Useful Genetics pt.

1

How different are we?
a. Introducing DNA and genomes
b. Genomes in life cycles
c. Differences between genomes
Learning Objectives:
-explain how little our DNAs differ
-interpret the word genome
-describe DNA changes through a life cycle

Phenotype:
-Original meaning: observable properties
-Modern meaning: observable and molecular properties
Genotype:
-original meaning: inferred cause (genes)
-modern meaning: DNA sequences of chromosomes

DNA Intro:
Each chromosome is a (very) long molecule of a polymer (long chain of subunits). There are 4
slightly different kinds of subunits: the bases A, G, T and C
The precise order of the bases is what holds the genetic information

The egg and sperm each contain one complete set of DNA molecules (of chromosomes).
So the fertilized egg contains 2 sets (one from mom and one from dad)
It grows and divides many times to become all the cells of our body. Each cell has the same
DNA as the fertilized egg did.
Whats in a complete set of DNA molecules?
-3 billion subunits (base pairs. In humans)
-strung together in 23 very long polymers (the chromosomes)
On average, 1/1000 bases is different between different people. i.e. 99.9% identical between
humans.
How much phenotypic difference do these genotypic differences make? Most of the 6,000,000
DNA differences do not make any detectable difference to phenotype. Because they are often
not in genes, or do not change the gene function. The rest of the differences cause all the
heritable differences between people. The same kinds of DNA differences cause the phenotypic
differences in all other species too.

Properties of DNA
a. DNA as a physical molecule and as information
b. How we represent DNA (5- to 3` convention)
c. DNAs evolutionary continuity
Learning objectives:
-explain how a physical molecule is also information
-use and interpret representations of DNA
-trace DNAs history
DNA is both a physical molecule (a polymer, a chain of identical or nearly identical subunits)
and genetic information. Sequence complementarity is a physical property of the bases; the
shape of each base determines which other base it can pair with.
Complementarity and H bonding:
1. Hold the srands together
2. Direct DNA replication
3. Direct synthesis of RNA
The order of the bases along the chain specifies protein sequences and other genetic functions.
The 2 strands have complementary information. This permits:
1. Error correction (informational redundancy)
2. Copying of information
3. Readout of information into RNA

The DNA in each chromosome is 2 very long single DNA strands wound around each other.
The sides of the paired bases are exposed and can interact with the regulatory proteins that sense
DNA sequence. The strands must physically separate (unzip) for DNA replication (copying)
and RNA transcription (readout). The bases and the bonds connecting them are asymmetric; the
2 strands run in opposite directions (polarity). The strands go from the 5`3`.

Classical genetics: we relied on indirect inferences about the nature of genes and how they
control phenotypes. Modern genetics: we now know a lot about the molecules, but we still cant
see them. The base sequences of some segments of the DNA are recognized by specialilzed
proteins that feel their shapes and control other events. The base sequences of other segments
(genes) are transcribed and translated into polymers of RNA and protein; the DNA sequence
specifies the RNA and protein sequences.
DNA polymerase acts at replication forks to synthesize new DNA.

What makes a DNA sequence a gene?
a. Genes are information in DNA
b. DNA information becomes protein information by transcription and translation
c. DNA sequeces are regulatory signals
Learning objectives:
-interpret genes as physical and informational entitities
-explain how regulatory sequences in DNA control gene expression
Physical entitites: genes are sections of DNA molecules (of chromosomes). They are not
physically different from any other part of the DNA. But they are different because of the
information, the sequences of DNA with promoter and terminator signals for transcription into
RNA
Two kinds of ways that they have promoters and terminators:
1. Functional RNAs of the protein synthesis machinery (rRNA, tRNA)
2. mRNAs that specify translation into amino acid sequences of proteins.
Each signal is a short sequence of bases. They function as binding sites for RNA polymerase,
which binds to the promoter (a specific sequence) and travels along the DNA, transcribing a
complementary strand of RNA until it reaches the terminator. RNA polymerase makes a single
strand of RNA; the promoter tells it where on the DNA to start and which DNA strand to use
(which direction to go). The terminator tells it where to stop.
Each protein-coding gene has 2 kinds of start-here signals: a promoter and a start codon. It also
has two kinds of stop-here signals: a stop codon and a terminator. The ribosome starts at the
start codon and travels along the mRNA, joining amino acids together into a protein polymer; it
stops at the stop codon. The order of the bases in the mRNA specifies which amino acids are
used to make the protein.
Promoter and terminator for RNA polymerase to start/stop transcription
Start and stop codon for ribosome to start/stop translation

The order of the bases in the mRNA specifies which amino acids are joined to make the protein.
Each group of three bases of the mRNA polymer specifies one amino acid of the protein
polymer.
Codon is an informational term. In a DNA sequence, every three-base sequence is a potential
codon. An open reading frame is a segment of sequence that starts with an ATG and ends with
the first in-frame stop codon. Other in-frame ATGs are treated as methionine codons, and out of
frame stop codons are ignored.
To a ribosome, only the first AUG of the mRNA (after the ribosome-binding site) is a start
codon. Downstream in-frame AUGs are codons for methionine and in frame UAA, UAG or
UGAs are stop codons. Out-of-frame combinations do not function as codons.

