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Biochemistry 1 > Unit 2 > Flashcards

Unit 2 Flashcards

1
Q

The 3-D conformation is able to fulfill a specific ________

A

Biologic function

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2
Q

The 3-D structure is also known as the _______ ______ that has a large number of favorable interactions within the protein

A

Native fold

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3
Q

There is a cost in _________ ________ of folding the protein into one specific native fold

A

Cost in conformational entropy

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4
Q

What are the favorable interactions in proteins?

A

Hydropphobic effect

Hydrogen bonds

London dispersion (Van der Waals)

Electrostatic interactions

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5
Q

The resonance causes the peptide bonds

  • to be _______ reactive compared to esters
  • to be quite ______ and nearly ______
  • to exhibit a large ________ _____ in the favored trans configuration
A

Less reactive
Rigid and nearly planar
Dipole moment

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6
Q

What type of linkages are seen in primary structures?

A

Covalent

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7
Q

Secondary structures contain what linkages and structures?

A

H-bonds

Alpha helices, beta sheets and beta turns

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8
Q

In the tertiary structure, what linkages are involved? And what are the linkages between?

A

Covalent
H-bond
Van der Waals
And hydrophobic

Linkages between the R groups

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9
Q

What is a peptide bond?

A

A bond formed by the carbonyl group and the amide group of another molecule

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10
Q

Quaternary structures contain all types of linkages except _______

A

Covalent

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11
Q

Where are the molecules bonded in quaternary structure?

A

Between subunits (mostly using R groups)

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12
Q

Virtually all peptide bonds in proteins occur in ______ configuration

A

Trans

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13
Q

What constitutes the polypeptide backbone?

A

The bond between the N and carbonyl carbon

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14
Q

The alpha helix is stabilized by H bonds between ________

A

Nearby residues

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15
Q

The beta sheet is stabilized by H-bonds between ________

A

Adjacent segments that may not be nearby

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16
Q

Irregular arrangement of the polypeptide chain is called the ________ _____

A

Random coil

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17
Q

Where does trypsin cleave at?

A

Lysine and arginine

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18
Q

Cyanogen bromide cleaves at ______

A

Methionine

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19
Q

Is the alpha helix right handed or left handed?

A

Right handed with 3.6 residues per turn

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20
Q

Peptide bonds are aligned roughly ______ with the helical axis

Side chains point out and are roughly_____ with the helical axis

A

Parallel

Perpendicular

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21
Q

What are strong helix formers? And what are some examples?

A

Small hydrophobic residues such as Alanine and Leucine are strong helix formers

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22
Q

What acts as a helix breaker and why?

A

Proline acts as a helix breaker because the rotation around the N-Ca bond is impossible

Glycine acts as a helix breaker because the R-group supports of conformations

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23
Q

What affects the formation of a helix?

A

Attractive or repulsive interactions etween side chains 3-4 amino acids apart

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24
Q

What is the functional insulin part?

A

C-peptide

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25
Q

In ______ ____, release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy

A

Hydrophobic effect

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26
Q

What are the favorable interactions in proteins?

A

Hydrophobic effect
H bonds
London dispersion
Electrostatic interactions

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27
Q

What are the hallmark features of primary structure of proteins?

A 
Covalent bonds (peptide bonds)
Made up of amino acid chains
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28
Q

What are the characteristics of secondary structures of proteins

A

H-bonds between peptide bonds

Types: alpha helix, beta sheets, beta turn

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29
Q

What is characteristic of tertiary proteins in terms of linkages

A

Covalent, H-bond, ionic, van der Waals and hydrophobic

Stability and linkages are formed based on the R groups

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30
Q

What are the types of tertiary structure?

A

Super-secondary structures such as motifs and domains

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31
Q

What is characteristic of quaternary structure?

A

All types of linkages except covalent

And interactions that form a quaternary structure is between subunits

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32
Q

What are types of quaternary structure?

A

Dimers and tetramers etc.

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33
Q

Structure of the protein is partially dictated by the properties of the ______ ______

A

Peptide bond

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34
Q

The ____ ______ is a resonance hybrid of two canonical structures

A

Peptide bond

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35
Q

The resonance causes the peptide bonds to be what 3 things?

