Review

1
Review
2
Fundamental properties of genes

• Genes are heritable units, arranged linearly
  along chromosomes.
• Complementation analysis of a large number of
  mutants defines genes that determine a function.
• E.g., biosynthetic pathway or DNA replication.
• Genetic techniques in microorganisms were used to
  determine the fine structure of a gene.
• Genes encode polypeptides
• Codons are triplets of nucleotides that encode an
  amino acid.

3
How genes encode proteins

• Genes are composed of a series of mutable sites
  that are also sites for recombination (now
  recognized as nucleotides).
• One gene encodes one polypeptide.
• The gene and the polypeptide are colinear.
• Single amino acids are specified by a set of
  three adjacent mutable sites this set is called
  a codon.

4
A simple view of DNA
AGCCTCGCAT TCGGAGCGTA
5
Forms of nucleic acid duplexes
6
Restriction maps and blots prob. 1.18
P
E
B
E
0 B H H P B B E H
10
7
6
5
4
3
2
1
DNA was digested with the indicated enzymes,
singly and in combination, and the resulting
fragments were resolved on an agarose gel.
7
A common plasmid cloning vector pUC
8
PCR, cycle 5 exponential increase in product
Cycle 5 Denature, anneal primers, and synthesize
new DNA
14 duplex molecules of desired product
9
cDNA clones and ESTs
5 UTR
3 UTR
Protein coding
Duplex inserts in cDNA clones
ESTs are sequences from each end of the cDNA
inserts
Unigene cluster is an group of overlapping ESTs,
likely from one gene
10
Expression profiling using microarrays
11
Human chromosomes sequenced
http//www.ncbi.nlm.nih.gov/genome/seq/
12
Human Genome Browser view
13
Model for replication fork movement in E. coli
14
Activities of DnaB and PriA in replisome
Sewing machine model
15
MutH, L, S action in mismatch repair1
16
MutH, L, S action in mismatch repair 2
17
Mismatch repair Excision of the misincorporated
nucleotide
18
Steps in the double strand break model
A1
B1
Endonuclease
5-3 exonuclease, Some 3-5 exo
Strand invasion
A2
B2
Repair synthesis
Repair synthesis
Ligate to form 2 joints
19
Effects of transposable elements depends on their
location
20
3-dimensional view of yeast RNA Pol II
Both yeast RNA Pol II and E. coli RNA polymerase
core Have a similar shape and have the channel
for DNA template.
Images from Dr. S. Darst
21
Evidence for a Pol II promoter
HBB, encodes beta-globin
Conserved in many Class II genes
Conserved in mammalian HBB genes
Directed mutation loss of trans- cription
Mutations cause beta-thalassemia
Specific binding of transcription factors
Mutation of gene encoding transcription factor
that binds here prevents HBB expression
22
Phosphotransfers for Group I vs. Group II
pre-mRNA
Exon 1
Exon 1
Exon 2
Exon 2
A
2
G
OH
OH
Exon 12
Exon 12

G

OH
Group II and pre-mRNA
Group I
23
EF-TuTs cycle for binding aa-tRNAs
24
From silenced to open chromatin
25
(No Transcript)