Introns and splicing
Most protein-coding genes contain segments called introns that are spliced out of the RNA
before it is translated into protein. The other segments are called exons.
The cellular machinery that does this (a protein-RNA complex called the spliceosome)
recognizes signals in the RNA specifying the parts to be cut out.

Real genes are the result of many generations of natural selection for a particular function. On
coding sequences for best combination of amino acids, on introns for correct excision, on
regulatory sequences for best timing and level of expression of a gene.
Cells identify genes because:
1. regulatory proteins recognize and bind to DNA near the promoter.
2. RNA polymerase binds to the promoter sequence
3. RNA polymerase makes a RNA version of one strand
4. RNA polymerase and other proteins recognize a terminator sequence and release the new
RNA
Genetic analysis: use crosses to investigate patterns of inheritance and infer differences in
genotypes
Bioinformatics: computer programs examine DNA sequences for long open reading frames, then
check for promoter and terminator sequences and check for similarities to known genes.

What makes these processes so confusing?
a. Common features of DNA replication, transcription and translation
b. Distinct functions of these processes
Learning objectives:
-recognize the common features of the information-flow processes
-practice keeping them straight


DNA replication: DNA copy of the DNAto make more cells. Central act of heredity; how
mutations happen
Transcription: RNA version of the DNA segmentRNA is the intermediate between DNA and
protein. How most gene activity is regulated
Translation: protein specified by an RNA segment to make protein informationproteins are the
machinery that does everything. Proteins do everything

Why is it so hard to keep them straight? They do things in a similar manner.
Always start with a molecular machine (polymerase of some sort: DNA/RNA/ribosome). It
binds to specific sequences it recognizes on the nucleic acid polymer (DNA or RNA) and creates
a product which is also a polymer, a sequence of bases (if DNA or RNA) or amino acids (if
proteins). When it reaches a stop sequence, it lets go.

Whats a chromosome?
a. One very long DNA molecule
b. Information for hundreds or thousands of genes
c. Regulatory signals
d. We each have 2 versions of each of 23 kinds
Learning objectives:
-relate the physical and informational properties of chromosomes
-recognize different representations
-use gene, allele and locus correctly

Chromosome structure:
One very long molecule of DNA, bound to and wrapped around proteins.
Chromosome information:
One very long DNA sequence, with genes and other functions embedded in
nonfunctional sequence.

For a molecule of DNA to function as a chromosome, it must carry specific information:
1. Signals recognized by DNA replication proteins (origins where DNA replication starts
and telomere at the chromosome ends)
2. A centromere signal that creates an attachment point for the fibers that pull replicated
chromosomes apart in cell division
3. Genes

Human chromosomes are pretty typical:
-23 different chromosomes (2 versions of each)
-named 1-22 from largest to smallest, and X/Y the 2 versions of sex chromosomes
-50-250 million bp long, with 400-4000 genes on each.
Locus: the location of a gene or other DNA sequence on a chromosome (refers to any and all
alleles of that gene)
Allele: a non-identical version of a gene, or more generally, of a DNA sequence
Gene: usually, a segment of DNA specifying a protein or functional RNA (often used where
allele or locus would be clearer

Life cycles and ploidy
a. The cell cycle
b. Typical plant/animal life cycles
c. Ploidy: haploid gametes shuffle DNA versions into diploid organisms
Unicellular: clonal/asexual reproduction. All offspring are genetically identical
Multicellular: stolon/asexual seeds which are also genetically identical to the parent
Sexual reproduction: usually have 2 sets of chromosomes, pollen/sperm and eggseed/zygote
that is genetically different than both of its parents.

