Biochemistry Exam2

Front 1

AA’s _______ through a condensation rxn to form ______ and proteins.

Back 1

polymerize

peptides

Front 2

Proteins can be covalently bound to organic molecules, ______, _____, and _________. These proteins are called _______ proteins and the prosthetic groups are necessary for the protein to function.

Back 2

metals
lipids
carbohydrates

conjugated

Front 3

What are the levels of protein structure?

Back 3

Primary

Secondary

Supersecondary

Tertiary

Quaternary

Front 4

What does each level of protein structure consist of?

Back 4

Primary- Amino Acids Residues

Secondary- Alpha Helix of amino acids

Tertiary- Polypeptide chains of alpha helices

Quaternary- Assembled units of polypeptide chains

Front 5

What is the purpose of hemoglobin?

Back 5

Oxygen Transport

Front 6

What is the purpose of myoglobin?

Back 6

Oxygen Storage

Front 7

What is the purpose of ribonuclease?

Back 7

(enzyme)
RNA hydrolysis

Front 8

What is the purpose of lysozyme?

Back 8

(enzyme)
Bacterial wall hydrolysis

Front 9

What is the purpose of cytochrome c?

Back 9

electron transport

Front 10

What is the purpose of immunoglobulin?

Back 10

(antibody)
Defense mechanism

Front 11

What is the purpose of keratin?

Back 11

Structural protein

Front 12

What is the purpose of elastin?

Back 12

Elasticity

Front 13

What is the purpose of actin?

Back 13

(protein)
Muscle Movement

Front 14

What is the purpose of collagen?

Back 14

Structural protein

Front 15

What is the purpose of myosin?

Back 15

(protein)
Muscle movement

Front 16

List globular proteins discussed:

Back 16

Hemoglobin
Myoglobin
Ribonuclease
Lysozyme
Cytochrome C
Immunoglobulin
Actin

Front 17

List fibrous proteins discussed:

Back 17

Collagen
Keratin
Myosin
Elastin

Front 18

What is the most basic way to detect a protein?

Back 18

UV light passing from a lamp through a monochromator at 280nm passing through a curvette.

Front 19

Absorbance of UV light by proteins is primarily due to the number of ___ and ____.

Back 19

Tyrosine
Tryptophan

Front 20

Proteins can be separated by what on the basis of their size, charge, and affinity for other proteins?

Back 20

Column chromatography

Front 21

Prion disease is not cause by microscopic pathogens such as viruses or bacteria but rather :

Back 21

misfolding of a normal cellular protein known as a prion protein PrP

Front 22

PrP =

Back 22

prion protein

Front 23

How is prion disease different from those caused by viruses or bacteria?

Back 23

does not involve dna or rna - an infectious protein was revolutionary discovery

Front 24

Prion disease involves conversion of PrPC into ?

Back 24

PrPSC

Front 25

What is the major difference between PrP and PrPSC?

Back 25

their tertiary conformations

Front 26

True or False

Prion disease involves a reduction in alpha-helical content with a concomitant increase in beta-sheet content

Back 26

True

Front 27

The conformational change in tertiary structure of PrP forms insoluble aggregates both inside the cell and in the form of extracellular ________ _____

Back 27

amyloid plaques

Front 28

PrPSC eventually kills ______ cells.

Back 28

neuronal

Front 29

PrPC C-terminal consists of ?

Back 29

three alpha helices and a short antiparallel beta sheet

Front 30

PrPC:

Helices two and three are held together by?

Back 30

disulfide bonding

Front 31

PrPC exhibits two features typical of extracellular proteins:

Back 31

disulfide linkage

carbohydrate groups

Front 32

The ___ terminal of PrPC is unstructured with two copper binding sites

Back 32

N

Front 33

What is the fastest way to get prion disease?

Back 33

intracerebral inoculation

Front 34

What causes a majority 85% of CJD cases?

Back 34

nothing - sporadic

Front 35

Close to 90% of individuals who develop CJD are homozygous for what codon?

Back 35

129

Front 36

What is the mean survival time for CJD?

Back 36

5 months

Front 37

CJD =

Back 37

Creutzfeldt-Jakob Disease

Front 38

What is the only certain way of diagnosing CJD?

Back 38

postmortem examination

Front 39

Elevated levels of what protein is effective in detecting sporadic CJD?

