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S2 E1 KCU COB > Biochem > Flashcards

Biochem Flashcards

1
Q

Which are the tiny AA?

A

C.A.G.S

Cysteine, Alanine, Glycine, and Serine

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2
Q

What are the small AA?

A

D P N T

Aspartate, Proline, Asparagine, Threonine

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3
Q

What are the medium AA?

A

E, V, H, Q

Glutamic Acid, Valine, Histidine, Glutamine

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4
Q

What are the large AA?

A

K R I L M

Lysine, Arginine, Isoleucine, Leucine, Methionine

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5
Q

What are the extra-large AA?

A

F Y W

Phenylalanine, Tyrosine, Trytophan

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6
Q

What are the essential AA?

A

PVT TIM HALL

Phenylalanine

Valine

Tryptophan

Threonine

Isoleucine

Methionine

Histidine

Arginine

Lysine

Leucine

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7
Q

What are the three stop codons?

A

UAA

UGA

UAG

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8
Q

What does statin intolerance cause to a patient that is treated with statins?

A

Statin inhibits the Selenocystein-tRNA from producing selenoproteins

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9
Q

What does selenium deficiencies lead to?

A

Oxidative distress is inhibited

(Oxidative stress continues)

Muscle death and myopathies

Immune incompetence

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10
Q

What is pyrrolysine and where can it be found?

A

Two lysines put together (An amino acid)

Found within methanogen bacteria found in the human’s GI system

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11
Q

What are the 4 interactions that govern protein folding and stability?

A

Van der Waals Interactions

Hydrogen bonds

Electrostatic (Salt bridges/Charges)

Hydrophobic interactions

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12
Q

What are the 4 determinants of protein folding?

A

Secondary Structure

Hierarchical folding

Hydrophobic effect

Context-dependent

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13
Q

What are the bonds found in alpha-helices?

A

Intrachain Hydrogen bonds leaving 4AA residues

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14
Q

What are the bonds that are found in Beta-sheets?

A

Hydrogen bonds between peptide chains

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15
Q

What causes compact and globular shapes for polypeptide chains?

A

Reversal directions

(Reverse turn, beta turn, hairpin loop, omega loops)

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16
Q

Where can loops and turns of secondary structures be found?

A

They can be found on the surface of a protein

(Hydrophilic)

They are used in interactions with other molecules or proteins

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17
Q

What uses the superhelix structure?

A

Keratin, collagen, cytoskeleton, and muscle

(Structural proteins: Things that need to be strong)

AND

Regulators of gene expression

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18
Q

What kind of protein uses intra-sulfur bonds?

A

Extracellular proteins

i.e. Insulin

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19
Q

What are the events of the folding funnel?

A
  1. Rapid formation of secondary structure
  2. Formation of domains through cooperative aggregation
    Concept of molten globule
    Possible structure, but unstable
  3. Adjustment of conformation
  4. Fine tuning of folding for native structure
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20
Q

What has a higher state of energy?

A higher state of entropy?

A

Denatured/unfolded proteins

They have a desire to be at a more stable state through protein folding into the native state

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21
Q

What does repeating motifs have in common? What is different?

A

Their final protein domains bind the same thing

i.e. calmodulin binds calciums

Their amino acid sequences are different

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22
Q

What kind of protein has the following characteristics

  1. Native-like
  2. Absence of specific tertiary structure
  3. Compact, but larger than native
  4. The loosely packed hydrophobic core
  5. Not specific
A

Molten globule proteins

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23
Q

How are molten globule proteins stabilized?

A

nonspecific hydrophobic interactions

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24
Q

Function of PDI

A

Protein Disulfide Isomerase

Fix misfolded proteins’ disulfide bonds

(Assists in refolding proteins so that correct disulfide bonds are created)

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25
Q

What is the purpose of accessory proteins

A

To fine-tune protein folding

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26
Q

Function of PPI

A

Peptidyl Prolyl Cis-Trans Isomerases

Changes the functional groups of a protein from trans to cis

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27
Q

T/F folding and unfolding is not an all or none process. It can be both

A

False.

All or none

It is either folded, or it is not

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28
Q

What are the methods of analysis of protein folding?

A

Turbidity: Proteins will create a clear semi-clear solution

Circular dichroism: Left and Right proteins bend light differently

Fluorescence: Aromatic structures absorb and emit light

Biological activity

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29
Q

What is the function of the 19s subunit of the proteosome?

A

Recognizes the ubiquitinated protein and allows entry into the degradation site (20s core)

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30
Q

What is the function of the 20s core in the proteosome?

A

A sealed barrel that contains proteolytic enzymes and a low pH for the degradation of proteins

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31
Q
A
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32
Q

What is the function of HSP 70

A

Coordinates cellular function by directing substrates for unfolding, disaggregation, and refolding or degradation

Works together with HSP 40

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33
Q

What is the function of HSP 40

A

HSP 40 is used to refold proteins

Does it on its own with soluble

Needs assistance from HSP 70 for insoluble

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34
Q

HSP 90

A

Helps fold signal transduction proteins

Inserts signaling functions at late folding stages

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35
Q

What are the functions of HSP 60 and HSP 10

A

They are chaperonins that have the barrel like structures

They create a hydrophobic microenviroment for folding of proteins

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36
Q

What are the three components of the cellular quality control system

A

Proteasomes: Protein degradation

Autophagy: Cellular digestion

ERAD: ER-Associated degradation (Sends useless proteins directly to proteasome)

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37
Q

What can improper degradation lead to?

