Molecular Flashcards
(91 cards)
1
Q
What are the stop codons
A
UAA
UGA
UAG
2
Q
What happens when a ribosome encounters a stop codon
A
Releasing factor proteins bind to the ribosome and stimulate release of the formed polypeptide chain and dissolution of the ribosome-mRNA complex
3
Q
What is the function of elongation factors
A
Facilitate tRNA binding and translocation steps of protein synthesis
4
Q
Enzyme in charge of converting dUMP to dTMP
A
Thymidylate synthase
5
Q
Cofactor needed by thymidylate synthase
A
5,10-methylene THF
6
Q
Name the 2 types of silencing RNA
A
- micro RNA (miRNA)
2. small interfering RNA (siRNA)
7
Q
Most important aminoacid in caspases and their function
A
- Cysteine
2. Cleavage of aspartic acid residues
8
Q
Molecular charge of the histone octamer that allows it to attach to DNA
A
Positive (DNA has a negative charge)
9
Q
Predominant aminoacids found in histones
A
Arginine and lysine
10
Q
Histone in charge of stabilizing the chromatin fiber
A
H1
11
Q
State of chromatin that appears darker on EM
A
Heterochromatin
12
Q
State of chromatin that is highly methylated, and therefore, sterically inaccesible (transcriptionally inactive)
A
Heterochromatin
13
Q
Barr bodies (inactive X chromosomes) exist in which state of chromatin
A
Heterochromatin
14
Q
State of chromatin that is highly acetylated, and therefore, sterically accesible (transcriptionally active)
A
Euchromatin
15
Q
Part of the DNA that, when methylated, represses transcription
A
CpG islands
16
Q
Components of nucleosides
A
Base + (deoxy)ribose
17
Q
Components of nucleotides
A
Base + (deoxy)ribose + phosphate
18
Q
How many rings do purines and pyrimidines have
A
Purines have 2, while pyrimidines have 1
19
Q
Deamination of cytosine makes…
A
Uracil
20
Q
Deamination of adenine makes…
A
Guanine
21
Q
Methylation of uracil makes…
A
Thymine
22
Q
How many H bonds does the G-C bond have
A
3
*Therefore, if DNA is high in G-C bonds, melting temperatura will increase, making DNA more resistant
23
Q
How many H bonds does the A-T bond have
A
2
24
Q
Enzyme inhibited by leflunomide
A
Dihydroorotate dehydrogenase
*Part of the pyrimidine synthesis pathway
25
Enzyme deficient in a patient with orotic aciduria but without hyperammonemia
UMP synthase
26
Pyrimidine synthesis pathway enzyme that is inhibited by hydroxyurea
Ribonucleotide reductase
*Inhibited reaction: UDP to dUDP
27
Pyrimidine synthesis pathway enzyme that is inhibited by 5-FU
Thymidylate synthase
28
Pyrimidine synthesis pathway enzyme that is inhibited by methotrexate/trimethoprim/pyrimethamine
Dihydrofolate reductase (therefore, reducing deoxythymidine phosphate)
29
Purine synthesis pathway enzyme that is inhibited by 6-MP (and its prodrug, azathioprine)
PRPP amidotransferase
30
Purine synthesis pathway enzyme that is inhibited by mycophenolate and ribavirin
Inosine monophosphate dehydrogenase
31
Pathogenesis of adenosine deaminase deficiency
ADA is required for degradation of adenosine and deoxyadenosine, its deficiency causes an increase in dATP, which is toxic to lymphocytes
*One of the major causes of autosomal recessive SCID
32
Pathogenesis of Lesch-Nyhan syndrome
Defective purine salvage due to absent HGPRT, resulting in excessive uric acid and de novo purine synthesis
33
Signs and symptoms of Lesch-Nyhan syndrome
* Hyperuricemia
* Gout
* Pissed off (aggression and self mutilation)
* Retardation (intelectual disability)
* dysTonia
34
Lesch-Nyhan syndrome treatment
Allopurinol or febuxostat
*They inhibit PRPP amidotransferase (as 6-MP), thereby reducing purine synthesis
35
Define the "wobble" feature of the genetic code
This refers to the fact that codons that differ in 3rd position may code for the same tRNA/aminoacid (base pairing is usually only required in the first 2 nucleotide positions of mRNA codon)
