Ch 7 - RNA and Genetic Code

Question 1

central dogma

Answer 1

• DNA replication
• DNA to RNA via transcription
  
  • opposite via reverse transcription
  • mRNA synthesized in 5-3 direction and is complementary to DNA template strand
• RNA to protein via translation
  
  • translate RNA from 5-3 direction
  • synthesize protein from N terminus to C terminus

Question 2

mRNA

Answer 2

• specify amino acid sequence for proteins
• transcribed via rna polymerase in the nucleus
• read in codons
• monocistronic - each mRNA molecule translates to one protein
  
  • eukaryotes
• polycistronic - different proteins depending on where on mRNA translation begins
  
  • prokaryotes

Question 3

tRNA

Answer 3

• transfer RNA
• anticodon to match codon on mRNA and retreive amino acid
• charged (activated) - when connected to amino acid
• aminoacyl-tRNA synthetase - activates amino acid
  
  • uses 2 high energy bonds from ATP
  • energy rich process
• CCA sequence where amino acid binds to 3’ end of tRNA

Question 4

rRNA

Answer 4

• ribosomal RNA
• synthesized in nucleolus
• ribosomal machinery
• ribozymes - enzyme made of RNA
• important in splicing out introns

Question 5

Codons

Answer 5

• anticodons - antiparallel to codons
• AUG - start codon (methionine)
• stop codons - UGA, UAA, UAG

Question 6

Mutations

Answer 6

• silent/degenerate - due to wobble base
  
  • no change to amino acid
• point - affect one nucleotide
  
  • missense - affect one amino acid
  • nonsense - introduce a stop codon
• frameshift - nucleotides added or deleted
  
  • insertion or deletion

Question 7

transcription

Answer 7

• helicase and topoisomersae unwind and prevent supercoiling
• synthesized from template strand
• synthesized by RNA polymerase
  
  • RNA polymerase II - mRNA and snRNA in eukaryotes
  • RNA polymerase I - rRNA in nucleolus
  • RNA polymerase III - tRNA and rRNA
• starts at promoter region
  
  • binds to TATA box
  • trasncription factors help polymerase bind
• travel in 3-5 direction in order to synthesize in 5-3
• +1 base is first to be transcribed
  
  • upstream from here are negative numbers
  • downstream are positive numbers
  • TATA box near -25
• continue until termination sequence
• DNA double helix reforms
• hnRNA - heterogeneous nuclear RNA is unmodified transcript

Question 8

Posttranscriptional processing

Answer 8

• splicing: introns and exons
• 5’ cap
• 3’ poly A tail

Question 9

Splicing

Answer 9

• remove introns (noncoding sequences)
• ligate exons (coding sequences) together
• Spliceosome - snRNA and small nuclear ribonucleoproteins (snRNPs)(snurps)
  
  • recognize introns and remove
  • lariat - lasso shaped structure of intron
  • intron degraded
• Alternatice splicing - make many different proteins from a limited number of genes
  
  • splice together in different ways

Question 10

5’ Cap

Answer 10

• 7-methylguanylate triphosphate cap
• protect from degradation in cytoplasm
• recognized by ribosome as the binding site

Question 11

3’ Poly A tail

Answer 11

• 3’ end of transcript
• protect from degradation
• longer tail will mean longer life outside of nucleus

Question 12

Ribosome

Answer 12

• A site - aminoacyl
• P site - peptidyl
• E site - exit
• Eukaryotes - 4 rRNA strands
  
  • RNA polymerase I and III transcribe rRNA
    
    • polymerase I in the nucleolus
  • 40S and 60S subunits join to make 80S (whole ribosome)
• Prokaryotes - 70S made from 50S and 30S subunits

Question 13

Translation Initiation

Answer 13

• eukaryotes - small subunit binds to 5’ cap
  
  • initiator tRNA binds anticodon to AUG in P site of ribosome
  • large subunit binds to small subunit
  • assisted by initiation factors
• prokaryote - small subunit binds to Shane Dalgarno Sequence (5’ untranslated region)

