Human Genetics

The Human Genome

Genome

The genome of an organism is the complete set of genes specifying how its phenotype will develop (under a certain set of environmental conditions).

Diploid organisms (like us) contain two genomes, one inherited from our mother, the other from our father.

The total DNA of an organism.Nuclear genome refers to the total DNA in the

nucleus, which is distinguished from organellar genomes of the mitochondria and chloroplast.

Genome size variation

Comparison of genome organization

Organism Genome Size(n)

# of Genes Chromosomes(n)

Human 3,000,000,000 35,000 23 linear

D.melanogaster

140,000,000 13,600 4 linear

C. elegans 97,000,000 19,000 6 linear

A. thaliana 125,000,000 25,500 5 linear

S. cerevisiae 13,000,000 5,800 16 linear

E. coli 4,700,000 4,000 1 circular

Human mtDNA 17,000 37 1 circular

Eukaryotic Genomes are Variable in Size

Marbled lungfish 139,000,000,000

Salamander 50,000,000,000

Homo sapiens 3,000,000,000

Pufferfish 400,000,000

Fruit Fly 165,000,000

Arabidopsis 100,000,000

Baker’s yeast 12,067,280

Why the big differences?

Do Marbled Lungfish differ from Pufferfish?

Are Lilies all that much different than Arabidopsis?

These differences exist because: Genomes have duplicated (chromosome

doubling) Individual genes have duplicated. DNA exists that has no coding function.

Gene structure

I. Gene definitionII. Genome organization (eukaryotic)

1. Genes and their noncoding regulatory sequences2. “Nonfunctional” DNA3. Duplicated genes4. Repetitive DNA

III. Mobile DNAIV. Gene Regulation

Some Terms

A duplicate of a gene may acquire mutations and emerge as a new gene.

Noncoding DNA: a sequence of DNA contained in eukaryotic genomes that does not encode any genetic information and often consists of repetitive sequences.

Expression: DNA transcribed into RNA and RNA turned into protein are expressed. The regulation of this process is called gene expression.

Nomenclature on DNA quantity

bp = one base pair within a double-stranded DNA

kb = 1,000 base pairs of double-stranded DNAmb = 1 million base pairs of double-stranded

DNAn = number of chromosomes in a haploid

genome2n = number of chromosomes in a diploid

genome

Definition(s) of a Gene

1. A hereditary unit that is composed of a sequence of DNA and occupies a specific position or locus.

2. Broadly, any genetic determinant of a specific functional gene product.

3. Molecular definition:

Entire nucleic acid sequence necessary for the synthesis of a functional polypeptide (protein chain) or functional RNA

Genes and Their ProductsThe majority of genes are expressed as

the proteins they encode. The process occurs in two steps:

Transcription = DNA -> RNA Translation = RNA -> protein

This is the “Central Dogma" of Biology: DNA makes RNA makes protein.

The Central Dogma of Molecular Biology

WHY? The DNA can retain integrity The RNA step allows amplification Multiple steps allow multiple points of control

DNA

RNA

Protein

TranscriptionTranslation

Most Genes Encode Proteins

Original Concept of the Gene: One gene = one enzyme

This concept does not hold for those proteins that consist of two or more different subunits.

Revised Concept: One gene = one messenger RNA = one

peptide.

RNA Genes

Some RNAs (tRNA, rRNA, snRNA, mtRNA) don’t code for proteins that are translated.

However, these are still referred to as genes-they are specific functional gene products.

Other DNA sequences regulate the transcription of other genes and can act like genes in some ways.

Genes are interspersed along DNA molecules, being separated by DNA sequence of unknown function (intergenic regions)

Coding region

Nucleotides (open reading frame) encoding the amino acid sequence of a protein

The molecular definition of gene includes more than just the coding region.

Noncoding regions

Regulatory regions RNA polymerase binding site Transcription factor binding sites

IntronsPolyadenylation [poly(A)] sites

“Nonfunctional” DNA

Higher eukaryotes have a lot of noncoding DNA

Some has no known structural or regulatory function (no genes)

80 kb

Duplicated genesEncode closely related (homologous)

proteinsClustered together in genomeFormed by duplication of an ancestral

gene followed by mutation

Five functional genes and two pseudogenes

Mobile DNA

Moves within genomesMost of moderately repeated DNA

sequences found throughout higher eukaryotic genomes L1 LINE is ~5% of human DNA (~50,000 copies) Alu is ~5% of human DNA (>500,000 copies)

Some encode enzymes that enable movement

Transposition

Movement of mobile DNAInvolves copying of mobile DNA element

and insertion into new site in genome

Why?

