Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

S2 E1 KCU COB > Biochem > Flashcards

Biochem Flashcards

(117 cards)

Start Studying
1
Q

Which are the tiny AA?

A

C.A.G.S

Cysteine, Alanine, Glycine, and Serine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the small AA?

A

D P N T

Aspartate, Proline, Asparagine, Threonine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are the medium AA?

A

E, V, H, Q

Glutamic Acid, Valine, Histidine, Glutamine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are the large AA?

A

K R I L M

Lysine, Arginine, Isoleucine, Leucine, Methionine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are the extra-large AA?

A

F Y W

Phenylalanine, Tyrosine, Trytophan

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the essential AA?

A

PVT TIM HALL

Phenylalanine

Valine

Tryptophan

Threonine

Isoleucine

Methionine

Histidine

Arginine

Lysine

Leucine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the three stop codons?

A

UAA

UGA

UAG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

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

A

Statin inhibits the Selenocystein-tRNA from producing selenoproteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What does selenium deficiencies lead to?

A

Oxidative distress is inhibited

(Oxidative stress continues)

Muscle death and myopathies

Immune incompetence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What are the 4 determinants of protein folding?

A

Secondary Structure

Hierarchical folding

Hydrophobic effect

Context-dependent

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are the bonds found in alpha-helices?

A

Intrachain Hydrogen bonds leaving 4AA residues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

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

A

Hydrogen bonds between peptide chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What causes compact and globular shapes for polypeptide chains?

A

Reversal directions

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What kind of protein uses intra-sulfur bonds?

A

Extracellular proteins

i.e. Insulin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

How are molten globule proteins stabilized?

