Biochem Test 1 Review

Front 1

What are the three major isoforms of nitric oxide synthases?

Back 1

neuronal NOS (nNOS; NOS I)
inducible NOS (iNOS; NOS II)
endothelial NOS (eNOS; NOS III)

Front 2

Which structure does NOT require the substrate to bind to function, P450 or NOS?

Back 2

NOS (Arginine does not have to be present for it to synthesis NO)

Front 3

What is sGC? Explain the structure. What does it convert?

Back 3

Soluble guanylate cyclase.

It is a heterodimer (one alpha, one beta chain), heme-containing protein.

Converts GTP to cGMP

Front 4

Where is nNOS found?

Back 4

Skeletal muscle and neurons

Front 5

What primarily activates NOS I?

Back 5

The binding of calcium (via large influx, as in with action potential) to calmodulin, which then binds to nNOS, producing NO

Front 6

What activates soluble guanylate cyclase?

Back 6

The binding of NO to the heme of sGC, which breaks the His-heme bond.

Front 7

Who is responsible for determining the nation's needs and interests?

Back 7

Strategists must weigh heavily the nations needs and interests. The process entails determining what interests and what national instruments of power are available and applicable.

Front 8

Which NOS isoform produces the most NO?

Back 8

iNOS (NOS II)

Front 9

Where is P450 found?

Back 9

Integral membrane protein

Front 10

Where does P450 get its name?

Back 10

It is the absorbance that is characteristic when CO is bound

"Pigment 450 nm"

Front 11

Explain the structure of P450

Back 11

Very similar to Hb, in that is has the protoporphyrin IX ring, but instead of His being bound, Cys is bound.

Front 12

What does NADPH stand for? How many H+ can it transfer at one time?

Back 12

Nicotinamide adenine dinucleotide phosphate

TWO

Front 13

What is the general P450 formula?

Back 13

NADPH + O2 + H + XH --> NADP+ + H2O + XOH

Front 14

Why does the substrate have to be bound in order for the p450 cycle to begin?

Back 14

The redox potential of non-bound P450 is -300 mV (low-spin, hexa-coordinated) which is higher than the FMN moiety (-270 mV). Once the substrate is bound, the complex becomes high-spin penta-coordinated, reducing the redox potential to -230, making it capable of accetping electrons.

Front 15

What does FAD stand for?

Back 15

oxidized flavin adenine dinucleotide.

Front 16

What does FADH2 stand for?

Back 16

reduced flavin adenine dinucleotide

Front 17

What does FMN stand for?

Back 17

flavin mononucleotide

Front 18

What does FMNH2 stand for?

Back 18

reduced flavin mononucleotide

Front 19

What structure do FAD and FMN have in common?

Back 19

Both contain the isoalloxazine ring from the vitamin B2 (riboflavin)

Front 20

What is the active redox group of the flavoprotein?

Back 20

Isoalloxazine ring

Front 21

Where is the P450 located in the ER? In the mitochondria?

Back 21

in the ER: embedded in the cytoplasmic side of the membrane

in the Mitochondria: on the inner membrane

Front 22

NADPH-cytochrome P450 reductase is a_____________ membrane protein which contains which two groups?

Back 22

peripheral;

FAD and FMN prosthetic groups

Front 23

Which is in more abundance, NADPH- cytochrome P450 reductase flavoproteins or P450s? what attracts the flavorproteins to the P450?

Back 23

NADPH- cytochrome P450 reductase flavoproteins

Electrostatic interactions (once substrate is bound the binding affinity for the flavoproteins is increased)

Front 24

What reactions are mitochondrial P450 involved in ? What is the enzyme that is used?

Back 24

steroid hydroxylation reactions

NADPH-adrenodoxin reductase

Front 25

Compare and contrast NADPH- cytochrome P450 reductase flavoproteins and NADPH-adrenodoxin reductase

Back 25

NADPH- cytochrome P450 reductase flavoproteins:

Found in ER P450
contains FAD and FMN

NADPH-adrenodoxin reductase:
found in mitochondria
does not contain FMN, but rather 2 adrenodoxin protein to transfer the electrons to P450

Front 26

Why do we care about P450?

Back 26

They affect the amount of time drugs stay in the body.

Front 27

How are P450's classified (named)?

Back 27

All start with CYP

Family= Number 40% aa sequence identity

Subfamily= Letter 50% aa sequence identity

Final # given based on the order it was found

Front 28

Why is CYP11A1 important? Where would you find this most often?

Back 28

All of the steroids in the body use CYP11A1

Adrenal gland

Front 29

What reaction does CYP11A1 catalyze?

