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BMS100 test 1 > central dogma- transcription and translation > Flashcards

central dogma- transcription and translation Flashcards

1
Q

what are the 2 nucleic acids

A

DNA: deoxyribonucleic acid
-genetic material, segments= genes which code for proteins= physical traits

RNA: ribonucleic acid

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2
Q

central dogma

A

DNA –> RNA –> protein

via transcription then translation

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3
Q

what are the 5 nitrogenous bases

and double vs single ring

A

adenine, guanine, cytosine, uracil, thymine

purine: double ring- A and G
pyrimidines: single ring- C, U, T

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4
Q

what are the 3 component of a nucleotide

A
  1. pentose sugar
  2. phosphate group
  3. nitrogenous base
    –>purine: double ring- A and G
    –>pyrimidines: single ring- C, U, T
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5
Q

DNA double helix

A

-sugar, phosphate backbone
-holds 2 strands by hydrogen bonds between complementary base pairs (A-T) and (G-C) [purine-pyrimidine]

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6
Q

DNA and RNA nitrogenous bases

A

DNA: ATGC (adenine, thymine, guanine, cytosine)
RNA: AUGC (adenine, uracil, guanine, cytosine)

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7
Q

3 forces to stabilize DNA helix

A
  1. hydrogen bonds
  2. sugar phosphate backbone (phosphodiester bonds)
  3. base stacking (bases stack parallel to each other and expel water - hydrophobic effects)
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8
Q

phosphodiester bonds in DNA and RNA; where are the found

A

join nucleotides on sugar phosphate backbone
-negative charges between phosphate groups repel and destabilize helix
–> positive Mg2+ helps to stabilize the negative charges on the phosphates

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9
Q

3 parts of DNA condensation

A

nucleosomes –> chromatin –> chromosomes

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10
Q

DNA condensation- nucleosomes

A

-package DNA
-147 base pairs wrapped around a histone core
-octamer; H2A, H2B, H3, H4
-H1 linker

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11
Q

DNA condensation- chromatin

A

-complex or DNA and tightly bound protein
-heterochromatin (dense and inactive)
-euchromatin (disperse, active)

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12
Q

DNA condensation- chromosomes

A

-in its most condensed form, DNA is packaged into chromosomes
-23 pairs, 46 total
-1 copy of each chromosomes from each parent (2n; diploid)
-maternal and paternal chromosome= homologous
-haploid (1 copy): egg and sperm
-autosomal chromosomes: 1-22; form homologous pairs
-sex chromosomes (non homologous, determine biological sex) female; 2x, male; 1x, 1y

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13
Q

DNA vs RNA
-compare 3 big differences

A

deoxyribose vs ribose sugar

thymine vs uracil

double strand vs single strand (can fold into many shapes)

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14
Q

genes

A

-functional unit of heredity
-chromosomes carry genes
-gene: segment of DNA containing instructions for making a particular protein
-exon= coding sequence of gene
-intron= non coding sequence of gene- removed via splicing after transcription

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15
Q

non-coding DNA

A

98.5% of the human genome, doesnt encode a protein
-for regulating gene expression
-promoter and enhancer regions- bind transcription factors
-binding sites for factors that organize chromatin structure
-non coding regulatory RNA (i.e. microRNA)
-mobile genetic elements (transposons)

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16
Q

exon vs intron

A

-exon= coding sequence of gene
-intron= non coding sequence of gene- removed via splicing after transcription

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17
Q

RNA

A

DNA–> mRNA (RNA transcript) –> protein
-premRNA –> mRNA via processing

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18
Q

non-coding RNA

A

-doesnt get translated into proteins
–> enzymatic, structural, and regulatory components

snRNA: in spliceosome, remove introns from pre-mRNA
-snRNA associated with protein subunits form small nuclear ribonucleoproteins (snRNPs) which form the core of the spliceosome

rRNA: structure of ribosome complex, involved in catalysis of peptide bond between amino acids

tRNA: needed in translation to carry correct amino acids to growing polypeptide chain, unique clover leaf shape
–> anticodon: 3 consecutive nucleotides that pair with complementary codon on mRNA molecule
–> amino acid binding site: short single-stranded region on 3’ end of tRNA, binds the amino acid that corresponds to the anti-codon on the tRNA

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19
Q

wobble hypothesis

A

64 nucleotide codons, 3 nucleotide codon, 20 amino acids = redundancy
-1 tRNA for many amino acids, a tRNA can base with > 1 codon
-1st 2 positions are accurate, 3rd position can tolerate mismatch

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20
Q

mRNA

A

messenger RNA; codes for proteins

DNA–> mRNA

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21
Q

non-coding RNA

A

snRNA, rRNA, tRNA, miRNA, siRNA, lncRNA

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22
Q

rRNA

A

ribosomal RNA; important constituents of ribosomes, catalyzes protein synthesis

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23
Q

tRNA

A

transfer RNA; adaptor between mRNA and amino acids

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24
Q

snRNA

A

small nuclear RNA; splicing of pre-mRNA

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25
Q

miRNA

A

microRNA; regulate gene expression, block translation of specific mRNA and promote its degradation

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26
Q

siRNA

A

small interfering RNA; regulate gene expression; direct specific mRNA degradation

27
Q

lncRNA

A

long non-coding RNA; regulate gene expression, can increase or decrease transcription

28
Q

what are the 3 RNA types that regulate gene expression?

