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STEP 1 (4) > Biochemistry-Molecular > Flashcards

Biochemistry-Molecular Flashcards

1
Q

How does DNA exist?

A

In a condensed, chromatin form in order to fit in the nucleus. Negatively charged DNA loops twice around positively carged histone octamers to form nucleosomes

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2
Q

What AAs are histones rich in?

A

lysine and arginine

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3
Q

What makes up the histone octamers?

A

(H2A, H2B, H3, and H4) x2

and H1 links them

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4
Q

DNA and histone synthesis occurs during what phase?

A

S

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5
Q

What is heterochromatin?

A

condensed, appears darker on EM

Transcriptionally inactive, sterically inaccessible

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6
Q

What is euchromatin?

A

less condensed, appears lighter

transcriptionally active, and sterically accessible

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7
Q

Describe DNA methylation

A

Template strand cytosine and adenine are methylated in DNA replication, which allows mismatch repair enzymes to distinguish between old and new strand in prokaryotes.

DNA methylation at CpG islands repressed transcription

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8
Q

Describe Histone methylation

A

Usuallu reveribly represses DNA trnscription, but can activate it in some cases (acetylation usually relaxes DNA coiling to allow for transcription)

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9
Q

Describe the nucleotides

A

PURines (A,G)- 2 rings PUR As Gold

PYrimidines (C,T,U)- 1 ring CUT the PY (pie)

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10
Q

More about nucleotides

A

Thymine has a methyl (found in DNA)

Deamination of cytosine makes uracil (found in RNA)

G-C bonds (3H) stronger than A-T bonds (2H). Higher G-C content= higher melting temp of DNA

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11
Q

What AAs are needed for purine synthesis?

A

Glycine

Aspartate

Glutamine

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12
Q

What is the difference between a nucleoside and a nucleotide?

A

nucleoside= base + deoxyribose (sugar)

nucleotide= based + deoxyribose + phosphate; linked by 3’-5’ phosphodiester bonds

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13
Q

What are the initial steps of pyrimidine base production?

A

1) Gutamate + CO2 (add 2 ATP and via carbamoyl phosphate syntthetase II) produces carbamoyl phosphate
2) carbamoyl phosphate + aspartate = orotic acid via dihydrooratate dehydrogenase

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14
Q

What drug blocks the conversion of carbamoyl phosphate + aspartate = orotic acid via dihydrooratate dehydrogenase?

A

leflunomide

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15
Q

What are the next steps in pyrimidine synthesis?

A

3) orotic acid + PRPP (from Ribose 5-P using PRPP synthetase) = UMP and then UDP
4) UDP converted to either CTP or dUDP via ribonucleotide reductase

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16
Q

What drug inhibits the conversion of UDP to dUDP via ribonucleotide reductase?

A

Hydroxyurea

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17
Q

What happens to dUDP in pyrimidine synthesis?

A

5) converted to dUMP
6) dUMP is converted to dTMP via thmidylate synthase by oxidizing N5N10- methylene THF to DHF (DHF is then made back into THF via dihydrofolate reductase)

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18
Q

What drug blocks thymidylate synthase?

A

5-FU

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19
Q

What drug blocks dihydrofolate reductase?

A

Methotrexate, Trimethoprim, pyrimethamine

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20
Q

How are purines made?

A

1) convert PRPP to IMP (6-MP, azathioprine (prodrug of 6-MP) blocks)
2) IMP to AMP or GMP via IMP dehydrogenase

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21
Q

What drug blocks conversion of IMP to GMP via IMP dehydrogenase?

A

mycophenolate, ribavirin

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22
Q

What other pathway besides de novo pyrimidine synthesis is carbamoyl phosphate involved in?

A

urea cycle

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23
Q

Purine salvage pathway- note that you can convert Adenosine to inosine using adenosine deaminase

A
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24
Q

What drugs inhibit the conversion of hypoxathine to xanthine and xanthine to uric acid?

A

allopurinol and Febuxostat

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25
Q

What does adenosine deaminase deficiency cause?

A

Excess ATP and dATP imbalances nucleotide pools via feedback inhibition of ribonucleotide reductase, which prevents DNA synthesis and thus, decreases lymphocyte counts (one of the major causes of AR SCID)

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26
Q

What is Lesch-Nyhan syndrome?

A

Defective purine salvage due to absent HGPT which converts hypoxanthine to IMP and guanine to GMP resulting in excess uric acid production and de novo purine synthesis

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27
Q

What is the MOA of Lesch-Nyhan syndrome?

A

X-linked recessive

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28
Q

How does Lesch-Nyhan syndrome present?

A

intellectual disability

self-mutilation

aggression

hyperuricemia

gout

dystonia

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29
Q

How is Lesch-Nyhan syndrome tx?

