Biochemistry Exam 1

ph \= pka + log10(A-/HA)

Henderson hasselbalch equation

No

is pH 7 always neutral?

2 O-H covalent bonds and two nonbonded hydrogens that can make bonds

what bonds are present in water

pH

an expression of the ionization of the concentration of protons over 14 orders of magnitude

\=log(H+)

pH \= ?

7.4

what is the pH of blood

titration

an analytical method used to determine how much acid is in solution by having a measured volume of acid solution and slowly adding a strong base of known concentration

pH \= pKa

when half the concentration of acid is neutralized...

buffers

solutions that resist changes in pH as acid and base are added. Consist of weak acid and its conjugate base

one

buffers can only be reliable within \___ pH unit of their pKA

imidazole

the \_______ group of Histidine works as an intracellular buffer

zwitterions

a neutral molecule with one positive and one negative charge

tetrahedral

amino acids have a \________ structure

hydrogen, carboxyl group, amino group, R chain

what are the four parts of an amino acid

condensation

the polymerization of amino acids is a \_____________ rxn

amino and carboxyl group

a peptide bond is formed between

(Pro, P): hydrophobic

Proline

(Gly, G): hydrophobic

Glycine

(Ala, A): hydrophobic

Alanine

(Val, V): hydrophobic

Valine

(Leu, L): hydrophobic

Leucine

(Ile, I): hydrophobic

Isoleucine

(Phe, F): hydrophobic

Phenylalanine

(Tyr, Y): hydrogen bonding, pKa of phenolic OH\=10.1

Tyrosine

(Trp, W): hydrogen bonding

Tryptophan

(Cys, C): hydrogen bonding, pKa of sulfhydryl\= 8.3

Cysteine

(Met, M): hydrophobic

Methionine

(Asp, D): acid, pKa of B carboxyl\=3.9

Aspartate

(Glu, E): acid, pKa of Y carboxyl\= 4.3

Glutamate

weaker

the carboxyl group of aspartate and glutamate are \___________ acids than the a carboxyl group

(Lys, K): basic, pKa of E amino group\= 10.5, hydrophilic

Lysine

(Arg, R): basic, pKa of guanidino group\= 12.5, hydrophilic

Arginine

(His, H): only aa that is buffer at physiological range, pKa of imidazole group\= 6.0, hydrophilic

Histidine

(Ser, S): pKa of hydroxyl\= 13, polar, h bond

Serine

(Thr, T): pKa of hydroxyl\= 13, polar, h bond

Threonine

(Asn, N): polar, h bond

asparagine

(Gln, Q): polar, h bond

glutamine

(Sec, U): natural amino acid, polar, acidic, anti-oxidant activity

Selenocysteine

(Pyl, O): in methanogenic archaea, polar, basic

Pyrrolysine

weak

amino acids are \___________ polyprotic acids

2

the pKa of any amino acids a-carboxyl group is

9

the pKa of any amino acids a-amino group is

isoelectric point

the pH at which a molecule carries no net electrical charge or is electrically neutral

(pKa1 +pKa2) / 2

pI (isoelectric point) \=

R,S nomenclature

which nomenclature is best for amino acids

trans to each other

the carbonyl oxygen and the amide hydrogen of the peptide bond are

40% double bond character

the peptide bond is a hybrid and has

jellyfish; tag; center; B-barrel

The green fluorescent protein (GFP) is found in \_________ and can be used in genetic engineering to \______ any protein, structure, or organelle in a cell. The luminescent chromophore of GFP lies in the \_________ of a \____________ protein structure

cyclization, oxidation, dehydration

What are the three steps of chromophore mutation of wild-type GFP

oligopeptide

12-20 amino acid residues

monomeric

one polypeptide chain

multimeric

more than one polypeptide chain

homomultimer

one kind of polypeptide chain

heteromultimer

two or more different polypeptide chains

shape and solubility

proteins are classified according to \___ and \___

fibrous proteins

class of proteins that are relatively simple, regular, linear structures. Mechanically strong, insoluble, structural

