Lectures 1 & 2

Front 1

There are over _ AA but only _ are coded only by DNA to appear in proteins

Back 1

300
20

Front 2

AA structure

Back 2

Carboxyl group
Amino group
H
Side chain

Front 3

All AA have an alpha Carbon except proline due to it's

Back 3

Side pyrroline ring which includes both alpha amino and alpha carbon forces a bend in a polypeptide

Front 4

AA geometry

Back 4

Tetrahedral

Front 5

AA are stereoisomers, meaning they can rotate plane-polarized light. Aka _

Back 5

Enantiomers

Front 6

Though they come in L/D, majority are in the _ form

Back 6

L

Front 7

Aliphatic groups AA

Back 7

Alanine, valine, leucine, isoleucine, glycine, methione

Front 8

Aliphatic

Back 8

Saturated hydrocarbon side chains, hydrophobic (found in membrane)

Front 9

Aromatic groups AA

Back 9

Phenylalanine, tyrosine, tryptophan

Front 10

Aromatic

Back 10

Aromatic side chains, nom polar, hydrophobic, found in all membrane, buried in the protein core

Front 11

Neutral, Polar AA

Back 11

Serine, Threonine, Cysteine, Proline, Asparagine, Glutamine

Front 12

Neutral, Polar

Back 12

Hydroxyl or amide, reversible phosphorylation

Front 13

Acidic AA

Back 13

Asphartate, Glutamatic

Front 14

Acidic

Back 14

Neg charged, carboxylic ionized at pH 7

Front 15

Basic AA

Back 15

Lysine, Aginine, Histidine

Front 16

basic

Back 16

Pos charged, protonated at pH 7

Front 17

Amphoteric

Back 17

Basic and acid groups

Front 18

Zwitteron

Back 18

Dominant at pH 7. Neutral; charges cancel each other out

Front 19

Titrated to acidic

Back 19

Alpha amine is protonated, pos charged

Front 20

Titrated to basic

Back 20

Alpha carboxyl is deprotonated

Front 21

Overall charge of protein depends on basic/acidic actual charge on protein varies with _

Back 21

PH of the solution

Front 22

Henderson-Hasselbalch Equation

Back 22

HA <-> H+ + A-
Conjugate acid <-> conjugate base

Front 23

Dissociation Constant (ka)

Back 23

Of weak acid. Equilibrium constant for The dissociation reaction. Half is dissociated.

Front 24

PH =

Back 24

-log[H]

Front 25

Isoelectric

Back 25

Intermediate b/t pk1and pk2; net charge 0

Front 26

Buffers

Back 26

Solutions that minimize a change in [H]; acid-base conjugate pair

Front 27

Maximal buffeting capacity

Back 27

Occurs at pH=pka

Front 28

Side chain reactivity of Cystine

Back 28

Oxidized 2cystines to form disulfide bonds, reduced by thiol reagents; bonds form protein structures

Front 29

Vasopressin vs. Oxytocin Spot #3

Back 29

Phe to IIe

Front 30

Vasopressin vs. Oxytocin Spot #8

Back 30

Arg to Leu

Front 31

1st Order

Back 31

Sequence of AA linked together by covalent peptide bonds. Planar.

Front 32

2nd Order

Back 32

Structure of polypeptide chain, determined by H-bond interactions b/t carbonyl oxygen of one and the amide of another.

Front 33

2nd Order is determined by _ nature of the peptide bond

Back 33

Planar

Front 34

Planar structure is stabilized by resonance b/t the C and N, confers _ restricting rotation

Back 34

Partial double band character on the peptide bond

Front 35

Ramachandran Plot

Back 35

Shows regular arrangement of AA that are located near to each other in the linear sequence

Front 36

A helix

Back 36

Stabilized by intra-H bonds formed b/t carbonyl oxygen and hydrogen attached to amide Hydrogen. 3.6 AA per turn

Front 37

A helix H bonds binding

Back 37

N + 4; H bonds to peptide 4 residues ahead

Front 38

B sheet

Back 38

H bonds formed b/t C=O of one peptide bond and the N of another. Inter-H bonds pleated b/c C-C bonds are tetrahedral. not planar.