A

nonspecific hydrophobic interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
What is the purpose of accessory proteins
To fine-tune protein folding
26
Function of PPI
Peptidyl Prolyl Cis-Trans Isomerases Changes the functional groups of a protein from trans to cis
27
T/F folding and unfolding is not an all or none process. It can be both
False. All or none It is either folded, or it is not
28
What are the methods of analysis of protein folding?
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
29
What is the function of the 19s subunit of the proteosome?
Recognizes the ubiquitinated protein and allows entry into the degradation site (20s core)
30
What is the function of the 20s core in the proteosome?
A sealed barrel that contains proteolytic enzymes and a low pH for the degradation of proteins
31
32
What is the function of HSP 70
Coordinates cellular function by directing substrates for unfolding, disaggregation, and refolding or degradation Works together with HSP 40
33
What is the function of HSP 40
HSP 40 is used to refold proteins Does it on its own with soluble Needs assistance from HSP 70 for insoluble
34
HSP 90
Helps fold signal transduction proteins Inserts signaling functions at late folding stages
35
What are the functions of HSP 60 and HSP 10
They are chaperonins that have the barrel like structures They create a hydrophobic microenviroment for folding of proteins
36
What are the three components of the cellular quality control system
Proteasomes: Protein degradation Autophagy: Cellular digestion ERAD: ER-Associated degradation (Sends useless proteins directly to proteasome)
37
What can improper degradation lead to?
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
38
What can improper localization lead to?
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
39
Nucleophilic substitution
Swap functional groups
40
Nucleophilic Addition
Add functional group
41
Carbonyl condensation
Change the number of carbons
42
Elimination
Change the bond order
43
Oxidation/Reduction
Move electrons
44
Oxidoreductases
Oxidation-Reduction rxn
45
Transferases
Group Transfer
46
Hydrolases
Breaking of a bond using water
47
Lysases
Breaking of a bond without using water May lead to double bonds
48
Isomerases
Intramolecular group transfers
49
Ligases
Ligation of two substrates at the expense of ATP hydrolysis Putting things together
50
NAD+
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
NADPH
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
FADH2
Coenzyme Made of vitamin B6 and adenine Found in oxidation reactions using FAD
53
FMNH2
Coenzyme Made of vitamin B6 and adenine Used in reduction reactions with FMN
54
ATP
Coenzyme to transfer a phosphate group Usually, gamma is moved
55
Pyridoxal phosphate
Coenzyme that transfers phosphates Made of Vitamin B6
56
SAM
Conenzyme: S-Adenosylmethionine A primary transferase that transfers a methyl group
57
Tetrahydrofolate
A coenzyme in a transferase process of a methyl group Made of Vitamin B9
58
5'deoxyadenoxylcobalamin
A coenzyme in methyl transferases Contains Vitamin B12 and cobalt
59
TPP
Coenzyme in ligase reactions Thiamine pryophosphate Made of Vitamin B1 and 2 phosphates Adds Aldehyde gropus
60
CoASH and Lipoamide
Coenzymes that add Acyl groups (-COR) Both have sulfurs
61
Biotin
Coenzyme that adds Adds CO2 Vitamin B7
62
Incomplete Enzymes that are inactive and require a cofactor or coenzyme
Apoenzyme
63
A whole enzyme that is active. Contains the cofactor/coenzyme
Holoenzyme
64
In terms of cooperativity on the hill plot: A slop of 1 is interpreted as
No cooperativity
65
In terms of cooperativity on the hill plot: A slope greater than 1 has
Positive cooperativity
66
In terms of cooperativity on the hill plot: A slope that is less than 1 has
Negative cooperativity
67
What are the subunits of embryonic Hb
Fetal hemoglobin is made of 2 zeta and 2 gamma
68
What are the subunits for HbF
Fetal Hb = 2 alpha and 2 gamma
69
What are the subunits of HbA
2 alpha 2 beta
70
What are the subunits for HbA2
2 alpha 2 delta
71
What hemoglobins are found in an adult?
HbA, HbA2, and HbF
72
When does HbA reach dominancy as the main type of Hb
After 1 year after birth/ Gestational age
73
What subunits are Alpha chains of Hb
Found on chromosome 16, alpha and zeta
74
What subunits are beta chains in Hb
Found on chromosome 11, epsilon, gamma, delta, and beta
75
What causes the formation of HbS
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
What is the proximal histidine and what is it bound to?
F8 histidine and is bound to the heme group (6th segment; 8th AA)
77
What is the distal histidine
E7 | (5th segment; 7th AA)
78
Where does oxygen bind to in Hb
On the distal histidine and the heme group
79
What happens to the iron atom when oxygen binds
It moves from out of the plane to into the plane This will pull the proximal histidine
80
T/F binding of oxygen is a cooperative process in myoglobin
False it is cooperative in hemoglobin
81
T/F When oxygen dissociates from hemoglobin, it makes it easier for other oxygens to dissociate
True: Reversibility of cooperativity
82
2,3 BPG induces what form of Hb?
The tense form which lowers the affinity
83
Absence of 2,3-BPG will do what to Hb?
It will increase affinity and keep Hb in the relaxed form
84
What correlation does pH have with Hb affinity?
As pH decreases so does the affinity | (more acidic)
85
What is HbA1c
Post-modification of the N-terminus in ß globulins Low at normal glucose levels High in diabetic patients that abuse glucose
86
What is Thalassemias
Reduced synthesis of a globulin that reduces the functionality of Hb
87
HbH
Excess beta globulins that will become tetramers
88
Alpha plus Thalasemia
Silent carrier: Deletion of 1/4 alpha genes
89
Alpha - Thalassemia
2/4 alpha genes are deleted
90
Microcytosis
Low mean cell volume Found in alpha thalassemia
91
Hypochromia
Low mean cell hemoglobin Found in alpha thalassemia
92
HbH Disease
3 alpha genes are affected Severe Anemia, hypochromic hemolytic anemia, hepatosplenomegaly, mild jaundice
93
Hydrops Fetalis
All (4/4) alpha genes are silenced Only gamma 4 Hb (Bart's Hb) Creates fetal onset of edema and anemia Kills newborns
94
ß Thalassemia
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
Covalent Catalysis
Binds covalently to transition state and stabilizes transition state
96
Acid-Base Catalysis
Partial proton transfer (Hydrogens: Think of what amino acids can participate)
97
Approximation
Spatial orientation and close contact so that electrons and protons can be exchanged
98
Electrostatic Catalysis
Stabilization of unfavorable charges on the transition state
99
Chymotrypsin
A serine protease (Hydrolase)
100
What is the active site of chymotrypsin?
The catalytic triad (Serine: Nucleophile Histidine: Base Aspartic Acid: Acid) **AND** Oxyanion Hole (Serine and glycine)
101
Specificity of Chymotrypsin
Hydrophobic specificity pocket
102
Carbonic Anhydrase
Hydrolase that assists in the removal of carbon dioxide
103
Carbonic anhydrase active site
zinc ion that coordinates to 3 histidines and a water Water facilitates the transition state
104
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
Carbonic anhydrase
105
Temporal control of gene expression Protein degradation Enzyme Compartmentalization Substrate availability
Regulation of the amount or availability (On/Off switch)
106
Myristolyation or Farnesylation
Post-translational modifications: addition of lipids
107
ADP ribosylation
Post-translational modifications: addition of nucleic acids
108
Ubiquination
Post-translational modifications: addition of proteins
109
Glycosylation
Post-translational modifications: addition of carbohydrates Addition onto side chain oxygen or nitrogen
110
y-Carboxylation
Post-translational modifications: addition of small molecules Adds onto gamma carbon
111
Acetylation or Methylation
Post-translational modifications: addition of acetyl or methyl group Adds onto nitrogen side groups (arginine and lysine)
112
Phosphorylation
Post-translational modifications: addition of phosphate kinases and phosphatases
113
Isozymes and Isoforms Covalent Modifications Allostery
Regulate the activity of the enzyme (volume control)
114
Isozyme and Isoforms
Catalyze the same reactions, but with different efficiencies
115
LDH is an example of ______ because it is made by \_\_\_\_\_\_\_.
Isozymes and Isoforms Chooses the first 4 available isoform units: It isn't picky
116
Zymgogens
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
In ATCase, what activates and inactivates the enzyme
Binding of CTP induces the T form (tense: Inactive) Binding of ATP prefers the R form (relaxed: active)

S2 E1 KCU COB (5 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions