CHE310 - Introduction + Proteins

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enantiomers

non-superimposable mirror images

chirality

when a carbon is bonded to 4 different groups

why is chirality important?

it determines the stereochemistry, handedness - how it can interact with other handed molecules in our body

there will be at least one chiral center in every amino acid except for

sidegroups with an NH2, H, or carboxyl group directly after the alpha carbon

amide

an amino group bonded to a carboxyl group

what is the chemical difference between amides and amines?

amides can't accept protons like amines can

general categories of amino acids

polar, nonpolar

subdivisions of polar amino acids

uncharged, charged

subdivisions of charged polar amino acids

acids, bases

subdivisions of nonpolar amino acids

aliphatic, aromatic, sulfur-containing

what is different about proline's r group and why is it important?

it's attached to the amino group of the amino acid, making it difficult to rotate it, which affects its secondary structure

polar groups tend to fold to the ______; nonpolar groups tend to fold to the _____ of a structure

outside, inside

aromatic

ring structures that exhibit resonance

resonance

when several atoms share several electrons simultaneously

what effect does the definition of aromatic structures have on the compound?

increase stability (and therefore difficult of breaking it down)

of the nonpolar amino acids, which is the most polar and why?

tyrosine because of its OH group

as polarity increases, Ka

increases

bad acids have ___ Ka values

low

is the C-S bond polar?

not very

R-S-R

thioether

R-SH

thiol (sulfhydryl)

describe the reaction of 2 molecules of cysteine

2cysteine ----> cystine + 2H+ + 2e-

will polar, uncharged amino acids act as acids or bases?

neither

what is special about threonine?

it has 2 chiral centers

what is another way of describing peptide bonds?

amide linkages

why don't peptide bonds and amide bonds rotate well?

resonance

a molecule's ability to act as an acid or a base depends on

the amount of H+ or H- floating around

describe the process of proton donation of arginine at pH = 0-2

all protonated forms are present

describe the process of proton donation of arginine at pH = 2-9

COOH turns into COO-

describe the process of proton donation of arginine at pH = 9-12

COO- remains, NH3+ (not side chain) becomes NH2

describe the process of proton donation of arginine at pH = 12-14

COO- and NH2 (not side chain) remain, NH2+ (side chain) becomes NH

describe the process of proton donation of arginine: at which pH is arginine the best acid?

0-2

describe the process of proton donation of arginine: which group is the best acid and why?

COOH because it gives up its proton when there are still a lot of other protons hanging around (NH3+ and NH2+)

Ka =

[H+][A-] / [HA]

sec-butyl

CH3-CH2-CH(CH3, __)

tert-butyl (t-butyl)

CH3-C(CH3,CH3)-

isobutyl

CH3,CH3>CH-CH2-

isopropyl

CH3,CH3>CH-

isoelectric point (Pi) or isoelectric pH

the pH at which the majority of molecules of a compound in solution have no net charge (equal to the pKa)

buffer

a weak acid and its conjugate base that resist changes in pH with the addition of H+ or OH- to the solution (pH=pKa)

the different levels of protein structure are important for:

protein folding and the types of bonds

primary structure

the sequence of amino acids that result from translation, which involves linking amino acids together via peptide bonds that are formed by condensing the alpha-COOH group of one with the alpha-NH2 gorup of another to make a dipeptide + H2O or OH-

why is resonance important for protein structures?

the amide linkage exhibits resonance, making it difficult for that bond to rotate and limiting the directions it can go and the other things it can interact with

the primary structure impacts:

the mechanism of protein action (polar w/ polar, hydrophobic w/ hydrophobic, etc.), structure of the globular protein (np inside, polar outside, etc.), relationship of aa's to other species

secondary structure

how rotation occurs around the peptide bond and how the structure is stabilized by attractive forces

what type of forces are involved in secondary structure?

hydrogen bonds, van der waals,

hydrogen bonding

a dipole-dipole interaction in which two molecules share a hydrogen atom

van der waals forces

attractions between opposite dipoles of two different molecules; can be dipole-dipole, dipole-induced dipole, or induced dipole-induced dipole

tertiary structure

the reaction between the R-groups to form a stabilized, folded structure from the secondary structure forces

quaternary structure

not all proteins have this; includes the way multiple polypeptide chains fold around each other

denaturation

the uncoiling of a protein (destruction of secondary, tertiary,and/or quaternary structures) that renders the protein biologically inactive

factors that can cause denaturation

heat, large changes in pH, detergents

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