Final review

Ghost in your genes movie

Human genome isnt as complex or have as many genes as plants

More genes does NOT imply more complex
Puppet kids- key seq of DNA is deleted from chromosome 15; the same
deletion had clearly been associated with a diff syndrome
2 completely diff disease caused by the same genetic abnormality
if the deletion was on the chromosome 15 child had inherited from father it
was one syndrome, if deletion from mother then angelman
DEPENDING ON PARENTAL ORIGIN caused diff diseases
Hwo would a chromosome 15 know where it came from? Altho the dna
sequence is the same, the diff sets of genes were being silenced depending
on whether it came from the mom or dad
Methylation affixes near the Aguti gene- shutting it down
Methyl molecules are tags; some tags attach to dna directly; some tags
wrap around histones to turn them on or off
This contact is hugging the dnaif these proteins hug dNA tightly, it is
hiding from cell and a cell that is hidden cant be utilized
Epigenetics is above the genomeif the genome is like a computer (the
hardware), the epigene would be like a software that tells the computer
when to work, how to work, and how much
Best example of epigenetics is skin, eyes, organs all have the same DNA
What distinguishes cells are not their genes bu how their genes are
switched on or off by epigenetics
Spigenetic switches are usually stable but CAN be switched occasionally
The epigenome determined how the book gets read
Dna is 100% the same, any influence should reveal influence of outside

world
Collected cells from identical twins began dissolving cells until left with
dna amplified ffragments of DNA revealing both the genes and their
epigenetic tags
Those that had been turned off were dark on the gel
When these genes were cut out and overlapped, the epigenetic effects stand
out especially when you contrast the genes of two sets of twins that differ
in age
Old twins genome may be the same but epigenome is NOT
Identical genes active in one twin may be shut down in the other
Epigenetic changes accumulate in twins and the rest of us
Epigenetics can change based on environment
We have static genome very hard to change but highly dynamic world
around us epigenome is inbetween creature built to respond to changes
around us

Experience itself changes the epigenome

Studied 2 kinds of rats

Epigenetics- above the genome

Methylation of DNA, histone
Software of computer (DNA sequence hardware)
What distinguishes cell types is gene expression, not presence of genes
epigenetic changes accumulate with age, what we eat, smoke, drink all
effect our epigenome
static genome, dynamic environment interface is epigenome

experience changes epigenome- mothers who were nurturing or not

interested in how these animal respond to stress- offspring of lowlicking
show greater inc. in blood pressure and in stress hormone production
its not the genes ethat the mother brings into the game, it is the behavior of
the moterh that has an impact on offspring
hwo does the rat remember what kind of care it received form its mother so
it has better or worse health conditions?
Must be some mark in genes that marks that memory
Extracted and analyzed a gene how its activity varied btwn high and low
licked lats
Less nurtured rates have multiple epigenetic marks silencing the gene
With the gene less active, stress levels in neglaeted rats soared
In stark contrast, nurtured rats could better handle stress bc they had
nothing dimming the genes activity
The maternal behavior scultpued the genome of their babies
JUST a behavior of one subject can change the gene expression
Injected anxious rats with drug known to remove epigenetic marks. As we
removed the mark the gene turned on and the behavior of the rat changed.
It became less anxious
We look at how the gene is marked in the brain we changed the
epitgenetic marking of the gene,

If you grow up in a family that involves abuse, neglect, etc you are
statistically more likely to develop depression, anxiety. You are more likely
to develop diabetes, heart disease, obesity
The stress hormones actively promote the development of these diseases
Some scientists believe epigenetic changes underlie human diseases
MDS is cancer in bone marrow epigenetic therapy. If one has a genetic
basis of cancer in mind, then yo9ure asking what causes genetic damage?

Cigarette smoking, etc. but if we say epigenetic damage can also cause
canceryou have to ask why this comes about
The trouble begins when our stem cells overwork. Every time a stem cell
has to repair injury it has to repair a little more
If you count age and how many times a stem cell has divided, then cancer
which copies cels continguously are extmrele yold
As epitgenetic changes pile up, the switches go on and off causing havoc
Turning on and turning off is getting epigenetic disease
Could misplaced tags be rearranged?
Drug to remove methyl tags silencing tumor repressor genes
Idea is to stay away form killing the cell we are trying to change the
instructions of the cnacer cells
Reminds the cell you are a human cell
Drugs that affect dna methylation have a profound effect on patients
drugs to reduce methylation being tried in cancer treatmentalzheimers to autism may have epigenetic triggers autism is
characterized by social withdrawal. No autism gene had been found.
Scanned the brains of healthy and autistic children searching for biological
cause
the way to diagnose autism used to be based on behavior
in comparing brain scans, they saw hippocampus was smaller in autistic
child. How could same gene create diff brain structures? Epigenetic
hypothesis have same genome but one of them has an epigenetic change
that is leading to difference in brain that yo udont see in the other twin

now searching for methyl marks

by binding identical genes that differ in their expression, cuases of autism
may emerge
environment molds epigenome, generational inheritance

environment molds epigenome but can it do more?

