Transcript Office Hours

Office Hours
My office hours are now officially Tuesday and
Thursday, 9:30-10:45 AM, Shantz 225
You can request an appointment outside of office
hours
Chad’s office hours are Tuesday and Thursday, 3:304:30 PM, Shantz 213
Rules about Falling Asleep
 You
pay for this class, so you can sleep through it
if you want.
 If you decide to sleep in class, I can decide to wake
you up however I want, whenever I want.
Genetics in the News
Bold New World for Bald Mice
By Kristen Philipkoski
http://www.wired.com/news/medtech/0,1286,64833,00.html?tw=wn_7techhead
Hairless mice of the world, rejoice. Scientists have found a way to grow
new hair follicles on your bald bodies using stem cells.
The study could be good news not just for furless mice. The Howard
Hughes Medical Institute researchers who performed the study are also
hoping the stem cells will grow hair, as well as skin and sebaceous
glands, in humans.
The study, which was published in the Sept. 3 issue of Cell, showed that
stem cells taken from the hair follicles of mice could self-renew in a dish,
and when grafted onto mice could grow into new follicles and hair.
"We are now looking at whether we can isolate human cells with the
same procedure," said Dr. Cedric Blanpain, a postdoctoral fellow at
Rockefeller University who is an author of the paper. "If that is the case,
it's promising for humans."
Besides replacing hair, the discovery could lead to better skin grafts for
burn victims, since grafts now can't grow hair or sebaceous glands.
The next step is to try implanting human stem cells, taken from hair
follicles, into the hairless mice. If the stem cells grow hair and skin like
the mouse cells did, then the researchers will try implanting the cells into
humans, Blanpain said……
The stem cells used in this study, however, were taken from the skin of
mice. Human adult skin, as well as bone marrow, blood, placenta and
brain tissue, is also a source of so-called adult stem cells. The same
groups that oppose embryonic stem cell research believe adult stem cells
should be studied for therapies instead.
The goal in both types of stem cell research is to coax the cells into
becoming replacements for a damaged liver, spinal cord, pancreas or
other organs.
Potency of stem-type cells
 Totipotent:
can differentiate along all pathways;
can become any kind of cell (early embryonic
only)
 Pluripotent: can differentiate along several
different pathways (late embryonic cells and adult
stem cells)
Review
 DNA is
a double helix of two strands, in opposite
orientations
 DNA is a polymer of nucleotides
 A nucleotide is composed of phosphate group(s),
asugar (deoxyribose) and a base (adenine, guanine,
thymine and cytosine)
 RNA is composed of phosphate group(s), a sugar
(ribose) and a base (adenine, guanine, uracil and
cytosine
Phosphate Group
Nitrogenous Base
5-Carbon Sugar
A Typical Nucleotide
The Central Dogma
DNA
RNA
PROTEIN
DNA
Transcription
RNA
PROTEIN
DNA
Transcription
RNA
Translation
PROTEIN
Information
 Information
in DNA and RNA is encoded by the
nucleotide sequence
 The nucleotide sequence confers contextual
information (e.g. sequence-specific protein binding
controls transcription of DNA)
 The nucleotide sequence confers processing
information (e.g. specifying splice junctions, 5’cap
and 3’ polyadenylation)
Information
 The
nucleotide sequence specifies amino acid
sequence of proteins translated from RNA
 Generally, proteins are polymers whose building
blocks are 20 amino acids
The Genetic Code
The Codon
Nucleotides in groups of three specify amino acids
Codon
Three letters per “word” (codon), four different
“letters” (bases: A, G, U/T, C)
43=64 possible codons
More than enough to specify 20 amino acids
The Code is Degenerate
 For
18 of the 20 amino acids, there is more than
one codon specifying a particular amino acid
 The first two nucleotides are the most important;
most degeneracy occurs in the third position
 The
third position is referred to as the “wobble
position”
The Amino Acids
Phenylalanine (Phe)
 Leucine (Leu)
 Isoleucine (Ile)
 Methionine (Met)
 Valine (Val)
 Serine (Ser)
 Proline (Pro)
 Threonine (Thr)
 Alanine (Ala)
 Tyrosine (Tyr)

Histidine
 Glutamine (Gln)
 Asparagine (Asn)
 Lysine (Lys)
 Aspartic Acid (Asp)
 Glutamic Acid (Glu)
 Cysteine (Cys)
 Tryptophan (Trp)
 Arginine (Arg)
 Gycine (Gly)