Molecular parasite: “selfish DNA”Probably have significant effect on

evolution by facilitating gene duplication, which provides the fuel for evolution, and exon shuffling

RNA or DNA intermediate

Transposon moves using DNA intermediate

Retrotransposon moves using RNA intermediate

LTR (long terminal repeat)Flank viral retrotransposons and retrovirusesContain regulatory sequences

Transcription start site and poly(A) site

LINES and SINESNonviral retrotransposons

RNA intermediate Lack LTR

LINES (long interspersed elements) ~6000 to 7000 base pairs L1 LINE (~5% of human DNA) Encode enzymes that catalyze movement

SINES (short interspersed elements) ~300 base pairs Alu (~5% of human DNA)

Human Disease and Mobile DNA

Movement (transposition) of LINES and SINES can cause mutations and genetic disease by insertion into essential genes Hemophilia (blood clotting factor VIII gene) Muscular dystrophy (DMD) Colon cancer (APC)

RNA Transcription

The process of releasing information contained in a DNA sequence, because DNA itself is used only for storage and transmission.

The sequence of bases in the DNA template is copied into an RNA sequence, which is either used directly or translated into a polypeptide.

Noncoding DNA can be Part of Transcribed Genes

Regulatory regions (Promoters)IntronsPoly A+ Addition sites5’ untranslated regions3’ untranslated regions.

Basic Gene Structure

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CAAT TATAGC

Prokaryotes like E. coli

Humans and other Eukaryotes

Bacterial Gene

Human Genes

Most have intronsProduce monocistronic mRNA: only one

encoded proteinLarge ( 1000->1,000,000 base pairs)

Gene Transcription and Regulation

A Puzzle about Cells

Each Cell has a complete copy of all the DNA. And yet, cells are different.

This is the theoretical basis of organism cloning.

So cells are only using some of the DNA to make RNA to make proteins at any time.

How does the cell know which DNA to chose to transcribe?

External environment sends signals that are recognized, and transcription is turned on or off in response to the signals.

Transcription

Transcription is the synthesis of RNA from a DNA template.

Main Types of RNA each have different roles in the cell: mRNA= Messenger RNA tRNA = Transfer RNA rRNA = Ribosomal RNA mtRNA = Mitochondrial RNA snRNA = Small nuclear RNA

rRNA and tRNA are Cogs in the Machinery

rRNA is a structural part of the ribosome

tRNA helps the protein machinery to read the mRNA

Neither of these types of RNAs actually carries any information

Messenger RNA

Messenger RNA carries the information in the DNA to the protein translation machinery (ribosomes)

Serves as the template for protein synthesis

Which mRNAs are transcribed in a cell decide the fate of that cell since they dictate which information in the DNA is read by the protein translation machinery

RNA moleculesSynthesized by RNA polymerases using DNA

as a template.Polymer of ribonucleotides, where each

consists of a phosphate group (PO4), ribose sugar, and a base (adenine, guanine, cytosine, or uracil).

Following synthesis of an RNA strand, it remains single-stranded.

Gene Regulation can occur at any of these steps

Initiation- highly regulated stepElongation- the rate at which the mRNA is

made can control how quickly its madeTermination- premature termination can

mean that the whole mRNA never gets made and neither does what it codes for: Like receiving only part of the instructions on

how to put together your “easy to assemble” bookcase/desk/whatever

Steps of RNA Transcription

Initiation Elongation Termination

All RNA transcription is performed by enzymes called RNA polymerases.

RNA transcription starts at a Promoter sequence (analogous to ORI for DNA replication).

Transcription of mRNA in Humans

Steps involved are the same as in prokaryotes: Initiation Elongation Termination

Mediated by RNA polymerase II: Very complex enzyme with many subunits

Human Transcription

Has to be more control of how more complex genetic material is read to create more variety (multicellular)

RNA has to be transcribed in the nucleus and then transported to the protein translation machinery in the cytoplasm before it can be read.

Protein

DNA

Nucleus

Human genes

Most have intronsProduce monocistronic mRNA: only one

encoded proteinLarge genes

Initiation

Initiation occurs at promoters as in prokaryotes- eukaryotic promoters are not well-characterized but have some well conserved elements- including the TATA box and CAAT box (both have A=T pairs)

In addition to the promoters there are region in the DNA called enhancers to which transcription factors bind and regulate which DNA is read and encoded in mRNA

mRNAPromoterEnhancer Gene

PromoterEnhancer Gene

Pol

TF

TF

TF

TFTF

TF

Transcription Factor Function

TF

TF= Transcription Factor

Transcription Factors

Although transcription is performed by RNA Polymerase, it needs other proteins to produce the transcript.

These proteins are either associated directly with RNA Polymerase or help it bind to the DNA sequences upstream of the initiation of translation..

These associated proteins are called transcription factors.

RNA transcription begins by the assembly of the RNA polymerase on a promoter region.

Orientation of promoter elements specifies the direction of transcription

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CAAT TATAGC

prokaryote

eukaryote

Transfer of Information

Gene

exon | intron | exon | intron | exon

mRNA

Exon - portion of the gene that contains DNA sequences that will be translated into protein.

Intron - portion of the gene that will be cut out before translation

Transfer of Information

Reading the Genes in the Genome

TranslatingProtein

mRNAAAAProcessing

Transcribing

Signal recognizing