NUTRITION AND GENE EXPRESSION Jan 23, 2014 Dr. Garry Handelman DEFINITION OF A GENE

NUTRITION AND GENE EXPRESSION

Jan 23, 2014

Dr. Garry Handelman

DEFINITION OF A GENE

WHAT IS A GENE?

From 1960-1980, it was defined as “the set of nucleic acids that codefor a certain protein”. Each gene wasknown to have a specific chromosomallocation.

For example, during that period,the gene for the enzyme LDHwas defined as the DNA sequencethat specified the messenger RNA(mRNA) to make the protein LDH.

WHAT IS THE NEW DEFINITIONOF 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 controlof the activity of that specific gene.

THUS, AT TPYICAL GENE CONSISTS

OF TWO COMPONENTS:

•A CODING domain, that specifiesthe amino acid sequence

•A REGULATORY domain, thatparticipates in turning thegene on and off.

IN THIS COURSE, WE WILL

DISCUSS BOTH THECODING DOMAIN, AND

THEPART OF THE GENE THAT

ISINVOLVED 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 showsbase pairing

In a textbook,this strand isshown:“Coding strand” This is the

“Template strand”,which is used tomake an RNA copy.

In this case, theCodon “CUA” willcode for LeucineTHIS RNA WAS

MADE AS A COPYFROM THE DNA!

WHAT HAPPENS AFTERCOMPLETION OF TRANSCRIPTION?

The strand of RNA is usually processed to make amessenger RNA (mRNA). The mRNA is then readby ribosomes to make proteins.

The genetic code specifies TRIPLETS on the mRNAwhich code for different amino acid.

Puffed-out regionof DNA in Drosophilachromosome:INTENSE synthesisof RNA occurring

You will use these RNA triplet codons, for specific aminoacids, 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 GENESIN DIFFERENT TISSUES

• MOST CELLS CONTAIN THE ENTIRE HUMANGENOME – ABOUT 25,000 GENES THAT CODEFOR PROTEINS. THERE ARE TWO COPIES OF MOST GENES: A COPY FROM THE MATERNAL DNA, AND FROM THE PATERNAL DATA.

• BUT – IN A TYPICAL CELL, ABOUT 10,000 GENES, ARE ACTIVE. THE RESTOF THE GENES ARE DORMANT. THESE EXTRAGENE 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 JUSTMAKE REGULATORY RNA: WE WILL ALSO DISCUSS THIS AREA, BUT THE STATE OF KNOWLEDGE ISVERY EARLY

THE COMPLETEHUMAN GENOME:We will focus in this lecture on genes that are located onChromosome 3

GENES IN CHROMOSOME 3

For illustration, we will discuss several different genes found on Human Chromosome 3:REMEMBER, YOU HAVE TWO COPIES OFTHIS CHROMOSOME, AND GENES ON BOTHARE 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 DEMONSTRATETHREE 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

LIVER CELL, MUSCLE CELL

PHOTORECEPTOR

PDH GENE:ACTIVE IN MOST CELLS

FATTY-ACID-CoA-Ligase:Highly Expressed in Cells thatUtilize Fatty Acids for Energy

RHODOPSIN GENE: ACTIVEONLY IN PHOTORECEPTORS

KEY CONCEPT: HOUSEKEEPING GENES

These are genes that are active at all times,in all cells in the body. There are about2,000 housekeeping genes.

Examples: Na/K-ATPase – enzyme that pumps Na out,and K out, to maintain normal ion distributioninside the cell

Pyruvate dehydrogenase (PDH): converts pyruvate toacetyl Co-A, at the entry point to the TCA cycle

Pyruvate dehydrogenase, beta-subunit:this gene is expressed in virtually all cells.

A HOUSKEEPING GENE!

GENES ON CHROMOSOME 3

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?

QUESTION:

-Is it necessary, for all the molecules of PDH in the cell to have the same amino acid sequence?

PDH complex (multi-protein): found in all cells that have mitochondria

This complex, includingthe beta-subunit, convertsPYRUVATE 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 selectedtissues, and remain dormant everywhere else.

Examples: Globin gene: makes globin chain for Hb.Only expressed on red cell precursor cellsin the bone marrow.

Rhodopsin gene: produces key visual protein.Only expressed in rod photoreceptors of the retina.

Rhodopsin (main human visual protein): expressed only in rod photoreceptors. VERY TISSUE SPECIFIC. Cannot be expressed, except in the retina.

GENES ON CHROMOSOME 3

A ROD PHOTORECEPTOR CELL

NO OTHER CELL EXPRESSESTHE GENE FOR RHODOPSIN!

Rhodopsin is locatedin this part of the cell,and responds tolight hitting the retina.

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 STUDYIN DETAIL DURING THIS COURSE.

Examples: TRPV-6 transport protein: up-regulated by calcitriol(the active metabolite of vitamin D); this proteinis needed to absorb Ca(2+) from the digestive tract

Fatty-acid-Co-Ligase: first step in beta-oxidationof fatty acids for energy, activated during fasting.

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 decreasedby high carbohydrate intake.

The conversion offatty acids to CoAderivatives is catalyzed by:

Fatty-Acid-CoA-Ligase

To BETA-OXIDATION

Pyruvate dehydrogenase, beta-subunit:this gene is expressed in virtually all cells.A HOUSKEEPING GENE!

REMEMBER, WE HAVE TWOCOPIES OF CHROMOSOME 3!

The PDH gene, beta-subunit is active at thesame 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 inyour DNA are active (unless one copy is defective).If you have one good copy, usually it’s OK.

FOR CLASSROOM DISCUSSION: WHAT GENESWOULD YOU EXPECT TO BE ACTIVE INTHE FOLLOWING TISSUES?

-WHITE CELLS

-PANCREATIC BETA CELLS

-CELLS THAT LINE THE STOMACH

-PITUITARY GLAND

Since each cell only activates a PORTIONof its total set of genes to make proteins –

HOW IS THAT REGULATED?

This is one of the fundamental questionsaddressed in human biology. The specific regulation of genes now consumesmuch of the effort in biology research.

THE STEPS IN PROTEIN SYNTHESIS.

CONTROL CAN OCCUR ATEACH STEP IN THE PATHWAY!

RNA initially transcribed

Processed to mRNA

mRNA read into Protein

Protein can be modified

R

MAKE THE INITIAL RNA

PROCESS TO mRNA

TRANSLATE TO PROTEIN

MODIFY THE PROTEIN

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 MATERIALWILL HELP US TO UNDERSTAND

GENE REGULATION.

YOU SHOULD BE MAKINGA SERIES OF PROGRESSIVELY

MORE DETAILED SKETCHES, ASYOU ADD INFORMATION TO

YOUR MODEL OF GENE EXPRESSIONAND THE GENOME