Back 39

14-3-3

Front 40

What is the significance of finding blue sclerae and multiple bone trauma?

Back 40

A mild case of osteogenesis imperfecta

Front 41

OI involves a _____ defect resulting in the replacement of glycine with ?

Back 41

type 1

cysteine

Front 42

Type 1 collagen forms triple helical structure involving what types of chains?

Back 42

(2) alpha 1 chains
(1) alpha 2 chain

Front 43

Where does the formation of the triple helix for type 1 collagen occur?

Back 43

in the endoplasmic reticulum

Front 44

Over 300 repeats of what tripeptide sequence makes up the helical region of each chain?

Back 44

Gly, Pro, Hydroxyproline

Front 45

Mutations that interfere with helix formation are example of ____ _____ mutations.

Back 45

dominant negative

Front 46

The mild case of OI in the case study was a less severe mutation involving a _______ bridged species because gel electrophoresis showed that a band appeared only under ______ conditions

Back 46

disulfide

nonreducing

Front 47

Precursor amyloid protein involves what amino acid?

Back 47

phenylalanine

Front 48

_________ Yields Aggregating β-Sheet Structure

Back 48

Proteolysis

Front 49

The native protein in PrPC is a ______ dimer of α-helices.

Back 49

soluble

Front 50

What type of protein does PrPSC act as while converting PrPC?

Back 50

chaperone protein

Front 51

_______ bond joins to amino acids together – chemically speaking it is an ______ bond

Back 51

Peptide

amide

Front 52

Doesnt always have to be amino acids bound to backbone to create funtional protein
Others are called :

Back 52

conjugated proteins

Front 53

If the group bound to backbone it is necessary for the protein to function =

Back 53

prosthetic groups

Front 54

Prosthetic groups:

Glycoproteins are covalently bound to ______

Back 54

carbohydrates

Front 55

What type of protein is globular?
Is it water soluble?

Back 55

functional proteins

globular proteins are soluble in water

Front 56

Fibrous proteins are used primarily for?

Back 56

Structure

Front 57

True or False:

Fibrous proteins are hydrophilic

Back 57

false - insoluble hydrophobic

Front 58

Beer Lamberts law:

Back 58

A = ELC

Front 59

Which has a greater absorptivity coefficient?

Tryptophan vs. Tyrosine

Back 59

Tryptophan

Front 60

Used primarily to locate proteins by running a buffer through a reservoir - which technique?

Back 60

Column Chromatography

Front 61

This technique is used primarily to quantitate known proteins

Back 61

affinity chromatography

Front 62

Protein too big to enter pours of matrix run on outside-elute first
Smaller proteins enter the pours of the beads- work through the maze- get hung up for a long time- slow – elute last

Technique?

Back 62

size exclusion chromatography

Front 63

solid beads – with chemically functional charged groups on them

Strength of protein binding depends on strength of charge of protein

Technique?

Back 63

ion exchange chromatography

Front 64

______ exchange:

A low concentration of ______ buffer would remove weakly positive proteins first.

Back 64

Cation

NaCl

Front 65

What can you modify in conditions of cation exchange chromatography to get a better separation? (2)

Back 65

1.Changing pH of buffer alters charges on substituent groups on protein- varying charges could lead to better separation

2.Increasing concentration of NaCl buffer in millimolars spreads out concentration gradient over longer stretch – better separation of proteins by altering gradient.

Front 66

Which chromatography involves binding antibodies to the porous beads?

Back 66

affinity chromatography

Front 67

What type of buffer solution could be used for cation exchange chromatography?

Back 67

Phosphate buffer would not compete for column for cation exchange

Front 68

SDS PAGE = ?

Back 68

sodium dodecyl sulfate

polyacrylamide gel electrophoresis

Front 69

What is the purpose of using sodium dodecyl sulfate in SDS PAGE?

Back 69

In order to ensure separation is only by molecular weight, SDS breaks down all tertiary structures and coats all proteins with a uniform negative charge.

Front 70

Native PAGE is used to separate proteins by _____ in order to obtain their _____ ______?

Back 70

charge

molecular weight

Front 71

Proteins in solution + ammonium sulfate = proteins that distrupt water the most fall out first those that disrupt it the least fall out last when ammonium sulfate is present

This is termed?

Back 71

salting out

Front 72

2D gel electrophoresis is based on the proteins what?

What type of gel is used?

