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Biochemistry I > SCT I - General Flashcards > Flashcards

SCT I - General Flashcards

1
Q

Name all 4 staining techniques for chromosomes

A

G-banding: Proteolysis + Giemsa
R-banding: Heat + Giemsa
C-banding: Barium Hydroxide + Giemsa
Q-banding: Quinacrine

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2
Q

Length and composition of a human gene

A

27 kilo-base-pairs
9 exons
8 introns

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3
Q

All 5 types of genetic alteration

A
  1. Insertion/deletion
  2. Tandem repeats
  3. Duplication
  4. Inversion
  5. Translocation
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4
Q

3 phases of DNA replication

A
  1. Initiation Phase: at G1
  2. DNA Synthesis
  3. Termination Phase
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5
Q

Which enzyme synthesizes DNA?

A
  1. DNA Polymerase α for 20 nucleotides
  2. DNA Polymerase δ + DNA Polymerase ε for the rest
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6
Q

Which enzyme unwinds DNA?

A

Helicase

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7
Q

Which enzyme places the RNA primer for DNA polymerase?

A

RNA Polymerase

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8
Q

Which enzyme supports DNA Polymerases?

A

PCNA

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9
Q

Which enzyme joins Okazaki fragments with phosphodiester bond?

A

DNA Ligase

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10
Q

Which enzymes solve the supercoil problem?

A

Topoisomerase Type 1: cuts one DNA strand, rotates the cleaved strand around the uncleaved strand, then ligates the DNA strands

Topoisomerase Type 2: cleaves both DNA strands to allow free rotation, then ligates them

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11
Q

Which enzyme is a reverse transcriptase?

A

Telomerase Enzyme

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12
Q

What are the two main types of mutation?

A

Point mutation: Alteration of a single nucleotide

Insertion/Deletion (Indel): Insertion or Deletion of one or a few nucleotides

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13
Q

What is transition in point mutations?

A

Transition: purine-purine/pyrimidine-pyrimidine changes

Example: Adenine to Guanine
Example: Cytosine to Thymine

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14
Q

What is transversion in point mutations?

A

Transversion: purine-pyrimidine/pyrimidine-purine changes

Example: Adenine to Cytosine
**Example: Guanine to Thymine

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15
Q

Deamination of Cytosine produces?

A

Uracil - Pairs with Adenine

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16
Q

Deamination of Adenine produces?

A

Hypoxanthine - Pairs with Cytosine

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17
Q

Deamination of Guanine produces?

A

Xanthine - Inhibits DNA Polymerase

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18
Q

Name all 5 types of Genotoxic Agents

A

Carcinogen: Causes tumors
Oncogen: Supports proliferation of tumors
Mutagen: Causes mutations
Teratogen: Causes embryonic abnormalities
Clastogen: Causes chromosomal breaks

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19
Q

Name all 4 effects of point mutations in the coding DNA region

A

Synonymous: different codon, encoding the same amino acid
Non-synonymous: different codon, encoding a different amin aocd
Nonsense: the mutation creates a stop codon
Readthrough: the mutation eliminates a stop codon

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20
Q

Name all 3 types of DNA repair

A

Excision repair: damaged nucleotide is excised (cut), and resynthesized correctly

Mismatch repair: mistmatched nucleotide is excised, and resynthesized correctly

Strand break repair: strand breaks are resynthesized or religated

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21
Q

Which enzyme recognize damaged nitrogenous bases in excision repair?

A

DNA Glycosylase

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22
Q

Which enzyme excises the affected DNA strand in excision repair?

A

AP Endonuclease

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23
Q

Which enzyme fills the excised gap in excision repair?

A

DNA Polymerase β

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24
Q

Which complex recognizes the mismatched basepairs?

A

MSH Protein Complex

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25
Q

What’s a primary protein structure?

A

An amino acid sequence

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26
Q

What’s a secondary protein structure?

A

Locally ordered structural elements

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27
Q

What’s a protein motif?

A

Super-secondary structure, that has a particular function & structure

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28
Q

What’s a protein domain?

A

Similar to motifs, has a broader function and is independently folded

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29
Q

What’s a tertiary protein structure?

A

Spatial conformation of a single polypeptide chain

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30
Q

What’s a quaternary protein structure?

A

Structure of a complex consisting of multiple protein chains

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31
Q

What type of amino acids are in living organisms?