A

Cystic Fibrosis

Good and bad proteins constantly being removed can lead to a build-up of half-assed proteins that were made too quickly to keep up

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38
Q

What can improper localization lead to?

A

Dual Toxicity

Improper folds cannot be sent to their respective site. Therefore there is a build-up of toxic proteins at one site and a loss of function at the other

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39
Q

Nucleophilic substitution

A

Swap functional groups

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40
Q

Nucleophilic Addition

A

Add functional group

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41
Q

Carbonyl condensation

A

Change the number of carbons

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42
Q

Elimination

A

Change the bond order

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43
Q

Oxidation/Reduction

A

Move electrons

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44
Q

Oxidoreductases

A

Oxidation-Reduction rxn

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45
Q

Transferases

A

Group Transfer

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46
Q

Hydrolases

A

Breaking of a bond using water

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47
Q

Lysases

A

Breaking of a bond without using water

May lead to double bonds

48
Q

Isomerases

A

Intramolecular group transfers

49
Q

Ligases

A

Ligation of two substrates at the expense of ATP hydrolysis

Putting things together

50
Q

NAD+

A

Coenzyme Made of vitamin B and Adenine

Used by dehydrogenases in catabolic reactions to OXIDIZE into NADH

(Oxidation is the loss of a proton/Hydrogen)

51
Q

NADPH

A

Coenzyme Made of Vitamin B3 and Adenine

Used by reductases in anabolic reactions to make NADP+

(Reduction is the addition of a proton/Hydrogen)

52
Q

FADH2

A

Coenzyme Made of vitamin B6 and adenine

Found in oxidation reactions using FAD

53
Q

FMNH2

A

Coenzyme Made of vitamin B6 and adenine

Used in reduction reactions with FMN

54
Q

ATP

A

Coenzyme to transfer a phosphate group

Usually, gamma is moved

55
Q

Pyridoxal phosphate

A

Coenzyme that transfers phosphates

Made of Vitamin B6

56
Q

SAM

A

Conenzyme: S-Adenosylmethionine

A primary transferase that transfers a methyl group

57
Q

Tetrahydrofolate

A

A coenzyme in a transferase process of a methyl group

Made of Vitamin B9

58
Q

5’deoxyadenoxylcobalamin

A

A coenzyme in methyl transferases

Contains Vitamin B12 and cobalt

59
Q

TPP

A

Coenzyme in ligase reactions

Thiamine pryophosphate

Made of Vitamin B1 and 2 phosphates

Adds Aldehyde gropus

60
Q

CoASH and Lipoamide

A

Coenzymes that add Acyl groups (-COR)

Both have sulfurs

61
Q

Biotin

A

Coenzyme that adds Adds CO2

Vitamin B7

62
Q

Incomplete Enzymes that are inactive and require a cofactor or coenzyme

A

Apoenzyme

63
Q

A whole enzyme that is active. Contains the cofactor/coenzyme

A

Holoenzyme

64
Q

In terms of cooperativity on the hill plot:

A slop of 1 is interpreted as

A

No cooperativity

65
Q

In terms of cooperativity on the hill plot:

A slope greater than 1 has

A

Positive cooperativity

66
Q

In terms of cooperativity on the hill plot:

A slope that is less than 1 has

A

Negative cooperativity

67
Q

What are the subunits of embryonic Hb

A

Fetal hemoglobin is made of 2 zeta and 2 gamma

68
Q

What are the subunits for HbF

A

Fetal Hb = 2 alpha and 2 gamma

69
Q

What are the subunits of HbA

A

2 alpha 2 beta

70
Q

What are the subunits for HbA2

A

2 alpha 2 delta

71
Q

What hemoglobins are found in an adult?

A

HbA, HbA2, and HbF

72
Q

When does HbA reach dominancy as the main type of Hb

A

After 1 year after birth/ Gestational age

73
Q

What subunits are Alpha chains of Hb

A

Found on chromosome 16, alpha and zeta

74
Q

What subunits are beta chains in Hb

A

Found on chromosome 11, epsilon, gamma, delta, and beta

75
Q

What causes the formation of HbS

A

In Sickle Cell hemoglobin, valine is substituted in place of glutamic acid in the 6th position of beta globulins

This causes polymerization of the Hb

76
Q

What is the proximal histidine and what is it bound to?

