SCT I - General Flashcards
(103 cards)
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
2
Q
Length and composition of a human gene
A
27 kilo-base-pairs
9 exons
8 introns
3
Q
All 5 types of genetic alteration
A
- Insertion/deletion
- Tandem repeats
- Duplication
- Inversion
- Translocation
4
Q
3 phases of DNA replication
A
- Initiation Phase: at G1
- DNA Synthesis
- Termination Phase
5
Q
Which enzyme synthesizes DNA?
A
- DNA Polymerase α for 20 nucleotides
- DNA Polymerase δ + DNA Polymerase ε for the rest
6
Q
Which enzyme unwinds DNA?
A
Helicase
7
Q
Which enzyme places the RNA primer for DNA polymerase?
A
RNA Polymerase
8
Q
Which enzyme supports DNA Polymerases?
A
PCNA
9
Q
Which enzyme joins Okazaki fragments with phosphodiester bond?
A
DNA Ligase
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
11
Q
Which enzyme is a reverse transcriptase?
A
Telomerase Enzyme
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
13
Q
What is transition in point mutations?
A
Transition: purine-purine/pyrimidine-pyrimidine changes
Example: Adenine to Guanine
Example: Cytosine to Thymine
14
Q
What is transversion in point mutations?
A
Transversion: purine-pyrimidine/pyrimidine-purine changes
Example: Adenine to Cytosine
**Example: Guanine to Thymine
15
Q
Deamination of Cytosine produces?
A
Uracil - Pairs with Adenine
16
Q
Deamination of Adenine produces?
A
Hypoxanthine - Pairs with Cytosine
17
Q
Deamination of Guanine produces?
A
Xanthine - Inhibits DNA Polymerase
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
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
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
21
Q
Which enzyme recognize damaged nitrogenous bases in excision repair?
A
DNA Glycosylase
22
Q
Which enzyme excises the affected DNA strand in excision repair?
A
AP Endonuclease
23
Q
Which enzyme fills the excised gap in excision repair?
A
DNA Polymerase β
24
Q
Which complex recognizes the mismatched basepairs?
A
MSH Protein Complex
25
What's a primary protein structure?
An amino acid sequence
26
What's a secondary protein structure?
Locally ordered structural elements
27
What's a protein motif?
Super-secondary structure, that has a particular function & structure
28
What's a protein domain?
Similar to motifs, has a broader function and is independently folded
29
What's a tertiary protein structure?
Spatial conformation of a single polypeptide chain
30
What's a quaternary protein structure?
Structure of a complex consisting of multiple protein chains
31
What type of amino acids are in living organisms?
α-L-Amino acids
32
What is the structure of a peptide bond?
Rigid and planar
33
Name all 4 chaperones
1. Hsp70
2. Hsp60
3. Protein disulfide-isomerase
4. Peptidyl-prolyl-cis/trans-isomerase
34
Define prion proteins
Are misfolded proteins that induce other proteins (mainly in the brain) to misfold too
35
Name the charged amino acids
LAG
Lysine
Arginine
Glutamate
36
Name the polar amino acids
SHTTAG
Serine
Histidine
Threonine
Tyrosine
Asparagine
Glutamine
37
Write the name of 2,3-BPG
2,3-Bisphosphoglycerate
38
What level of Hb(A1c) is diabetic?
greater than or equal to 6.5
39
What can hemoglobin bind to?
1. Glycated Hemoglobin (N-terminal)
2. CO2 (N-terminal)
3. CO (Heme)
4. O2 (Heme)
40
What's methemoglobin?
Mutated hemoglobin that contains some ferric-iron that is non-functional
41
What's hemoglobin S?
Sickle Cell Anemia hemoglobin - BCL11A gene
42
What are the three phases of transcription?
1. Initiation
2. Elongation
3. Termination
43
Name the 3 stop codons
UAA
UAG
UGA
44
Name the start codon
AUG - coding for methionine
45
Name all 3 sites of the ribosome
**A-site**: aminoacyl-tRNA binding site
**P-site**: peptidyl-tRNA binding site
**E-site**: exit site
46
List the 4 steps of translational termination
1. Binding to eRF-1
2. Dissociation of polypeptide chain
3. Release of last tRNA
4. Dissociation from ribosome
47
What does the mitochondrial genome code for?
1. 13 mitochondrial proteins
2. 22 tRNA
3. 2 rRNA
48
What's the mechanism of the antibiotic chloramphenicol
Prevents the formation of the peptide bond by binding to the transfer site
49
What's the mechanism of the antibiotic puromycin
Inhibits both prokaryotic and eukaryotic translation by binding to the A-site of the ribosome
50
What's the mechanism of the antibiotic tetracycline
REVERSIBLY binds to the 30S ribosomal subunit and blocks the binding of the charged aminoacyl-tRNA to the acceptor site
51
What's the mechanism of the antibiotic streptomycin
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
Name all 6 types of enzyme catalyzed post-translational modifications and their dependencies
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
Name all 3 types of non-enzymatic post-translational modifications and their metabolites
1. Oxidation (ROS dependent)
2. Succinylation (Succinate dependent)
3. Glycation (Glucose dependent)
54
Name the 4 structural features required for catalysis
1. Catalytic triad
2. Oxyanion hole
3. Primary substrate binding pocket
4. Main chain structure binding
55
What is one unit (U)?
Amount of enzyme activity needed to catalyze 1 micromole of the substrate per minute at STP
56
What is one katal (kat)?
Catalytic activity that will raise the rate of the reaction by 1 mole per second in a specified assay system
57
What gives the Michaelis-Menten equation validity?
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
What's the meaning of Km?
Is the substrate concentration when the rate is half of Vmax
59
What happens to Km and Vmax when a competitive inhibitor is brought in?