collagen

example of a fibrous protein that forms a triple helix and is the principle component in tendons, cartilage, bones, and teeth

globular proteins

class of proteins that are very abundant with a roughly spherical shape and are very soluble. Hydrophobic core and hydrophilic surface

myoglobin

example of a globular protein

membrane proteins

class of proteins that associate with the various membranes of the cell

bacteriorhodopsin

example of a membrane protein

primary

structure level of protein that is just the amino acid sequence connected by peptide bonds

secondary

structure level of protein that is when local structures are stabilized by h bonds

tertiary

level of protein structure that is the overall 3D shape of a protein. Interactions between alpha and B sheets

quaternary

level of protein structure that consists of more than one amino acid chain and has subunit organization

structure; motion

function depends on \_________ and \____________ enabled function

N terminus to C terminius

amino acid sequences are numbered from

carbonyl and the amino

intramolecular hydrogen bonding between \_______ and \______ make the a helix and B sheets possible

prosthetic group

the non amino acid part of the structure of the protein, being tightly linked to the apo-protein

post-translational modifications

chemical changes made to protein after synthesis. ex: phosphorylation, acetylation, methylation, acylation, prenylation, ADP-ribosylation, adenylylation

nucleophilic ones (S,T,Y,K,R,C,H)

post translational modifications happen on which amino acids

r groups

\____________ hydrogen bond on the protein surface

stabilize

a hydrogen bond in the interior of a protein serves to

electrostatic or repulsive

ionic interactions can either be

surface

charged residues are normally located on the protein \____________ where it can interact w solvent

van der waals

force that is the result of instantaneous dipole-induced dipole interactions that arise bc of fluctuations in the electron charge distributions of adjacent nonbonded atoms

flat; rotate

the peptide bond is \______ and not free to \_____

psi bond

bond linking the a carbon with the carbon of the peptide bond

phi bond

the bond linking the nitrogen of the peptide bond and the adjacent a carbon

n+4 rule

an alpha helix is spontaneously created bc the carbonyl forming a hydrogen bond with the amino group of the 4th residue ahead in the sequence

3.6

a helix residues per turn

1.5 A

rise per residue in an a helix

5.4 A

rise per turn (pitch) in an alpha helix

c terminus to n terminus

the dipole moment in a a helix goes from

parallel b sheet

b sheet that have strands going the same direction

antiparallel b sheet

b sheet that has adjacent strands running in opposite directions

a keratin

type of fibrous protein found in claws, fingernails, hair, and horns that is composed of a central a-helix-rich rod

fibroin and B keratin

what are the two types of fibrous proteins that form extensive beta sheets, found in silk and bird feathers, have an alternating sequence

proline

which amino acid acts as a helix breaker due to fixed psi angles

domains/modules

two or more recognizable and distinct structures found in larger globular proteins. Usually have different functions

protein sectors

quasi-independent groups of correlated amino acids. Physically connected to tertiary structure and each has a distinct role. Ex: substrate binding, protein core, catalytic domain

random coil

the segment of a protein that are not helices or sheets. Usually organized and stable but don't conform to any frequently recurring pattern. Strongly influenced by side chain interactions

true

t/f: proteins with different structures can carry out similar functions and vice versa

cooking an egg to its Tm (melting temperature)

what is an everyday example of protein denaturation

guanidine-HCl or urea

proteins can be denatured by high concentrations of

entropy

the largest thermodynamic contribution to protein folding is \______ for the interaction of nonpolar residues w the solvent. Liberates solvent molecules when nonpolar folds inward

a proteins

when the entire protein is a helices

b proteins

when the entire protein is b sheets

a /b proteins

protein in which helices and sheets are intermingled

a \= b proteins

proteins which contain separate a-helical and b-sheet domains