Back 29

The committed step in steroid biosynthesis (cleaving the bond between C20 and C22 to form pregnenolone (21 carbon) and isocaproic aldehyde (6 carbon)

Front 30

Explain the steps of steroid synthesis

Back 30

step 1:
in the adrenal mitochondria, CYP11A1 hydroxylates cholesterol (a 27 carbon) at C22 to produce 22-hydroxycholesterol

step 2: CYP11A1 hydroxylate at C20 to produce 20,22-dihydroxycholesterol (a diol)

step 3:
CYP11A1 cleaves the bond between C20 and C22 to produce pregnenolone (21 C) and isocaproic aldehyde (6 C)

Front 31

Which is the only amino acid that is not chiral?

Back 31

Glycine

Front 32

All of the biologically active chiral alpha C's have _____________ configuration

Back 32

Levorotary

Front 33

All the biologically acitve chiral alpha carbons have __________ absolute configuration except __________.

Back 33

Sinister;
Cysteine

Front 34

Describe polarity.
Valine

Back 34

nonpolar

Front 35

Describe polarity.
Leucine

Back 35

nonpolar

Front 36

Describe polarity.
Isoleucine

Back 36

Nonpolar

Front 37

Describe polarity.
Phenylalanine

Back 37

Nonpolar

Front 38

Describe polarity.
Tyrosine

Back 38

Nonpolar

Front 39

Describe polarity.
Tryptophan

Back 39

Nonpolar

Front 40

Describe polarity.
Histidine

Back 40

Nonpolar

Front 41

Describe polarity.
Aspartate

Back 41

Polar

Front 42

Describe polarity.
Glutamate

Back 42

Polar

Front 43

Describe polarity.
Lysine

Back 43

Polar

Front 44

Describe polarity.
Arginine

Back 44

Polar

Front 45

Describe free energy.
Arginine

Back 45

Very large negative free energy

Front 46

Describe free energy.
Glutamate

Back 46

Very large negative free energy

Front 47

Decribe free energy.
Aspartate

Back 47

Very large negative free energy

Front 48

Describe free energy.
Lysine

Back 48

Very large negative free energy

Front 49

Describe Free energy.
Tyrosine

Back 49

Positive free energy (hydrophobic)

Front 50

Describe free energy.
Isoleucine

Back 50

Positive free energy (hydrophobic)

Front 51

Describe free energy.
Phenylalanine

Back 51

Positive free energy

Front 52

decribe free energy.
Tryptophan

Back 52

Positive free energy

Front 53

How would you describe an amino acids with free energy near zero and both hydrophobic and hydrophilic parts?

Back 53

Amphoteric

Front 54

Two cysteines oxidize to form ___________. What is the name of this bond? Is it covalent or noncovalent?

Back 54

Cystine
Disulfide Bond
Covalent

Front 55

What is the bond called in involved in polymerization?

Back 55

Peptide bond

Front 56

What kind of a reaction is polymerization?

Back 56

Dehydration reaction

Front 57

a polymer of less than or equal to 50 aas is called a __________. A polymer of greater than or equal to 50 aas is called a ____________.

Back 57

Peptide

Protein

Front 58

What is the bond length of a peptide bond?

Back 58

1 & 1/2

(There are 2 resonance structures)

Front 59

What are some characteristics of peptide bonds?

Back 59

Rigid, do not rotate
Plane established

Front 60

Is the alpha carbon- gamma carbon bond allowed to rotate?

Back 60

Yes (only the C=N cannot rotate)

Front 61

Which conformation has a lower free energy state, trans or cis? Which is more stable?

Back 61

Trans; Trans

Front 62

In what situation would you be most likely to find cis conformation?

Back 62

Enzymes (used to provide energy for catalysis)

Front 63

Alpha carbons of two neighboring residues are usually found in the (trans/cis) conformation.

Back 63

Trans

Front 64

Preproinsulin is how many aas in length?

Back 64

110

Front 65

What are the two major factors in protein folding?

Back 65

Hydrophobicity and charge

Front 66

What does pI stand for? This is called the ____________ form.

Back 66

Isoelectric pH (the pH where all the + plus - charges equal to zero).

Zwitterion form

Front 67

If pH is less than pI, the molecule is (+/-) charged.

If pH is greater than pI, the molecule is (+/-) charged.

Back 67

Positive

Negative

Front 68

Which level of structure?
Local folding of the backbone

Back 68

secondary

Front 69

What type of bonds hold together the secondary structure?