Back 72

Isoelectric point

Isoelectric focusing gel

Front 73

Which techniques would be used to to separate first by pI then by MW?

Back 73

2D gel electrophoresis

SDS PAGE

Front 74

Solution of complex mixture of proteins- matrix is hit by lazer causing it to dissinegrate and ionize
Type of monochromator specific for mass : charge ratios
Set monochromator to a set ratio to study specific ions which hit detector

technique?

Back 74

Mass spec - Mass spec

Front 75

= Medium – Molecular weight less than 10kDa = 10,000 (about 100 amino acids)

Back 75

Polypeptide

Front 76

= Large – Has a molecular weight greater than 10 kDa

Back 76

Protein

Front 77

= Small – 10 or less amino acids

Back 77

Peptide

Front 78

Free rotation between alpha carbon – carbonyl group =

Back 78

psi

Front 79

Free rotation between alpha carbon - alpha amino group =

Back 79

phi

Front 80

Alpha helices are stablized by ____-helical hydrogen bonding of alpha amino and alpha _____ group of every 4th residue

Back 80

intra

carbonyl

Front 81

What type of hydrogen bonding holds beta sheets together?

Back 81

inter-strand

Front 82

What is the major difference between parallel and anti-parallel beta sheets?

Back 82

Parallel involves termini of the same charge - leading to a twisting that creates an angle and decreases the stability of the inter-strand hydrogen bonding

Front 83

How many amino acids must be involves in a beta turn?

Back 83

4

Front 84

What amino acids will always be present in a beta turn?

Back 84

Proline and glycine

Front 85

alpha helix, beta sheets, random coils
are all _______ structures.

Back 85

secondary

Front 86

What is the prosthetic group involved in myglobin and hemoglobin?

Back 86

heme

Front 87

What drives the formation of tertiary proteins?

Back 87

hydrophobic

Front 88

The Alpha-Beta Barrel is best described a variation of which type of secondary structure?

Back 88

random coil

Front 89

True or false:

The Beta-Alpha-Beta Loop is antiparallel

Back 89

false

Front 90

The Beta-Barrel, Alpha-Beta Barrel, and Beta-Alpha-Beta Loop are all _________ structures.

Back 90

super-secondary

Front 91

structural- independently folded region of super-secondary structure within a protein

Back 91

Protein domain

Front 92

______ protein domains differ in that they involve binding

Back 92

Functional

Front 93

A functional domain on an enzyme is called?

Back 93

Active site

Front 94

Proteins whos highest level of structure is tertiary =

Back 94

monomer

Front 95

Proteins with highest level of structure - quaternary

Back 95

oligomer

Front 96

This protein is made of up two alpha-2 and two beta-2 subunits

Back 96

Hemoglobin

Front 97

What drives protein folding?

Back 97

hydrophobic effect

Front 98

What are the two chaotropic agents discussed in denaturing of proteins?

Back 98

Urea , Guanadinium Ion

Front 99

How do chaotropic agents work?

Back 99

Water loves to H-bond with chaotropic agents - no longer will water interact with non-polar proteins - hydrophobic effect is taken away - protein unfolds

Front 100

True or false:

The super helix formed in keratin's quaternary structure is a left handed helix

Back 100

True

Front 101

Put in order from lowest to highest

Protofibril, Protofilament, Super Helix

Back 101

Super Helix

Protofilament

Protofibril

Front 102

True or false:

Hair would have more disulfide bonds than fingernails because there are higher levels of conformations involved in hair

Back 102

False

more disulfide = more rigid = fingernails

Front 103

Which attraction would demonstrate a lower Kd?

Enzyme + Sustrate
vs.
Antibody + Antigen

Back 103

antibody + antigen = lower kd = higher affinity

Front 104

Hyperbolic shape of a binding curve indicates ____________ binding process

Back 104

noncooperative

Front 105

True or false

Both Myoglobin and Hemoglobin have quaternary structure?

Back 105

False

Myoglobin = tertiary

Front 106

What type of bond ?

One atom donates both electrons to the bond

Back 106

Coordinate Covalent bond

Front 107

Valence on bottom of the protoporforyin ring system on the heme group makes ________ _______ bond with _____ nitrogen

Back 107

coordinate covalent

proximal

Front 108

What prevents iron in the heme group of myoglobin / hemoglobin from being oxidized to a +3 state?