A

miRNA, siRNA, lncRNA

29
Q

3 parts of a transcriptional unit

A
  1. promoter region (has consensus sequence i.e. TATA box)
  2. coding region (transcribed into mRNA)
  3. terminator region (specifies end of transcription)
30
Q

template strand

A

antisense strand
DNA–> RNA

31
Q

non-template strand

A

complimentary strand on DNA (sense strand)

32
Q

RNA polymerase

A

enzyme
-unwinds DNA helix just ahead of active site for polymerization
-catalyzes new phosphodiester bond on the newly formed RNA strand
-reads DNA template strand 3’ to 5’
-makes RNA in 5’ to 3’
-RNA polymerase makes more mistakes than DNA polymerase bc mRNA quick turnover, make many proteins, but if error in DNA then effect more

33
Q

4 stages of transcription

A
  1. initiation
  2. elongation
  3. processing
  4. termination
34
Q

which way is DNA template strand read and which way is RNA made?
3’ or 5’ … and by which enzyme

A

RNA polymerase
-reads DNA template strand 3’ to 5’
-makes RNA in 5’ to 3’

35
Q

transcription: initiation

A

RNA polymerase recognizes where to start via transcription initiation factors

prokaryotes: sigma factor
eukaryotes: many i.e. TFII (transcribes all protein coding genes)

A) TFII binds consensus sequence in promotor region (i.e. TATA box)
-i.e. TATA box ~25 nucleotides upstream from transcription start site
-TFIID is specific TFII to bind TATA box

B) other transcription factors join

C) RNA polymerase II joins

D) transcription initiation complex is complete and transcription can begin

–> regulation:
-negative: repressor proteins bind upstream to silencers to inhibit gene transcription
-positive: transcriptional activator proteins bind upstream to enhancers to increase rate of transcription, attracts RNA polymerase II enzyme

36
Q

transcription: elongation

A

-after RNA polymerase starts transcribing DNA, release general transcription factors (TFII)
-TFII can now initiate another round of transcription with new RNA polymerase
-transcribe coding region: use elongation factors to decrease likelihood of RNA polymerase dissociating from DNA before it reaches the end of a gene

-eukaryotes also require:
-chromatin remodelling complexes: help RNA polymerase navigate chromatin structure
-histone chaperones partially disassemble and reassemble nucleosomes as an RNA polymerase passes through
-as RNA polymerase moves along DNA double helix it generates supercoils
–> DNA topoisomerase (eukaryotes): removes super-helical tension

37
Q

transcription: processing (3 things needed)

A

pre-mRNA –> mRNA
1.splicing
2. 5’ cap
3. polyadenylation 3’ tail

-7-methyl guanosine cap (modified guanine nucleotide) added to 5’ end of pre-mRNA
-facilitates export of mRNA from nucleus for translation

-introns and exons transcribed into RNA
-RNA splicing: remove introns
-spliceosome: requires snRNA and proteins complexed into snRNPs
-snRNP= spliceosome once its complexed with pre mRNA

38
Q

transcription: processing and termination

A

-3’ end; DNA signals are translated into RNA and then bind to proteins to cleave mRNA from RNA polymerase

-once cleaved ~200 nucleotide poly A tail added to mRNA
-poly-A-polymerase (PAP) enzyme catalyses

-tail protects mRNA from degradation and facilitates export from the nucleus
-poly A binding proteins then bind poly A tail

-cleavage stimulation factor (CstF), and the cleavage and polyadenylation specificity factor (CPSF) are necessary for 3’-terminal processing of polyadenylated mRNAs

39
Q

what are the transcription initiation factors in prokaryotes and eukaryotes?

A

prokaryotes: sigma factor
eukaryotes: many i.e. TFII

40
Q

what factors make sure RNA polymerase stays on DNA?

A

elongation factors

41
Q

in eukaryotes, what is needed during elongation?

A

chromatin remodelling complexes, histone chaperones, DNA topoisomerase

42
Q

DNA topoisomerase

A

DNA topoisomerase (eukaryotes): removes super-helical tension

breaks phosphodiester bond to remove tension. allows 2 sections of DNA helix to rotate. phosphodiester bond reforms when DNA topoisomerase leaves

43
Q

how does 1 gene create many different proteins

A

alternative splicing

44
Q

prokaryotes transcription

A

-no processing of mRNA (no 5’ cap, splicing, poly A tail)
-no export from nucleus therefore transcription starts right away
-mRNA transcript is polycistronic (codes >1 protein)

45
Q

what is polycistronic?