Haploid: one complete set of DNA sequences (chromosomes), one complete genome
Diploid: two complete sets of DNA sequences
N: number of chromosomes in one complete set. 2N=total number of chromosomes in diploid

Genetic consequences of sexual reproduction:
Each generation gets new genetic combinations from the previous generation. New
combinations of chromosome versions (always in full sets). New combinations within each
chromosome

Homology and variation
a. Homology
b. How DNA sequences are compared
c. Alleles, variants, SNPs and indels
d. Genetic variation reflects evolutionary history
-Homology: similarity due to shared ancestry. Ex: homologous genes in fruit flies, mice,
humansthe genes have similar sequences, functions and order on the chromosome. Gene
sequences can be homologous too
Possible causes of similarity:
-chance
-selection for the same function (convergent evolution)
-common ancestry (homology)
The logic of inferring homology:
Are the similarities too strong to have arisen by chance and too arbitrary to have arisen by
convergent evolution? If so, homology
Once weve decided that DNA or protein sequences are homologous, their degree of
similarity tells us how recent their common ancestor was
Alleles: non-identical versions or variants of a gene or more generally of a dna sequence
SNVs: single-nucleotide variant; the presence of different nucleotides at homologus positions in
two DNA sequences
Indel: a genetic difference created by insertion or deletion of a bp or a longer DNA segment
Haplotype: the genotype of a short segment of a chromosome
Chromosomes that carry different versions of the same information are called homologous
chromosomes. The same genes are on each, in the same order. DNA sequenes differ by only
about 0.1%, because they share very recent ancestry i.e. sexual reproduction
Rare variant: a genetic differene present in less than 1% of the population
Polymorphism: a genetic difference present in at least 1% of the population
SNP: single nucleotide polymorphism; a SNV present in at least 1% of the population

Genetic and evolutionary relationships of human populations
a. Shared differences
b. Human evolutionary history
a. Out of Africa
b. After Africa
Learning objective:
Interpret human genetic differences in their evolutionary context

Within-species diversity in humans: 99.9% of sequenes are identical. We are a young species; we
are more similar to each other than most other species.
How different are the genomes of people from different parts of the world? What does this tell us
about human evolutionary history? They examined 4 genes in 14000 people from around the
world:
-98 different haplotypes for these 4 genes in Europeans, 73 variations in Asians, 199 in
Africans. Then they checked and found that almost all the genetic variation found in the other
groups were also found in Africans. So: all humans are genetically very similar. Genetic
variants found in one group are usually present in other groups. Non-african groups have subsets
of the variation present in modern (and ancestral) Africans
Out of Africa explanation of human evolution:
Humans arose and diversified in Africa. One group left Africa and continued to diverge as they
spread out through the rest of the world. All non-africans are descended from these people.
The ancestors of non-african modern humans mated with Neanderthal humans before the pure
Neanderthals went extinct. So, some Neanderthal alleles live on in non-african genomes. Thiss
has been proved by sequencing DNA from ancient bones of 6 neanderthals and compared the
DNA to modern humans and found 2-3% Neanderthal alleles and haplotypes in non-african
people.

Mutations:
-physical changes and informational changes (damage and mutation)
-molecular machines make mistakes
-immediate changes and evolutionary changes
-harm and benefits
-stability and variation
-research significance and personal significance

Mutation basics:
a. Definition
b. Why they are so important
c. How they arise
d. How often and why
e. Consequences
f. Evolutionary history

A mutation is a change in DNA sequence. A different sequence than the
normal/standard/functional DNA. It is structurally normal DNA and can be inherited.
Why do we care about mutations?
Some mutations reduce fitness, pain, suffering and death in individuals and extinction of species.
They generate diversity; without them we wouldnt be able to evolve. They cause cancer. Risk
of mutations causes anxiety.
Mutations arise as errors in DNA replication
Most mutations begin as mismatches by DNA polymerase. But, most mismatches dont become
mutations.
-proofreading by DNA polymerase
-correction by mismatch-repair enzymesnot in structurally normal DNA

New mutations rarely arise because DNA polymerase is very accurate. In humans, from parent
to child there are only 1 or 2 *10^-8 new mutations per base pair per generation. This means
about 60-120 new mutations per diploid genome. On average, each new baby has 1 new
mutation that changes an amino acid in a protein. And because cells have evolved ways to
minimize and repair DNA damage using: proofreading by DNA polymerase, mismatch repair,
excision repair, recombinational repair

Most new point mutations are from the father, not the mother. Why?

Mutations usually have neutral or harmful consequences. Most are neutral because most DNA
changes are in places where they dont affect gene function. So few are beneficial because living
systems are already very well-adapted, the chance of a random change being beneficial is very
small.
Neutral mutations accumulate over generations, so we inherit many DNA-sequence differences
that arose as neutral or near-neutral mutaitons. And a few differences that would be seriously
harmful if we didnt also have a good copy of that gene.

