Transcript 1) Lecture notes: mechanisms of gene activation

Nutrition and
Gene Expression
Lecture, part 1, Feb 5, 2015
Overview: Gene Activation
WHAT IS A GENE?
•A gene is usually defined as sequence of
DNA that codes for a protein. Control
elements are also part the gene, and are
critical to regulation of its expression
•The coding sequence is first read into an RNA
sequence, which is processed to a message
(mRNA). This is called TRANSCRIPTION.
•The mRNA is then read by ribosomes to make
the protein. This is called TRANSLATION.
The basic structure of genes of course is DNA.
Standard cartoon view
View that shows
base pairing
In a textbook,
this strand is
shown:
“Coding strand”
This is the
“Template strand”,
which is used to
make an RNA copy.
In this case, the
Codon “CUA” will
code for Leucine
CODING STRAND: template for RNA synthesis
HYPOTHETICAL SMALL CHROMOSOME:
Double-stranded DNA, 1 million base pairs long
A
B
C
D
E
These 5 genes (A-E) occupy only 100,000 base pairs (about
(20,000/gene). The DNA in between has roles to be defined.
A
B
C
D
E
Let’s focus on one gene, B.
Region that is read into
primary RNA transcript
SIMPLIFIED STRUCTURE FOR A GENE
Transcription factor
binds here
ATGCTAATGTGCCTATATACGATGTCGCGTATAATTGAT
TACGATTACACGGATATATGCTACAGCGCATATTAACTA
Sequence to be copied into RNA
If there is a protein transcription factor to bind to the
RED DNA SEQUENCE, then the GREEN SEQUENCE
will uses as a template for a primary RNA transcript.
THE STRANDS SEPARATE BEFORE RNA IS MADE!
WHAT IS TRANSCRIPTION?
The synthesis of a complementary RNA strand,
that matches the sequence of the DNA strand.
This is the process where most regulation occurs,
during gene expression.
This will be illustrated with some very simple
examples of this process.
Coding strand: If a textbook shows only one sequence, it
will be this strand. It’s the same as the RNA transcript,
except that the RNA has U instead of T.
DNA: ATATGCTACAGCGCATAT
RNA: AUAUGCUACAGCGCAUAU
DNA: TATACGATGTCGCGTATA
Template strand: used by RNA-polymerase-II to make
a complementary RNA copy
Thymine (T)
Uracil (U)
RNA: AUAUGCUACAGCGCAUAU
DNA: TATACGATGTCGCGTATA
During RNA synthesis:
A pairs with T on the DNA
U pairs with A
C pairs with G
G pairs with C
Like DNA double strand, except RNA has U instead of T.
THE CORE QUESTION IN REGULATION OF
GENE EXPRESSION –
IS THERE A PROTEIN TRANSCRIPTION
FACTOR TO START RNA SYNTHESIS?
Otherwise, the DNA is usually not
transcribed into RNA.
In a typical cell, manyof the genes
(about 60%) are hardly ever transcribed.
TRANSCRIPTION FACTORS THEMSELVES ARE
PROTEINS.
THESE PROTEINS FUNCTION TO ACTIVATE THE
GENES THAT MAKE OTHER PROTEINS.
EFFECTS OF BINDING OF SPECIFIC
TRANSCRIPTION FACTOR (TF)
A) TF protein binds to CONTROL SITE
ATGCTAATGTGCCTATATACGATGTCGCGTATAATTGAT
TACGATTACACGGATATATGCTACAGCGCATATTAACTA
B) RNA Pol-II binds to the START SITE
Pol-II
ATGCTAATGTGCCTATATACGATGTCGCGTATAATTGAT
TACGATTACACGGATATATGCTACAGCGCATATTAACTA
RNA SEQUENCE, COMPLEMENTARY TO DNA, IS MADE
AS POL-II MOVES ALONG DNA SEQUENCE
AU
ATGCTAATGTGCCTATATACGATGTCGCGTATAATTGAT
TACGATTACACGGATATATGCTACAGCGCATATTAACTA
AUAUGC
ATGCTAATGTGCCTATATACGATGTCGCGTATAATTGAT
TACGATTACACGGATATATGCTACAGCGCATATTAACTA
AUAUGCUACAGCGCAUAU
ATGCTAATGTGCCTATATACGATGTCGCGTATAATTGAT
TACGATTACACGGATATATGCTACAGCGCATATTAACTA
TRANSCRIPTION COMPLETE
ATGCTAATGTGCCTATATACGATGTCGCGTATAATTGAT
TACGATTACACGGATATATGCTACAGCGCATATTAACTA
AUAUGCUACAGCGCAUAU
Primary transcript made, ready
for splicing and translation
NOTE: RNA-Pol-II will fall off the gene, and
can then start transcription again.
FRUCTOSE METABOLIC PATHWAY:
WHY ALDOLASE B IS NEEDED
FROM DIET
ALDOLASE B
NEEDED
AT THIS STEP
For discussion of the papers on hereditary fructose
intolerance, we will review a database maintained
on this disorder at Boston University:
http://www.bu.edu/aldolase/HFI/hfidb/hfidb.html