Topic Dec 2
Uses of PCR - cloning YFG, identifying viruses in clinical or env samples
ALSO: Forensics - DNA Fingerprinting
In many regions of our genome there are repetitive sequences - CACACA or
Repeats can be anywhere from 4 to 40 times.
1. Chemical basis of life
2. Amino acids
3. Protein structure
4. Protein function
5. Enzyme catalysis
6. Protein purification
By the end of today you will:
1. Understand the pH scale
2. Understand Ka and pKa
3. Be able to calculate pH and p
Michael B. Boffa, Ph.D.
Dept. of Biochemistry
TAFIa: PDB 3LMS
2288A only: Written assignment due 4 pm, Sept 29th
Available on OWL
Late assignment pe
Topic Nov 30
To be sure that YFG is correct, it should be sequenced.
We are still scared that what we have extracted is incorrect so that is why we do this.
Chemical sequencing - by Maxam and Gilbert - involved base specific c
Biochem Topic Nov 27
Last class- we made cDNA from a tissue we knew expressed YFG. Used PCR to amplify. Ran it
on agarose gel to purify it. No we clone it.
To get YFG into E. Coli we put it into a plasmid.
What is a plasmid?
A fragment of DNA that replic
Biochem: Topic Nov 25
Last class: Denaturation of DNA - intrinsic factors that affect the Tm
Extrinsic factors that affect the Tm
What does adding salt - NaCl - to the solution do to the Tm of the DNA? - raise the Tm
o The charged Phosphate backbones wil
Topic November 20
Charging of tRNAs
Amino acyl rRNA synthase
Some energy from ATP in high energy ester linkage which will be used in protein
tRNA aminoacyl tRNA synthetase complex
Bc of contact bw enzyme and anti
Nov 18 - Biochem 2280 - Brandl
Introns are spliced consecutively at 2 sites with 2 transesterification rxns
Attack at 3' OH and 5' splice junction
Machinery for splicing - spliceosome
Composed of snRNPs - contain both RNA and
Dr. Brandl - Nov 16
Trp operon KNOW Lac operon - no detail in lecture bc have worked on it before in 1st year - but know
E. Coli for utilization metabolism of lactose
Negative control - lac repressor
Positive control - catabolite activat
Why is there an RNA step in gene expression? - 3 reasons that the RNA step is useful
Provides a differential amplification which contributes to differential gene expression. some genes make more or less RNA
Since RNA can be degraded, expre
Topic Dec 9
Exam will provide the genetic code
Read the questions PROPERLY - read question, look at answers, read question and break it down
(highlighting/ underline) and then determine the answer.
3 hours - it will probably take just over 2 - do not rush
Topic Dec 7
Caused by UNCONTROLLED DIVISION of ABNORMAL CELLS
Genetic and biochemical problems related to cancer
Cancer can hit people of any age but it tends to be more prevalent with older people
More prevalent once you get past 40.
Why is that?
Bc a s
Topic Dec 4
Annotating the Sequenced Genome
What in does the genome contain - expressed and nonexpressed regions
Today - protein coding regions
Also want to annotate for promoters, terminators - will not really talk about these two
Looking for a pr
i. RNAP holoenzyme binds to promoters -10 & -35 via sigma factor-> closed complex
1. Note: NO PRIMER!
ii. RNAP unwinds a bit of DNA at start site-> open complex
iii. Elongation 5->3. After 5-10 nucleotides, si