All genetic differences started out as new mutations, mutations lead to natural genetic variation
and adaptive differences

Most mutations are neutral because:
1. most DNA is not part of genes. About half is genetic parasite repeates (LINEs, SINEs,
LTR and DNA transposons) mobile genetic elements. Another 20% of our genome
has no known function, 8% is duplications that we dont know what they do. Only about
28% of our DNA is genes.
2. DNA in genes is mostly in introns, which later get excised out, os therefore they dont
have negative effects on our phenotype. Only 2% of our genome is protein-coding genes.
Mutations in some non-coding sequences do affect phenotype (secondary effects. Ex: change
shape of tRNA, change DNA polymerase):
-Sequences that affect regulation:
-when DNA is transcribed
-cell types where DNA is transcribed
-how strongly DNA is transcribed
-how efficiently mRNA is translated into protein
-Intron sequences that affect splicing
-genes that function as RNA
-tRNAs, rRNAs
-regulatory RNAs
3. Many changes to coding sequences dont change an amino acid. The genetic code is
redundant
4. Many amino acid changes dont affect protein function. (At least half of non-silent
SNVs are neutral)

Types of mutations and their consequences
Kinds of mutational changes to DNA sequences:
a. DNA polymerase errors
b. Insertion of mobile elements
c. Duplications and deletions
d. Rearrangements
e. Ploidy changes
Different types have different consequences
Explain how mobile elements accumulate in chromosomes and explain why different kinds of
mutations have different consequences

Types of mutations and their consequences:
1. Replication errors by DNA polymerase in protein-coding sequences
a. Wrong base (mismatch)- may change an amino acid or create a stop codon, which
can cause a neutral or loss-of-function mutation
b. Skips or adds an extra base-can cause a frameshift. The new reading frame has
not been subject to natural selection, so it specifies nonfunctional amino acids and
frequent stop codons. Usually loss of function
c. Skips or adds multiple bases. If it is a multiple of three, doesnt cause a
frameshift, just adds/skips a single amino acid. Usually loss of function
2. Other errors in protein-coding sequences
a. Insertions of mobile elements (genetic parasites): disrupts translation, causes
frameshift mutation, knockout mutation. Strongly selected against mobile
elements in protein coding sequences. Introns began as mobile elements. Usually
loss of function
b. Duplications or deletions of large segments-usually result as an attempt to repair
DNA damage. Duplications are usually neutral because you still have a working
copy of the gene. Deletions are usually more harmful, loses functional genes.
Change gene dosage, loss of function
c. Breaks and joins of parts of chromosomes- change gene dosage, gene loss of
function
d. Changes in chromosome number-change in gene dosage, often very harmful.
Change gene dosage, meiosis problems

Somatic and germline mutations
a. Our bodies consist of germline and somatic cells
b. Mutations accumulate in both
c. For somatic mutations, benefits to cells can harm the organism

Germline cells: become reproductive tissues
Somatic cells: create the rest of the body

The somatic/germline distinction doesnt usually apply to plant cells, because most plant cells
can have descendants that become gametes. i.e. can take tissues from different structures and
have them grown into whole new plants

All our somatic and germline cells are ever-so-slightly different from each other because they
each accumulated different mutations. Mutations in these cause very different problems.

In females: about 30 germline cell divisions from zygoteegg so any given egg cell has on
average 20 new mutations than the zygote
In males: about 400 cell divisions from zygote to sperm (depending on age). Because mutations
accumulate with cell division, sperm generally has more mutations
Usually if there is a mutation, the zygote will still have a normal allele and will be heterozygous
so a normal phenotype. If it is a harmful mutation, the zygote usually fails to develop normally
and results in a miscarriage.

In any specific tissue, some somatic mutations will be:
1. Harmful to the cell (reduce growth or viability)cell death, doesnt affect organism
overall because there are so many
2. Neutral to the cell (no change)cluster of cells with this mutation, but doesnt change
much.
3. beneficial to the cell (increase growth or viability)lots of cells with this mutation, can
be detrimental to the organism which can be pre-cancerous or cancerous.
Sometimes, a mutation will benefit the cell but will be detrimental to the organism as a whole.

Many chromosomal changes occur in early embryogenesis. Tissues whose cells no longer divide
(terminally differentiated cells, ex: neurons) often have high numbers of mutations. Tissues
whose cells divide many times often accumulate high numbers of point mutations.
A mutation doesnt make your whole body mutant. It initially affects one cell, and if not harmful
can give rise to a cluster of somatic or germline cells. Only mutations in germline cells can
affect your offspring. Somatic cells with beneficial mutations can lead to cancer.

Mutagens
a. Agents that damage DNA
b. Kinds of mutations
a. Radiation
b. Chemical
c. How UV causes mutations
d. What mutagens and exposures should/shouldnt we worry about
e. Mutations and birth defects


Major causes of mutations:
Bad luck (uncontrollable and unpredictable events):
-chance shifts in molecular sructures of the basesDNA polymerase errors
-reactions of DNA with cellular metabolites DNA damage
-cosmic rays and other background radiationDNA damage
Mutagens (factors that increase the chance of a mutation):
-radiation (above background) DNA damage
-chemical mutagens (natural and unnatural) DNA damage
DNA damage=any chemical change from the standard physical structure of DNA:
Oxidation of base, bulky adduct, break in phosphodiester backbone, crosslinking bond between
bases, crosslinking bond between strands. They block DNA polymerase

How UV light causes mutations:
Energy from UV light causes thymidine dimers (covalent bonds between T-T) which creates a
bump in the backbone and causes DNA polymerase to stop working on this strand. Error-prone
DNA polymerase comes in, and put in whatever bases seem to fit, which often creates mutations,
but it allows the rest of the strand to be replicated.