A

α-L-Amino acids

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32
Q

What is the structure of a peptide bond?

A

Rigid and planar

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33
Q

Name all 4 chaperones

A
  1. Hsp70
  2. Hsp60
  3. Protein disulfide-isomerase
  4. Peptidyl-prolyl-cis/trans-isomerase
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34
Q

Define prion proteins

A

Are misfolded proteins that induce other proteins (mainly in the brain) to misfold too

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35
Q

Name the charged amino acids

A

LAG

Lysine
Arginine
Glutamate

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36
Q

Name the polar amino acids

A

SHTTAG

Serine
Histidine
Threonine
Tyrosine
Asparagine
Glutamine

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37
Q

Write the name of 2,3-BPG

A

2,3-Bisphosphoglycerate

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38
Q

What level of Hb(A1c) is diabetic?

A

greater than or equal to 6.5

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39
Q

What can hemoglobin bind to?

A
  1. Glycated Hemoglobin (N-terminal)
  2. CO2 (N-terminal)
  3. CO (Heme)
  4. O2 (Heme)
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40
Q

What’s methemoglobin?

A

Mutated hemoglobin that contains some ferric-iron that is non-functional

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41
Q

What’s hemoglobin S?

A

Sickle Cell Anemia hemoglobin - BCL11A gene

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42
Q

What are the three phases of transcription?

A
  1. Initiation
  2. Elongation
  3. Termination
43
Q

Name the 3 stop codons

A

UAA
UAG
UGA

44
Q

Name the start codon

A

AUG - coding for methionine

45
Q

Name all 3 sites of the ribosome

A

A-site: aminoacyl-tRNA binding site

P-site: peptidyl-tRNA binding site

E-site: exit site

46
Q

List the 4 steps of translational termination

A
  1. Binding to eRF-1
  2. Dissociation of polypeptide chain
  3. Release of last tRNA
  4. Dissociation from ribosome
47
Q

What does the mitochondrial genome code for?

A
  1. 13 mitochondrial proteins
  2. 22 tRNA
  3. 2 rRNA
48
Q

What’s the mechanism of the antibiotic chloramphenicol

A

Prevents the formation of the peptide bond by binding to the transfer site

49
Q

What’s the mechanism of the antibiotic puromycin

A

Inhibits both prokaryotic and eukaryotic translation by binding to the A-site of the ribosome

50
Q

What’s the mechanism of the antibiotic tetracycline

A

REVERSIBLY binds to the 30S ribosomal subunit and blocks the binding of the charged aminoacyl-tRNA to the acceptor site

51
Q

What’s the mechanism of the antibiotic streptomycin

A

Belongs to aminoglycosides; it binds to the 30S ribosome and inhibits the formation of initiation complex by preventing the binding of aminoacyl-tRNA to the A-site of the ribosome

52
Q

Name all 6 types of enzyme catalyzed post-translational modifications and their dependencies

A
  1. Phosphorylation (ATP dependent)
  2. Acetylation (AcetylCoA dependent)
  3. Ubiquitination (Ubiquitine dependent)
  4. Methylation (SAM dependent)
  5. Palmitoylation (Plamitoyl-CoA dependent)
  6. O-glycosylation (UDP-Gal-Nac dependent)
53
Q

Name all 3 types of non-enzymatic post-translational modifications and their metabolites

A
  1. Oxidation (ROS dependent)
  2. Succinylation (Succinate dependent)
  3. Glycation (Glucose dependent)
54
Q

Name the 4 structural features required for catalysis

A
  1. Catalytic triad
  2. Oxyanion hole
  3. Primary substrate binding pocket
  4. Main chain structure binding
55
Q

What is one unit (U)?

A

Amount of enzyme activity needed to catalyze 1 micromole of the substrate per minute at STP

56
Q

What is one katal (kat)?

A

Catalytic activity that will raise the rate of the reaction by 1 mole per second in a specified assay system

57
Q

What gives the Michaelis-Menten equation validity?

A
  1. Second step of the reaction is irreversible
  2. Kinetically stable ES complex formed
  3. Concentration of substrate doesn’t change
  4. No enzyme-product complex made
  5. Only one substrate molecule is bound to the active site of the enzyme

K3 is far smaller than K1 and K2

58
Q

What’s the meaning of Km?

