Chapters 7-8

Chapter 7-8 Review!

Transcription

1. Unwind DNA to expose a portion of bases

2. Template strand is used for complementary base pairing

3. RNA polymerase builds mRNA

4. mRNA is complementary to DNA

5. DNA double helix reforms

Multiple Choice

Which enzyme produces the mRNA transcript?

• Dna polymerase

• Rna primase

• RNA polymerase II

• DNA ligase

• catalyzes addition of deoxyribonucleotides

• requires an RNA primer

• adenine binds to thymine (still 2 bonds in both!!)

DNA polymerase

• catalyzes addition of ribonucleotides (nucleotide with ribose)

• does not need a primer to initiate transcription

• adenine binds to uracil

RNA polymerase

Differences between polymerases

Multiple Choice

Pick the correct statement below

• RNA is only single stranded

• RNA uses uracil

• Uracil and adenine bind with 3 H-bonds

• DNA polymerase makes the mRNA transcript

• Bacterial transcription: RNA polymerase slides along DNA until it recognizes a promoter

• RNA polymerase latches to DNA

• DNA and new RNA is released

• RNA polymerase re-associates with a free sigma factor and searches for another promoter to begin the process again

  • A sigma factor is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters.

Prokaryotic

• 3 types of RNA polymerase: I, II & III.

• Require accessory proteins (Transcription factors - assemble at promoter before polymerase can begin transcription)

• DNA packed into nucleosomes

  • nucleosome = dna wrapped around histones

Eukaryotic

Fill in the Blanks

How many types of RNA polymerases are in eukaryotic organisms? type a number

General Transcription Factors

GTFs enable promoter recognition and initiation

• Assemble at promoter

• Position RNA polymerase

• Pull apart the double helix to expose template

• Launch RNA Polymerase

How do GTFs work?

1. TFIID (Transcription Factor II D) binds to short DNA sequence primarily composed of As and Ts (TATA box)

2. TATA-binding protein (TBP) subunit of TFIID causes local distortion in DNA; necessary for assembly of others proteins to promoter

3. TFIIB then binds

4. TFIIE, TFIIH, TFIIF and RNA polymerase II assemble at promoter

5. TFIIH pries apart DNA at start site using energy from ATP hydrolysis

6. TFIIH phosphorylates RNA polymerase II on polypeptide ‘tail’, releasing it from general factors, to begin elongation
   

Transcription Initiation Complex

GTFs + RNA Polymerase II

RNA processing

• protects mRNA from degradation

• aids in exporting the mature mRNA to the cytoplasm

• involved in binding proteins to initiate translation

3' poly A tail

• a specially altered nucleotide on the 5′ end of mRNA

• protects transcript from degradation

5' cap

Spliceosome

• small nuclear RNAs (snRNAs) help cut out introns

• packaged with additional proteins to form small
  nuclear ribonucleoprotein particles (snRNPs or “snurps”)

• snRNPs: RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs

Mature mRNA -> Cytoplasm

Cap and poly-A tail of mature mRNAs are ‘marked’ by proteins
that recognize these modifications
•Once found to be mature mRNA it is exported out of the nucleus
through the nuclear pore

Multiple Choice

How does the mature transcript reach the cytoplasm?

• Nuclear pore

• Protein transport

• Golgi apparatus

• Cell membrane

Codons & Ribosomes

• Three consecutive nucleotides (triplet) specify an amino acid

  • start codon = AUG (methionine)

  • stop codons = UAA, UAG, UGA

• Ribosomal subunits each made from more than 30 different proteins

  • (ribosomal proteins) and several RNA molecules - ribosomal RNAs (rRNAs)
    • rRNAs are synthesized in the nucleolus

  • terminating translation: Ribosome releases mRNA and dissociates into 2 subunits
    

Multiple Choice

Select the start codon

• UGA

• AUT

• AUG

• AUU

tRNA

Each ribosome has a small & large subunit

• 3’ end holds amino acid corresponding with the mRNA code

• Anticodon recognizes matching codon sequence

• Carry amino acids to the ribosome for incorporation into a polypeptide

tRNA cont.

• aminoacyl-tRNA synthetases covalently couple amino acids to the
  acceptor arm of tRNA

• 20 synthetases in all - one for each amino acid

• Produces a high-energy bond between tRNA and the amino acid.

• The energy of this bond will be used later to link the amino acid covalently to the polypeptide chain

Fill in the Blanks

How many aminoacyl-tRNA synthetases are there? type a number

CHAPTER 8: control of gene expression

• All cells contain the same information but how that information is expressed determines a cell's final role in an organism

• Differentiation – process by which a non-specialized cell becomes specialized

Chromatin Structure

• Gene activator proteins can recruit histone-modifying enzymes and chromatin remodeling complexes to the promoter region of a gene

  • histone = protein that DNA wraps around

    • histone acetylase = attach acetyl group to lysines to open DNA

    • lysine = an amino acid

    • histone deacetylase = remove acetyl group to decrease accessibility (closed DNA)

  • chromatin = material that makes up chromosomes

  • promoter = region where proteins bind to initiate transcription

    • DNA sequence surrounding TATA box where GTFs & RNA poly II assemble

Multiple Choice

Does acetylation open or close DNA?

• open

• close

Regulatory Sequences

Serve as binding sites for gene regulatory proteins whose presence on the DNA affect the rate of transcription initiation
- regulatory sequences can be located adjacent to the promoter, far upstream of it, or downstream of the gene

Transcriptional regulators

aka Transcription Factors - proteins which recognize regulatory DNA sequences

• affect the rate of transcription

• regulators bind specifically into a defined shaped via H-bonds, ionic bonds, and hydrophobic interactions

• protein-DNA interactions are among the tightest & most specific

Multiple Choice

Only one activator needs to bind to the promotor

• True

• False

Multiple Choice

Activator proteins can be bound upstream or downstream from the gene.

• True

• False

• Activator proteins don't bind anywhere

On-Off Switch

• repressors are proteins that bind to promoters in a way that impedes subsequent binding of RNA polymerase

• activity altered by phosphorylation

Turning genes off

• chromatin must be opened

• activators must bind

• general transcription factors must bind

• activators can be activated by secondary messengers

• activity of activators altered by phosphorylation

Turning genes on!

Combinatorial Control

• groups of regulatory proteins work together to determine the final rate of transcription initiation

  • typical gene controlled by dozens of transcription factors

  • both repressors and activators

  • help determine the final level of expression for a gene

  • can create different cell types

• shape of the 5' UTR regions affect binding of activators/repressors to the ribosome binding site altering translation

  • The 5' and 3' untranslated regions (UTRs) are mRNA domains that control critical post-transcriptional gene regulation processes. As regions that are transcribed, but seldom translated, the 5' and 3'UTRs contain regulatory elements involved in pre-mRNA processing.

UTR regions

• introns - noncoding

• exons - expressed

• UTR - untranslated regions (important for gene expression b/c contains regulatory elements involved in mRNA-processing)

Alternative Splicing

Post-transcriptional Controls

• process where enzymes break proteins down

• proteases hydrolyze peptide bonds between amino acids

• ubiquitination

Proteolysis

• cause degradation of mRNA by guiding mRNA cleavage or direct DNA methylation (OFF)

Small regulatory RNAs can silence genes

Post-transcriptional controls