A

prokaryotic mRNA transcript
–> codes >1 protein

46
Q

what 4 components are needed for translation?

A

mRNA, tRNA, small and large ribosomes

47
Q

translation; where does it occur; how it is read

A

-after transcription, mRNA exported from nucleus via nuclear pore complexes
-in cytosol, mature mRNA is translated into protein

-mRNA is read in sets of 3 nucleotides = codon
–> 64 combos, 20 amino acids = redundant

48
Q

what is the start codon/ reading frames for eukaryotic and prokaryotic translation?

A

prokaryotes: shine dalgarno sequence

eukaryotes: AUG (Methionine)

49
Q

how is tRNA prepared; which enzyme

A

-each tRNA corresponds to one of the 20 amino acids
-enzyme amino acyl-tRNA synthetase catalyzes the attachment of correct amino acids to tRNA

50
Q

what do ribosomes do?

A

protein synthesis
-rRNA (small and large subunits)
-help maintain correct reading frame and ensure accuracy of codon-anticodon interaction

51
Q

3 steps of translation

A
  1. initiation
  2. elongation
    a) tRNA binding
    b) peptide bond formation
    c) large subunit translocation
    d)small subunit translocation
  3. termination
52
Q

translation initiation

A

-AUG is 1st/ start codon translated on mRNA
-initiator tRNA carries methionine therefore all new proteins have 1st amino acid as methionine at the N terminal
-forms initiator tRNA-methionine complex (met-tRNAi)
-met-tRNAi is loaded into small ribosomal subunit with initiation factors (eIFs)
-small ribosome binds to 5’ end of mRNA
-5’ 7-methyl guanosine cap helps with recognition of 5’ end
-small ribosome moves on mRNA 5’ –> 3’ scan for AUG (requires ATP hydrolysis)
-initiation factors dissociate and large ribosome subunit assembles to complete the ribosome complex

53
Q

translation initiation in prokaryotes

A

-mRNA polycistronic: an additional recognition sequence is needed for ribosome binding: shine dalgarno sequence

54
Q

translation elongation

A
  1. tRNA binding at A site of ribosome complex
  2. peptide bond formation
    -carboxyl end of polypeptide chain is released from tRNA at the p site and joins the amino acid linked to the tRNA at the a site
    -new peptide bond is catalyzed by peptidyl transferase enzyme contained within the large ribosomal subunit
  3. translocation of large subunit: large subunit moves relative to the mRNA held by the small subuit
    -2 tRNAs are shifted to the E and P sites
  4. translocation of small subunit
    -small subunit shifts 3 nucleotides
    -tRNA in E site is ejected
    –> cycle repeated for new incoming amino acyl-tRNA

–> elongation factors (EFs): enter and leave ribosome during each cycle and are coupled with GTP hydrolysis

55
Q

translation termination

A

-peptidyl transferase catalyzes addition of water molecule rather than amino acid to free carboxyl end and release the polypeptide

-ribosome releases mRNA and dissociates into small and large subunits
-subunits recycled to begin new round of protein synthesis

56
Q

polysomes

A

-synthesis of protein occurs on polyribosomes (or polysomes)
-multiple interactions take place on each mRNA molecule begin translation
-as soon as the preceding ribosome has translated enough of the nucleotide sequence to move out the way, a new ribosome complex is formed
-helps speed up rate of protein synthesis

57
Q

post-translational

A

-protein folded into 3D structure
-modified in ER (I.e. glycosylate- add mono or oligosaccharide)
-sent to proper cellular location

58
Q

where does protein synthesis occur?

A

polysomes/ polyribosomes

59
Q

what enzymes catalyzes transcriptional termination? and what does it add?

A

peptidyl transferase

catalyzes addition of water molecule rather than amino acid to free carboxyl end and release the polypeptide

60
Q

what starts translation initiation?

A

methionine forms complex with tRNA
-go into small ribosome with initiation factors (eIFs)

61
Q

what end of mRNA does translation start and what helps to recognize it? what binds it?

A

5’ end and by 5’ 7-methylguanosine cap
-small ribosome binds 5’ end of mRNA

62
Q

ribosome complex; what’s it composed of

A

small and large ribosome subunits

A site, P site, E site

63
Q

what bonds are formed between amino acids during translation elongation in ribosome complex? what enzyme does this and where is it found?

A

peptide bonds

-new peptide bond is catalyzed by peptidyl transferase enzyme contained within the large ribosomal subunit

BMS100 test 1 (24 decks)

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