Are pregnant women more at risk from mutagens? Exposure to mutagens during pregnancy does
not increase the risk of birth defects in the baby. Most birth defects are not due to mutations, but
are just accidents of development; a few are due to chemicals (teratogens) that directly interfere
with fetal development. A mutation occurring in a developing embryo will not normally cause a
birth defect, because it will be a somatic mutation. To reduce new mutations in our children,
everyone who might someday have children should avoid exposure to mutagens, but most
mutations are due to background events we cant control (chemical properties of DNA; natural
metabolism).

We should worry about acute radiation sickness and chemotherapy toxicity (caused by high
levels of DNA damage that prevent cell divisioin. Effects are similar for accidental and
therapeutic whole-body irradiation and for chemo), cancer (cells become cancerous because of
changes to their DNA. Mutagens are also carcinogens. Various mutations can disrupt regulation
of cell division, so the cell grows when it shouldnt) and mutations in germline cells (these can
be passed on to the next generation, but effects on birth-defect rates are usually undetectable).

Mobile elements are mutagenic. They are used as knockout mutations in lab testing, because
they completely break the gene.

Mutations and natural selection
a. Many factors influence mutations
b. But NOT the consequences of the mutation for the survival or well-being of the
organism
c. The environment doesnt affect which mutations happen
d. Organisms havent evolved mechanisms to control which mutations happen or when they
happen
e. Explain why we cant reprogram our DNA/why organisms cant control the kinds of
mutations they get
\
Many factors influence when and what kidn of mutations happen. BUT the effect a mutation
will have on the organisms ability to survive and reproduce is not a factor.
Mutations arise randomly with respect to their functional consequences; they cannot be directed.
Natural selection didnt evolve ways to direct mutations because the processes that cause
mutations have no way to detect the specific functions of the DNA sequences they change. And
they have no way to predict which changes would be beneficial.
We dont see all the mutations that arise, only those that persist. Same is true for horizontal gene
transfer and genetic recombination. The beneficial mutations are also amplified by natural
selection.

If mutations are mostly bad, why arent they zero? If they are good why arent they higher?
1. Almost all new mutations are neutral or harmful
2. Preventing mutations is expensive for the cell
3. If there were no new beneficial mutations, adaptation would stop and species would go
extinct
4. But, natural selection doesnt really care whether species go extinct

Evolution of new genes and gene families
Genome sizes vary dramatically (changes in junk DNA and in gene number)
New genes begin as copies of existing genes
1. From within a genome-duplication within a genome (of a segment, chromosome or
genome), then mutation and divergence and selection to distinct functions
2. DNA inserted from another species genome. (less common)
Much of the difference we see in genome size is due to mobile elements
Genes that arose as copies of an ancestral gene form a gene family. In humans, many metabolic
genes and most structural and regulatory genes are members of gene families.

What causes DNA duplications (most common way of acquiring new genes)?
-mistakes by DNA polymerase (slips, stalls and restarts)
-integrated viruses
-mobile elements
-miscellaneous chromosome errors
-chromosome duplications
-whole genome duplications

What causes horizontal/lateral DNA transfer (from other species genomes)?
-infecting viruses
-genomes of commensal or pathogenic cells
-mobile elements
-many genes have been transferred to the chromosomes from mitochondria and chloroplasts

Initial consequences of DNA duplications and transfers:
DNA must become part of the germ line, not just a somatic cell if you will see it in future
generations
Often what is transferred are fragments of genes and other nonfunctional DNA more junk
DNA
If it is intact genes, could be bad (unbalanced gene dosage or unneeded function), could be
neutral or even good (useful dosage increase or new function)

Divergence of duplicated genes: selection is released (organism doesnt need 2 copies), one copy
can accumulate mutations, usually becomes defective but sometimes gains a modified function.

DNA differences reveal evolutionary history
a. Lineages of species accumulated both shared and distinguishing mutations
b. Shared differences reveal shared ancestry
c. Phylogenetic trees are diagrams of evolutionary relationships.

Evolutionary trees are inferred from DNA sequence divergence
Neutral mutational changes accumulate over generations, not just within a species, but through
all of lifes history. If we understand how this happens, we can read evolutionary history from
our genes.
We can infer divergence backward in time, to common ancestors. First: get homologous
sequences. Then, count the differences. The more differences there are, the farther back they are
related and the more time they have had to diverge and evolve away from each other.