A

allopurinol or febuxostat

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30
Q

Genetic code features

A

Unambiguus- each codon specifies only 1 AA

Degenerate/Redundant- most AAs are coded by multiple codons (exceptions: methionine and tryptophan are encoded y only 1 codon, AUG and UGG, respectively)

Commaless, nonoverlapping- read from a fixed starting pt as a continuous sequence of bases

Universal- genetic code is conserved throughout evolution (except in mitochondria)

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31
Q

Describe the origin of replication of DNA

A

particular consensus sequence of base pairs in genome where DNA replication begins. May be single (prokaryotes) or multiple (eukaryotes)

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32
Q

What is the replication fork in DNA replication?

A

Y-shaped region along dNA where the leading and lagging strands are made

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33
Q

What does helicase do?

A

unwinds DNA template at the replication forks (single-stranded binding proteins prevent the strands from reannealing)

34
Q

What do DNA topoisomerases do?

A

create single or double stranded DNA breaks to add or remove supercoils (fluoroquinolones inhibit prokaryotic enzymes topo II (DNA gyrase) and topo IV)

35
Q

What does primase do?

A

Makes an RNA primer on which DNA polymerase III can initiate replication

36
Q

Describe DNA polymerase III

A

Prokaryotic only. Elongates the leading strand by adding deoxynucleotides to the 3’ end and elongates the lagging strand until itreaches the primer of the preceding fragment

so, DNA polymerase III has 5’-3’ activity and proofreads with 3’-5’ exonuclease

37
Q

Describe DNA polymerase I

A

Prokaryotic only. Degrades RNA primer and replaces it with DNA

Has same function as DNA polymerase III but also excises RNA primer with 5’-3’ exonuclease

38
Q

What does DNA ligase do?

A

catalyzes the formation of a phosphodiester bond with a strand of double-stranded DNA (i.e. joins Okazaki fragments)

39
Q

What is telomerase?

A

An RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication (eukaryotes only)

40
Q

Severity of damage in DNA mutation types

A

silent < missense < nonsense < frameshift

41
Q

What is a ‘transition’ mutation? Transverse?

A

Transition- purine to purine (e.g. A to G) or pyrimidine to pyrimidine (e.g. C to T)

Transversion- purine to pyrimidine (e.g. A to T) or vice-versa

42
Q

What is a silent mutation?

A

when nucleotide substitution codes for the same AA; often the result of a base change in the 3rd position

43
Q

What is a missense mutation?

A

substitution causes a new AA to be inserted (e.g. valine for glutamic acid in SCD)

44
Q

Describe the Lac operon

A

Glucose is the preferred metabolic substrate in E. Coli but when it is absent and lactose is available, the lac operon is activated to switch to lactose use.

45
Q

How does the shift from glucose to lactose use in E. Coli occur?

A

Low glucose increases adenylyl cyclase actvity to increase generation of cAMP from ATP which activates catabolite activator protein (CAP) to induce transcription of Lac Z, Y, and A (glucose inhibits adenylyl cyclase normally)

Similarly, high lactose unbinds a repressor protein (Lacl) from the repressor/operator site to induce transcription

So you need both low glucose AND high lactose for this mechanism to occur (in other words, just having low glucose wont produce more lactose)

46
Q

How does nucleotide excision repair occur?

A

specific endonucleasaes release the oligonucleotides containing damaged based; DNA polymerase and ligase fill and reseal the gap, respectively.

Occurs in G1 phase

47
Q

Nucleotide excision repair is defective in what disease?

A

Xeroderma pigmentosum, which prevents repair of pyrimidine dimers because of UV light exposure

48
Q

How does base excision repair occur?

A

Base specific glycosylase removes altered based and creates an AP site (apurinie/apyrimidinic)\

One or more nucleotides are removed by AP-endonuclease, which cleaves the 5’ end. Lyase cleaves the 3’ end. DNA polymerase-B fils the gap and DNA ligase seals it.

Occurs throughout the cell cycle

49
Q

How does mismatch repair occur?

A

Newly synthesized strand is recognized, nucleotides are removed, and the gap is filled and sealed

Occurs mostly in G2

50
Q

Mismatch repair is defective in what disease?

A

Hereditary nonpolypopis colorectal cancer

51
Q

What is nonhomoglous end joining?

A

Brings together 2 ends of DNA fragments to repair double-strand breaks. No requirement for homology. Some DNA may be lost

52
Q

Nonhomoglous end joining is mutated in what diseases?

A

ataxia telangiectasia and Fanconi anemia

53
Q

DNA/RNA?protein synthesis direction

A

DNA and RNA are both synthesized 5’-3’. The 5’ end of the incoming nucleotide bears the triphosphate (energy source for bonds)

Protein synthesis is N-terminus to C-terminus

54
Q

What is the mRNA start codon?

A

AUG (or rarely GUG)

In eukaryotes, codes for methionine, which may be removed before translation is complete

In prokaryotes, codes for N-formylmethionine (fMet)

55
Q

What does fMet do in prokaryotes?

A

neutrophil chemotaxis

56
Q

What are the mRNA stop codons?