A

Less reactive compared to esters
Rigid and nearly planar
Exhibit a large dipole moment in the favored trans configuration

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36
Q

What bond constitutes the polypeptide backbone?

A

N and alpha carbon carbonyl

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37
Q

What are the 5 functions of globular proteins?

A 
Storage of ions and molecules
Transport of ions and molecules 
Defense against pathogens
Muscle contraction
Biological catalysis
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38
Q

What globular proteins function in storage of ions and molecules?

A

Myoglobin and ferritin

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39
Q

What globular proteins function to transport ions and molecules?

A

Hemoglobin and serotonin transporter

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40
Q

What globular proteins funciton in defense against pathogens

A

Abs and cytokines

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41
Q

What are examples of globular proteins that function in muscle contraction?

A

Actin and myosin

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42
Q

What are some examples of globular proteins that function in biological catalysis?

A

Chymotrypsin and lysozyme

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43
Q

A molecule that binds to a protein is called a _______

A

Ligand

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44
Q

A region in the protein where the ligand binds is called the _______ _____

A

Binding site

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45
Q

Ligand binds via same ________ forces that dictate protein structure

A

Noncovalent

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46
Q

What allows the interactions of globular proteins with other molecules to be transient?

A

Ligands binds via noncovalent forces

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47
Q

What is the kinetics process?

A

The association rate constant Ka or the dissociation constant Kd

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48
Q

How do you know the Ligand and protein binding have reached equillibrium?

A

When the association and dissociation rates are equal

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49
Q

The ______ _______ is characterized by the equillibrium constant Ka

A

Equillibrium constant

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50
Q

What does Kd equal?

A

The concentration of ligand at which half of the available ligand-binding sites are occupied

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51
Q

If Kd is low, the binding affinity is _______

A

Tight

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52
Q

The lower the binding constant, the ________ the affinity

A

Higher

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53
Q

______ is the main oxygen storage protein

A

Myoglobin

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54
Q

______ is a circulating oxygen binding protein

A

Hemoglobin

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55
Q

The lower the affinity, the ______ the Kd value

A

Higher

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56
Q

Some transition metals bind O2 well but would generate _____ _______ if free in solution

A

Free radicals

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57
Q

Only _________ of Fe can be bound to myoglobin

A

Fe2+

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58
Q

_________ is free heme that is not bound to myoglobin

A

Fe3+

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59
Q

What are the components of heme?

A

Organic component: Protoporphyrin IX

Inorganic component: Iron (Fe2+)

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60
Q

How many coordination bonding sites are on the Heme-Fe?

A

4 bonded to the nitrogen atoms of the protoporphyrinIX and 2 perpendicular to the plane of the ring

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61
Q

The perpendicular sites on the heme are made up of what?

A

His residue on the proximal side

Oxygen binding site on the distal side

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62
Q

_________, ___, is the typical globular protein with most nonpolar a.a. Inside (except for the 2 Histidines which bind ______ and ______

A

Myoglobin, Mb,

Fe and O2

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63
Q

Where is myoglobin typically located?

A

Heart, muscle and liver

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64
Q

Binding to O2 is _______, it only depends on the [Mb] and on the pO2

A

Simple

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65
Q

Myoglobin has _____ helices terminate by _____ or Beta turns and loops

A

8

Proline

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66
Q

Fe3+ or the ferric state is also known as _________, and Oxygen cannot bind to it

A

Metmoglobin

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67
Q

The iron ion in the ferric state (or metmoglobin) _________ bind to oxygen

A

Doesn’t

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68
Q

______ blocks funciton of myoglobin, hemoglobin and mitochondrial cytochromes that are involved with oxidative phosphorylation

A

Carbon monoxide

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69
Q

Which has a higher affinity for hemeoglobin, oxygen or carbon monoxide?

A

Carbon monoxide

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70
Q

Why cant myoglobin transport O2?

A

Because it would not release the oxygen to the tissues because of its high affinity

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71
Q

______ is a tetrameric protein of 2 identical globin subunits

A

Hemoglobin

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72
Q

What makes up hemoglobin?