DNA and protein sequences reveal phylogeny better than phenotypes do:
-more characters
-unambiguous homology
-more neutral
Once we know the phylogeny, we can learn about evolutionary processes by comparing
phenotypes.

Protein Basics:
a. Polymer of amino acids
b. N and C termini
c. Fold spontaneously into active structure, driven by hydrophobic effects and hydrogen
bonds
d. Natural selection shapes amino acid sequences for specific function
e. Mutations change phenotype by changing protein structure/function or regulation

Proteins are polymers-long chains of varying combinations of 20 different types of amino acid
subunits. All subunits are classed as amino acids because they all have an amino (NH2)
chemical group on one side and a carboxylic acid (COOH) group on the other side. The COOH
on one amino acid forms a peptide bond with the NH2 on the next. Each amino acid has a
different chemical structure between its N and C ends. The order of the amino acids is
determined by the order of the 2-base codons in the gene that specifies the protein.
Primary structure: amino acid sequence
Secondary structure: simple local folding. Either an alpha helix or a beta sheet.
Tertiary structure: final complex folding. Disordered, open ends, alpha helices and beta sheets
associate with each other
Quaternary structure: subunits are bound to each other.
The properties of its amino acid side chains cause each protein chain to fold up into a specific 3D
structure, generally folding in a way that the hydrophobic side chains are inside and hydrophilic
on the outside and positive-negative charges usually interact as well.

Protein folding is so critical to protein function, cells have evolved special folding-assistance
proteins called chaperonins. They provide a sheltered environment for unfolded proteins,
where they promote appropriate interactions and gently discourage inappropriate ones.

Protein sequences have been shaped by natural selection so that each folded protein will carry
out a specific function (a specific interaction or chemical activity). That activity, like the folding
is caused by interactions of the different amino acids with each other and with other molecules in
the cell.
Protein functions:
-catalytic (enzymes)
-structural
-regulatory
Many proteins fall into more than one of these categories. Ex: actin and myosin catalyze muscle
contraction, but they also form the structural fabric of muscle

Catalytic Proteins (enzymes)
a. Enzymes are flexible molecular machines that catalyze biochemical reactions
a. Almost all are proteins (rarely RNA)
b. Binding to substrate causes specific shape change
c. Shape change promotes a chemical change in the substrate (it becomes the
product)
d. This chemical change causes the product to separate from the protein
Ribozyme-RNA catalyst. Folds up like a protein to expose active sites where reactions happen.
Active site is where the catalysis actually happens. Most of a proteins function is to bring
everything together into the right palces so the active has the right reactive groups in place and
the right flexibility to cause a reaction. The substrate binds to the active site, the presence of the
interactions of the substrate and the enzymes cause the enzyme to change its shape, bringing new
reactive groups into contact with the substarate which cause the substrate to undergo a
biochemical reaction and the substrate turns into the product and is released.

Ex: Phenylalanine hydroxylase. A tetramer, each subunit has 3 domains: catalytic domain,
regulatory domain and interaction domain (bind 4 tetramers together). The enzyme converts
phenylalanine into tyrosine, an important part of our metabolism.
Tyrosine is a precursor for other important chemicals (thyroid hormones, adrenaline, and
dopamine) in our body. If there is a problem in the enzyme, the phenylalanine gets converted
instead into phenyl-pyruvate (phenyl-ketones). Phenylketonuria causes mental retardation when
the enzyme doesnt work and the phenylalanine swamps the brain and stops it from taking up
other amino acids. If the babies are treated with a low-phenylalanine diet, they have no problems
whatsoever.

Structural, transport and carrier proteins
a. Why we need structural proteins: can be function. Ex: elastin
b. Why we need transport proteins. Ex: voltage-gated NA+ channel
c. Why we need carrier/storage proteins. Ex: apolipoproteins, ferritin

We need structural proteins:
Assemble in multimers to form fibers that form body structures. Usually fibers, but also the
crystalline lens of the eye
One or a few kinds of subunits, often interwoven
Protein-protein interactions hold fibers strongly together
Many structural fibers also have catalytic activities, ex: muscle fibers, tubulin

Elastin (structural protein):
Individual elastin monomers fold into a loos tangle that can stretch out when under tension.
Important in all elastic tissues (walls of arteries, lungs, skin, bladder, cartilage), added to skin-
care products. Covalent cross-links between lysines allow it to stretch.

Membrane transport proteins:
Lipid bilayer membrane encloses all cells, hydrophobic molecules that repel large polar
molecules and ions, while allowing small lipophilic molecules and small polar molecules
through. The large polar molecules and the ions need to get into the cell, but can only do it
through a membrane-transport protein which provides a channel through the membrane allowing
even ions and large polar molecules to get through, using ATP for an energy source.