36
Organisms that can have multiple origins of replication
Eukaryotes
37
DNA replication direction
5' to 3' direction
38
Enzyme that unwinds DNA template at replication fork
Helicase
39
Gene that codes for DNA helicase
BLM gene
*Deficiency leads to Bloom syndrome (growth retardation, facial abnormalities, photosensitive skin rash, and immunodeficiency)
40
Molecule that prevents DNA strands from reannealing during DNA replication
Single-stranded binding proteins
41
Molecules that create breaks in the DNA helix during DNA replication to add or remove supercoils
Topoisomerases
42
Drugs that inhibit eukaryotic topoisomerase 1
Irinotecan/topotecan
43
Drugs that inhibit eukaryotic topoisomerase 2
Etoposide/teniposide
44
Antibiotics that inhibits prokaryotic topoisomerase 2 (DNA gyrase) and 4
Fluoroquinolones
45
Molecule that adds an RNA primer on the template strands during DNA replication
Primase
46
Molecule that during DNA replication, elongates leading strand by adding deoxynucleotides to the 3' end
DNA polymerase 3 (only found in prokaryotes)
47
Molecule active during DNA replication that has 5' to 3' synthesis and 3' to 5' exonuclease (proofreading) activities
DNA polymerases
48
Molecule active during DNA replication (in prokaryotes only) that degrades the RNA primer and replaces it with DNA
DNA polymerase 1
*Excises primer with 5' to 3' exonuclease (only DNA polymerase with this activity)
49
Molecule that catalyzes the formation of a phosphodiesther bond within a strand of double-stranded DNA during DNA replication (joins Okazaki fragments)
DNA ligase
50
RNA-dependent DNA polymerase that adds DNA to 3' ends of chromosomes to avoid los of genetic material
Telomerase
51
Eukaryotic molecule that polymerizes the primer in eukaryotes
alpha DNA polymerase
52
Most severe DNA mutation
Frameshift
53
For point mutations, a change from purine to purine or pyrimidine to pyrimidine is called...
Transition
54
For point mutations, a change from purine to pyrimidine (or viceversa) is called...
Tranversion
55
What is a silent mutation
Nucleotide substitution that codes for the same aminoacid (often in 3rd position of codon)
56
What is a missense mutation
Nucleotide substitution resulting in changed aminoacid (called conservative if new aminoacid is similar in chemical structure)
i.e. Sickle cell disease (substitution of glutamic acid with valine)
57
What is a nonsense mutation
Nucleotide substitution resulting in early stop codon
* Usually results in a nonfunctional protein
i. e. beta talasemia major
58
What is a frameshift mutation
Its a deletion or insertion of a number of nucleotides NOT DIVISIBLE BY 3, resulting in misreading of all nucleotides downstream
* Protein may be shorter or longer, and its function may be disrupted or altered
i. e. Duchenne muscular dystrophy, Tay-Sachs disease
59
What is an in-frame mutation
Its a deletion or insertion of a number of nucleotides DIVISIBLE BY 3
i.e. Cystic fibrosis
60
Type of mutation that results in a retained intron in the mRNA
Mutation at a splice site
61
Región of the DNA recognized by RNA polymerase
Promoter region
62
Mechanism of DNA repair in charge of repairing bulky helix-distorting lesions
Nucleotide excision repair
63
Molecules used in nucleotide excision repair
1. Specific endonucleases (reléase oligonucleotides containing damaged bases)
2. DNA polymerase
3. DNA ligase
64
Nucleotide excision repair occurs during which phase of the cell cycle
G1 phase
65
Defective nucleotide excision repair results in what patholgy
Xeroderma pigmentosum
66
Mechanism of DNA repair in charge of repairing spontaneous/toxic deamination
Base excision repair