A

2 alpha globins and 2 beta globins and each globin molecules is structurally similar and folds like myoglobin

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73
Q

In hemoglobin, each globin molecule has a ______ group

A

Heme

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74
Q

Interactions in hemoglobin between the alpha and beta globins is _____ than interactions between the 2alphabbeta dimers

A

Stronger

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75
Q

What is the difference between myoglobin and hemoglobin’s oxygen saturation curve?

A

Myoglobin saturation curve is more hyperbolic meaning it has a higher affinity for myoglobin.
Hemoglobin saturation curve is more S shaped to where it has high affinity but not as strong as myoglobin

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76
Q

_______ binds too tightly to be useful in O2 transport

A

Mb

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77
Q

______ binds O2 cooperatively

A

Hb

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78
Q

Binding of O2 at heme-Hb site ________ the likelihood that O2 binds ar the remaining unoccupied sites and vice versa

A

Increases

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79
Q

What is the make up of hemoglobin?

A

2 alpha globulins and 2 beta globulins

Each has a heme group and behaves like a protein made of 2 identical dimers (alphaBeta)2

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80
Q

The interaction between the alpha and beta globins is mostly _________. The interaction between the alphabeta dimers is mostly ________

A

Hydrophobic

Ionic

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81
Q

Hb is mainly a transporter protein for ____ but it also binds and transports ______

A

O2

CO2

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82
Q

Adult Hb is identified as ______

Fetal Hb is identified as __________

A

HbA (alphabeta)2

HbF (alphagamma)2

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83
Q

Hb__ binds with greater affinity to O2 than Hb___ does

A

HbF; HbA

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84
Q

What are the two states of Hb?

A

Relaxed and tense state

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85
Q

O2 binding triggers a conformational change from the _____ state to the _____ state

A

T-state-> R state

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86
Q

Conformational change from the T state to the R state involves what?

A

Breaking ion pairs between the alpha1-Beta-2 interface

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87
Q

What triggers the conformational change from T to R state?

A

The binding of O2 to the histidine residue

Slide 28

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88
Q

Conformation change from the T state to the R state involves breaking what?

A

Breaking ion pairs between the alpha1 and beta 2 interface

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89
Q

The pH difference between the lungs and metabolic tissues _______ efficiency of the O2 transport

A

Increases

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90
Q

What is the Bohr effect?

A

The pH difference between lungs and metabolic tissues increases efficiency of the O2 transport

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91
Q

H+ binds to Hb and stabilizes the _____ state of Hb

A

T state

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92
Q

Explain how H+ binding to Hb stabilizes the T state

A

Protonates His146 which then forms a sal bridge with Asp94 -> leads to the release of O2 in the tissues

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93
Q

At a higher pH O2 has a _______ affinity for Hb

At a lower pH O2 has a ______ affinity for Hb

A

Higher

Lower

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94
Q

_______ forms additional salt bridges stabilizing the T state

A

Carbamate

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95
Q

CO2 is exported out of the peripheral tissues as what 3 forms?

A

Carbamate on the amino terminal residues of each polypeptide subunits

Bound to Heme as CO2

Exported as dissolved bicarbonate

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96
Q

CO2 conversion to bicarbonate produces _____ leading to a ______ in pH

A

Proton; decrease

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97
Q

What promotes the release of O2 from Hb in peripheral tissues?

A

Protons and CO2

98
Q

What form of Hb does lower pH and higher CO2 stabilize?

A

The T state of Hb facilitating the release of bound oxygen

99
Q

What is another name for the R form of Hb?

A

Oxyhemoglobin

100
Q

Oxyhemoglobin (R form) prevails in the ______

A

Lungs

101
Q 
The R form or oxyhemoglobin form prevails when (high or low):
PO2 \_\_\_\_\_\_
PCO2\_\_\_\_\_\_
[H+] \_\_\_\_\_
pH \_\_\_\_\_\_
[BPG] \_\_\_\_\_\_
A 
pO2 high
pCO2 low
[H+] low
pH high 
[BPG] low
102
Q

What is another name for the T form of Hb?

A

Deoxyhemoglobin

103
Q

Where does the Deoxyhemoglobin (T form) prevail at in the body?