Ion channel mutations and epilepsy
Voltage-gated sodium channel: several hundred distinct mutations in brain voltage-gated sodium
channel genes cause inherited forms of epilepsy.

Carrier/storage proteins. Reversibly bind and release small molecules for storage and transport.
Controls availability of key supplies and keep small molecules away from dangerous
environments.
Why do fats and cholesterol need a special carrier structure? Otherwise they would just join the
first membrane they bumped into. Proteins ApoA, B, C and E bind fat and cholesterol for
transport in the bloodstream. Have a monolayer surrounding hydrophobic, fatty molecules
(triacylglycerol and cholesterol). In the membrane are apolipoproteins which deliver the fat and
cholesterol to the specific places they need to go. The apolipoproteins stop them from just
joining any molecule they meet.
Why does iron need a special carrier structure? Ferritin carries iron in our blood. Made of 24
subunits, allows the cell to target the cell to where its needed so the iron doesnt just go around
anywhere. Also, iron is reactive, the ferritin shields the iron from other molecules it might react
with, and it also protects bacteria from getting iron, which they need to survive.

Regulatory proteins and RNAs
a. Regulation of gene expression
b. By proteins and RNAs
a. Ex: flower color, blood oranges, homeotic floral mutations
c. Regulation of protein activity by proteins and small molecules
d. GMO potato (antisense RNA)

Regulation of transcription (=gene expression). Regulation of gene expression is almost always
at the transcriptional level, not before or after. There are lots of regulators, transcriptional
acitvators which bind to the regulatory sequences, often the first causes a conformational change
allowing the second to bind which causes a conformational change which allows the RNA
polymerase to bind to the promoter and begin transcription.

Regulation of catalysis =protein activity
Features of catalytic proteins:
Activeproduces product
and regulatory site inhibitor binds and causes conformational change which changes the active
site and makes it impossible for the substrate to bind.
small molecule binds protein or protein binds protein

regulation by Antisense RNA
potatoes contain 2 kinds of starch, amylose and amylopectin. Amylopecuin is used by industry,
but is hard to purify away from amylose. Directed genetic modification of potato introduced an
antisense RNA gene into the potato genome. This RNA base-pairs with the mRNA of the gene
for amylose synthase. The double-stranded mRNA cant be translated, so these potatoes make
no amylose.

Diploids: homozygous phenotypes
ABO blood type alleles:
ABO-A allele codes for an enzyme that puts a sugar modification on the surface of red blood
cells: alpha1->3 N-acetylgalactosaminyl transferase
The ABO-B allel codes for a very similar enzyme that puts a different sugar on red blood cells:
alpha1->3 galactosyl transferase.
ABO-B differs from ABO-A by seven substitutions in the coding sequence; four of these change
amino acids, and together these change the sugar specificity.
Te ABO-O allele doesnt specify a functional enzyme. There is a deletion from ABO-A of a
single base pair at aa87 of the 354aa protein, causing a frameshift mutation so no sugar is bound

Cystic fibrosis:
Caused by common mutation affecting the cystic fibrosis transmembrane regulator (CFTR), a
complex protein that transports Cl- ions across the cell membrane and has a regulatory domain
which regulates the transport of Cl- across the membrane. About 1/20 north americans (?) are
heterozygous for a mutation in this gene, because it is a very big gene with enourmous introns,
making it a very big target for mutation. Many different kinds of CFTR defects can cause cystic
fibrosis.

Dominance:
a. Definition of dominance
b. Other usage of dominance
c. Dominance in context
d. Why mutant alleles are often recessive to their wild-type counterparts
e. Why Mendel always saw dominance
f. Considering more than 2 alleles
Dominance: consider 2 alleles that give different phenotypes when homozygous. If a
heterozygous individual has the same phenotype as one of the homozygotes, geneticists say that
allele is dominant to the other.
Dominance describes a relationship between two alleles, not a property of a single allele.
If the heterozygote has an in-between phenotype, we say this is a blended or additive
phenotype.
If the heterozygote has both phenotypes: we say that both phenotypes are seen.

Why are defective alleles typically recessive to functional alleles? Because, for many functions,
half the usual amount of protein is enough. Haplo-sufficiency is good, i.e. half the usual
amount is enough.

Many genes have 3+ alleles. Each pair has their own dominance relationship. Ex: homologous
genes control coat color in many mammals. The dominance relationships of these alleles from
an allelic series.