Back 69

Hydrogen

Front 70

How are beta sheets arrangeD?

Back 70

Antiparallel pleated sheets(read N--> C)

Front 71

Where are the side groups arranged in a helix? What level of structure is the helix? What level would tell you where the side groups are located?

Back 71

Most side groups in a helix are located on the outside of the helix (when they are arrranged on the inside of the helix, it is usually a specialixed protein and the position is related to the function)

Helix- Secondary

Side groups- Tertiary

Front 72

How much is an Angstrom?

Back 72

1/10 nm

Front 73

How many residues/turn are present in an alpha-helix? What is the pitch? This forces every ___th and ___th side chain to be in contact with the 1st side chain

Back 73

n= 3.6

p= 5.4 angstroms

3rd and 4th

Front 74

Which level of structure? The arrangement of polypeptide chains in a multichain protein.

Back 74

Quaternary

Front 75

What kinds of bonds are present in quaternary structure?

Back 75

Noncovalent (exception being the covalent bonds of disulfide bonds)

Front 76

How are the 4 subunits of Hb held together?

Back 76

Noncovalently

Front 77

Compare and contrast HbA1 and HbS

Back 77

Normal adult hemoglobin (HbA1) is a heterotetramer (a2b2). HbS has a mutation in the beta chain (position 6 Glu is replaced by Valine). This replacement of a hydrophilic aa for a hydrophobic one causes HbS to have a lower affinity for carrying O2. Also it causes deoxy-HbS to polymerize with other deoxy-HbS forming fibrils which precipitate inside the red blood cell

Front 78

What % of African Americans are homozygous for HbS? Heterozygous?

Back 78

0.4%; 10%

Front 79

What type of a sequence does a protein have that needs to be secreted?

Back 79

N-terminal signal peptide sequence

Front 80

What halts cytosolic translation for peptides that are being secreted?

Back 80

SRP (signal recognition particle)

Front 81

Describe the secretory pathway.

Back 81

1) Cytosolic ribosome synthesizes a N-terminal signal peptide sequence

2) A SRP (signal recognition particle) binds halts translation

3) The ribosome moves to the ER, where the SRP binds to a docking protein.

4) The ribosome is transferred to a translocon. Translation resumes inside the ER.

5) Protein is modified, passed to the golgi apparatus and eventually secreted from the cell

Front 82

__- linked glycosolation is an example of cotranslational glycosylation

Back 82

N

Front 83

__- linked glycosolation is an example of posttranslational glycosylation

Back 83

O

Front 84

What sequence is necessary for N-linked glycosylation?

Back 84

Asn-X-Thr/Ser (where X is any aa except Pro or Asp)

Front 85

Explain the location of where everything happens in N-linked glycosylation

Back 85

The oligosaccharide is partially assembled on the ER cytosolic side, then flipped to the lumenal side to be linked to the amide on the Asn (after the signal peptide is already cleaved from the protein chain)

Front 86

Which type of glycosylation can affect protein folding?

Back 86

N-linked (the O-linked occurs after the protein is already folded)

Front 87

where (organell) does O-linked glycosylation occur?

Back 87

Golgi apparatus

Front 88

What sequence is required for O-linked glycosylation?

Back 88

No specific sequence is required, however an non-aromatic oxygen is required, therefore the substrate must by Ser or Thr or hydroxylated Lys

Front 89

What determines the type of sugars that are attached during glycosylation? Are the oligosaccharides heterogeneous or homogeneous?

Back 89

The types of glycosyltransferases present determine which sugars will be attached.

Heterogeneous because the glycosyltransferases compete to add the sugars.

Front 90

What type of modifications determine where a protein goes and what is does?

Back 90

Post-translational

Front 91

Explain what happens when a protein is supposed to go to a lysosome

Back 91

Glycosyltransferases add N-acetylglucosamine phosphate (GlcNAc-P) to high mannose-type oligosaccharides on proteins destined to go to lysosomes

A glycosidase removes the GlcNAc, forming a mannose 6-phosphate which signals for that protein to be transported to the lysosomes

Front 92

Give an example of cotranslational proteolysis

Back 92

When signal peptidase cleaves the N-terminal signal peptide sequence during entry to the ER (prior to N-linked glycosylation)

Front 93

What enzyme cleaves the connecting peptide (C-peptide) of proinsulin? What are the sites in which it is cleaved?

Back 93

carboxypeptidase E
Between T30-R31 and R65-G66

Front 94

Describe the structure of insulin. Can insulin be easily reformed if these disulfide bonds are broken?

