to C6

beta - OH is cis to C6

1. What mechanism allows for the formation of cyclic sugars?

cyclization, which creates a new chiral center at C1 and forms either alpha or beta anomers

What are anomers? How do they interconvert?

anomers are the result of cyclization of linear carbohydrates

alpha is for OH on opposite side of C6, beta is for same side

they interconvert by un-cyclizing and re-cyclizing to the other anomer

interconversion is called mutarotation

1. Be able to identify different anomers

look at directions of alpha carbon and OH

same direction is beta, opposite is alpha

Can a given sugar linearize and switch forms? When can’t it?

usually yes

disaccharides where both anomeric carbons are involved cannot linearize because glycosidic bond breakage would be required

ex: sucrose

Be able to identify or create glycosidic bonds between saccharides

1. identify

   1. if only one anomeric carbon is involved, the bond has same anomeric state as that carbon

   2. if both are involved and have same anomeric states, bond has same name as state

   3. if both are involved and have different states, then bond is both

   4. numbers go in front (C# of originating molecule)-(C# of receiving molecule)

   5. ex 1-4 alpha-glycosidic bond

2. create

   1. condensation reaction between 2 OH’s on monosaccharides

   2. take away a water and connect C-O-C

      1. at least one C must be anomeric carbon

For all four polysaccharides we’ve discussed, be able to connect structure with function, and be able to recognize any of these structures; also know linkages

1. Cellulose (β-1,4)

   1. alternating glucoses

   2. strong interchain and intrachain hydrogen bonds lead to high tensile strength

   3. used for structure in plants

2. Chitin (β-1,4)

   1. N-acetyl-D-glucosamine 

   2. basically glucose but has amide groups

   3. alternating structure

   4. strong interchain and intrachain hydrogen bonds

   5. insect and crab exoskeletons

3. Amylose (α-1,4)

   1. alpha-D-glucose

   2. no branching

   3. humans break down for energy

   4. but it forms a spiral instead of a straight chain

4. Glycogen (α-1,4) and (α-1,6 every 8-10 residues creating a branch)

   1. alpha-D-glucose

   2. energy storage in animals

      1. multiple branches means it is broken down fast

Understand the basic roles of lipids

1. long term energy storage

2. make cell membranes

3. intracellular and intercellular cell signaling

Fatty acids – Be able to name a fatty acid (e.g. linoleic acid has the symbol 18:2n-6)

(total carbon #):(# double bonds)n-(# carbons counting backward until first double-bonded carbon is reached)

so start counting from carbon at opposite end of carbonyl carbon

What’s the basic structure of a fatty acid?

carboxylic acid with aliphatic chain

What is the relationship between length and melting point? Degree of unsaturation and melting point?

1. longer = higher melting point

   1. better IMF

2. saturated = higher melting point 

   1. less kinks means stacking means better IMF

TAGs – Know the basic structure of TAGs (what are its parts?)

1. triacylglycerol

2. a glycerol (CH2CH2CH2) attached to 3 fatty acids

1. How do TAGs compare with carbohydrates as energy storage molecules?

1. long term energy storage

How do TAGs and carbohydrates impact osmotic pressure differently (and what are the consequences of this difference)?

1. carbohydrates significantly increase osmotic pressure due to hydrophilicity

   1. cannot be stored as monomers or cell would swell

2. hydrophobicity means TAGs do not affect osmotic pressure much

   1. can be stored without issue, they just accumulate

1. How are TAGs broken down? What is the basic metric telling you how much energy (relative amount, not absolute) you can get from a TAG?

1. lipolysis

   1. one glycerol and three fatty acids

2. beta oxidation

   1. fatty acid is oxidized, NAD+/FAD is reduced, acetyl-CoA is produced

   2. 2 carbons make roughly 1 acetyl-CoA

1. How do lipids get transported? Why do they have to have special transport?

1. lipoproteins

   1. phospholipid monolayer with several apolipoproteins

   2. lots of TAGs and cholesterol inside

2. they are hydrophobic and would just accumulate in blood instead of dissolving and moving

1. Phospholipids – What comprises the cellular membrane?

1. proteins and phospholipids

1. How do membranes form?

1. they self-assemble by putting their tails together like hydrophobic collapse

1. Know the basics of membrane permeability

1. basically only small, nonpolar things can get through

1. Know the basic structure of glycerophospholipids (e.g. glycerol, two fatty acids, polar head group)

1. like a TAG but the third fatty acid is replaced by polar head group such as serine

1. You do need to be able to identify the precursor molecule, and know the roles glycerophospholipids play

1. signaling pathways

1. What’s PIP2? What’s its role and where does it operate?

1. glycerophospholipid that works in signaling pathways

Phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine(!!) are important in later topics (flip, flop, scramble)

1. phosphatidylcholine

   1. mostly in outer leaflet

2. phosphatidylethanolamine

   1. mostly in inner leaflet

3. phosphatidylserine

   1. all in inner leaflet

1. Know the basic structure of sphingolipids

1. sphingosine backbone

   1. basically a normal backbone but the top fatty acid is replaced by =CH-(CH2)12-CH3

2. fatty acid in the middle

3. X group replaces third fatty acid

1. You do need to be able to identify the precursor molecule and know the roles sphingolipids play

1. outer leaflet signaling

Sphingomyelin is important in later topics (flip, flop, scramble)

mostly in outer leaflet

How do phospholipids diffuse? Which forms of diffusion are harder and why?

