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First Aid - Biochemistry > Molecular > Flashcards

Molecular Flashcards

1
Q

Chromatin

A

DNA exsits in condenssed, chromatin form in order to fit into the nucleus

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2
Q

Chromatin structure

A
  • ‘beads on a string’
  • (-) charged DNA wraps around (+) charged histone twice to form a nucleosome = ‘bead’
  • Histones= rich in AA lysine and arginine
  • H1 binds nucleosome and ‘linker DNA’ thereby stabilizing chromatin fiber
    • have nucleosome core ( H2A, H2B, H3, H4 x2) and the core are connected by **H1 ( **only histone not in the core)
  • mitosis = DNA condenses to form chromos
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3
Q

Heterochromatin

A

Condensed, transcriptionally inactive, sterically inaccessible

HeteroChromatin= Highly Condensed

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4
Q

Euchromatin

A

Eu = true –> truly transcirbed

Less condensed, transcriptionally active, sterically **accessible **

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5
Q

DNA methylation

A

template strand cytosine and adenine methylated in DNA replication

allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes

DNA methylation at **CpG islands **represses transcription

‘CpG Methylation makes Mute’

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6
Q

Histone methylation

A

reversible repression of DNA transcription BUT can activate it sometimes

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7
Q

Histone acetylation

A

relaxes DNA coiling and allows for transcription

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8
Q

Nucleotides

A

base + deoxyribose+ phosphate

linked by **3’-5’ phosphodiester bone **

are Purines and Pyrimidines

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9
Q

purines

A

Adenine

Guanine

2 rings

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10
Q

Pyrmidines

A

Cytosine, Thymine and Uracil

1 ring

uracile ONLY in RNA and thymine in DNA

deamination of cytosine makes uracil

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11
Q

Bonds between nucleotides

A

A:T = 2

C:G = 3

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12
Q

Purine synthesis: de novo

A

start with sugar + phosphate ( PRPP)

Add base

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13
Q

Things necessary for purine synthesis

A

GAG: **glutamine, aspartate and glycine **

and THF

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14
Q

Pyrimidine synthesis: de novo

A

**requires aspartate **

make temporary base ( orotic acid)

  1. add sugar + phosphate ( PRPP)
  2. Modify base
  3. rubonucleotides are synthesizes first and are converted to deoxyribonucleotides by **ribonucleotide reductase **
  4. Carbamoyl phosphate is involved in 2 metabolic pathways: **de novo pyrimidine synthesis and urea cycle **
  5. various anti-neoplastic and antibiotic drugs function by interfering with nucleotide synthesis
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15
Q

Drugs affecting nucleotide synthesis

A
  1. Leflunomide - inhibits dihydrorotate dehydrogenase
  2. Mycophenolate and ribavirin = inhibit **IMP dehydrogenase **
  3. Hydroxyurea = inhibits **ribonucletide reductase **
  4. 6-mercaptopurin and its’ prodrug azathioprine - inhibit **de novo purine sythesis **
  5. 5-fluorouracil ( %-FU) - inhibit thymidylate synthase ( decreases dTMP)
  6. Methotrexate (MTX), trimethoprim( TMP) and pyrimethamine - inhibits DHFR ( dihydrofolate reductase) –> decreases dTMP in humans, bacteria and protozoa
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16
Q

Purine salvage deficiencies

A

adenosine deaminase deficiency

Lesch-Nyhan syndrome

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17
Q

Adenosine deaminase deficiency

p.68 for drawing

A

excess ATP and dATP imbalances nucleotide pool via feedback inhibitionof ribonucleotide reductase –> prevents DNA synthesis and thus decrease lymphocyte count

is one of the major causes of **autosomal recessive SCID **

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18
Q

Lesch-Nyhan syndrome

p.68 for drawing

A

defective purine salvage due to absent **HGPRT ( **converts hypoxanthine –> IMP and guanine –> GMP)

results in excess uric acid production and **de novo purine synthesis **

**X-linked recessive **

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19
Q

Lesch-Nyhan syndrome findings

A

HGPRT:

Hyperuricemia

Gout

Pissed off ( aggression and self-mutilation)

Retardation ( intellectual disability)

DysTonia

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20
Q

Lesch-Nyhan syndrome Tx

A

allopurinol

febuxostat ( 2nd-line)

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21
Q

unambiguous genetic code

A

each codon specifies only 1 AA

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22
Q

degenerate/ redundant genetic code

A

most AA are coded by multiple codons

Exceptions: methionine( AUG) and tryptophan(UGG) endcoded by only 1 codon

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23
Q

Severity of mutations

A

frameshift > nonsense > missense>> silent

  • For silent, missense and nonsense mutations:
    • Transition: purine to purine OR pyrimidine to pyrimidine
    • Transversion: purine to pyrimdine and vice versa
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24
Q

Silent Mutation

A

nucleotide substitution but still codes for the same AA; often a base change in 3rd position of codon - tRNA wobble