A

Is the substrate concentration when the rate is half of Vmax

59
Q

What happens to Km and Vmax when a competitive inhibitor is brought in?

A

Km increases
Vmax stays the same

60
Q

What happens to Km and Vmax when a non-competitive inhibitor is brought in?

A

Km stays the same
Vmax decreases

61
Q

What happens to Km and Vmax when an uncompetitive inhibitor is brought in?

A

Km decreases
Vmax decreases

62
Q

What are the two types of homotypic ubiquitin modifications?

A

Homotypic K48
Homotypic K63

63
Q

Name the three components of the ubiquitin proteasome system

A

E1 - Ubiquitin activating enzyme
E2 - Ubiquitin conjugating enzyme
E3 - Ubiquitin protein ligase

64
Q

Name the three types of autophagy

A
  1. Macroautophagy: Intracellular components aggregate
  2. Microautophagy: directly, molecules are internalized into lysosome
  3. Chaperone mediated autophagy: special molecules are involved
65
Q

Name all the regulatory agents for macroautophagy

A

TOR: Inhibits process
Insulin: Inhibits process
PI3K: Starts process
Glucagon: Starts process

Bcl-2: Phosphorylates
Beclin-1: Is released

66
Q

Name the three types of enzyme regulation

A

Enzyme amount:
gene expression

Enzyme activity:
1- Modulating the substrate conc.
2- Allosteric effectors
3- Product inhibition
4- Covalent modification

Enzyme localization

67
Q

Classify the regulatory process by its speed and duration

A

Allosteric: Fastest, but short lasting
Covalent: Intermediate and mid lasting
Gene Level: Slowest, but long lasting

68
Q

Explain the three stages of cellular respiration

A
  1. AcetylCoA yield from carbs, fats, and proteins
  2. Kreb’s Cycle to yield 1 NADH + 3 FADH2
  3. Oxidation of reduced coenzymes to produce electrons

Electrons are then sent to the Electron Transport Chain to yield ATP

69
Q

Name the 5 cofactors involved in the oxidation of Pyrucate to AcetylCoA

A
  1. FAD (Vit. B2: Riboflavin)
  2. NAD (Vit. B3: Niacin)
  3. TPP (Vit. B1: Thiamin)
  4. CoA (Vit. B5: Pantothenic Acid
  5. Lipoic acid (fatty acid)
70
Q

Name the three enzymes that make up the pyruvate dehydrogenase complex

A

E1 - Pyruvate dehydrogenase (most sensitive)
E2 - Dihydrolipoyl transacetylase
E3 - Dihydrolipoyl dehydrogenase

71
Q

What’s the function of E1 in PDH complex?

A

Pyruvate Dehydrogenase

  1. Decarboxylation of pyruvate with the use TPP/vitamin B1 (Thiamine)
  2. Transfers acetyl group onto E2
72
Q

What’s the function of E2 in PDH complex?

A

Dihydrolipoyl Transacetylase

  1. Uses Lipoic Acid and CoA/vitamin B5 (Pantothenic Acid) through transesterification to yield AcetylCoA
73
Q

What’s the function of E3 in PDH complex?

A

Dihydrolipoyl Dehydrogenase

  1. Uses FAD/vitamin B2 (Riboflavin) to reduce FAD to FADH2.
  2. Uses NAD/vitamin B3 (Niacin) to dehydrogenate FADH2 forming NADH and FAD

Regenerates the reductive power of FAD

74
Q

What are the main products of the PDH complex reaction?

A
  1. AcetylCoA
  2. NADH
  3. CO2
75
Q

How is the PDH complex regulated

A

Negative feedback - the products of the complex inhibit the mechanism when there’s an abundance of products

76
Q

How is the PDH complex regulated allosterically?

A

High levels of AcetylCoA, NADH, ATP, and Fatty Acids provide negative feedback to the PDH complex

High levels of CoA, NAD, AMP, and Ca2+ provide positive feedback to the PDH complex

77
Q

How is the PDH complex regulated covalently?

A

Insulin & Glucagon dephosphorylate/phosphorylate the mechanism, respectively.

Ca2+ & Mg2+ activate phosphotases which DEphosphorylates the complex (activates)

78
Q

Where else is the PDH complex located?

A

The nucleus, where it provides AcetylCoA for the modification of histones

79
Q

What are the final products of the TCA cycle?