A

The peripheral tissues

104
Q 
The deoxyhemoglobin (T-form) prevails when the following are high or low?
pO2 \_\_\_\_\_\_
pCO2 \_\_\_\_
[H+]\_\_\_\_\_
pH \_\_\_\_\_
[BPG] \_\_\_\_\_
A 
pO2 low
pCO2 high
[H+] high 
pH low 
[BPG] high
105
Q

What is an example fo a negative heterotropic regulator of Hb function

A

2,3 Bisphosphoglycerate (2,3 BPG)

106
Q

What Small negatively charged molecule binds to the positively charge central cavity of Hb and stabilizes the T state?

A

2,3 BPG

107
Q

Why is 2,3 BPG important in erythrocytes?

A

Without 2,3 BPG Hb would be extremely inefficient in transporting O2 releasing only 8% of its cargo in the tissues

108
Q

2,3 BPG is a(n) ________ ______ because biding to Hb affects its binding to O2

A

Allosteric regulator

109
Q

2,3 BPG binds mostly to ______ amino acids in the Bet globins in the center of the tetramer of Hb. This pocket is only present in the ____ form of Hb

A

Basic

T form

110
Q

On the T-to-R transition what happens to 2,3 BPG

A

The pocket where 2,3 BPG binds collapses and 2,3BPG is released

111
Q

In order for the structural transition from T to R to take place what must happen to the bonds between Hb and 2,3 BPG?

A

They must be broken

112
Q

What has a higher oxygen-binding affinity, HbF (fetal Hb) or HbA (adult Hb)?

A

HbF

113
Q

What amino acid exchange goes on leading to the sickle cell shape of RBCs in sickle cell anemia?

A

Valine replaces glutamic acid

114
Q

How does the exchange of glutamic acid for valine in th beta chain of Hb result in sickle cell?

A

Glutamic acid is a hydrophilic amino acid while valine is a hydrophobic branched chain amino acid. The different properties of these amino acids results in a change from the biconcave disc to a sickled cell shape

115
Q

Imbalance in production of Hb chains results in ________

A

Thalassemias

116
Q

What happens in alpha-thalassemia?

A

Alpha globins are not produced in sufficient amounts

Some Hb contains only the beta globins that bind to O2 highly with very poor release of O2

117
Q

What happens in beta thalassemia?

A

Beta globins are not produced in sufficient amounts

Alpha globins form aggregates that precipitate inside immature RBC producing anemia

118
Q

What small protein is found in RBC that binds to alpha chains and keeps them properly folded and in solution?

A

AHSP (alpha-hemoglobin stabilizing protein)

119
Q

Muscle contraction occurs through a series of conformational changes to protein structure due to what 3 things?

A

Binding
Hydrolysis
Release of ATP and ADP

120
Q

What are the four steps to the actomyosin cycle?

A

1) ATP binds to myosin -> myosin dissociates from actin
2) ATP is hydrolyzed -> conformational change of myosin
3) myosin reconnects tot he actin filament at a different location -> release of Pi
4) release of Pi-> power stroke where myosin returns to initial state; shifting actin filament relative to the myosin tail -> release of ADP

121
Q

What regulates the availability of Myosin-binding sites on actin?

A

Tropomyosin and troponin

122
Q

____ causes conformation changes to tropomyosin-troponin complex exposing myosin binding sites

A

Ca2+

123
Q

The ______ is stabilized by H bonds between nearby residues

A

Alpha helix

124
Q

The ______ stabilized by H bonds between adjacent segments that may not be nearby

A

Beta sheet

125
Q

Irregular arrangement of the polypeptide chain is called the ________

A

Random coil

126
Q

What amino acids are examples of strong helix formers?

A

Alanine and Leucine

127
Q

What amino acids act as Helix breakers?

A

Proline and Glycine

128
Q

What affects formation of helix and its stability?

A

Attractive or repulsive interactions between side chains 3-4 amino acids apart

129
Q

What 5 amino acids are common in beta sheets?

A 
Valine 
Isoleucine 
Tyrosine
Cysteine 
Tryptophan
130
Q

In _____ beta sheets the H-bonded strands run in the same direction

A

Parallel

131
Q

In ______ beta sheets the H bonded strands run in opposite directions

A

Antiparallel

132
Q

_______ beta sheets results in bent H bonds

A

Parallel

133
Q

________ beta sheets result in linear H bonds

A

Antiparallel

134
Q

________ beta sheets are stronger than ______ beta sheets

A

Antiparallel; parallel

135
Q

What 3 amino acids are common in beta turns?

