Download 1) Definition of the gene

NUTRITION AND GENE EXPRESSION
Jan 22, 2015
Dr. Garry Handelman
DEFINITION OF A GENE
WHAT IS A GENE?
From 1960-1980, it was defined as
“the set of nucleic acids that code
for a certain protein”. Each gene was
known to have a specific chromosomal
location.
For example, during that period,
the gene for the enzyme LDH
was defined as the DNA sequence
that specified the messenger RNA
(mRNA) to make the protein LDH.
COMMENT: What is mRNA?
In the process called TRANSCRIPTION, the DNA helix
separates, and one strand is copied into an RNA strand.
That RNA strand will then be processed to make an mRNA.
IN GENE FUNCTION
BOTH RNA AND
DNA OCCUR AS
POLYMER STRANDS
WE WILL DISCUSS RNA VS DNA ALL SEMESTER:
Notice one important difference. The ribose sugar in
RNA has two free OH groups, and DNA has only one free OH.
WHAT IS THE NEW DEFINITION
OF A GENE?
In the last 30 years, the gene was redefined.
It includes the DNA that codes for the protein,
AND the DNA that participates in the control
of the activity of that specific gene.
THUS, AT TPYICAL GENE CONSISTS
OF TWO COMPONENTS:
• A CODING domain, that specifies
the amino acid sequence
• A REGULATORY domain, that
participates in turning the
gene on and off.
IN THIS COURSE, WE WILL
DISCUSS BOTH THE
CODING DOMAIN, AND THE
PART OF THE GENE THAT IS
INVOLVED IN REGULATION.
To understand the gene, consider
the structure of DNA
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 RNA WAS
MADE AS A COPY
FROM THE TEMPLATE STRAND
OF THE DNA!
This is the
“Template strand”,
which is used to
make an RNA copy.
In this case, the
Codon “CUA” will
code for Leucine
WHAT HAPPENS AFTER
COMPLETION OF TRANSCRIPTION?
The strand of RNA is usually processed to make a
messenger RNA (mRNA). The mRNA is then read
by ribosomes to make proteins.
The genetic code specifies TRIPLETS on the mRNA
which code for different amino acid.
PLEASE COPY THE DRAWINGS I MAKE ON
THE BOARD INTO YOUR NOTES
Puffed-out region
of DNA in Drosophila
chromosome:
INTENSE synthesis
of RNA occurring:
ARGUMENT: SHOW
RNA SYNTHESIS
RIGHT HERE!!!
VIDEO IS OK.
You will use these RNA triplet codons, for specific amino
acids, for exercises throughout the semester.
For exercises on
TRANSLATION of
genetic code: amino
acid side chains
THE CORE CONCEPT IN GENE EXPRESSION:
SELECTIVE ACTIVITY OF GENES
IN DIFFERENT TISSUES
•
MOST CELLS CONTAIN THE ENTIRE HUMAN
GENOME – ABOUT 25,000 GENES THAT CODE
FOR PROTEINS. THERE ARE TWO COPIES OF
MOST GENES: A COPY FROM THE MATERNAL DNA,
AND FROM THE PATERNAL DATA. Comment: DRAW
ACTIVITY OF GENES BOTH COPIES
•
BUT – IN A TYPICAL CELL, ABOUT 10,000 GENES,
ARE ACTIVE. THE REST
OF THE GENES ARE DORMANT. THESE EXTRA
GENE REMAIN IN THE NON-ACTIVE STATE.
•
THE CELL ONLY EXPRESSES THE GENES,
AND MAKES THE PROTEINS, THAT IT NEEDS
•
THERE IS A NEW CLASS OF GENES THAT JUST
MAKE REGULATORY RNA: WE WILL ALSO DISCUSS
THIS AREA, BUT THE STATE OF KNOWLEDGE IS
VERY EARLY
THE COMPLETE
HUMAN GENOME:
We will focus in this
lecture on genes
that are located on
Chromosome 3
GENES IN CHROMOSOME 3
For illustration, we will discuss several
different genes found on Human Chromosome 3:
REMEMBER, YOU HAVE TWO COPIES OF
THIS CHROMOSOME, AND GENES ON BOTH
ARE USUALLY ACTIVE
-A gene that is active in almost all tissues
(pyruvate dehydrogenase, or PDH)
-Another gene on Chromosome 3, only active in
photoreceptors of the retina (rhodopsin)
-Finally, a gene that is activated during fasting,
when you burn fatty acids for energy
(fatty-acid-CoA-ligase)
THESE GENES ARE UTILIZED TO DEMONSTRATE
THREE KEY CONCEPTS IN GENE EXPRESSION:
•
Genes that are active, continually, in most cells
•
Genes that only operate in a very restricted set
of cells, not affected by diet
•
Finally, genes that operate in a variety of tissues,
and respond to dietary and other changes
FIBROBLAST
PHOTORECEPTOR
PDH GENE:
ACTIVE IN MOST CELLS
RHODOPSIN GENE: ACTIVE
ONLY IN PHOTORECEPTORS
FATTY-ACID-CoA-Ligase:
Highly Expressed in Cells that
Utilize Fatty Acids for Energy
LIVER CELL,
MUSCLE CELL
KEY CONCEPT:
HOUSEKEEPING GENES
These are genes that are active at all times,
in all cells in the body. There are about
2,000 housekeeping genes.