A
  1. 3 NADH
  2. 1 FADH2
  3. 1 GTP
80
Q

Name a terminal electron acceptor in the case of hypoxia/stress

A

Fumarate

81
Q

Which complex houses cytochrome B and cytochrome C1?

A

Complex III: Ubiquinone-Cytochrome Oxidoreductase

82
Q

Which complex houses cytochrome A and cytochrome A3?

A

Complex IV: Cytochrome Oxidase

83
Q

What inhibits ADP Synthase?

A

Oligomycin

84
Q

What inhibits Adenine Nucleotide Translocase (Antiporter)?

A

Atractylozide

85
Q

What is the mode of action of the inhibitor Retenone?

A

Prevents the oxidation of NADH for Complex I (NADH Dehydrogenase)

86
Q

What is the mode of action of the inhibitor Malonate?

A

Binds to the active site of Complex II (Succinate Dehydrogenase)

87
Q

What is the mode of action of the inhibitor Antimycin A?

A

Blocks Complex III (Ubiquinone-Cytochrome C Oxidoreductase)

88
Q

What is the mode of action of the inhibitors CO and Cyanide?

A

Block terminal oxidation, O2 cannot be used as a terminal electron acceptor for Complex IV

89
Q

How much ATP do you get from oxidizing one NADH?

A

2.5-3 ATP

90
Q

How much ATP do you get from oxidizing one FADH2?

A

1.5-2 ATP

91
Q

Why is mitochondrial DNA more susceptible to genetic mutations than normal DNA?

A

Because it does not have a repair system

92
Q

What is the normal blood-glucose range?

A

~5mM (4.4-6.1mM)

93
Q

Name all the important carbohydrate transporters and their function

A

GLUT5 → Fructose uptake into enterocyte

SGLT → A symporter (2ndry active transporter), Glucose and Galactose enter the enterocyte only with Na+ coming with it

GLUT2 → Fructose, Glucose, and Galactose transporter from the enterocyte into the blood

94
Q

Name the location of all 5 GLUT proteins

A

GLUT1 → RBC, Brain, Adipose Tissue
GLUT2 → Liver, Pancreatic β-cells, Kidney, GI
GLUT3 → Brain (neurons)
GLUT4 → Muscle, adipose tissue (insulin dependent)
GLUT5 → Fructose transporter

95
Q

What’s the role of GLUT2?

A

Help regulate blood-glucose levels by being activated at 15-20mM - Liver stores glucose as glycogen, pancreas release insulin, and kidney works harder idk

96
Q

Where does Glycolysis take place?

A

Cytoplasm

97
Q

What happens to pyruvate (product of glycolysis) in anaerobic conditions?

A

It is converted to lactate, and forms net 2 ATP only

98
Q

When is glucokinase or hexokinase used?

A

Hexokinase at low Km of blood-glucose
Glucokinase at high Km of blood-glucose

99
Q

Which steps of glycolysis are regulated?

A

Step 1: Glucose → Glucose-6-Phosphate (Hexokinase/Glucokinase)
Step 3: Fructose-6-Phosphate → Fructose-1,6-Bisphosphate (Phosphofructo Kinase)
Step 9: Phosphoenolpyruvate → Pyruvate (Pyruvate Kinase)

  • Most kinases except Phosphoglycerate Kinase
100
Q

How is step 1 of glycolysis regulated?

A

Glucose-6-Phosphate grants negative feedback to the reaction, inhibiting Hexokinase

If Glucokinase is used, Fructose-6-Phosphate will grant negative feedback instead.

101
Q

Name the types and location of the aldolases

A
  1. Type A Aldolase: Muscle - Glycolysis
  2. Type B Aldolase: Liver - Glycolysis, Gluconeogenesis
  3. Type C Aldolase: Brain - Glycolysis
102
Q

Which step is effected by low levels of NAD+ in glycolysis?

A

Glyceraldehyde-3-Phosphate → 1,3-Bisphosphoglycerate
Glyceraldehyde-3-Phosphate Dehydrogenase

  • NAD+ → 2x NADH
103
Q

How can RBCs have a higher affinity to release oxygen into tissue?

A

By binding to 2,3-Bisphosphoglycerate, 15-20% of glucose in RBCs is converted to this substance, which is a side reaction of the reaction between 1,3-Bisphosphoglycerate and 3-Phosphoglycerate

This forfeits the ATP production

Biochemistry I (12 decks)

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