Some are seeing evidence that genes may not be all the passes form
generation to generation
The evidence comes from Swedish villages archives records track birth,
deaths, and harvests. Had a hard time when there was famine
Famine might affect people almost a century later, even if they had never
experienced a famine themselves. So past and future genetations might be
linked in ways no one imagined. Epigenetics explains phenomenon.
Food supply of ancestors was affecting mortality of the next generation
Diabetes might show environment and epigenetics were involved
A grandon was 4x more likely to die from diabetes if grandfather had more
food to eat during childhood
Did not directly cause genetic mutation but could affect offspring
Mechanism transferring environmental info from generations to gen.
Looked at food supply every year in grandparents only certain periods
in ancestors development when they can trigger transgenerational
response sensitive periods of development
When famine could trigger an effect was diff for grandma than grandpa
Connections btwn gender, diet, and health most pronounced 2
generations later
Men who experienced famine around 10 had paternal grandsons that lived
much longer than those whose grandpas experienced plenty
Link btwn generations diet in one and life expectancy in another
Why does this affect only appear in paternal line of inheritance? Why
should famine be both harmful and beneficial ?
Raises prospect that impact of famine can be captured by egg and sperm
and memory of this event can be carried foreward to affect children 2
generations later
Changing the view of what inheritance is

Skinner triggers a similar effect with pesticides

He wanted to see how these chemicals affected pregnant rats and their
offspring
Treated mom with compounds and started seeing a whole host of other
diseases tumors to prostate disease, kidney disease
Chacked that there were no genetic mutations
Then breeded the rats
Did several repeats among generations then realized that the pheonomena
was real major diseases occurred of all animals of every generation
If an individual was exposed to environmental toxin, they can get disease
state
Toxin no logner affects just that individual but generations down the line
This means that what youre grandma was exposed to could cause a disease
in you even tho u had no exposure
Can stress, smoking, generate such effects?
Mapping human epigenome will tell us why organisms functions, etc
The epigenome varies from tissue to tissue, btwn individuals, and over time
This is a huge challenge

DNA Replication
Meselson-Stahl experiment
Semi-conservative, bidirectional replication
Primer template requirements

Chemistry and directionality of DNA synthesis

Differences and similarities between DNA and RNA

polymerases

Replication

fork,

leading

strand,

lagging

strand,

discontinuous synthesis vs continuous syn.

Okazaki fragments
Roles of Pol I and Pol III in replication
Trombone model: why it was proposed (what it explains)

Accessory proteins: general names, not genetic names:

ligase, helicase, beta-clamp, single-stranded binding protein,
topoisomerase

Initiation: occurs at origins of replication and requires

initiator protein which are regulated
Telomerase and maintenance of telomeres
Mutagenesis and Repair
Transitions vs transversions
Silent, missense, nonsense, frameshift mutations
Common types of mutations
Deamination, depurination, bulky group addition, thymine dimmers
DNA repair
Lesion bypass (last resort)
Direct reversal (Photoreactivation, Removal methyl groups)
Damage removal: know steps and types of enzymes needed, not
genetic names
Base excision: repairs damage to a single base caused by
oxidation, alkylation, hydrolysis, or deamination
Removes single base and replaces it
Nucleotide excision: repairs bulky helix distorting damage

(and thymine dimmers)

Removes a segment of DNA (12-13 bases long and repairs it)
Mismatch repair: repairs mismatches but otherwise normal
bases
Uses hemimethylated sites to distinguish old and new strands,
removes all dna between damage and GATC site
Double stranded break repair
Uses either non-homologous end joining or HRE.

Recombinant DNA technology

Restriction/modification system
Gene cloning, antibiotic resistant genes and transformation
Blunt vs sticky ends (5 overhang vs 3 overhang)
Difference between cloning a gene and cloning an organism
Vector vs insert
Antibiotic resistance as screen for inserts (become antibiotic sensitive) and
as a selection for transformation
Blue white screen for inserts
Genomic vs cDNA library
Western blots, ELISA
PCR, DNA sequencing both based on in vitro DNA synthesis (leading
strand synthesis)
Reporter genes- promoter fusions

AIDS Lecture

AIDS-Acquired Immunodeficiency Syndrome-caused by HIV virus,

retrovirus (ssRNA genome) that infects a type of white blood cell known as
T helper cells (CD4+)
Copies of HIV mRNA is inversely proportional to CD4+ lymphocyte count
(these are the cells HIV infects)
Tests generally measure the levels of antibodies against HIV proteins either
in an ELISA assay, an oral test or by western blot
HIV life cycle:
attachment, uncoating and reverse transcription,
integration, transcription, viral assembly, budding
Medications block many steps in life cycle- if only block one step likely to
evolve resistant version of HIV
AZT blocks reverse transcriptase by acting as a chain terminating
nucleotide analog
Non-nucleotide reverse transcriptase inhibitors (NNRTI) directly
interact with RT to inhibit its function
Drugs also include integrase inhibitors, protease inhibitors and
fusion inhibitors
ART- anti retroviral therapy