A

UGA, UAA, and UAG

57
Q

Parts of a eukaryotic gene

A

Enhancer- Promoter (TATA box)- start of transcription- Introns/Exons- Termination Signals

58
Q

What is the promoter region?

A

region where RNA polymerase II and multiple other transcription factors bind to DNA upstream from the gene locus (AT-rich sequence with TATA and CAAT boxes)

Pormoter mutation commonly results in a dramatic decrease in the level of gene transcription

59
Q

What is the enhancer region?

A

Stretch of DNA that alters gene expression by binding trnscription factors

Enhancers and silencers may be located close to, far from, or even within (in an intron) the gene

60
Q

What is a silencer?

A

site where negative regulators (repressors) bind

61
Q

What RNA polymerases do Eukaryotes have?

A

I (makes rRNA)

II (makes mRNA, larged RNA; opens DN at promoter sites)

III (makes tRNA, smallest)

No proofreading function, but can initiate chains.

62
Q

What is a-amanitin?

A

Found in Amanita phaloides, (death cap mushrooms) this inhibits RNA polymerase II and causes severe hepatotoxicity if ingested

63
Q

How many RNA polymerases do prokaryotes have?

A

1 polymerases (multisubunit complex) makes all 3 kinds of RNA

Rifampin inhibits RNA polymerase in prokaryotes

64
Q

RNA processing (eukaryotes)

A

The initial transcript is called heterogeneous nucleus RNA (hnRHA). hnRHA is then modified and becomes mRNA.

The following processes occur in the nucleus following transcription:

Capping of 5’ end (addition of 7-methylguanosine cap)

Polyadenylation of 3’ end (200 A’s)

Splicing out of introns

Capped, tailed, and spliced transcript is called mRNA

65
Q

What happens to newly made mRNA?

A

transported out of the nucleus into the cytosol, where it is translated.

mRNA quality control occurs at cytoplasmic P-bodies, which contain exonucleases, decapping enzymes, and microRNAs

66
Q

How does splicing of pre-mRNA occur?

A

1) Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form spliceosomes
2) Lariat-shaped (looped) intermediate is formed
3) Lariat is released to precisely remove intron and join 2 exons

67
Q

Abs to spiceosomal snRNPs (anti-Smith bodies) are highly specific for what disease?

A

SLE

68
Q

Anti-U1 RNP Abs are highly specific for what disease?

A

Mixed CT Disease

69
Q

Describe exons and introns

A

Exons contain the actual genetic info coding for proteins and introns are intervening noncoding segments

Different exons are frequently combined by alternative splicing to produce a larger number of unique proteins

70
Q

Describe the structure of tRNA

A

75-90 nucleotides with a 2ndary structure of a cloverleaf form, anticodon end/loop is opposite the 3’ aminoacyl end.

All tRNAs, eukaryotic and prokaryotics, have CCA at the 3’ end along with a high percentage of chemically modified bases

The incoming AA is covalently bound to the 3’ end of the tRNA

71
Q

What does the t-arm of tRNA do?

A

contains the TyC (thymine, pseudouracil, and cytosine) sequence needed for tRNA-ribosome binding

72
Q

What does the D-arm of tRNA do?

A

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

NOTE: The acceptor stem contains the 5’-CCA’-3’

73
Q

Describe tRNA charging

A

Aminoacyl tRNA synthetase (uses ATP) scrutinizes AAs before and after it binds to tRNA. If correct, the bond is hydrolyzed.

The AA-tRNA bond has energy for formation of peptide bond.

74
Q

What is ‘wobble’?

A

Accurate base pairing is usually required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd wobble position may code for the same tRNA/AA

75
Q

What are the 3 steps of protein synthesis?

A

Initiation

Elongation

Termination

76
Q

Describe protein Initiation

A

Initiated by GTP hydrolysis; initiation factors help assemble the 40S ribosomal subunit with the initiatory tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex

77
Q

What are the subunits of eukaryotic ribosomes?

A

40S + 60S - 80S

78
Q

What are the subunits of prokaryotic ribosomes?

A

30S + 50S - 70S

79
Q

Describe elongation protein synthesis

A

1) Aminoacyl-tRNA binds to the A site (except for the intitiator methionine)
2) rRNA (“ribozyme”) catalyzes the peptide bond formation, transfers growing polypeptide to AA in the A site
3) Ribosome advances 3 nucleotides toward the 3’ end of the mRNA, moving peptidyl tRNA to P site (translocation)

80
Q

Describe termination protein synthesis

A

Stop codon is recognized by release factor and the complete polypeptide is released from the ribosome

81
Q

What posttranslational modifications occur to proteins?

A

1) Trimming: removal or N- or C-terminal propeptides from zygomen to generate mature protein
2) Covalent alterations including: Phosphorylation, glycoylation, hydroxylation, methylation, acetylation, and ubiquitination

82
Q

What are Chaperone proteins?

A

Intracellular proteins involved in facilitating and/or maintaining protein folding.

STEP 1 (4) (18 decks)

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