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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)
3,000,000,000
# of Genes
35,000
Chromosomes
(n)
23 linear
D.
melanogaster
C. elegans
140,000,000
13,600
4 linear
97,000,000
19,000
6 linear
A. thaliana
125,000,000
25,500
5 linear
13,000,000
5,800
16 linear
4,700,000
4,000
1 circular
17,000
37
1 circular
Human
S. cerevisiae
E. coli
Human mtDNA
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 definition
II. Genome organization (eukaryotic)
1. Genes and their noncoding regulatory
sequences
2. “Nonfunctional” DNA
3. Duplicated genes
4. Repetitive DNA
III. Mobile DNA
IV. 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 DNA
mb = 1 million base pairs of double-stranded
DNA
n = number of chromosomes in a haploid
genome
2n = 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 Products
The 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
Protein
DNA
Transcription
RNA
Translation
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
Introns
Polyadenylation [poly(A)] sites
“Nonfunctional” DNA
80 kb
Higher eukaryotes have a lot of
noncoding DNA
Some has no known structural or
regulatory function (no genes)
Duplicated genes
Encode closely related (homologous)
proteins
Clustered together in genome
Formed by duplication of an ancestral
gene followed by mutation
Five functional genes and two pseudogenes
Mobile DNA
Moves within genomes
Most 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 DNA
Involves 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
retroviruses
Contain regulatory sequences
Transcription start site and poly(A) site
LINES and SINES
Nonviral 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)
Introns
Poly A+ Addition sites
5’ untranslated regions
3’ untranslated regions.
Basic Gene Structure
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Prokaryotes like E. coli
GC CAAT TATA
Humans and other Eukaryotes
Bacterial Gene
Human Genes
Most have introns
Produce monocistronic mRNA: only one
encoded protein
Large ( 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 molecules
Synthesized 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 step
Elongation- the rate at which the mRNA is
made can control how quickly its made
Termination- 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 introns
Produce monocistronic mRNA: only one
encoded protein
Large 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
Transcription Factor Function
TF
TF
TF
TF
Enhancer
TF
TF
TF
Enhancer
Pol
Promoter Gene
mRNA
Promoter
Gene
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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prokaryote
GC CAAT TATA
eukaryote
Transfer of Information
Gene
mRNA
exon | intron |
exon
| intron
| exon
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
Signal recognizing
Transcribing
Processing
AAA mRNA
Translating
Protein