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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
miRNA
microRNA; regulate gene expression, block translation of specific mRNA and promote its degradation
26
siRNA
small interfering RNA; regulate gene expression; direct specific mRNA degradation
27
lncRNA
long non-coding RNA; regulate gene expression, can increase or decrease transcription
28
what are the 3 RNA types that regulate gene expression?
miRNA, siRNA, lncRNA
29
3 parts of a transcriptional unit
1. promoter region (has consensus sequence i.e. TATA box) 2. coding region (transcribed into mRNA) 3. terminator region (specifies end of transcription)
30
template strand
antisense strand DNA--> RNA
31
non-template strand
complimentary strand on DNA (sense strand)
32
RNA polymerase
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
4 stages of transcription
1. initiation 2. elongation 3. processing 4. termination
34
which way is DNA template strand read and which way is RNA made? 3' or 5' ... and by which enzyme
RNA polymerase -reads DNA template strand 3' to 5' -makes RNA in 5' to 3'
35
transcription: initiation
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
transcription: elongation
-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
transcription: processing (3 things needed)
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
transcription: processing and termination
-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
what are the transcription initiation factors in prokaryotes and eukaryotes?
prokaryotes: sigma factor eukaryotes: many i.e. TFII
40
what factors make sure RNA polymerase stays on DNA?
elongation factors
41
in eukaryotes, what is needed during elongation?
chromatin remodelling complexes, histone chaperones, DNA topoisomerase
42
DNA topoisomerase
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
how does 1 gene create many different proteins
alternative splicing
44
prokaryotes transcription
-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
what is polycistronic?
prokaryotic mRNA transcript --> codes >1 protein
46
what 4 components are needed for translation?
mRNA, tRNA, small and large ribosomes
47
translation; where does it occur; how it is read
-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
what is the start codon/ reading frames for eukaryotic and prokaryotic translation?
prokaryotes: shine dalgarno sequence eukaryotes: AUG (Methionine)
49
how is tRNA prepared; which enzyme
-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
what do ribosomes do?
protein synthesis -rRNA (small and large subunits) -help maintain correct reading frame and ensure accuracy of codon-anticodon interaction
51
3 steps of translation
1. initiation 2. elongation a) tRNA binding b) peptide bond formation c) large subunit translocation d)small subunit translocation 3. termination
52
translation initiation
-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
translation initiation in prokaryotes
-mRNA polycistronic: an additional recognition sequence is needed for ribosome binding: shine dalgarno sequence
54
translation elongation
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
translation termination
-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
polysomes
-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
post-translational
-protein folded into 3D structure -modified in ER (I.e. glycosylate- add mono or oligosaccharide) -sent to proper cellular location
58
where does protein synthesis occur?
polysomes/ polyribosomes
59
what enzymes catalyzes transcriptional termination? and what does it add?
peptidyl transferase catalyzes addition of water molecule rather than amino acid to free carboxyl end and release the polypeptide
60
what starts translation initiation?
methionine forms complex with tRNA -go into small ribosome with initiation factors (eIFs)
61
what end of mRNA does translation start and what helps to recognize it? what binds it?
5' end and by 5' 7-methylguanosine cap -small ribosome binds 5' end of mRNA
62
ribosome complex; what's it composed of
small and large ribosome subunits A site, P site, E site
63
what bonds are formed between amino acids during translation elongation in ribosome complex? what enzyme does this and where is it found?
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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