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High Yield General Principles > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

What is the charge of DNA?

A

negative

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2
Q

which histone binds ot the nucleosome to stabilise the chromatin fiber?

A

H1

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3
Q

What is the structure of heterochromatin? How does it appear on EM? Is it active transcriptionally?

A

HeteroChromatin = Highly Condensed

Darker on EM

Inactive transcriptionally

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4
Q

What is the structure of euchromatin? How does it appear on EM? is it active transcriptionally?

A

less condensed

lighter on EM

active

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5
Q

How do prokaryotes distinguish between old and new strands during DNA replication?

A

template strand cytosine and adenine are methylated

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6
Q

What does methylation of DNA at CpG islands do?

A

Represses transcription

CpG Methylation Makes DNA Mute

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7
Q

What does histone methylation do?

A

can repress or activate DNA transcription depending on methylation location

Histone Methylation Mostly Makes DNA Mute

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8
Q

What does histone acetylation do?

A

Relaxes DNA coiling to allow for transcription

Histone Acetylation makes DNA Active

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9
Q

which nucleotides are purines? What is a purine?

A

PURines have 2 rings

A, G

PURe As Gold

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10
Q

Which nucleotides are pyrimidines? What is the structure of a pyrimidine?

A

PYrimidine has 1 ring

C, U, T

CUT the PY

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11
Q

How many H bonds does a G-C form and an A-T form? What does this mean for the melting temperature of DNA?

A

G-C forms 3. A-T forms 2

Therefore more G-C = higher melting temp of DNA

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12
Q

How can cytosine form uracil?

A

Deamination of cytosine –> uracil

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13
Q

What AAs are necessary for purine synthesis?

A

GAG - Glycine, Aspartate, Glutamine

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14
Q

What is a nucleoSide and a nucleoTide?

A

NucleoSide = base + ribose Sugar

NucleoTide = base + ribose sugar + phosphaTe

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15
Q

Describe the de novo synthesis of purines

A

Start with a sugar and phosphate (PRPP) and add the base

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16
Q

Describe the de novo synthesis of pyrimidines

A
  1. Make a temporary base of orotic acid
  2. Add sugar + phosphate (PRPP)
  3. modify the base to what you want
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17
Q

What converts ribonucleotides to deoxyribonucleotides?

A

ribonucleotide reductase

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18
Q

How does leflunomide work?

A

immunosuppressive that inhibits dihydrooratate dehydrogenase

Interterferes with nucleotide synthesis

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19
Q

How does mycophenolate and ribavirin work?

A

inhibit IMP dehydrogenase interfering with nucleotide synthesis

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20
Q

How does hydroxyurea work?

A

inhibits ribonucleotide reductase interfering with nucleotide synthesis

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21
Q

How does 6-MP work? What is its prodrug?

A

prodrug - azathioprine

inhibits de novo purine synthesis

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22
Q

How does 5-FU work?

A

Inhibits thymidylate synthase and stops nucleotide synthesis

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23
Q

How does methotrexate, trimethoprim, and pyrimethamine work??

A

Inhibits dihydrofolate reductase and interferes with nucleotide synthesis in humans, bacteria and protozoa respectively

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24
Q

How does adenosine deaminase deficiency lead to SCID?

A

Excess ATP and dATP imbalances nucleotide pool by inhibiting ribonucleotide reductase via feedback inhibition. This leads to more purines than pyrimidines. This prevents DNA synthesis and thus decreases lymphocyte count –> SCID

Since developing T and B cells are the most mitotically active, the immune system suffers the most.

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25
Q

How does Lesch-Nyhan syndrome lead to excess uric acid production and de novo purine synthesis?

A

Defective purine salvage due to absent HGPRT enzyme. This enzyme converts IMP and guanine to GMP. This leads to excess uric acid and de novo purine synthesis.

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26
Q

What are the symptoms of Lesch-Nyhan syndrome

A

Hyperuricemia

Gout

Pissed off

Retardation

dysTonia

HGPRT enzyme involved

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27
Q

How should Lesch-Nyhan syndrome be treated?