Back 94

Two aa chains (A and B) held together by disulfide bonds.

NO!

Front 95

Why does one develop an insulin resistance over time (to exogenous insulin)?

Back 95

Since bovine and porcine insulin are not excatly the same as human insulin, the body can trigger an immune response. Anti-insulin antibodies can produce an insulin resistance over time

Front 96

Which type of insulin is closest in sequence to human insulin (and therfore produces the least side effects)?

Back 96

Porcine

Front 97

What is the primary insulin used for humans?

Back 97

Recombinant

Front 98

Collagen is an example of ____________ hydroxylation and ___________ glycosylation.

Back 98

cotranslational hydroylation and posttranslational glycosylation

Front 99

Procollagen is contains cotranslational ____________ to form ____________ and ________.

Back 99

hydroxylation

3-hydroxyproline and 4-hydroxyproline

Front 100

Where does O-linked glycosylation occur in procollagen

Back 100

On the 5-hydroxylysine (formed by cotranslational hydroxylation)

Front 101

Procollagens are ______________

Back 101

Glycoproteins

Front 102

What is the repeating sequence of procollagens?

Back 102

Gly-X-Y (where every 1/3 X positions are Pro and 1/3 Y positions are Hyp)

Front 103

What does Hyp stand for?

Back 103

3- or 4-Hydroxyproline

Front 104

The Pro or Hyp every 3 aas in procollagen forms a __________ type __ helix. What part of the chain points toward neighboring chains? What type of strong bonds does this allow for?

Back 104

Polyproline type II helix ;

carbonyl points toward neighboring chains

allows for strong interchain H-bonds

Front 105

Which type of aa in procollagen allows for an apolar edge?

Back 105

Glycine (at every 3rd residue)

Front 106

Three chains of procollagen wind around each other to form a ___________.

Back 106

Superhelix

Front 107

Where and when is procollagen cleaved to form collagen?

Back 107

At both N- and C-terminal ends once inside vesicle

Front 108

Collagen super helices assemble into fibrils by end-to-end and side-to-side aggregation. Which extracellular enzyme is responsible for cross-linking the lysine side chains to provide the collagen with its strength?

Back 108

Lysyl oxidase

Front 109

what is the final step in collagen formation?

Back 109

Cross-linking

Front 110

Cross-linking of collagen involves formation of an ___________ derivative of lysine. What is this derivative called?

Back 110

Aldehyde;

Allysine

Front 111

Two allysines can react to form an ________________.

Back 111

Aldol cross-link

Front 112

Allysine can react with lysine to form a _______________.

Back 112

lysinonorleucine cross-link

Front 113

How many lysines (or derivatives) are needed to cross-link collagen?

Back 113

two

Front 114

Elastin uses ______ lysines to form a ____________ cross-link. This forms a rings, allowing it to stretch

Back 114

4 (3 allysines and one lysine);
desmosine.

Front 115

What is the half life of human lens crystallines?

Back 115

NEVER replaced

Front 116

What is the half-life of Hb?

Back 116

60 days

Front 117

What is the half-life of Factor VIII?

Back 117

20 hours

Front 118

What are the 3 factors which determine protein half-life?

Back 118

1. N-terminal AA
2. Proteins rich in PEST aas are rapidly degraded
3. Tagging by Ubiquitin-protein ligase (E3) for digestion.

Front 119

What is the half-life of Methionine?

Back 119

>20 hours

Front 120

What is the half-life of alanine?

Back 120

>20 hrs

Front 121

What is the half-life of Serine?

Back 121

>20 hrs

Front 122

What is the half-life of threonine?

Back 122

>20 hrs

Front 123

What is the half-life of valine?

Back 123

>20 hrs

Front 124

What is the half-life of glycine?

Back 124

>20 hrs

Front 125

What is the half-life of arginine?

Back 125

2 min

Front 126

What is the half-life of lysine?

Back 126

2 min

Front 127

what is the term for adding multiple ubiquitins to a protein?

Back 127

Polyubiquitination

Front 128

what degrades a protein which is marked by polyubiquitination?

Back 128

Proteosome

Front 129

E3 transfers activated UB to the condemned protein forming an ____________ bond to a _______.

Back 129

isopeptide; Lysine

Front 130

What happens to UBs and AAs after protein degradation by the protesome?

Back 130

They are released and recycled

Front 131

Apoptosis activates which enzyme which digests the cell?

Back 131

Cysteine aspartyl proteases (caspases)

Front 132

What are calpains and what do they do?

Back 132

calcium dependent thiol proteases;

perform limited proteolysis