Question 14

Translation Elongation

Answer 14

• ribosome moves 5-3
• synthesize N to C terminus
• A site - hold aminoacyl-tRNA complex, next amino acid, determined by codon
• P site - hold growing peptide chain
  
  • form peptide bond - polypeptide transferred from P to A site tRNA via peptidyl transferase
    
    • GTP used
• E site - uncharged tRNA pauses and then leaves
• EF factors - elongation factors - locate and recruit amnioacyl tRNA and GTP, remove GTP

Question 15

Translation Termination

Answer 15

• release factor binds to terminal codon (stop codon)
  
  • UAA, UAG, UGA
• add water to peptide chain - peptidyl transferase and termination factors hydrolyze peptide from last tRNA
• released from P site
• ribosome subunits dissociate

Question 16

Posttrasnlational processing

Answer 16

• chaperones - fold protein
• cleavage - inactive peptide must be cleaved before active
• phosphorylation - add PO4 2- via kinase
• carboxylation - add carboxylic acid
• glycosylation - add oligosaccharides in ER and golgi
• prenylation - add lipids to membran bound enzymes

Question 17

signal sequences

Answer 17

• designate destination for a protein
• some direct to endoplasmic reticulum
  
  • ribosomes on ER to complete translation
• then to Golgi apparatus and secrete via vesicle and exocytosis

Question 18

Prokaryote Gene expression

Answer 18

• Operon - cluster of genes transcribed as a single mRNA
  
  • described by Jacob-Monod Model
  • strucutreal gene - protein of interest
  • operator site - binds repressor protein
  • promoter site - RNA polymerase binds
  • regulator gene - codes for repressor protein
• Inducible and Repressible Systems

Question 19

Inducible System (operator system)

Answer 19

• repressor binds to operator system and stops transcription
• negative control - reduce transcription due to binding of molecule
• Inducer binds to repressor to allow RNA polymerase to transcribe the gene
  
  • similar to competitive inhibition
• ex. Lac operon (negative inducible)
  
  • only used when lactose is high and glucose is low
    
    • induced by presence of lactose
    • catabolite activator protein (CAP) - transcriptional activator when glucose is low
    • low glucose - high cAMP - binds to CAP - CAP conformational change - CAP bind to promoter - increase transcription of lactase gene
    • positive control - increase transcription of gene due to binding of molecule

Question 20

Repressible Systems

Answer 20

• constant production of protein
• repressor must bind to corepressor to be active
  
  • complex binds operator site
  • negative feeback
  • final structure may be the corepressor
• trp operon - negative repressible
• trp operon - tryptophan is high - acts as corepressor
  
  • repressor binds to operator when 2 tryptophans bound to it - stop making tryptophan

Question 21

Transciption factors

Answer 21

• Eukaryotes
• search DNA for DNA binding motifs
• DNA binding domain - binds specific sequence in promoter region or DNA response element
• Activation domain - binds other transcription factors and regulatory proteins

Question 22

Gene Amplification

Answer 22

• increase transcription due to hormones, growth factors, intracellular conditions
• Enhancers - several response elements (DNA sequences) grouped together to cause increase in transcription
  
  • form hairpin turn in DNA to mean up with promoter region
  • enhancer binds transcription factors that cooperate with the promoter region transcription factors
• Gene duplication - can duplicate to have many duplicates on one chromosome

Question 23

Chromatin Structure

Answer 23

• Heterochromatin - tightly coiled DNA, dark under microscope
• Euchromatin - looser, light under microscope
  
  • genes are active
• Histone acetylation - histone acetylase, acetylate lysine residue on histone proteins
  
  • decreases positive charge and weaken interaction with DNA
  • open chromatin and easier access
  • histone deacetylase - closes chromatin to decrease expression
• DNA methylation - DNA methylase - add methyl group to cytosine and adenine
  
  • silences gene expression
  • heterochromatin is more methylated