A

Proline
Glycine
Asparagine

136
Q

What amino acid is common in type 1 beta turns?

A

Proline

137
Q

What amino acid is common in type 2 beta turn?

A

Glycine

138
Q

What does the tertiary structure refer to?

A

The overall spatial arrangement fo atoms in a protein

139
Q

What are the two major classes of tertiary structure?

A

Fibrous and globular ( water or lipid soluble)

140
Q

______ proteins always have combination of secondary structures and turns are always present

______ protein mostly one type of secondary structure

A

Globular

Fibrous

141
Q

_______ proteins are practically insoluble

_____ proteins are fully soluble or membrane bound

A

Fibrous

Globular

142
Q

The main function of ______ proteins are mostly dynamic roles

The main function of ____ proteins are mostly structural roles

A

Globular

Fibrous

143
Q

______ proteins are located mostly intracellularly while ______ proteins are located mostly extracellualrly

A

Globular

Fibrous

144
Q

What are examples of globular proteins?

A

Hemoglobin
Myoglobin
Enzymes

145
Q

What are examples of fibrous proteins?

A

Collagen
Keratin
Elastin

146
Q

_______ proteins are mostly primary and secondary structures while ______ proteins all have tertiary structures (simple) and many complex have quaternary structure

A

Fibrous; Globular

147
Q

_____ proteins provide support for cells and tissues

A

Fibrous

148
Q

______ is an important constituent of CT

A

Collagen

149
Q

What is each collagen chain made of?

A

Long glycine and proline rich left handed helix

150
Q

Three collagen chains intertwine into what?

A

A right handed superhelical triple helix

151
Q

Many ________ assemble into a collagen fibril

A

Triple helicies

152
Q

Type 1 collagen is present in what 5 tissues?

A 
Skin
Bone
Tendon
Blood vessels
Cornea
153
Q

Type 2 collagen is present in what 3 tissues?

A

Cartilage
Intervertebral disk
Vitreous body

154
Q

Type 3 collagen is present in what 3 tissues?

A

Blood vessels skin and muscle

155
Q

What types of collagen are fibril forming?

A

Type 1, 2 and 3

156
Q

What types of collagen are network forming?

A

Type 4 and type 8

157
Q

What types of collagen are fibril associated?

A

Type 9 and type 12

158
Q

In the synthesis and processing of collagen what occurs inside the cells?

A
  • Synthesis of pro-alpha-chains on ribosome ER to facilitate secretion
  • Hydroxylation of selected Pro and Lys residues catalyzed by Pro and Lys hydroxylases
  • Glycosylation of selected OH-Lys residues via an enzyme catalyzed process
  • Spontaneous process of triple helix formation of Pro-collagen molecule
  • Secretion of procollagen molecule
159
Q

In synthesis and processing of collagen, what processes occur outside cells?

A
  • Cleavage of extension peptides (may take place before secretion)
  • Assembly into micro fibril
  • Crosslink formation
  • Assembly into mature collagen fibril
  • Aggregation of collage fibrils to form a collagen fiber
160
Q

Cleavage of extension peptides occurs ________ cells and is catalyzed by what?

A

Outside cells

Catalyzed by procollagen peptidases

161
Q

What are the spontaneous processes that occur outside the cell in the synthesis and processing of collagen?

A

Assembly into micro fibril
Assembly into mature collagen fibril
Aggregation of collagen fibrils to form a collagen fiber

162
Q

What causes cross-link formation in synthesis and processing of collagen?

A

Lysyl oxidase

163
Q

What collagen genetic disease is associated with type 1 collagen?

A

Osteogenesis imperfecta

-weak bones that fracture easily

164
Q

What collagen genetic disease is associated with type 2?

A

Chondriodysplasias

-abnormal cartilage, bone and joint deformities

165
Q

What collagen genetic diseases are associated with type III and type V

A

Ehlers- Danlos syndrome

Fragile skin and blood vessels (type III aorta rupture) and hyper- mobile joints (type V)

166
Q

What are motifs (folds)?