A

Allopurinal or febuxostat

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28
Q

How does the term ‘unambiguous’ describe the genetic code?

A

Each codon is specific to only 1 amino acid

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29
Q

How does the term ‘degenerate’ describe the genetic code?

A

Most amino acids coded by multiple codons

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30
Q

How does the term ‘nonoverlapping or commaless’ describe the genetic code?

A

Read from a fixed starting point as a continuous sequence of bases

31
Q

How does the term ‘universal’ dsecribe to the genetic code?

A

Genetic code is conserved throughout evolution

32
Q

Describe the process of DNA replication

A
  1. DNA replication begins at a particular sequence of base pairs
  2. DNA topoisomerases create a single or double stranded break in the helix to add or remove supercoils
  3. DNA helicase unwinds the DNA template at the replication fork
  4. Single stranded binding proteins prevent the strands from reannealing
  5. Primase makes an RNA primer on the DNA
  6. DNA polymerase I and III initiates replication (in prokaryotes only). Both have a 5’ to 3’ synthesis but pol 3 has a 3’ to 5’ proofreading exonuclease.
  7. DNA pol 1 then degrades the RNA primer and replaces it with DNA.
  8. DNA ligase then joins the okazaki fragments
  9. Telomerase adds DNA to 3’ ends of chromosomes to avoid loss of info. Eukaryotes only
33
Q

What is a missense mutation? What is a nonsenes mutation?

A

Missense - different amino acid codon

Nonsense - premature stop codon

34
Q

What is the lac operon? When is it activateD? In what bacterium does it

A

Gene in e.coli which when on switches cell to lactose metabolism

Activated when low glucose and high lactose

35
Q

Describe the process of activation of the lac operon

A
  1. Low glucose –> increased adenylyl cyclase activity –> increased generation of cAMP –> activation of catabolite activator protein (CAP) –> increased transcription
  2. high lactose –> unbinds repressor protein from operator site –> increases transcription of lac genes

Requires both processes to strongly express the lac genes. if lactose unavailable to amount of low glucose will activate the lac genes.

36
Q

What is nucleotide excision repair?

A

Single stranded DNA repair which Repairs damaged oligonucleotides through UV. Repairs bulky helix distorting lesions.

Occurs in G1 phase of cell cycle

37
Q

Which DNA repair mechanism is defective in xeroderma pigmentosum?

A

Nucleotide excision repair

38
Q

What is base excision repair?

A

Single stranded DNA repair that Removes and repairs 1-10 altered bases. Repairs small non helix distorting lesions. Occurs throughout cell cycle.

39
Q

What is mismatch repair?

A

Single stranded DNA repair that reapirs mismatched nucleotides in a newly synthesised DNA strand. Occurs in G2 of cell cycle.

40
Q

What DNA repair mechanism is defective in hereditary nonpolyposis colorectal cancer?

A

mismatch repair

41
Q

What is non homologous end joining?

A

Double stranded DNA repair that reapirs double stranded breaks. No requirement for homology. Some DNA might be lost.

42
Q

Which DNA repair mechanism is defective in ataxia telangiectasia?

A

nonhomologous end joining

43
Q

Which DNA repair mechanism is defective in fanconi anemia?

A

nonhomologous end joining

44
Q

What is the direction of DNA and RNA synthesis?

A

5’ to 3’

45
Q

What is the direction of protein synthesis?

A

N-terminus to C-terminus

46
Q

What is the direction in which mRNA is read?

A

5’ to 3’

47
Q

What is the mRNA start codon?

A

AUG

AUG inAUGrates protein synthesis

48
Q

What is the start codon in eukaryotes and in prokaryotes?

A

eukaryotes - methionine

prokaryotes - fMet

49
Q

What are the mRNA stop codons?

A

UGA, UAA, UAG

UGA = U Go Away

UAA = U Are Away

UAG = U Are Gone

50
Q

Draw the functional organisation of a eukaryotic gene

A
51
Q

What would happen if the promoter sequence was mutated?

