Biomg 3300 Quiz 1

Write methyl

Ethyl

Phenyl

Carbonyl (aldehyde)

Carbonyl (ketone)

Carboxyl

Hydroxyl (alcohol)

Enol

Ether

Ester

Acetyl

Anhydride

Amino

Amido

Imine

N-Subsituted Imine

Schiff Base

Guanidinium

Imidazole

Sulfhydryl

Disulfide

Thioester

Phosphoryl

Phosphoanhydride

Mixed anhydride

carboxylic acid and phosphoric acid: acyl phosphate

What are the prefixes for nano, micro, and mili?

nano: 10 -9

micro: 10 -6

mili: 10 -3

How do you know what the stronger acid is based off the Keq?

the larger the Keq is, the stronger the acid

How does pKa determine how strong an acid is?

lower pKA= stronger acid

At what pH does concentration of acid equal that of its conjucate base?

when pH=pKa

Define what a buffer is and explain how a buffer system works.

maintains constancy of pH with weak acid and conjucate base

flattest point on titration curve

At what pH does a cmpd have maximium buffering capacity?

When pH= pKa

What is the pH range over which the cmpd is useful as a buffer?

the flat portion

Glycine

Gly, G

Alanine

Ala, A

Proline

Pro, P

Valine

Val, V

Leucine

Leu, L

Isoleucine

Ile, I

Methionine

Met, M

Phenylalanine

Phe, F

Tyrosine

Tyr, Y

Tryptophan

Trp, W

What has a lower pKa value?

carboxylic acid --> this means the H gets deprotonated off of here first

What is the first rule of thumb to see if something has a polar side chain?

If it has N, O, or S

How can you tell when something will be a hydrogen bond acceptor vs donor?

acceptor: any molecule that has a relatively electronegative atom

donor: electronegative atom bond to a hydrogen

If the pH is below the pKA, what form is it in?

protonated so its pos

What are the exceptions to the polar side chain rule, these are actually?

Tyr, Trp, Cys, Met

- nonpolar

What is the hydropathy index?

tells you if it is hydrophobic or hydrophilic

pos: hydrophobic

neg: hydrophilic

Which amino acids can hydrogen bond?

ASK

Which amino acids can interact ionically?

lysine, arginine, histidine, aspartate, glutamate, tyrosine, cysteine

What is the general rule of thumb when looking at how pH is relative to pKa?

2 units below pKa: 0.01

1 unit below: 0.1

= pKa: 1

1 unit above: 10.0

2 units above: 100

What are most amino acids?

zwitterions: neutral amino acid

How should you solve which 2 forms of an amino acid predominate at any given pH value?

draw out titration curve: make the first one fully protonated

and then go from there

How do you determine the PI of the amino acid that has ionizable side chains?

take the average of the pKA of the ones that are flanking the neutral amino acid

What is the structure of the peptide bond, draw out the full one with N terminal and C terminal

Serine

Ser, S

Threonine

Thr, T

Cysteine

Cys, C

Asparagine

Asn, N

Glutamine

Gln, Q

What should you look at when seeing how many hydrogen bonds a molecule can form?

O and N with lone pairs --> 2 lone pairs, 2 hydrogen bonds

Then look for number of hydrogens that can accept

What happens to entropy when you place a hydrophobic molecule in water? How can we minimize this?

When you place a hydrophobic molecule in water, the entropy of water decreases

We can minimize this by allowing the hydrophobic molecules to aggregate--> this is called the hydrophobic effect

How do you know when an amino acid is drawn in the L configuration?

amino group is on the left, all amino acids in proteins are in L configiguration

What is important when seeing the word predominate?

It needs to be above or below that pKa value, at the pKa value it is equal

How do you know the dirction of migration?

When a pH is below the pI, it is protonated so it is pos so it will move to the negative side

What is an ester made up of?

carboxylic acid and alcohol

What is an amide made up of?

acid and ammonia

What is an acid anhydride made up of?

2 molecules of acetic

What are the 4 types of non-covalent interactions that stabilize biomolecules?

hydrogen, ionic, van der Waals, hydrophobic effect

Negatively charged R groups are?

acidic

Lysine

Lys, K

Arginine

Arg, R

Histidine

His, H

Aspartate

Asp, D

Glutamate

Glu, E

What is a phosphoester?

R-CH2 and then phosphate group with another R

How do you calculate the charge on a peptide?

use the pH, find the forms that are deprotonated/protonated--> then add up the overall charge