Genetics and Molecular Genetics

Genes basic unit of heredity

Genetics - science of biological heredity and variation

Molecular genetics study of the structure and

function of genes at a molecular level
employs the methods of genetics and molecular
biology
 Genome

In classical genetics, refers to a full set of

chromosomes in a gamete
regular somatic cell contains two full sets of genomes
(2N)
haploid organisms, e.g., bacteria, contain only a single
set of the genome

In modern molecular biology the genome of an

organism is its hereditary information encoded in
DNA
 Genotype: encoded in chromosomes

Chromosome - a long strand of DNA, packaged together with

proteins and other molecules

Number of
Organism Chromosome
Pairs
Tomato 12 Pairs
Mouse 20 Pairs
Human 23 Pairs
Dog 39 Pairs
What are chromosomes made of?

Chromosomes are made

up of DNA and proteins
 Amino acids and proteins
Proteins = polymers of amino acids.
20 amino acids are commonly found in proteins
Each amino acid has a similar, yet unique structure
The four DNA bases
1944
Oswald Avery, Colin
MacLeod, and Maclyn
McCarty report
evidence that, at least Avery

in bacteria, the
molecule that carries
genetic information is
MacLeod
deoxyribonucleic acid
(DNA)

McCarty
 DNA is the genetic material

"S" or SMOOTH coat strain: lethal to mice "R" or rough strain; non-lethal

heat-killed S: mouse lives mixture of the heat-killed S and R strain

mouse dies
Avery's results were either ignored or attributed to trace
contamination of his DNA fractions with protein.
 Chargaffs Rules

Erwin Chargaff documented that that in all species,

[ A ] = [ T ] and [ C ] = [ G ]
1952
Martha Chase and Alfred
Hershey provide final proof
that DNA is the substance
that transmits inherited
traits from one generation
to the next
Hershey receives a Nobel
Prize in 1969 for this work
 Elucidating DNA structure

1953
James Watson and Francis Crick determine that the structure of
the DNA molecule is a double helix
They elucidate DNA structure using X-ray crystallography images
The DNA bases are of four types (A, C, G, & T): pairing always occurs between A
& T, and C & G.
The DNA double helix acts as a template
for its own duplication
Double strand arises from H-bonding
between G C and A - T
DNA Replication
Completion of bacterial
replication
Eukaryotic replication
Chromatin
packing
 Gene Expression

The genes in a genome do not have any effect on

cellular functions until they are "expressed

Different types of cells express different sets of

genes, thereby exhibiting various shapes and
functions

"Gene expression" = production of a protein from

its gene
Figure 4-6 Molecular Biology of the Cell ( Garland Science 2008)
 Proteins
Proteins fulfill a very wide range of functions, including:

1. Catalysis of chemical reactions

Enzymes

2. immunological response to infection

Antibodies

3. Oxygen transport
Hemoglobin, myoglobin

4. Acting as chemical messengers to regulate growth,

development, reproductive function, and metabolism
Transcription factors
 The flow of genetic
Information

Figure 6-2 Molecular Biology of the Cell ( Garland Science 2008)

 1961
Brenner, Jacob, and
Meselson identify the role
of RNA
Brenner Jacob
They determine that mRNA
carries genetic information
from DNA in the nucleus
into the cytoplasm

The cell uses mRNA to

make specific proteins.
Meselson
Central dogma of molecular
biology
"DNA makes RNA, RNA makes protein, and
proteins make us."

Francis Crick
The flow of genetic information
DNA transcription produces a single-stranded RNA
molecule that is complementary to one strand of DNA
Transcription
Translation
The genetic code
 Translation in prokaryotes

As soon as mRNA starts getting transcribed, ribosomes attach to translate

An mRNA can be translated by multiple ribosomes at the same time,
forming a polyribosome
 RNA Splicing
a process that removes introns and joins exons in a primary
transcript.
An intron usually contains a clear signal for splicing

Structure of two human genes showing the arrangement of exons and introns
 smallest protein-coding gene in the human genome is only
500 nucleotides long and has no introns.
encodes a histone protein

largest human gene encodes dystrophin, which is missing or

non-functional in the disease muscular dystrophy.
2.5 million nucleotides in length
>16 hours to produce a single transcript.
>99% of the gene is made up of its 79 introns.
The procedure of RNA processing for protein genes
 Exon skipping
Intron splicing requires an essential signal: "GT........AG".
If the splice acceptor site AG is mutated (e.g., A to C), the splicing
machinery will look for the next acceptor site.
As a result, the exon between two introns is also removed.
2 types of splicing errors. Cryptic splicing signals are nucleotide
sequences of RNA that closely resemble true splicing signals.
 Alternative splicing

Alternative splicing of the -tropomyosin gene from rat

Alternative splicing of
the HIV-1 primary
transcript
(i) Unspliced
(ii) to (iv) - singly
spliced
(v) and (vi) - doubly
spliced.

The resulting mRNA (i),

(iv) and (vi) are
bicistronic.
The star "*" indicates
the location of the
initiation codon
(AUG).
 The flow of genetic
Information

Figure 6-2 Molecular Biology of the Cell ( Garland Science 2008)

 Exceptions to the Central Dogma

DNA methylation can be

inherited

DNA

retroviruses use reverse transcriptase

mRNA introns (splicing) to replicate their genome
(Philip Sharp and Richard Roberts) (David Baltimore and Howard Temin)

RNA editing RNA viruses

RNA

ribozymes can catalyze an

enzymatic reaction
(Thomas Cech, Sidney Altman)
Protein Prions (Stanley Pruisner)
 Prions
proteinaceous infectious particle which resist
inactivation by procedures that modify nucleic acids

infectious agent composed only of protein

cause a number of diseases in a variety of animals

e.g., bovine spongiform encephalopathy (BSE, or "mad
cow disease") in cattle
e.g., Creutzfeldt-Jakob disease (CJD) in humans

Affect structure of brain or other neural tissue

Currently untreatable and fatal.

