*BIOL 3020 Lecture 2 (Water & Noncovalent Interactions)

ionic interaction is referred to what in biochemistry?

salt bridge

the strength of ionic interactions is determined by what three things?

charges, distance, and dielectric constant of the medium

what does a high dielectric constant?

it can effectively reduce the electrostatic forces between charged particles.

the strength of ionic interactions increased or decreased in aqueous solution? why?

decreased because water has a high dielectric constant (able to weaken positive and negative charges in solution)

what is the H-bond donor and acceptor have?

H-bond donor: electronegative atom

H-bond acceptor: LPE

H-bonds are strongest when all three of the involved atoms (the two electronegative atoms, the hydrogen atom) are in what orientation?

collinear

H-bonds are found in what part of the DNA?

holding the double helix structure of DNA together

networks of H-bonding make water highly…

cohesive

what is the function of urea?

to denature proteins

how does urea denature proteins?

it disrupts the water structure and prevents hydrophobic interactions which maintains a protein’s structure

what is urea produced by and as what kind of waste?

the kidney as nitrogen waste

hydrophobic effect

nonpolar substances aggregate in aqueous solutions to minimize their exposure to water, leading to increased entropy of the surrounding water molecules. This effect is crucial in the formation of cell membranes and protein folding.

why is hydrophobic effect not considered electrostatic in nature?

the driving force is the release of surrounding water molecules not charges

what do nonpolar molecules do when in water?

they are forced together, away from contact with water molecules

why are nonpolar molecules driven together? is it because they have a high affinity for each other or is it because of entropy?

entropy-driven

hydrophobic effects drive a protein to fold into what kind of conformation?

a compact conformation

in a compact conformation, is the nonpolar side inside or outside?

inside, buried

name two places hydrophobic interactions are found:

driving formation of membrane and spontaneous folding of polypeptide chain

weak interactions are strong/weak cumulatively and strong/weak individually

strong, weak

higher pka, weak/strong acid

weak

know how to use the henderson hasselbalch equation

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

low pH = high/low H+ concentration

high H+ concentration

what is the physiological range of pH

6.5-8

what is acidosis

blood pH drops to 7.2

the DNA double helix structure falls apart when there is an increase or decrease in pH?

increase

why does DNA double helix lose its structure as pH increases?

increasing pH will lead to deprotonation of guanine since there is less H+ in solution. This makes guanine lose a hydrogen bond donor, causing its inability to base-pair with C

changes in pH can alter what on proteins?

the surface charge

a higher pH will make the protein have a + or - charge

negative charge

protein molecules in aqueous solution become increasingly/decreasingly protonated and more positively/negatively charge as the pH decreases

increasingly, positively

buffer

weak acid and its conjugate base

buffer system for pH control of blood

carbonic acid-bicarbonate buffer system

buffer system for controlling intracellular pH due to its pKa near 7.0

dihydrogen phosphate-hydrogen phosphate system

do proteins contain a lot of weakly/strongly acidic or basic groups and why?

weakly acidic or basic groups because proteins are abundant in cells and body fluids, where pH buffering is very strong

what is used to help buffer blood?

carbonic anhydrase

how does the bicarbonate buffer system restore blood pH

when blood pH drops, excess H+ in the blood increases the amount of CO2 exhaled (pt breathes rapidly), which shifts it to the side with more CO2 and promotes loss of H+ to bring blood levels back to normal

what else might contribute to intracellular buffering?

phosphates and histadines

what are the four parts of all amino acids?

alpha carbon, amino group (NH2), carboxyl group (COOH), and side chain (R)

many amino acids exist as what at physiological pH?

zwitterions

chiral molecule (aka stereocenter, asymmetric carbon)

when a carbon atom has four different substituents attached to it

The L isomer rotates polarized light to the right/left

right

The D isomer rotates polarized light to the right/left

left

When H is in the back and CORN is clockwise, is it L/D form?

D form

When H is in the back and CORN is counterclockwise, is it L/D form?

L form

When H is in front and CORN is clockwise, is it L/D form?

L form

When H is in front and CORN is clockwise, is it L/D form?

D form

Only D/L amino acids are constituents of proteins

L amino acids

in a Fischer projection, horizontal bonds are coming in/out from the page and vertical lines are coming in/out of the page?

horizontal are coming out, vertical are coming in

the lowest priority substituent (hydrogen) is pointed to or away from the viewer?

away from

if the progression from highest to lowest is counterclockwise, this is R/S? (assume H is pointed away)

S

if the progression from highest to lowest is clockwise, this is R/S? (assume H is pointed away)

R

for almost all amino acids, the L isomer has what kind of configuration?

S configuration

what is the amino acid exception in which its L isomer has R absolute configuration?

cysteine because of the sulfhydrl group

what are the four groups of amino acids?

hydrophobic (nonpolar)

polar (neutral)

positively charged at pH 3

negatively charged at pH 2

non-polar residues are present in the interior/exterior of the globular protein?

interior

if the center carbon is the alpha carbon, what are the next three carbons after that called?

beta, gamma, delta

what two amino acids are found on the surface of a protein?

glycine and proline (gly and pro)

turn region of a protein

region of protein chain that needs to change direction

where can you find the turn region of a protein

surface

why is glycine suitable for a turn in protein?

smallest side chain, very flexible

why is proline suitable for a turn in protein?

unique cyclic side chain makes it compatible with a turn conformation.

which three amino acids are branched side chains?

valine, leucine, isoleucine

in amino acids with a hydroxyl group, it can react with what through phosphorylation?

ATP

phosphorylation

hydroxyl group being modified with a phosphoryl group

a disulfide bond formed between two cysteines becomes what?

cystine

what drives the formation of a disulfide bond between two cysteine residues?

oxidation

reduction, which is the gain of an electron, will make or break a disulfide bond?

break

the aromatic side chains absorb UV lights at what value?

280 nm

spectrophotometry

scientists use this technique to measure the concentration of tryptophan and tyrosine in a protein

what are the two rare genetically encoded amino acids?

selenocysteine and pyrrolysine

selenocysteine and pyrrolysine are known as what?

21st and 22nd amino acids, respectively.