A

Specific arrangement of several secondary structure elements

167
Q

___________ structure is formed by the assembly of individual polypeptides into a larger functional cluster

A

Quaternary

168
Q

What are intrinsically disorder proteins composed of (amino acids)?

A

Composed of amino acids whose higher concentration forces less defined structure

Lys, Arg, Glu, and Pro

169
Q

_________ _______ proteins facilitate interaction with numerous different partner proteins

A

Intrinsically disordered proteins

170
Q

A proteins function depends on what?

A

It’s 3D structure

171
Q

Loss of structural integrity with accompanying loss of activity is called __________

A

Denaturation

172
Q

What denatures proteins?

A 
Heat or cold
pH extremes 
Detergents
Reducing agents: DTT and Mercaptoethanol
Chaotropic agents: urea
173
Q

What reduces disulfide bonds?

A

Beta-Mercaptoethanol

174
Q

Adding a chaotropic agent will _____ the protein but when the chaotropic agent is removed it causes the ______ of the protein and that protein is now catalytically active

A

Denature

Renature

175
Q

What are 4 examples of protein misfolding and neurodiseases?

A

Alzheimer’s disease
Parkinson’s disease
Huntington’s disease
Prion disease

176
Q

Alzheimer’s, Parkinson’s, Huntington and creutzfeldt- Jakob diseases result in deposition of protein aggregates called ______

A

Amyloid fibrils or plaques

177
Q

Alzheimer’s, Parkinson’s, Huntington’s and creutzfeldt Jakob’s disease are called ______

A

Amyloidoses

178
Q

What is a common feature of amyloidoses?

A

Normally soluble proteins are converted into insoluble fibrils rich in beta sheets

179
Q

What is the major proteopathy in Parkinson’s disease?

A

Alpha-synuclein

180
Q

Alpha-synuclein can form insoluble aggregates or ______________ that are a major part of Parkinson’s disease

A

Lewy bodies

181
Q

Where is the site of synthesis of pepsinogen?

A

Stomach

182
Q

What is the site of synthesis for chymotrypsinogen, trypsinogen, procarboxypeptidase and proeleastase?

A

Pancreas

183
Q

What activates trypsinogen into trypsin?

A

Enteropeptidase

184
Q

What activates chymotrypsinogen, proelastase and procarboxypeptidase?

A

Trypsin

185
Q

What activates pepsinogen, what is its source, and what is its target?

A

[H+]/ pepsin activates
Source is the stomach
Target is Phe

186
Q

What activates trypsinogen, what is its source and what is its target?

A

Enteropeptidase and trypsin activates it
Source is pancreas
Target is lys and arginine residues

187
Q

What activates chymotrypsin, what is its source and what’s its target?

A

Trypsin and chymotrypsin activates it
Source is the pancreas
Targets aromatic and bulky amino acids

188
Q

Different carriers transport the families of amino acids based on what?

A

The nature of the R groups

189
Q

In protein digestion and absorption, free amino acids use secondary active transport using what type of gradient?

A

Sodium concentraiton gradient

190
Q

What are enzymes?

A

Catalysts that increase reaction rates without being used up

191
Q

What are examples of oxidoreductases?

A

Dehydrogenases
Reductases
Oxidase

192
Q

What are examples of transferase?

A

Kinase and transaminases

193
Q

What are examples of hydrolases?

A

Lipase and proteases

194
Q

What are examples of lyases?

A

Anhydrases
Dehydratases
Hydratases

195
Q

What are examples of isomerases?

A

Isomerase
Mutase
Epimerases

196
Q

What are examples of ligases?

A

Carboxylases and synthetase

197
Q

_______ are required by inactive app-enzymes to convert them into active holo-enzymes

A

Cofactors

198
Q

What activated carriers carry electrons?

A

NADH, NADPH
FADH2
FMNH2

199
Q

What activated carrier carries phosphoryl group?

A

ATP

200
Q

What activated carrier carries an aldehyde?

A

Thiamine pyrophosphate

201
Q

What activated carrier carries CO2?

A

Biotin

202
Q

What activated carrier carries one carbon units?

A

THF (tetrahydrofolate)

203
Q

What activated carrier carries glucose?

