Biochem Final

What is an aquaporin and what does it do?

prevents proton hopping and transports water across membranes, is a glycoprotein and is a homotetramer

carbohydrates

carbon-based molecules rich in hydroxyl groups (CH2O)6

* monosaccharides: aldehydes or ketones with 2+ OH groups, exist in many different isomeric forms
* disaccharides: 2 monosaccharides
* polysaccharides: oligosaccharides 2+ linked by O-glycosidic bonds (OH groups like Ser and Thr), other polysaccharides can have N-links (N groups like Asn)

aldoses

carbohydrate monosaccharide with an aldehyde group

ketoses

carbohydrate monosaccharide with a ketone group

polysaccharide bonding

* 1,4 glycosidic bonds
* 1,6 glycosidic bonds form branches

isomers

have the same molecular formula but different structures

constitutional isomers

differ in order of attachment of atoms

stereoisomers

atoms connected in the same order but differ in spatial arrangement, includes: enantiomers and diastereomers → which include epimers and anomers

enantiomers

nonsuperimposable mirror images

diastereomers

isomers that are not mirror images

epimers

diastereomer that differs at one of several asymmetric carbon atoms

anomers

isomers that differ at a new asymmetric carbon atom formed on ring closure

starch

made of amylopectin (branched) and amylose (unbranched) and is water insoluble due to layered semi-crystalline form, alpha linkages

cellulose

straight chains that form string fibrils, strong and durable, made of beta 1,4 linkages

glycogen

alpha glucose subunits, highly branched (1,4 and 1,6 linkages)

glycoproteins

carbohydrates attached to proteins, largest component by weight is protein

proteoglycans

protein attached to glycosaminoglycan, important for structural roles (cartilage), composed of repeating disaccharide with sulfate modification

mucins/mucoproteins

predominantly carbohydrate, pretein attached to carbohydrate N-acetylgalactosamine

phosphorylation in carbohydrates

excessive phosphorylation disrupts branching pattern and structure of glycogen, can lead to neurodegeneration

starch degredation

outermost layer becomes water soluble

lipids

non-polymer, water insoluble, critical for energy storage and signaling

* free fatty acids
* triglycerols
* phospholipids
* glycolipids
* steroids

fatty acids

long hydrocarbon chain, can be saturated (solid) or unsaturated (liquid, double bond),

18: 2n-6 means 18 carbons, 2 double bonds, double bond 6 from omega (CH3) end

Triglyceride

esterified fatty acids, storage form of fatty acids

glycerophospholipids

They have four components: fatty acids (2 or \n more), a glycerol platform , a phosphate, and \n an alcohol

glycolipids

carbohydrate-containing lipids, important for cell signaling

cholesterol

helps maintain membrane fluidity, less van der waals, worse packing, increases fluidity

lipid-bilayer

2 molecules thick of phospholipids, semi-permeable, creates 2 environments

passive transport

mediated by ionophores

ion channels

highly selective for an ion, removes water in interior wall through selectivity filter (S4 is Arg rich +), are gated

Porins

transport ions and nonpolar solutes, transport bigger molecules than ion channels, beta barrel

Transporters

alternate between 2 conformations to move substances from one side to another

secondary transporters

* Symporters power the transport of a molecule against its concentration \n gradient by coupling the movement to the movement of another molecule \n down its concentration gradient, with both molecules moving in the same \n direction


* Antiporters also use one concentration gradient to power the formation of \n another, but the molecules move in opposite directions

ABC transporters

pump ions, sugars, amino acids, polar and non polar substances (outward facing to inward)

enzymes

increase reaction rates by lowering activation energy, usually proteins but can be RNA, provide specific environment and reaction takes place in confined space called the active site

induced fit model

substrate and enzyme are not exact fit, adapts shape

lock and key model

enzyme and substrate are exact fit (not always true)

substrate specificity

geometric specificity and electronic specificity

how enzymes work

* regenerate
* lower activation barrier
* do not change equilibrium
* activation E reflects rate of reaction
* reaction reaches equilibrium faster

enzyme reactions

\
* Enzymes function as catalysts \n by stabilizing the transition

state
* Active site matches the shape of the \n transition state leading to product
* Active site possesses functional \n groups that interact more strongly \n with the transition state structure \n than with the substrate

how is activation energy lowered

the binding of the substrate to the enzyme releases energy that is later used to lower the activation energy

in transition state what interactions are optimized?

weak interaction between enzyme and substrate

cofactors

enhance the range of enzymatic reactions (metal ions and coenzymes)

active form

holoenzyme

inactive form

apoenzyme

enzyme kinetics importance

* insight to reaction mechanisms
* might need to know how quickly a reaction happens
* regulation of reaction mechanisms
* gives foundational understanding of living organisms and gives us the ability to modulate

Vmax

max velocity at enzyme saturation

Vo

initial velocity a \[S\]

Km

michaelis-menton constant, describes substrate concentration needed to achieve half of Vmax (specific to substrate, temp, and pH)