Back 108

hydrophobic pocket

Front 109

_______ shape of binding curve indicates cooperative binding process

Back 109

Sigmoidal

Front 110

How many binding sites on hemoglobin for O2?

Back 110

4

Front 111

Positive allosteric modulator ________ affinity for ligand and shifts curve to the ____

Back 111

increases

left

Front 112

How is cooperativity in allosteric binding determined?

Back 112

Hill Coefficient

Front 113

n < 1 =

Back 113

negative cooperative binding process

Front 114

cuffed porphoryin ring system around iron – oxygen electron clouds interact – repulsion - hard to bind = low affinity state

Back 114

T-state

Front 115

Which amino acid acts as a doorway to the binding site that is easier to get by in the R-state?

Back 115

Valine

Front 116

In the transformation from T-state to R-state ___ _______ are replaced by ___ _________ as a stabilizing factor

Back 116

salt bridges

h-bonding

Front 117

What are the two disputed models of O2 binding to hemoglobin?

which one is described more in this class?

Back 117

Concerted vs. Sequential


Sequential - cooperative

Front 118

what two factors ensure that CO will not outbind O2 on hemoglobin thus leading us to all die?

Back 118

There is more O2 in the environment

Distal histidine forces CO and O2 to bind at an angle to the heme group - this decreases the affinity for CO to bind but increases stability of O2

Front 119

What is the Bohr effect- general explanation.

Back 119

Hemoglobin will readily release oxygen around working tissue where this is a high concentration of hydrogen ions and CO2, it will readily bind oxygen in the lungs where hydrogen ion concentration is low and CO2 is released by breathing

Front 120

_____ is our bodies adaptation to higher altitudes, more of it is produced in the body because it readily ______ oxygen and stabilizes the __ state

Back 120

BPG

releases

T

Front 121

Sickle cell anemia involves a point mutation of ________ changing to ______, causing hemoglobin to stick together when they bump together.

Back 121

Glutamic Acid

Valine

Front 122

What is the only accepted treatment of sickle cell anemia?

Back 122

Hydroxyurea

Front 123

A substance that increases the rate of a chemical rxn but is unaffected by the rxn.

Back 123

Catalyst / Enzyme
(enzyme acts as a catalyst)

Front 124

6 General classes of enzymes:

Back 124

Lyases
Isomerases
Ligases
Oxidoreductases
Transferases
Hydrolases

Front 125

Enzymes usually require ________ to be biologically active.

Back 125

cofactors / coenzymes

Front 126

Enzymes with cofactors are termed

without cofactors are termed

Back 126

holo-enzymes

apo-enzymes

Front 127

True or False

A protein is denatured when stripped of its cofactor

Back 127

false

Front 128

– antioxidant – formation of collagen

Back 128

Vitamin C

Front 129

– eye sight – anti-oxidant – take too much = turn orange + lose hair

Back 129

Vitamin A

Front 130

prevent bone loss – helps calcium absorbtion – activates transcription of calcium absorbers

Back 130

Vitamin D

Front 131

antioxidant- must be lipophilic to be active

Back 131

Vitamin E

Front 132

blood clotting + proper bone formation

Back 132

Vitamin K

Front 133

Induced-Fit:

Reactions occur between

Back 133

enzyme + transition state

Front 134

rate of reaction increases with a loss in ________ after substrate binds to enzyme

Back 134

entropy

Front 135

Steric Strain- Increases the free energy of the substrate- lowers ____

Back 135

energy of activation

Front 136

- inhibitor binds to the active site of the enzyme

Back 136

Competitive

Front 137

– inhibitor binds to another site on the enzyme

Back 137

Noncompetitive

Front 138

- inhibitor binds after the substrate is already bound to active site on enzyme

Back 138

Uncompetitive

Front 139

What are the three types of chemical catalysis?

Back 139

Acid Base
Covalent
Metal Ion

Front 140

Transfer of a proton by a functional group on the enzyme with no change in pH.

Back 140

General Acid-Base Catalysis

Front 141

A nucleophilic functional group forms a covalent bond with the _________ resulting in a highly reactive reaction intermediate.

Back 141

substrate

Covalent catalysis

Front 142

Binds to substrate and places it is proper orientation for reaction.
Mediates oxidation-reduction reactions through reversible changes in the metal ion's oxidation state.
Electrostatic stabilization of charged reactant.

Back 142

Metal ion catalysis