Front 39

B turn

Back 39

Segments in which the polypeptide changes directions (Glycine and Proline)

Front 40

3rd Order

Back 40

Spontaneous stabilized by side chain interactions (non covalent)

Front 41

4th Order

Back 41

Formed by interactions b/t peptide chains. Held together by covalent forces.

Front 42

monomeric proteins

Back 42

proteins consist of a single polypeptide chain

Front 43

multimeric proteins

Back 43

proteins that consist of two or more polypeptide chains

Front 44

eghomodimer

Back 44

structurally identical

Front 45

heterodimer

Back 45

structurally totally unrelated

Front 46

Hemoglobin is held together by

Back 46

hydrophobic interaction, H-bonds and ionic interactions

Front 47

Hemoglobin structure

Back 47

a2b2 heterotetramer. Binding of O2 increases affinity for O2.

Front 48

cytochrome oxidase

Back 48

multimeric proteins. oxidase in the mitochondrial electron transport chain and the pyruvate dehydrogenase complex.

Front 49

Protein Denaturation

Back 49

results in the unfolding and disorganization of the protein’s structure and is commonly defined as any noncovalent change in the structure of a protein.

Front 50

Protein Denaturation effects these proteins structures

Back 50

the secondary, tertiary or quaternary structure of the molecules

Front 51

The most common observation in the denaturation process is the precipitation or _ of the protein

Back 51

coagulation

Front 52

Denaturing agents

Back 52

excess heat, chaotropes such as urea and guanidine hydrochloride, organic solvents, such as alcohol, mechanical mixing or shearing, strong acids or bases, such as HCl or NaOH, detergents, such as sodium dodecylsulfate and heavy metal ions such as lead and mercury that typically react with free sulfhydryl groups.

Front 53

Protein Purification

Back 53

cells are disrupted by grinding or homogenization in buffered isotonic solutions at physiological pH to minimize degradation.

Front 54

The Anfinsen Experiment

Back 54

determined how the primary structure of a protein determines its 2* & 3* structure

Front 55

The analysis of primary structure, or sequence analysis, reveals the effects of _ and _

Back 55

genetic mutations and shows homologies within families of proteins

Front 56

There are three major steps in the analysis of primary structure

Back 56

1) Amino acid composition
2) Fragment sequencing
3) Fragment linking

Front 57

Amino acid composition is determined by quantitative analysis following _ by complete acid hydrolysis which cleaves all peptide bonds liberating the individual amino acid residues.

Back 57

protein digestion

Front 58

Fragment sequencing: Specific hydrolysis by chemicals or proteolytic enzymes cleaves peptide bonds at specific residues to produce small, easy-to-manage peptide fragments. This is followed by _

Back 58

Edman degradation of each fragment to identify each of the amino acid residues and their sequence in the peptide.

Front 59

Trypsin hydrolyzes the carboxyl side of _ and _

Back 59

K and R residues

Front 60

Chymotrypsin hydrolyzes the carboxyl side of

Back 60

aromatic residues (F, Y and W).

Front 61

Cyanogen bromide cleaves on the carboxyl side of

Back 61

M

Front 62

Edman degradation involves the sequential removal and identification of N-terminal amino acid by reaction with _; it is used for peptide sequences up to 50-60 residues long.

Back 62

phenylisothiocyanate

Front 63

Fragment linking

Back 63

Cleavage of the protein at different points produces overlapping fragments

Front 64

Methods for studying primary structure

Back 64

Mass spectrometry

Front 65

Mass spectrometry

Back 65

used to identify molecular mass and sequence of polypeptides

Front 66

Methods for studying secondary structure

Back 66

CD spectra

Front 67

Methods for studying tertiary structure

Back 67

X-ray crystallography
NMR