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25
Q

Missense Mutation

A

nucleotide substitution resulting in changed AA

called conservative if AA is similar in chem structure

ex: sickle cell

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26
Q

Nonsense mutation

A

nucleotide substitution resulting in early stop codon

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27
Q

Frameshift mutation

A

deletion or insertion of a number of nucleotides not divisible by 3 resuling in misreading of all the nucleotides downstream

usually results in a truncated or non-functional protein

ex: duschenne muscular dystrophy

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28
Q

Types of single strand DNA repair

A

Nucleotide excision repair

Base excision repair

Mismatch repair

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29
Q

Nucleotide excision repair

A

type of DNA repair

specific endonucleases release the oligonucleotide containing damaged bases

DNA polymerase and ligase fill and reseal the gap

mech to repair **bulky, helix-distorting lesions **

defective in xeroderma pigmentosum - inability to repair pyrimidine dimers due to UV exposure

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30
Q

Base excision repair

A

type of DNA repair

base-specific glycosylases recognize altered base and create AP site ( apurinic/apyrimidinic)

one or more nucleotides are remved by Ap-endonucleases which cleave the 5’ end

lyase cleaves the 3’ end

DNA-polymerase-Beta fills the gaps

DNA ligase seals it

important in repair of spotaneous/toxic deamination

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31
Q

Mismatch repair

A

Newly synthesized strand recognized

mismatched nucleotides are removed

gap is refilled and resealed

defective in hereditary non-polyposis colorectal cancer (HNPCC)

32
Q

Doble stranded DNA repair

A

**non-homologous end joining **

brings together 2 ends of DNA fragments to repair DB-stranded breaks

no requirement for homology

mutated in **ataxia taelangiectasia **

33
Q

5’ –> 3’

A

direction in which DNA and RNA are **synthesized **

5’ end = incoming nucleotides bear the triphosphate ( energy source for bond)

triphosphate bond is the target for the 3’ hydroxyl attack

drugs blocking DNA synthesis often have a modified 3-OH grp to prevent further DNA elongation - chain termination

34
Q

5’ –> 3’

A

direction in which RNA is read

35
Q

N –> C

A

direction of protein synthesis

36
Q

mRNA start codon

A

AUG or GUG( rarely) - AUG inAUGrates DNA synthesis

Eukaryotes - AUG codes for methionine which may be removed before trnalstion is complee

Prokaryotes - AUG codes for formylmethionin ( f-met)

37
Q

mRNA stop codons

A

UGA - U Go Away

UAA- U Are Away

UAG - U Are Gone

38
Q

elements involved in regulation of gene expression on a DNA strand

A

Promoter

Enhance

Silencer

39
Q

DNA strand - promoter

A

site where RNA polymerase and other multiple transcription factors bind to DNA upstream from gene locus

is an AT-rich sequence with TATA and CAAT boxes

mutation results in dramatic decrease in gene transcription

40
Q

DNA strand - enhancer

A

stretch of DNA that alters gene expression by binding transcription factors

can be locate far, close or within ( intron) of the gene whose expression it reguates

41
Q

DNA strand - silencer

A

site where negative regulators ( repressor) bind

can be locate far, close or within ( intron) of the gene whose expression it reguates

42
Q

RNA polymerase - eukaryotes

A

RNA polymerase I, II, III

numbered in order of when their products are used in protein synthesis

have **no **proofreading function but **can **initiate chains

43
Q

RNA polymerase I

A

makes rRNA

most numerous

r = rampant

44
Q

RNA polymerase II

A

mRNA

is the largest RNA

opens DNA at promoter site

alpha-amantin - found in death cap muschrooms inhibits RNA polym II and causes severe hypotoxicity if ingested

45
Q

RNA polymerase - prokaryotes

A

onne RNA polymerase ( multiunit) - makes all 3 kinds of RNA

46
Q

RNA processing

A

initial transcript = hnRNA ( heterogeneous RNA)

hnRNA modified to become hnRNA via these processes:

Capping on 5’ end ( addition of 7-mehylguanosin cap

polyadenylation of 3’ end ( approx 200As)

splicing out of introns

capped tailed and spliced transcript called = mRNA and is transported out of nucleus into cytsol to be translated

47
Q

Polyadenylation

A

carried out by Poly-A polyemrase which does NOT require a template

polyadenylation signal = AAUAAA

48
Q

mRNA quality control

A

occurs at cytoplasmic P-bodies which contain exinucleases, decapping enzymes and microRNAs

mRNAs may be stored here for future translation

49
Q

pre-mRNA splicing

A

primary transcript combines with small nuclear ribonuclearproteins ( snRNPs) and other proteins to form spliceosome

lariat-shaped( looped) intermediate is generate

lariat is released precisely to remove intron and join 2 exons

auto-Abs to spliceosomal snRNPs ( anti-Smith Abs) are highly specific for SLE

Anti-U1 RNP Abs are highly assoc with mixed CT disease

50
Q

tRNA - structure

A

clover leaf form

anticodon is at the 3’ aminoacyl end

ALL tRNA, eukaryotic and prokaryotic have CCA at the 3’ end with a high percentage of chemically modified bases

the AA covalently binds 3’ end of tRNA

T-arm = contains thymnie, pseudouridine, cytosine sequence necessary for tRNA-ribosome binding