1. lateral diffusion

   1. move sideways and stay on same leaflet

   2. easier because heads/tails don’t mix into the wrong areas

2. transverse diffusion

   1. flip into other leaflet

   2. harder because the head has to move through the tail area

How is phospholipid asymmetry maintained? What proteins manage this asymmetry and how do they work?

1. flippase

   1. inward movement

   2. uses ATP

2. floppase

   1. outer movement

   2. uses ATP

What protein disrupts this asymmetry? Under what conditions does it get triggered? What are the consequences of this disruption?

1. scramblase

2. cell damage → Ca2+ signaling → scramblase activation

3. moves serine to the outer leaflet

4. aids in cell death (apoptosis)

How do cells regulate their membrane composition in response to temperature changes?

1. cells add saturated fatty acids when it’s hot and unsaturated fatty acids when it’s cold

   1. the membrane naturally increases fluidity with temperature

   2. saturated fatty acids decrease this fluidity

   3. unsaturated fatty acids increase it

2. cholesterol is always present

   1. rigid four-ring structure keeps fluidity

   2. IMF formed with phospholipids decreases fluidity

Be familiar with the basic structures of the different membrane proteins, including lipid anchored proteins

1. integral proteins

   1. alpha helix

      1. one helix perpendicular to membrane 

   2. helical bundle

      1. many helices parallel to each other but perpendicular to membrane

   3. Beta-barrel

      1. a barrel inside membrane and parallel to its direction

2. peripheral proteins

   1. do not cross both layers of the membrane

   2. otherwise, have varying degrees of “involvement” in the membrane

Eicosanoids and sterols – What are the differing roles of these classes of lipids? What are their precursors? Would you be able to identify an eicosanoid or sterol? How would you inhibit prostaglandin production?

1. eicosanoids  do autocrine and paracrine (local) signaling

   1. derived from arachidonic acid

   2. 1-2 benzene rings

2. sterols

   1. membrane components and global signaling, bind to nuclear receptors

   2. subset of steroids

   3. four non-aromatic rings

What is compartmentalization? How does this synergize with catalysis to create efficient processing?

1. compartmentalization is the separation/concentration of bio-components in specified subcellular sections

2. molecules must collide for a reaction to happen, so putting reactants all in the same place makes it easier for that to happen

What are the thermodynamics of an enzyme-catalyzed reaction?

1. the activation energy is reduced

   1. more collisions are likely to have the necessary energy to start the reaction

2. the starting and ending energy levels and overall change in energy stay the same

1. Understand the activation energy and transition state concepts well

enzymes stabilize the transition state, because if they just stabilized the reactants then the reaction would never proceed

Be able to discuss the intermediates of an enzyme catalyzed reaction and place them on a reaction coordinate diagram

1. the first dip is ES and represents enthalpic stabilization

2. the second dip represents EP

3. final state is E + P

Why would enzymes deliberately strain the E-S complex?

when you don’t go as low you don’t have as high to go later

Why are the best competitive inhibitors transition state analogs?

1. enzymes bind best to transition state, so something structurally similar to a transition state would bind tightly 

2. the analog doesn’t actually proceed with the reaction

What is the induced-fit model? What does it say about enzymes?

the enzyme binds the substrate moderately well at first, but then undergoes a conformational change which strengthens the bond

How do enzymes create stereospecific interactions with chiral (or pro-chiral) molecules?

they have pockets which only fit some groups in some order

Enzymes have optimal pHs and temperatures. Why is this the case? What happens when you stray outside of these optimal regions?

1. the amino acids which receive/donate protons to further the reaction would become inappropriately protonated/deprotonated and would no longer be able to catalyze the reaction

2. high temperatures denature the enzyme and at low temperatures, the molecules may not have enough KE to proceed

Know the classes of enzymes and be able to identify them based on a provided reaction

1. oxidoreductases

   1. transfer electrons and change oxidation state of atom

2. transferases

   1. transfer functional groups from one molecule to another

3. hydrolases

   1. break a substrate into two parts using water

4. lyases

   1. remove a group to form a double bond

   2. do not need to use water

5. ligases

   1. form one product from two substrates

6. isomerases

   1. intramolecular rearrangements within a single molecule

Know the mechanisms

1. Proximity and orientation

   1. Substrates confined in proper orientation for reaction to occur

2. Acid catalysis

   1. An enzyme active site donates a proton to stabilize a leaving group

3. Base catalysis 

   1. An enzyme active site accepts a proton to create a strong nucleophile

4. Covalent catalysis

   1. Enzyme forms a temporary covalent bond with the substrate 

5. Electrostatic catalysis

   1. Charges in the active site stabilize the transition state

6. Metal-ion catalysis

   1. Metal ion in the active site participates in catalysis

Understand the basics of kinetics (chemical reaction → rate of production

rate of production = forward rate constant (reactant concentration) - backward rate constant (product concentration)

What assumptions are needed to derive Michaelis-Menten kinetics? Be able to connect these assumptions to specific points in the derivation. What did these assumptions allow for?

1. assume second step is rate-limiting

   1. get rid of k-2 term

2. assume steady state, so [ES] is constant

   1. get rid of [ES] term because we can’t measure it

3. assume we are at beginning of reaction so [P] = 0

How do these assumptions constrain our measurements/data?

can only be used for basic substrate-enzyme interactions

How do you read a MM plot? Interpret it?

1. velocity vs substrate

2. limit as [S] approaches infinity is Vmax

3. at half Vmax, [S] = Km is reached

4. reaction is initially first order (linear with respect to [S])  and finally 0th order

How does one gather the data points that become a MM plot? (specifically, what kind of data do you need to collect?)

1. initial velocity

2. various substrate concentrations