**Km** increases
**Vmax** stays the same
60
What happens to Km and Vmax when a non-competitive inhibitor is brought in?
**Km** stays the same
**Vmax** decreases
61
What happens to Km and Vmax when an uncompetitive inhibitor is brought in?
**Km** decreases
**Vmax** decreases
62
What are the two types of homotypic ubiquitin modifications?
Homotypic K48
Homotypic K63
63
Name the three components of the ubiquitin proteasome system
E1 - Ubiquitin activating enzyme
E2 - Ubiquitin conjugating enzyme
E3 - Ubiquitin protein ligase
64
Name the three types of autophagy
1. Macroautophagy: Intracellular components aggregate
2. Microautophagy: directly, molecules are internalized into lysosome
3. Chaperone mediated autophagy: special molecules are involved
65
Name all the regulatory agents for macroautophagy
**TOR**: Inhibits process
**Insulin**: Inhibits process
**PI3K**: Starts process
**Glucagon**: Starts process
**Bcl-2**: Phosphorylates
**Beclin-1**: Is released
66
Name the three types of enzyme regulation
**Enzyme amount**:
gene expression
**Enzyme activity**:
1- Modulating the substrate conc.
2- Allosteric effectors
3- Product inhibition
4- Covalent modification
**Enzyme localization**
67
Classify the regulatory process by its speed and duration
**Allosteric**: Fastest, but short lasting
**Covalent**: Intermediate and mid lasting
**Gene Level**: Slowest, but long lasting
68
Explain the three stages of cellular respiration
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
Name the 5 cofactors involved in the oxidation of Pyrucate to AcetylCoA
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
Name the three enzymes that make up the pyruvate dehydrogenase complex
E1 - Pyruvate dehydrogenase (most sensitive)
E2 - Dihydrolipoyl transacetylase
E3 - Dihydrolipoyl dehydrogenase
71
What's the function of E1 in PDH complex?
**Pyruvate Dehydrogenase**
1. Decarboxylation of pyruvate with the use TPP/vitamin B1 (Thiamine)
2. Transfers acetyl group onto E2
72
What's the function of E2 in PDH complex?
**Dihydrolipoyl Transacetylase**
1. Uses Lipoic Acid and CoA/vitamin B5 (Pantothenic Acid) through transesterification to yield AcetylCoA
73
What's the function of E3 in PDH complex?
**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
What are the main products of the PDH complex reaction?
1. AcetylCoA
2. NADH
3. CO2
75
How is the PDH complex regulated
Negative feedback - the products of the complex inhibit the mechanism when there's an abundance of products
76
How is the PDH complex regulated allosterically?
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
How is the PDH complex regulated covalently?
Insulin & Glucagon dephosphorylate/phosphorylate the mechanism, respectively.
Ca2+ & Mg2+ activate phosphotases which DEphosphorylates the complex (activates)
78
Where else is the PDH complex located?
The nucleus, where it provides AcetylCoA for the modification of histones
79
What are the final products of the TCA cycle?
1. 3 NADH
2. 1 FADH2
3. 1 GTP
80
Name a terminal electron acceptor in the case of hypoxia/stress
Fumarate
81
Which complex houses cytochrome B and cytochrome C1?
Complex III: Ubiquinone-Cytochrome Oxidoreductase
82
Which complex houses cytochrome A and cytochrome A3?
Complex IV: Cytochrome Oxidase
83
What inhibits ADP Synthase?
Oligomycin
84
What inhibits Adenine Nucleotide Translocase (Antiporter)?
Atractylozide
85
What is the mode of action of the inhibitor Retenone?
Prevents the oxidation of NADH for Complex I (NADH Dehydrogenase)
86
What is the mode of action of the inhibitor Malonate?
Binds to the active site of Complex II (Succinate Dehydrogenase)
87
What is the mode of action of the inhibitor Antimycin A?
Blocks Complex III (Ubiquinone-Cytochrome C Oxidoreductase)
88
What is the mode of action of the inhibitors CO and Cyanide?
Block terminal oxidation, O2 cannot be used as a terminal electron acceptor for Complex IV
89
How much ATP do you get from oxidizing one NADH?
2.5-3 ATP
90
How much ATP do you get from oxidizing one FADH2?
1.5-2 ATP
91
Why is mitochondrial DNA more susceptible to genetic mutations than normal DNA?
Because it does not have a repair system
92
What is the normal blood-glucose range?
~5mM (4.4-6.1mM)
93
Name all the important carbohydrate transporters and their function
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
Name the location of all 5 GLUT proteins
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
What's the role of GLUT2?
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
Where does Glycolysis take place?
Cytoplasm
97
What happens to pyruvate (product of glycolysis) in anaerobic conditions?
It is converted to lactate, and forms net 2 ATP only
98
When is glucokinase or hexokinase used?
Hexokinase at low Km of blood-glucose
Glucokinase at high Km of blood-glucose
99
Which steps of glycolysis are regulated?
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
How is step 1 of glycolysis regulated?
Glucose-6-Phosphate grants negative feedback to the reaction, inhibiting *Hexokinase*
If *Glucokinase* is used, Fructose-6-Phosphate will grant negative feedback instead.
101
Name the types and location of the aldolases
1. Type A Aldolase: Muscle - Glycolysis
2. Type B Aldolase: Liver - Glycolysis, Gluconeogenesis
3. Type C Aldolase: Brain - Glycolysis
102
Which step is effected by low levels of NAD+ in glycolysis?
Glyceraldehyde-3-Phosphate → 1,3-Bisphosphoglycerate
*Glyceraldehyde-3-Phosphate Dehydrogenase*
- NAD+ → 2x NADH
103
How can RBCs have a higher affinity to release oxygen into tissue?
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