Neural degeneration in a prion infection. This micrograph shows a slice from the
brain of a person who died of kuru. Kuru is a human prion disease, very similar to
BSE, that was spread from one person to another by ritual mortuary practices in
New Guinea. The large fluid-filled holes are places where neurons have died.
 prion protein found in infectious material has a
different structure and is resistant to proteases

normal form of the protein = PrPC

C = cellular or common PrP

infectious form = PrPSc

Sc = 'scrapie; prion disease in sheep
Usually a misfolded form of the normal form
Protein aggregation causes prion diseases

misfolded version of protein induces normal PrP

protein it contacts to change conformation

misfolded protein prone to aggregation, but not

infectious
protease-resistant protein aggregates found in a variety of
human neurological diseases,
e.g., Alzheimers

structure of infectious form not yet known with

certainty because of aggregation
 Human prion diseases

CJD: Creutzfeld-Jacob Disease

GSS: Gerstmann-Straussler-Scheinker
syndrome
FFI: Fatal familial Insomnia
Kuru
Alpers Syndrome
 Creutzfeldt-Jakob disease
(CJD)

occurs spontaneously in 1 in 106 individuals

10% of cases are inherited mutations in the PRPN

gene

Usually strikes people age 50 to 75

Symptoms: dementia, muscle twitching, vision

problems
 Lines of evidence supporting a protein-
only model of infection

Nucleic acid not necessary for

infectivity
low ratio of nucleic acid to
infectious material.
resistance of infectivity to
agents which modify or
damage nucleic acids but
infectivity is susceptible to
reagents which destroy
proteins
 PrPsc associated with scrapie infectivity

purification of scrapie infectivity results in

preparations highly enriched for PrPsc

purification of PrPsc results in enrichment of scrapie

activity

purification of PrPsc by SDS-PAGE also recovers

infectivity

PrPsc can be denatured, renatured without loss of

infectivity
 Ribozymes
RNA enzymes; can catalyze a chemical reaction

Many natural ribozymes catalyze either their own cleavage or

the cleavage of other RNAs

Have also been found to catalyze ribosome aminotransferase

activity

discovered by Sidney Altman and Thomas Czech (Nobel Prize

in Chemistry, 1989)

Ribozymes may be single-use or re-usable (like protein

enzymes)
RNA template-directed protein synthesis links
the RNA and protein worlds

Why is DNA more stable than RNA? RNA

RNA remarkably stable
(-) charges in backbone protect it from attack by OH-
ions that would lead to hydrolytic cleavage
However, 2-OH susceptible to base-catalyzed
hydrolysis
Removal decreases the rate of hydrolysis by
approximately 100-fold
conversion of the genetic material from RNA into
DNA chemical stability.
 What is the first biomolecule?
DNA needed to make proteins
Proteins needed to make DNA

RNA world theory proposes that RNA = 1st

biomolecule
Since RNA can be used to store genetic info, but may also
contain catalytic properties

plausible that RNA was utilized to store genetic

information early in the history of life
Eventually replaced by DNA
Figure 6-110 Molecular Biology of the Cell ( Garland Science 2008)
 Viruses

Genetic material may be

1. ds DNA
2. ss DNA
3. ssRNA
 Retroviruses
genome = RNA molecule ~8500 nts

RNA genome reverse transcribed to form dsDNA

dsDNA integrated into host chromosome

integration required for e synthesis of new viral RNA

molecules by the host cell RNA polymerase
 Epigenetics
Epigenetics = study of inherited changes in
phenotype or gene expression caused by
mechanisms other than mutations

Unlike mutations, epigenetic events are reversible

important mechanism by which environmental factors,
such as diet, can influence biological processes and
phenotypes, including disease

Epigenetic alterations include changes in DNA

methylation, histone regulation
 Epigenetics and the epigenome
Epigenetics: comes from epi- (Greek: - over,
above) genetics
epigenome" is a parallel to the word "genome"
refers to the overall epigenetic state of a cell

changes may remain through cell divisions for the

remainder of the cell's life and may also last for
multiple generations
http://learn.genetics.utah.edu/content/epigeneti
cs/intro/
 Epigenetics
shows that
environmental
factors can
affect the DNA
that you pass
on to your kids
 Epigenetics vs evolution
Runs counter to the concepts of evolution and
genetics
We have had a long-standing deal with biology:
whatever choices we make during our lives might
ruin our short-term memory or make us fat or
hasten death, but they won't change our genes
our actual DNA. Which meant that when we
had kids of our own, the genetic slate would be
wiped clean.
 Evolutionary theory says that evolutionary changes
take place over many generations and through
millions of years of natural selection

However, historical evidence suggests that powerful

environmental conditions (e.g., near death from
starvation) can leave an imprint on DNA in eggs and
sperm
can short-circuit evolution, pass along new traits in a
single generation
Epigenetics: experimental evidences
1. fruit flies exposed to geldanamycin show unusual
outgrowths on their eyes that can last through at least 13
generations of offspring even though no change in DNA
has occurred
generations 2 through 13 were not directly exposed to the drug

2. roundworms fed with a kind of bacteria can feature a

small, dumpy appearance and a switched-off green
fluorescent protein
changes last at least 40 generations
 Changes may not be permanent
biological response to an environmental stressor
response can be inherited through many
generations via epigenetic marks
If environmental pressure is removed, the
epigenetic marks will eventually fade

Read more:
http://www.time.com/time/health/article/0,859
9,1951968-3,00.html#ixzz0eQydjL4Y