central dogma- transcription and translation Flashcards
what are the 2 nucleic acids
DNA: deoxyribonucleic acid
-genetic material, segments= genes which code for proteins= physical traits
RNA: ribonucleic acid
central dogma
DNA –> RNA –> protein
via transcription then translation
what are the 5 nitrogenous bases
and double vs single ring
adenine, guanine, cytosine, uracil, thymine
purine: double ring- A and G
pyrimidines: single ring- C, U, T
what are the 3 component of a nucleotide
- pentose sugar
- phosphate group
- nitrogenous base
–>purine: double ring- A and G
–>pyrimidines: single ring- C, U, T
DNA double helix
-sugar, phosphate backbone
-holds 2 strands by hydrogen bonds between complementary base pairs (A-T) and (G-C) [purine-pyrimidine]
DNA and RNA nitrogenous bases
DNA: ATGC (adenine, thymine, guanine, cytosine)
RNA: AUGC (adenine, uracil, guanine, cytosine)
3 forces to stabilize DNA helix
- hydrogen bonds
- sugar phosphate backbone (phosphodiester bonds)
- base stacking (bases stack parallel to each other and expel water - hydrophobic effects)
phosphodiester bonds in DNA and RNA; where are the found
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
3 parts of DNA condensation
nucleosomes –> chromatin –> chromosomes
DNA condensation- nucleosomes
-package DNA
-147 base pairs wrapped around a histone core
-octamer; H2A, H2B, H3, H4
-H1 linker
DNA condensation- chromatin
-complex or DNA and tightly bound protein
-heterochromatin (dense and inactive)
-euchromatin (disperse, active)
DNA condensation- chromosomes
-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
DNA vs RNA
-compare 3 big differences
deoxyribose vs ribose sugar
thymine vs uracil
double strand vs single strand (can fold into many shapes)
genes
-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
non-coding DNA
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)
exon vs intron
-exon= coding sequence of gene
-intron= non coding sequence of gene- removed via splicing after transcription
RNA
DNA–> mRNA (RNA transcript) –> protein
-premRNA –> mRNA via processing
non-coding RNA
-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
wobble hypothesis
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
mRNA
messenger RNA; codes for proteins
DNA–> mRNA
non-coding RNA
snRNA, rRNA, tRNA, miRNA, siRNA, lncRNA
rRNA
ribosomal RNA; important constituents of ribosomes, catalyzes protein synthesis
tRNA
transfer RNA; adaptor between mRNA and amino acids
snRNA
small nuclear RNA; splicing of pre-mRNA
miRNA
microRNA; regulate gene expression, block translation of specific mRNA and promote its degradation
siRNA
small interfering RNA; regulate gene expression; direct specific mRNA degradation
lncRNA
long non-coding RNA; regulate gene expression, can increase or decrease transcription
what are the 3 RNA types that regulate gene expression?
miRNA, siRNA, lncRNA
3 parts of a transcriptional unit
- promoter region (has consensus sequence i.e. TATA box)
- coding region (transcribed into mRNA)
- terminator region (specifies end of transcription)
template strand
antisense strand
DNA–> RNA
non-template strand
complimentary strand on DNA (sense strand)
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
4 stages of transcription
- initiation
- elongation
- processing
- termination
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’
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
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
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
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
what are the transcription initiation factors in prokaryotes and eukaryotes?
prokaryotes: sigma factor
eukaryotes: many i.e. TFII
what factors make sure RNA polymerase stays on DNA?
elongation factors
in eukaryotes, what is needed during elongation?
chromatin remodelling complexes, histone chaperones, DNA topoisomerase
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
how does 1 gene create many different proteins
alternative splicing
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)
what is polycistronic?
prokaryotic mRNA transcript
–> codes >1 protein
what 4 components are needed for translation?
mRNA, tRNA, small and large ribosomes
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
what is the start codon/ reading frames for eukaryotic and prokaryotic translation?
prokaryotes: shine dalgarno sequence
eukaryotes: AUG (Methionine)
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
what do ribosomes do?
protein synthesis
-rRNA (small and large subunits)
-help maintain correct reading frame and ensure accuracy of codon-anticodon interaction
3 steps of translation
- initiation
- elongation
a) tRNA binding
b) peptide bond formation
c) large subunit translocation
d)small subunit translocation - termination
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
translation initiation in prokaryotes
-mRNA polycistronic: an additional recognition sequence is needed for ribosome binding: shine dalgarno sequence
translation elongation
- tRNA binding at A site of ribosome complex
- 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 - 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 - 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
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
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
post-translational
-protein folded into 3D structure
-modified in ER (I.e. glycosylate- add mono or oligosaccharide)
-sent to proper cellular location
where does protein synthesis occur?
polysomes/ polyribosomes
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
what starts translation initiation?
methionine forms complex with tRNA
-go into small ribosome with initiation factors (eIFs)
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
ribosome complex; what’s it composed of
small and large ribosome subunits
A site, P site, E site
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