Other Codons
 AUG
(met) is also the initiation codon
UAG, UGA are stop codons
 These two types of codons specify the beginning
and ending of the DNA sequence that will be
transcribed into RNA
 UAA,
Alterations in DNA (Mutation) that
Affect Transcription and Subsequent
Translation
Nonsense: alteration that results in a stop codon,
which produces a truncated polypeptide
AUG UGC ACC CAU
Met Cys Thr His
AUG UGA ACC CAU
Met STOP
Alterations in DNA (Mutation) that
Affect Transcription and Subsequent
Translation
Frameshift: insertion or deletion of one or two
nucleotides that shifts the reading frame such that
the codons are changed
G
AUG UGC ACC CAU
AUG UGG CAC CCA U
Met Cys Thr His
Met Trp His
Pro
Other Characteristics of the Code
 Non-overlapping: After translation begins, a given
RNA nucleotide is part of only ONE triplet codon
 Unambiguous: A codon specifies ONE item, either a
single amino acid or the stop function
 Without
“punctuation”: Once translation begins, the
codons are read continuously without breaks
 Universal: The coding dictionary is used by almost all
viruses, prokaryotes, archebacteria and eukaryotes
The Triplet Code
Again, the four bases possible at each of the three
positions in a codon allows for 64 different
combinations for codons.
The universal designation of those codons demands
an examination of philosophy, which can never be
divorced from objective science.
Perspectives on Information
To be or not to be….
How long would it take a monkey at a typewriter to
generate this famous sentence if he randomly
selected among the six possible letters, accounting
for the relative frequencies of the different letters,
and worked continuously?
Hmmm?
A few years?
A few millenia?
In fact, it would take a billion, billion
(2 x 1018) years!
Given that the age of the earth is
estimated to be only a few billion
years, you should now be
wondering…
What is the origin of our information?
Is it possible to generate information
from scratch?
Or, can information arise out of
chaos?
Transcription
Occurs in the nucleus (as opposed to
translation,which occurs on ribosomes out in the
cytoplasm)
The enzyme responsible is RNA Polymerase, a
multi-subunit protein associated with a complex of
other proteins (transcription factors) that
direct placement of the polymerase on the DNA
molecule.
Transcription
Transcription: Synthesis of an RNA molecule on a
DNA template
Sense
Antisense
Sense
~2,000 NT
5,00050,000 NT
Transcription
Initiation: Formation of the transcription complex,
consisting of RNA Polymerase and other proteins
that drive transcription and determines the
transcription start site
Elongation: Synthesis of the RNA molecule
Termination: Synthesis ends and the RNA molecule
is released
Initiation
Promoters are specific DNA sequences that are
upstream (5’) of the point where transcription of
the RNA molecule begins.
Promoters determine the efficiency of transcription.
Promoters contain a number of sequences that
determine where transcription factors bind
Consensus Sequences
Consensus Sequences are similar (homologous)
sequences that
1. Appear in different genes of the same organism
2. In one or more genes related organisms
Conservation across organisms indicates their critical
role in gene expression.
Consensus Sequences
A prime example is the TATA box, located 10-35
bases upstream of the site of transcription
inititiation.
The TATA box directs the RNA polymerase where to
“sit down” in the most basic sense (transcription
factors also influence this)
Enhancers
Consensus sequences located farther upstream that
increase transcription efficiency.
May be located a relatively long distance upstream.
Promoter with Proteins Bound
Elongation
Chain lengthening as RNA polymerase moves along,
reading the DNA template and adding
corresponding RNA nucleotides
Termination
RNA synthesis terminates when a stop codon is
encountered
RNA polymerase dissociates along with associated
transcription factors
RNA Processing
Heteronuclear RNA (hnRNA) is the “raw”
RNA transcribed off DNA.
This RNA is processed before leaving the nucleus.
Introns and Exons
Exons are spans of RNA that are retained in the
final transcript (mRNA) that exits the nucleus; may
encode amino acids.
Introns are spans of RNA that are removed from
hnRNA after termination, during processing.
hnRNA
Exons
Introns
Introns may be very large (20,000 NT) compared to
exons (200-300 NT)
Removal of introns is sequence specific (splice
junctions) recognized by processing enzymes
Splicing to remove introns
Splicing
Other processing steps

5’ cap: 7-methylguanosine (7mG) attached to 5’ end of the
transcript, usually during elongation

3’ poly-A tail: ~200 adenine added to the 3’ end of the
transcript
Attachment of the poly-A tail is directed by a consensus
sequence toward the 3’ end of the transcript
Summary of Transcription