A

F8 histidine and is bound to the heme group

(6th segment; 8th AA)

77
Q

What is the distal histidine

A

E7

(5th segment; 7th AA)

78
Q

Where does oxygen bind to in Hb

A

On the distal histidine and the heme group

79
Q

What happens to the iron atom when oxygen binds

A

It moves from out of the plane to into the plane

This will pull the proximal histidine

80
Q

T/F binding of oxygen is a cooperative process in myoglobin

A

False it is cooperative in hemoglobin

81
Q

T/F When oxygen dissociates from hemoglobin, it makes it easier for other oxygens to dissociate

A

True: Reversibility of cooperativity

82
Q

2,3 BPG induces what form of Hb?

A

The tense form which lowers the affinity

83
Q

Absence of 2,3-BPG will do what to Hb?

A

It will increase affinity and keep Hb in the relaxed form

84
Q

What correlation does pH have with Hb affinity?

A

As pH decreases so does the affinity

(more acidic)

85
Q

What is HbA1c

A

Post-modification of the N-terminus in ß globulins

Low at normal glucose levels

High in diabetic patients that abuse glucose

86
Q

What is Thalassemias

A

Reduced synthesis of a globulin that reduces the functionality of Hb

87
Q

HbH

A

Excess beta globulins that will become tetramers

88
Q

Alpha plus Thalasemia

A

Silent carrier: Deletion of 1/4 alpha genes

89
Q

Alpha - Thalassemia

A

2/4 alpha genes are deleted

90
Q

Microcytosis

A

Low mean cell volume

Found in alpha thalassemia

91
Q

Hypochromia

A

Low mean cell hemoglobin

Found in alpha thalassemia

92
Q

HbH Disease

A

3 alpha genes are affected

Severe Anemia, hypochromic hemolytic anemia, hepatosplenomegaly, mild jaundice

93
Q

Hydrops Fetalis

A

All (4/4) alpha genes are silenced

Only gamma 4 Hb (Bart’s Hb)

Creates fetal onset of edema and anemia

Kills newborns

94
Q

ß Thalassemia

A

Not enough ß chains are being made compared to alpha chains

This leads to alpha chains precipitating out and cause oxidative stress and hemolysis and destruction of immature erythroblasts in bone marrow

They do NOT form a tetramer

95
Q

Covalent Catalysis

A

Binds covalently to transition state and stabilizes transition state

96
Q

Acid-Base Catalysis

A

Partial proton transfer

(Hydrogens: Think of what amino acids can participate)

97
Q

Approximation

A

Spatial orientation and close contact so that electrons and protons can be exchanged

98
Q

Electrostatic Catalysis

A

Stabilization of unfavorable charges on the transition state

99
Q

Chymotrypsin

A

A serine protease (Hydrolase)

100
Q

What is the active site of chymotrypsin?

A

The catalytic triad

(Serine: Nucleophile

Histidine: Base

Aspartic Acid: Acid)

AND

Oxyanion Hole

(Serine and glycine)

101
Q

Specificity of Chymotrypsin

A

Hydrophobic specificity pocket

102
Q

Carbonic Anhydrase

A

Hydrolase that assists in the removal of carbon dioxide

103
Q

Carbonic anhydrase active site

A

zinc ion that coordinates to 3 histidines and a water

Water facilitates the transition state

104
Q

Reaction mechanism to what enzyme:

  1. Water binds to zinc and lowers its pKa (water then loses a hydrogen)
  2. Approximation as substrates enters active site
  3. Nucleophilic addition (adds hydroxyl group)
  4. Release of product and regeneration of enzyme
A

Carbonic anhydrase

105
Q

Temporal control of gene expression

Protein degradation

Enzyme Compartmentalization

Substrate availability

A

Regulation of the amount or availability

(On/Off switch)

106
Q

Myristolyation or Farnesylation

A

Post-translational modifications: addition of lipids

107
Q

ADP ribosylation

A

Post-translational modifications: addition of nucleic acids

108
Q

Ubiquination

A

Post-translational modifications: addition of proteins

109
Q

Glycosylation

A

Post-translational modifications: addition of carbohydrates

Addition onto side chain oxygen or nitrogen

110
Q

y-Carboxylation

A

Post-translational modifications: addition of small molecules

Adds onto gamma carbon

111
Q

Acetylation or Methylation

A

Post-translational modifications: addition of acetyl or methyl group

Adds onto nitrogen side groups (arginine and lysine)

112
Q

Phosphorylation

A

Post-translational modifications: addition of phosphate

kinases and phosphatases

113
Q

Isozymes and Isoforms

Covalent Modifications

Allostery

A

Regulate the activity of the enzyme (volume control)

114
Q

Isozyme and Isoforms

A

Catalyze the same reactions, but with different efficiencies

115
Q

LDH is an example of ______ because it is made by _______.

A

Isozymes and Isoforms

Chooses the first 4 available isoform units: It isn’t picky

116
Q

Zymgogens

A

Need to be proteolytically cleaved in order to activate

Proteases: Digestive enzymes, collagenase, and caspases

Examples of zymogens: collagen, blood clotting factors, Insulin/hormones, chymotrypsin

117
Q

In ATCase, what activates and inactivates the enzyme

A

Binding of CTP induces the T form

(tense: Inactive)

Binding of ATP prefers the R form

(relaxed: active)

S2 E1 KCU COB (5 decks)

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