Kcat

turnover number (number of reactions for unit time)

kcat/km

specificity number (measure of enzyme efficiency)

catalytic perfection reached at

10^8 to 10^9 M-1\*s-1

michaelis menton equation

Vo = (vmax \[S\]) / (Km + \[S\])

kinetic perfection

catalytic velocity is restricted only by the rate at \n which they encounter substrate in solution

types of inhibition

* irreversible
* reversible
* competitive
* uncompetitive
* non-competitive

competitive inhibitors

reduces the concentration of free enzyme available \n for substrate binding

allosteric regulation

molecules that can bind to enzyme at active site, increase or decrease enzyme activity

free energy equation

ΔG = ΔH - TΔS and ΔG^o = -RTln(Keq)

driving force for protein folding and membrane formation

hydrophobic effect

hydrophobic effect

The tendency of water molecules to minimize their \n contact with hydrophobic molecules

buffers

mixtures of a weak acid and its conjugate base that \n resist change in pH when either strong acid or strong base is added

does a strong acid have a high or low pKa?

low

buffer pH range

\+/- 1 of the Pka

Zwitterion

a molecule that possesses both a positive and negative charge (an amino acid at neutral pH is an example)

Isoelectric point (PI)

the pH where an amino acid has a net charge of zero (avg of pk1 + pk2 …)

peptide bond

the bond between amino acids (between C and N), resonance stabilized

peptide

linear polymer of amino acids

dipeptides

two linked amino acids

Oligopeptides

4–20 amino acids

Polypeptides

20 or more amino acids linked together

Almost all peptide bonds are in the trans conformation, what is the exception?

proline linkages

what stabilizes the secondary protein structure

H-bonds

what amino acids may disrupt alpha helices?

Valine, threonine, and isoleucine tends to \n destabilize because of steric clashes

Serine, aspartate and asparagine tend to \n disrupt the helix because of their side chains \n has hydrogen bonding potential

Glycine destabilizes a-helix because absence of \n side chain results in greater freedom of rotation \n

Proline produces a kink in an a-helix because \n cyclic structure occupies space that neighboring \n amino acid would otherwise occupy

motifs

combinations of secondary features

domain

independently folded unit within a protein

globular proteins

water soluble proteins that fold into compact structures

fibrous proteins

have repeating secondary structures (like keratin or collagen, coiled coils)

how are tertiary structures stabilized?

hydrophobic effect is the largest contributor, then non-covalent charge-charge interactions (salt bridges) and Van der Waals, then disulfide bonds and metal ions, some steric repulsions as well

how do proteins fold?

through the progressive stabilization of intermediates, entropy and free energy decrease as it folds

Proteins can be denatured reversibly, what does this prove?

proof that tertiary structure of a protein is coming from its sequence

protein folding

Hydrophobic Collapse Model (entropy-driven): Protein collapses rapidly around hydrophobic side-chains with the release of bound, water molecules

Nucleation Model (hydrogen bonding): Neighboring residues in sequence form some element of the native secondary structure (e.g., a-helix) that acts as a nucleus for cooperative folding \n

Van der Waals, Charge-Charge \n

Many small proteins fold spontaneously. Others need assistance.

Intrinsically Disordered Proteins (IDP)

inherently unstructured proteins, tend to participate in regulation and signaling mechanisms

myoglobin role

Facilitates oxygen diffusion in \n the muscle cells and functions as a oxygen storage \n protein in aquatic mammals

where does oxygen bind in myoglobin?

prosthetic heme group

role of proximal histidine

makes Fe stay in the Fe2+ state

hemoglobin

transports oxygen throughout the body, does not have a heme group because it needs to be able to both take in and drop off oxygen

what is this graph

oxygen binding curve for hemoglobin and oxygen, more oxygen needed to saturate hemoglobin, hemoglobin exhibits cooperative binding

hemoglobin states

T-state: not bound to O2

R-state: bound to O2

how does cooperativity work?

Initial binding of first O2 shifts Fe+2, proximal His and its associated a-helix toward the plane of the porphyrin ring

How does 2,3- BPG effect hemoglobin binding?

it binds to allosteric sites and stabilized deoxygenated hemoglobin, so it increases oxygen unloading capacities at the tissue level

Bohr effect

lowered pH decreases hemoglobin affinity to bind to O2, thus offloading ability of hemoglobin increases (seen at the tissue level)

fetal hemoglobin

has higher oxygen binding affinity that that of the mother

proteins must be what in order to be purified?

proteins must be released from the cell in order to be purified

ways to purify a protein

by solubility, size/mass, charge, binding affinity,

cryo-electron microscopy

direct images of proteins (sum of photos from different directions), good for large proteins

what are nucleotides composed of?

nitrogenous base, sugar, and a phosphate

role of both DNA and RNA

store and decode genetic information

properties of nitrogenous bases

Aromatic, planer, and heterocyclic molecules

what are the purines?

Adenine (A) and Guanine (G)

what are the pyrimidines?

Cytosine (C), Thymine (T), and Uracil (U)

phosphodiester linkages

ester bonds that form between sugar and phosphate to form the backbone of nucleic acids.