Biol-K 324 Lec 3: Basic Genetic Mechanisms

Front 1

structure of nucleic acids

Back 1

1. linear polymers

2. chemical directionality

3. 5'-->3'

4. linked by phosphodiester bonds

5. G:C 3H bonds

6. A:T 2H bonds

7. antiparallel

8. double stranded

Front 2

Who solved DNA structure and when?

Back 2

Watson, Crick, Franklin, and Wilkins in 1953

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purines

Back 3

1. Adenine and Guanine

2. 2-rings

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pyrimidines

Back 4

1. Cytosine, Thymine, and Uracil

2. single ring

Front 5

What difference between RNA and DNA helps to explain the greater stability of DNA?

Back 5

1. The 2' hydroxyl group in RNA

2. acts as a nucleophile and breaks the phosphodiester bond

3. supercoiled structure is more energetic

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DNA supercoiling

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1. Topoisomerases

2. necessary for DNA replication, RNA polymerization, and chromatin folding

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Topoisomerases

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1. add or relieve torsional stress on DNA

2. form of DNA supercoiling

Front 8

RNA Structure

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1. Uracil replaces Thyamine

2. single stranded

3. fold into a variety of structures

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What are some structures RNA can fold into?

Back 9

1. hairpin

2. stem-loop

3. pseudoknot

4. tRNA

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transcription

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1. synthesis of genetically encoded, functional RNAs from the DNA

2. mRNA, rRNA, tRNA, ncRNA

3. +1 transcription start site

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ncRNA

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1. noncoding RNA

2. includes miRNA, microRNA

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What regulates transcription initiation?

Back 12

promoter

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transcription initiation

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1. promoter regulates transcription

2. +1 transcription start site

3. coding sequence

4. where most regulation occurs

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stages of transcription

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1. initiation

2. elongation

3. termination

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transcription initiation

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1. closed complex

2. open complex

3. phosphodiester linkage

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closed complex

Back 16

Polymerase bidns to promoter sequence in duplex DNA

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open complex

Back 17

polymerase melts duplex DNA near transcription start site forming a transcription bubble

Front 18

phosphodiester linkage

Back 18

polymerase catalyzes phosphodiester linkage between two initial rNTPs

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transcription elongation

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polymerase advances 3'-->5' down template strand, melting duplex DNA and adding rNTPs to growing RNA

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transcription termination

Back 20

1. polymerase releases completed RNA and dissociates from DNA at transcription stop site

2. very processive

3. does not stop until STOP codon recognized

4. release factors involved

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prokaryotes vs eukaryotes (gene organizatiom)

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prokaryotes: operons

eukaryotes: chromosomes, genes have a single protein coding region

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operon

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1. arrangement of genes in a functional group that are transcribed as a unit

2. multiple translational start sites

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eurkaryotic RNA processing

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1. 5' methylated cap

2. 3' polyadenylation

3. splicing out introns from hnRNA

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alternative splicing

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fibronectin splicing

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fibronectin splicing

Back 25

1. produces tissue forms and circulating forms for different functions

2. with EIIIB and EIIIA, fibroblast cells attach to this FN in their ECM

3. hepatocyte FN is secreted into blood, and cells only normally bind in blood clots

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3 roles of RNA in translation

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1. mRNA

2. rRNA

3. tRNA

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genetic code

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1. 64 possible triplet codons

2. most encode specific amino acids

3. 3 are stop codons

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charging tRNAs

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aminoacyl-tRNA synthetas

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aminoacyl-tRNA synthetase

Back 29

1. charging tRNAs

2. process is an important proofreading step in translation

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tRNA genes

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1. prokaryotes: 30-40 tRNA genes

2. eukaryotes: 50-100 tRNA genes

Front 31

can you explain why there are not 61 tRNAs?

Back 31

Wobble

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ribosomes

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1. most abundant RNA protein complex in the cell

2. catalyze protein synthesis at an elongation rate of 3-5 amino acids per second

3. ribosome specific composition and component structure is known

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translation initiation

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1. pre-initiation complex forms with Met-tRNA

2. mRNA bound by eIF4 complex and PABP complexes

3. pre-initiation complex binds to mRNA and scans for AUG

4. AUG recognition

5. 60S subunit joining to 40S subunit

6. ready for elongation

Front 34

protein synthesis

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elongation

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translation termination

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1. stop codon is reached

2. eRF-1, eRF3-GTP produces peptidyl-tRNA cleavage and disruption of the translation complex

Front 36

polysomes

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circular mRNA structure produces an organization that increases translation efficiency

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DNA replication

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1. semi-conservative replication

2. revealed by the Meselson-Stahl experiment

3. bi-directional

4. discontinuous replication in lagging strand

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Requirments for DNA replication

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1. DNA template

2. dNTPs

3. 3-OH

4. RNA primer

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DNA replication enzymes involved

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1. helicase

2. topoisomerase

3. primase

4. DNA polymerase

5. ligase

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central dogma

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DNA --> RNA --> protein

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untranslated region

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region after stop codon

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introns

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1. intervening sequence

2. gets removed

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5' methylated cap

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1. found in eukaryotic RNA

2. processing

3. will be degraded if cap is absent

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exon

Back 44

expressed sequence

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rRNA

Back 45

catalytic

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tRNA

Back 46

has anticodon and attached to amino acid

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Wobble

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1. in the third nucleotide

2. more than 1 nucleotide can be recognized that codes for the same amino acid

3. anti codon can recognize more than one codon

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ribosome and protein synthesis

Back 48

high degree of conservation between eukaryotes and prokaryotes

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elongation steps

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1. methionine complex binding

2. entry of next tRNA

3. GTP is hydrolyzed --> locks tRNA/aa in place

4. conformational change

5. peptide formation (peptide bond)

6. elongation factor recognized

7. translocated ribosome --> opens up new space for next tRNA to bind

Front 50

RNA primer

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1. does not need a template

2. can synthesize primer for DNA replication

3. leading strand: 1 RNA primer

4. laggin strand: multiple RNA primers

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DNA helicase

Back 51

unwinds DNA

Front 52

DNA topoisomerase

Back 52

relieves torsial strain

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DNA primase

Back 53

makes RNA primer

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DNA polymerase

Back 54

makes new DNA

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DNA ligase

Back 55

joins Okazaki fragments together

Front 56

Exam question: What protein is involved in translation?

Back 56

aminoaceyl-tRNA synthase