D-arm = contains dihydrouracil residues necessary for tRNA recognition by the correct **aminoacetyl-synthetase **

51
Q

acceptor stem of tRNA

A

3’ CCA is the amino acid accpetor site

52
Q

aminoacyl-tRNA synthetase: charging

A

1 per amino acid; matchmaker; uses ATP

scrutinizes AA before **and **after it binds to tRNA

if incorrect, the bond is hydrolyzed

the AA-tRNA bond has energy for formation of a **peptide bond **

a mischarged tRNA reads usual codon but inserts wrong AA

aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of AA selection

53
Q

IF2

A

initiation factor for tRNA

54
Q

tRNA wobble

A

accurate base pairing required only in the first 2 nucleotide positions of an mRNA codon so codons iddfering the 3rd, ‘wobble’ position may code for the same AA/tRNA as a results of the **degeneracy **of genetic code

55
Q

three steps of protein synthesis

A

initiation

elongation

termination

56
Q

initiation of protein synthesis

A

initiates by GTP hydrolysis

inititation factors ( eukaryotic IFs) help assemble 40S ribosomal subunit with the initiator tRNA and are rleased when mRNA and the ribosomal 60S unit assemble with the complex

57
Q

Ribosomal subunits

A

Eukaryotic:40S + 60S ( Even)

Prokaryotic: 30S + 50S ( Odd)

58
Q

ATP and GTP in protein synthesis

A

ATP - tRNA Acitvation ( charging)

GTP - tRNA Gripping and going places ( translocation)

59
Q

Elongation: Protein synthesis

A
  1. aminoacyl-tRNA binds to A site ( **except for initiator methionine) **
  2. rRNA ( ‘ribozyme’) catalyzes peptide bond formation, transfers growing polypeptide to AA in the A site
  3. ribosome advances 3 nucleotides towards 3’ end of mRNA, moving peptidyl tRNA to P-site ( translocation)

think APE

  • A site = incoming aminoacyl-tRNA
  • P site = accomodates growing peptide
  • E-site = holds Empty tRNA as it Exits
60
Q

Termination: protein synthesis

A

stop codon is reconized by release factor, and complete polypeptide released from ribsome

61
Q

types of pottranslational modifications

A

trimming

covalent alterations

62
Q

trimming

A

a kind of post-transaltional modification

removal of N or C-terminal propeptides from zymogen to generate mature protein

63
Q

Covalent alterations

A

a kind of post-transaltional modification

phosphorlation/glycosylation/hydroxylation/methylation/acetylation/uniquitination

64
Q

Chaperone protein

A

intracellular protein involved in facilitating or maintaining protein folding

in yeast, some are heat shock prteins expressed at high temps to prevent prtein denaturing/misfoldings

65
Q

commaless, nonverlapping genetic code

A

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

66
Q

universal genetic code

A

code conserved throughout evolution

excpetions in humas: mitochondria

67
Q

DNA replication

A

is both prokaryotes and eukaryotes is **semi-conservative **and involves bth continuous and discontinuous ( Okazaki fragment) synthesis

68
Q

origin of replication

A

particular consensus sequence of base pairs in genome where DNA replication begins

have multiple in eukaryotes and single in prokaryotes

69
Q

replication fork

A

Y-shaped refgion where leading and lagging strands are synthesized

70
Q

helicase

A

unwinds DNA template at the replication fork

71
Q

Single stranded binding proteins

A

prevents strands from reannealing

72
Q

DNA topoisomerases

A

create single or DB-stranded breaks in the helix to remove or add supercoils

fluoroquinolones - inhibit DNA gyrase ( prokaryotic topoisomerase II)

73
Q

Primase

A

makes RNA primer on which DNA polymerase III can intitiate replication

74
Q

DNA polymerase III

A

prokaryotic ONLY

elongate leading strand by adding deoxynucletides t the 3’ end

elongs lagging strand until it reaches primer of preceding fragment

3’ –> 5’ exonuclease activity ‘proofreadds’ each added nucleus

SO: DNA polymerase III has 5’ –> 3’ synthesis and proofreads 3’ –> 5’ exonuclease

75
Q

DNA polymerase I

A

prokaryotic only

degrades RNA primaer and replaces it with DNA

has same functions as DNA polym III but ALSO excises RNA primer with 5’ –> 3’ exonuclease

76
Q

DNA ligase

A

catalyzes the formation of a phosphodiester bond within a strand of DB-stranded DNA - aka joins okazaki fragments

77
Q

Telomerase

A

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

First Aid - Biochemistry (2 decks)

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