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Step 1 biochemistry > Molecular biochem > Flashcards

Molecular biochem Flashcards

(65 cards)

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1
Q

How is DNA stored?

A

Chromatin
- DNA wrapped 2x around + histone = nucleosome
Beads on a string

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2
Q

Histones made mostly of?

A

Lysine and arginine

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3
Q

H1 histone binds?

A

Nucleosome and linker DNA

Stabilizes chromatin fiber

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4
Q

DNA and histone synthesized during what phase in cell cycle?

A

S phase

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5
Q

When does DNA condense to form chromosomes?

A

Mitosis

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6
Q

HeteroChromatin

A 
Highly Condensed 
EM darker
Transcriptionally inactive 
Sterically inaccessible
Barr bodies (inactive X chromosome) made of
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7
Q

Euchromatin

A

Less condensed
EM lighter
Transcribed
Sterically accessible

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8
Q

DNA methylation

A

CpG Methylation Makes DNA Mute

Allows mismatch repair enzymes to distinguish from old and new strands during DNA replication

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9
Q

During DNA replication what is methylated

A

Cytosine and adenine on template strand

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10
Q

Histone methylation

A

Reversible repression DNA transcription (some locations activate)

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11
Q

Histone acetylation

A

Relaxes DNA coil, make DNA active for transcription

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12
Q

NuceolSide

A

Base + (deoxy)ribose (Sugar)

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13
Q

NucleoTide

A

Base + (deoxy)ribose + phosohaTe

Linked by 3’-5’ phosophodiester bond

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14
Q

PURines

A

(A, G) = PURe As Gold

2 rings

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15
Q

PYrimidines

A

(C, U, T) = CUT the PY

Thymine has a methyl

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16
Q

G-C bond

A

3 H bonds

Increase GC content = increases melting temp DNA

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17
Q

Which AA required for Purine synthesis

A

Glycine
Aspartate
Glutamine

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18
Q

Things that disrupt pyrimidine synthesis

A

Leflunomide: inhibit dihydroorotate dehydrogenase
Methotrexate (MTX), trimethoprim (TMP), and pyrimethamine: inhibit dihydrofolate reductase
5-fluorouracil (5-FU): forms 5-F-dUMP, which decreases dTMP

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19
Q

Disrupt purine synthesis

A 
6 mercaptopurine (6-MP): inhibit de novo synthesis
Mycophenolate and ribavirin: inhibit inosine monophosphate dehydrogenase
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20
Q

Disrupt purine and pyrimidine synthesis

A

Hydroxyurea: inhibit ribonucleotide reductase

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21
Q

Adenosine deaminase deficiency

A

Defect purine salvage pathway
Autosomal recessive SCID
Decrease aATP -> toxicity in lymphocytes

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22
Q

Leach-Nyhan syndrome

A 
Defect purine salvage pathway: defect convert hypoxanthine to IMP and guanine to GMP
X linked recessive 
HGPRT:
Hyperuricemia (orange sand in diaper)
Gout
Pissed off (self mutilation and aggression)
Retardation 
DysTonia
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23
Q