Examples:
Na/K-ATPase – enzyme that pumps Na out,
and K out, to maintain normal ion distribution
inside the cell
Pyruvate dehydrogenase (PDH): converts pyruvate to
acetyl Co-A, at the entry point to the TCA cycle
GENES ON CHROMOSOME 3
Pyruvate dehydrogenase, beta-subunit:
this gene is expressed in virtually all cells.
A HOUSKEEPING GENE!
QUESTIONS:
The PDH gene is shown on one copy
of chromosome 3.
- How many copies are there of this
chromosome, in a typical cell?
- Is the gene for PDH only active, on
one copy of that chromosome?
PDH complex
(multi-protein):
found in all cells that
have mitochondria
This complex, including
the beta-subunit, converts
PYRUVATE to ACETYL-CoA,
which is then used in the
TCA cycle, to make ATP.
KEY CONCEPT:
TISSUE-SPECIFIC GENES
These are genes that are only active in selected
tissues, and remain dormant everywhere else.
Examples:
Globin gene: makes globin chain for Hb.
Only expressed on red cell precursor cells
in the bone marrow.
Rhodopsin gene: produces key visual protein.
Only expressed in rod photoreceptors
of the retina.
GENES ON CHROMOSOME 3
Rhodopsin (main human visual protein):
expressed only in rod photoreceptors.
VERY TISSUE SPECIFIC. Cannot be
expressed, except in the retina.
Rhodopsin is located
in this part of the cell,
and responds to
light hitting the retina.
NO OTHER CELL EXPRESSES
THE GENE FOR RHODOPSIN!
A ROD PHOTORECEPTOR CELL
KEY CONCEPT:
GENES THAT RESPOND TO DIET
These are genes that active in some tissues
(not all), and which change with change in diet.
THESE ARE THE GENES WE WILL STUDY
IN DETAIL DURING THIS COURSE.
BLACKBOARD GRAPHIC
Examples:
TRPV-6 transport protein: up-regulated by calcitriol
(the active metabolite of vitamin D); this protein
is needed to absorb Ca(2+) from the digestive tract
Fatty-acid-Co-Ligase: first step in beta-oxidation
GENES ON CHROMOSOME 3
FATTY-ACID CoA LIGASE:
This gene is activated when fatty acids
are delivered to tissues for catabolism,
such as during fasting.
Can be expressed in heart muscle,
skeletal muscle, liver, kidney.
Its mRNA can also be decreased
by high carbohydrate intake.
The conversion of
fatty acids to CoA
derivatives is catalyzed by:
Fatty-Acid-CoA-Ligase
To BETA-OXIDATION
REMEMBER, WE HAVE TWO
COPIES OF CHROMOSOME 3!
Pyruvate dehydrogenase, beta-subunit:
this gene is expressed in virtually all cells.
A HOUSKEEPING GENE!
The PDH gene, beta-subunit is active at the
same time on EACH chromosome
(maternal and paternal): this protein is made
from the PDH gene on each chromosome.
As a general rule, both copies of each gene in
your DNA are active (unless one copy is defective).
If you have one good copy, usually it’s OK.
FOR CLASSROOM DISCUSSION: WHAT GENES
WOULD YOU EXPECT TO BE ACTIVE IN
THE FOLLOWING TISSUES?
-WHITE CELLS
-PANCREATIC BETA CELLS
-CELLS THAT LINE THE STOMACH
-PITUITARY GLAND
Since each cell only activates a PORTION
of its total set of genes to make proteins –
HOW IS THAT REGULATED?
This is one of the fundamental questions
addressed in human biology.
The specific regulation of genes now consumes
much of the effort in biology research.
THE STEPS IN PROTEIN SYNTHESIS.
CONTROL CAN OCCUR AT
EACH STEP IN THE PATHWAY!
RNA initially transcribed
Processed to mRNA
mRNA read into Protein
Protein can be modified
MAKE THE INITIAL RNA
PROCESS TO mRNA
TRANSLATE TO PROTEIN
MODIFY THE PROTEIN
R
AS THE COURSE MOVES ON, WE WILL
DISCUSS CONTROL OF
EACH OF THESE FOUR STEPS
WE WILL REVIEW IN DETAIL THE
PATHWAYS OF GENE EXPRESSION.
THIS BACKGROUND MATERIAL
WILL HELP US TO UNDERSTAND
GENE REGULATION.
YOU SHOULD BE MAKING
A SERIES OF PROGRESSIVELY
MORE DETAILED SKETCHES, AS
YOU ADD INFORMATION TO
YOUR MODEL OF GENE EXPRESSION
AND THE GENOME