A

UDP- glucose (uridine diphophate glucose)

204
Q

Enzymes alter only the ________ and not the _________

A

Reaction rate

Not the equilibrium

205
Q

Enzyme ________ ______. Are complimentary to the transition state of the reaction

A

Active sites

206
Q

Enzymes bind to __________ better than substrates

A

Transition states

207
Q

The ________ of enzymes is a 3D cleft or crevice that takes up a small part of the total volume of an enzyme

A

Active site

208
Q

How do substrates bind to the enzyme?

A

By multiple weak interactions depending on the precisely defined arrangement of atoms in an active site

209
Q

Define Vmax

A

Maximal velocity when the enzyme is saturated with substrate

210
Q

Nonlinear michaelis-menten plot should be used to calculate what?

A

Km and Vmax

211
Q

Linearized double-reciprocal plot is good for what?

A

Analysis of two-substrate data or inhibition

212
Q

What processes take place in the mitochondria?

A

TCA cycle
FA oxidation
Oxidation of pyruvate

213
Q

What cellular processes occur in the cytosol?

A

Glycolysis
Pentose phosphate pathway
FA synthesis

214
Q

What cellular processes occur in the nucleus?

A

DNA and RNA synthesis

215
Q

What cellular processes occur in the lysosome?

A

Degradation of complex macromolecules

216
Q

What are the factors that affect reaction velocity?

A

Substrate concentration
Temperature
pH

217
Q

Large Km = ______ affinity of enzyme for substrate

Small Km = ______ affinity of enzyme for substrate

A

High Km= low affinity

Low Km= high affinity

218
Q

At low concentration of substrate, the velocity of the reaction is what?

A

Proportional to the substrate concentration

First order

219
Q

What high concentration of substrate, the velocity of the reaction is what?

A

constant and independent of substrate concentration

Zero order

220
Q

T/F: allosteric enzymes do obey Michaelis-Menten kinetics

A

False; they do not obey Michaelis-Menten kinetics

221
Q

Kinetics of allosteric enzymes display _______

A

Cooperativity

222
Q

What is cooperativity?

A

Binding of substrate to one active site faciliatates the binding of the substrate to the other active sites

223
Q

In competitive inhibition, what does the inhibitor bind to and how does it effect the Km and Vmax

A

Inhibitor binds to Enzyme only
Raises Km
Vmax unchanged

224
Q

In uncompetitive inhibition, what does the inhibitor bind to and what is its effect on Km and Vmax?

A

Inhibitor binds to enzyme substrate ONLY
Lowers both Km and Vmax

Ratio Km/Vmax remains unchanged

225
Q

In noncompetitive inhibition, what does the inhibitor bind to? And what its its effect on Km and Vmax?

A

Inhibitor binds to enzyme OR enzyme substrate complex
Lowers Vmax
Km remains unchanged

226
Q

Describe feedback inhibition

A

The products of one pathway will inhibit further production of that product

227
Q

What are examples of regulation of enzyme activity?

A

Feedback inhibition

Covalent modification

228
Q

What are examples of covalent modification?

A

The addition and removal of phosphate groups

229
Q

Zymogen activation and the blood coagulation cascade use what?

A

Irreversible covalent modification

230
Q

What are the two most common types of cofactors?

A

Inorganic ions (metal) and coenzymes

231
Q

Apoenzyme = ______
Holoenzyme= _______
Apoenzyme + cofactor -> _________

A

Inactive
Active
Holoenzyme

232
Q

What is the cofactor for pyruvate dehydrogenase?

A

Thiamine pyrophosphate

233
Q

What is the cofactor for pyruvate carboxylase?

A

Biotin

234
Q

What is the cofactor for Lactate dehydrogenase?

A

Nicotinamide adenine nucleotide

235
Q

What is the cofactor for methylamlonyl mutase?

A

5’ deoxyadenosyl cobalamin

236
Q

What is the cofactor for thymidylate synthase?

A

Tetrahydrofolate (THF)

237
Q

What is the cofactor for carbonic anhydrase?

A

Zn2+

238
Q

What is the cofactor for hexokinase?

A

Mg2+

239
Q

What is the cofactor for glutathione peroxidase?

A

Se

240
Q

What is the cofactor for superoxide dismutase?

A

Mn

Biochemistry 1 (4 decks)

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