Treatment Leach-Nyhan syndrome

A

Allopurinol or febuxostat

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24
Q

Helicase

A

Unwind DNA

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25
DNA topoisomerase
Remove supercoil
26
Primase
Makes RNA primer than DNA ploymerase III initiate DNA replication
27
DNA ligase
Joins Okazaki fragments
28
DNA polymerase I
Prokaryotic only | Degrade RNA primer and replace with DNA
29
Telomerase
Dysregulated in cancer = unlimited replication Eukaryotes only Adds DNA to the 3' end to avoid loss genetic material
30
Types of single strand DNA repair?
1. NucleoTide excision repair 2. Base excision repair 3. Mismatch repair
31
Types of double stranded DNA repair?
1. Nonhomologous end joining | 2. DNA/RNA/protein synthesis direction
32
What is defective in xeroderma pigmentosum?
Defective nucleotide excision repair= prevent repair pyrimidine dimmers from UV light damage
33
Defect nucleotide excision repair results in?
Xerderma pigmentosum
34
What type of repair for spontaneous/toxic deamination?
Base excision repair
35
What is defective in Lynch Syndrome
Defective Mismatch repair = hereditary nonpolyposis colorectal cancer
36
Mismatch repair defect results in?
Lynch syndrome
37
Mutation in nonhomologous end joining (double strand break repair) occurs in?
Ataxia telangiectasia and Fanconi anemia
38
Direction of DNA and RNA synthesis and protein synthesis
5' to 3' for DNA and RNA | N terminus to C terminus for protein synthesis
39
Drug blocking DNA replication often modify what?
Triphosphate bond of 3' OH modified to prevent addition of next nucleotide
40
mRNA start codons
AUG (rarely GUG)
41
mRNA stop codons
``` UGA = U Go Away UAA = U Are Away UAG = U Are Gone ```
42
Prokaryotes start codons code for?
N-formlymethionine (fMet) = neutrophil chemotaxis
43
Eukaryotes start codons code for?
Methionine
44
Severity of damage based on mutations in DNA?
Silent<
45
Types of point mutations?
Silent, missense, nonsense
46
What is a missense mutation and name one disease that is caused by a missense mutation
Nucleotide substitution cause change in AA, sickle cell disease (substitution glutamic acid with valine)
47
What is a frameshift mutation?
- Deletion or insertion in nucleotides by number not divisible by 3 = misread nucleotides downstream - function disrupted or altered
48
Diseases caused by frameshift mutation?
Duchenne muscular dystrophy and Tay-Sachs disease
49
Lac operon in E coli
- Glucose preferred over lactose - lactose metabolism activated by lac operon if glucose low and lactose present - low glucose = activate ardently cyclase= increase cAMP = increased CAP = increased transcription - high lactose = increase transcription
50
Promoter regulation in gene expression?
- Site RNA polymerase II binds to DNA upstream | - AT rich and contains TATA and CAAT boxes
51
Name Eukaryotes RNA polymerases and what they make
RNA polymerase I: rRNA (rampant) RNA polymerase II: mRNA (massive) RNA polymerase III: tRNA (tiny) and 5S rRNA
52
Alpha-amanitin inhibits?
- inhibit RNA polymerase II - causes hepatotoxicity - Found in death cap mushrooms
53
Rifampin inhibits?
Prokaryotes RNA polymerase
54
Actinomycin D inhibits?
Prokaryotes and eukaryotes RNA polymerase
55
P bodies do what?
Quality control of mRNA in cytoplasm
56
What RNA modification occurs in the nucleus of eukaryotes?
1. 5' cap 2. Polyadenylatiom- 3' tail 3. Splice out introns
57
Introns
- Non-coding DNA | - spliced out and stay in nucleus
58
Exons
-coding DNA that get expressed
59
microRNA
- Small, non-coding RNA - post-transcriptionally regulated protein expression - inactivate target mRNA = decrease translation into protein
60
What part of tRNA binds to AA?
Can Carry Amino acids -CCA is a 3' end for eukaryotes and prokaryotes
61
tRNA components
1. T arm: ribosome binding 2. D arm: contains dihydrouridine which helps aminoacyl tRNA synthetase recognize matches 3. Acceptor stem: 5'-CCA-3' AA acceptor site
62
Wobble position
3rd position of codon, closest to D arm
63
Protein synthesis steps
1. Initiation: Eukaryotes: 40S + 60S -> 80S Even) ; ProkaryOtes: 30S+ 50S-> 70S (Odd) 2. Elongation : going APE A site= incoming Aminoacyl-tRNA P site= accomadates growing Peptide E site= holds Empty tRNA as it Exits 3. Termination : release factor recognize stop codon and release polypeptide from ribosome
64
Post-translational modifications
1. Trimming : zymogen to mature protein (trypsiinogen to trypsin) 2. Covalent alterations: phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination
65
Chaperone proteins
Facilitate and maintain protein folding

Step 1 biochemistry (6 decks)

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