A

decrease in level of gene transcription

52
Q

How is the promoter site activated?

A

RNA pol 2 binds to TATA box in promoter

53
Q

What is an enhancer or silencer of gene expression?

A

Enhancer - stretch of DNA that alters gene expression by binding transcription factors

Silencer - Site where repressors bind.

54
Q

What does RNA polymerase I, II, and III do in eukaryotes?

A

pol I - makes rRNA

pol II - makes mRNA

pol III - makes tRNA

55
Q

What effect does ingestion of death cap mushrooms have and how?

A

Causes severe hepatotoxicity due to α-amanitin which inhibits RNA pol 2.

56
Q

What does rifampicin do?

A

Inhibits RNA polymerase in prokaryotes

57
Q

What does actinomycin D do?

A

inhiits RNA polymerase in both eukaryotes and prokaryotes

58
Q

What does the RNA polymerae in prokaryotes do?

A

1 RNA polymerase makes all 3 kinds of RNA, rRNA, tRNA, mRNA

59
Q

Describe the process of RNA processing in eukaryotes in the nucleus

A
  1. Initial transcript made is called heterogenous nuclear RNA (hnRNA)
  2. hnRNA is then capped at 5’end with 7-methylguanosine cape
  3. 3’ end is polyadenylated
  4. Introns spliced out.
  5. Becomes mRNA post processing
60
Q

What occurs to the mRNA after it leaves the nucleus?

A

Goes to cytosol for translation

Can enter P-bodies for quality control which contains enzymes and microRNAs. mRNA can also be stored here for future translation.

61
Q

What is the genetic signal for polyadenylation?

A

AAUAAA

62
Q

Describe the process of pre-mRNA splicing

A
  1. pre-mRNA combines with snRNPs and other proteins to form spliceosome
  2. lariat-shaped (Looped) intermediate is generated
  3. Lariat is released to remove intron and join 2 exons
63
Q

What are anti-smith antibodies?

A

antibodies to spliceosomal snRNPs found in systemic lupus erythmetasus and mixed conntective tissue disease.

64
Q

What are anti-U1 RNP antibodies associated with?

A

mixed connective tissue disease (MCTD)

65
Q

How many nucleotides can be found in tRNA?

A

75-90

66
Q

What is the overall shape and structure of tRNA?

A

cloverleaf shape

anticodon end is opposite the 3’ end

Contains a T-arm, a D-arm, variable arm

67
Q

What can be found on the 3’ end of tRNA?

A

amino acid attached to CCA codon

Can Carry Aminoacids

68
Q

What is found in the T-arm of the tRNA?

A

Cotnains TΨC (thymine, pseudouracil, cytosine) sequence necessary for tRNA-ribosome binding

69
Q

What is found in the D-arm of tRNA?

A

dihydrouracil residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase

70
Q

Describe how tRNA is charged

A
  1. Aminoacyl-tRNA synthetase (1 per AA) recognizes D-arm and attaches AA to 3’ end CCA
  2. If incorrect bond is hydrolyzed by aminoacyl-tRNA synthetase
71
Q

Explain the Wobble hypothesis

A

Accurate base pairing required only for first 2 nucleotide positions of an mRNA codon. the 3rd ‘wobble’ position may form an unconventional base pair if not correct (degenerecy of genetic code)

72
Q

Explain how protein synthesis is initiated

A
  1. Initiated by GTP hyrdrolysis.
  2. Initiation factors (IF) help assemble 40S ribosomal subunit with the initator tRNA
  3. IFs released when mRNA and 60S subunit assemble with complex

GTP - tRNA Gripping and Going places (translocation)

73
Q

What is the ribosomal subunits found in eukaryotes and in prokarytoes?

A

Eukaryotes: 40S + 60S –> 80S (Even)

prOkaryotes: 30S + 50S –> 70S (Odd)

74
Q

Describe the process of elongation in protein synthesis

A
  1. Aminoacyl-tRNA binds to A site
  2. rRNA

High Yield General Principles (2 decks)

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