67
Molecules used in base excision repair
1. Glycolase (removes altered base and creates AP site)
2. AP-Endonuclease (removes one or more nucleotides by cleaving the 5' end)
3. Lyase (cleaves de 3' end)
4. DNA Polymerase beta (fills the gap)
5. Ligase (seals the thing)
"GEL PLease"
68
DNA repair process deficient in Lynch syndrome
Mismatch repair
69
DNA repair process that carries the risk of losing genetic material
Nonhomologous end joining
*Brings together 2 strands of DNA fragments to repair double-stranded breaks
70
Prokaryotic aminoacid that is coded by the start codon and that, additionally, stimulates neutrophil chemotaxis
N-formylmethionine (fMet)
71
Function of promoter regions in the regulation of gene expression
Sites where RNA polymerase 2 and other transcription factors bind to DNA upstream from gene locus
*AT-rich sequences (TATA and CAAT boxes)
72
How many base pairs away are CAAT and TATA boxes from the site of transcription start
* CAAT: 75 bp
| * TATA: 25 bp
73
Regions of DNA that alter gene expression by binding positive (transcription factors) or negative regulators
Enhancers and silencer
*May be located close to, far from, or within the gene
74
Mechanism through which transcription factors alter gene expression
They facilitate bending of DNA
75
Primary site of ribosomal RNA transcription
Nucleolus
76
State the types of RNA transcribed by each type of euokaryote RNA polymerase
* RNA polymerase 1: rRNA
* RNA polymerase 2: mRNA
* RNA polymerase 3: tRNA
*1, 2, and 3 are numbered in the same order that their products are used in protein synthesis
77
RNA polymerase inhibited by alpha-amanitin
RNA polymerase 2
78
Modifications to hnRNA that take place in the nucleus before it can be considered mRNA
1. Capping of the 5’ end (addition of 7-methylguanosine cap)
2. Polyadenylation of 3’ end (~200 A’s)
3. Splicing out of introns
79
Cytosolic sites which contain exonucleases, decapping enzymes, and microRNAs; and where mRNAs can be stored for future translation
P-bodies
80
Name the steps in pre-mRNA splicing
1. Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form the spliceosome
2. Lariat-shaped (looped) intermediate is generated
3. Lariat is released to precisely remove intron and join 2 exons
81
Antibodies to snRNPs (anti-Smith) are specific for what pathology
SLE
82
What is the function of microRNAs
Regulate gene expression by targeting the 3’ untranslated region of specific mRNAs for degradation or translation repression
83
Part of the tRNA that covalently binds aminoacids
The 3’ end is the acceptor stem, it is a CCA end
84
tRNA arm in charge of binding to the ribosome
T-arm
*Contains ribothymidine, pseudouridine, cytidine / T-arm tethers tRNA molecule to ribosome
85
tRNA arm necessary for tRNA recognition by the correct aminoacyl tRNA synthetase
D-arm
*Contains dihydrouridine residues
86
Name the 2 groups of posttranslationsl modifications done to mRNA
1. Trimming (removal of N- or C- terminal propeptides from zymogen to generate mature protein)
2. Covalent alterations
87
Function of chaperone proteins
Intracellulr proteins involved in facilitating and/or maintaining protein folding
88
Enzyme required for the degradation of adenosine and deoxyadenosine into inosine
Adenosine deaminase (ADA)
89
One of the enzymatic deficiencies that can lead to severe combined immunodeficiency (SCID) that can be found in the purine salvage pathwat
Adenosine deaminase (ADA)
90
Substrate that is accumulated in adenosine deaminase (ADA) deficiency that inhibits ribonucleotide reductase
dATP
*This leads to inhibition of both nucleotide synthesis pathways
91
Cell types that are most affected by adenosine deaminase (ADA) deficiency
T- and B-cells