How genes are named:
a. Genes/loci are named by their discoverers
a. Discovered by genetic analysis
b. By sequence analysis
c. More than one discoverer
b. Devise gene and allele names that are helpful for problem solving
c. Use convenient shorthand notation

Genetic analysis: geneticists use crosses to find patterns of inheritance of phenotypes and from
them infer differences in genotypes
Naming:
1. For what is changed in the mutant (usually, what goes wrong). Ex: the white gene
encodes an enzyme that makes a red pigment, the eyelss gene is needed for making eyes
2. As a clever pun or joke
3. Personal reasons
Bioinformatics: computer programs examine DNA sequences for long open reading frames.
Then they check fro promoter and terminator sequences. Then for similarity to known genes.
Naming:
1. For the name of a homologous gene or gene family. Ex: ANKRD15ankyrin repat
domain protein 15
2. If no homologs, use obscure technical naming convention tied to genome position
If a gene has more than one discoverer it probably has more than one name.
Usually alleles are named as versions of the gene name. example wt drosophila eyes are red=
white+, or white cherry for pink eyes, white apricot, white eosin

Is the big allele always dominant to the little one?
If the names of two alleles are distinguished only by their capitalization, you can safely assume
that the uppercase one is dominant to the lowercase.
Dominance is indicated by the greater than sign >
A implies an unspecified allele


Gene interaction in biochemical pathways:
a. Most phenotypes depend on multiple genes
b. Alleles at one locus can mask effects of alleles at another locus
c. Biochemical pathways depend on upstream steps
d. Some genes act redundantly
e. Some genes act cooperatively

Sometiems, alleles at different loci interfere with each others phenotypes. Ex: cant tell what
hair color if you dont have any hair

Regulatory interactions:
a. Simplified regulatory interactions: stop and go genes in embryonic and adult cells
b. Effects of knowckout and promoter-up mutations in embryonic and adult cells
c. Germline and somatic mutations
d. Connectedness of genes

How somatic mutations cause cancer
a. How cancer cells are different
b. Each tumor is an evolving population of cells
c. Cancer cells mutate at a high rate
d. Caner begins with mutations causing cells to grow when they shouldnt
e. Environmental and inherited factors can increase the risk of these mutations
f. Bad luck

Normal cells: stay put, stop growing when signaled, dont co-opt blood supply, cant grow
forever, grow only wen signaled, die when not needed.
Tumor cells: ignore signals to stop growth, co-opt blood supply, can grow forever, make own
growth signals, ignore death signals, invasion and metastasis
Cancer cells change by a kind of natural selection, as if they were cells of an independent
species, not well-behaved parts of our bodies.

Cancer cells make more genetic mistakes. Chromosomes are lost and gained in mitosis
(aneuploidy), DNA damage is frequent and badly repaired, DNA replication is not synchronized,
cell-cycle checkpoints are ignored.
Cancer cell populations evolve, accumulating genetic changes that improve growth or drug
resistance.
Medical goals are to use chemotherapy to block the effects of these mutations without favoring
new mutants and prevent the late mutations (keep cells genetically stable). Very difficult to do
because every cancer/tumor is unique and the genetic changes arise at random and cannot be
predicted. And the phenotypic consequences of these mutations are hard to predict because the
genetic background due to other mutations is so variable.

What genetic changes create the initial tumor cell?
-Mutations in proteins that stimulate cell growth (activating mutations) proto-oncogenes
-proteins that suppress cell growth (loss of function mutations)tumor-suppressor genes
Proteins that tell cells when to die) loss of function mutationsapoptosis genes

Genetic background we inherit affects the consequences of new cancer-causing mutations.
Inherited alleles can also affect our mutation rate directly.
Environmental mutagens can increase the risk of new cancer-causing mutations. Environmental
mutagens dont usually affect subsequent events in cancer.
Cancer founder cells arise by random mutations. Tumors become more aggressive by random
mutations

Sex Chromosomes and sex determination
a. In humans and most animals, development of male sexual characteristics is induced by
the SRY gene product
b. SRY is only on the Y chromosome, so inheriting a Y chromosome causes development
into a male
c. X and Y are called sex chromosomes; the others are autosomes. Females have two X
chromosomes, males have an X and a Y
d. The large X chromosome has about 2000 genes unrelated to sex, the Y has few genes,
most male-specific.
e. When male cells go through meiosis, the Y chromosome behaves as if it were a homolog
of the X chromosome

X chromosome:
- 155,000,000 bp
- About 2000 genes
o Defective alleles cause hemophilia, muscular dystrophy, hemophilia
Y chromosome:
- 58,000,000 bp
- SRY and a few other male-specific genes
Autosomes: for 22 of 23 pairs of chromosomes, males and females are exactly the same

The 2000 genes on the X chromosome are for functions shared by males and females. In this, X
chromosomes are like autosomes. Theyre also like autosomes in their inheritance. The 2 X
chromosomes in females behave exactly like autosomes (with one exception).

SRY and the few other genes on the Y chromosome are expressed only in males (only males
have this chromosome). In male meiosis, the Y chromosome pretends to be an autosome by
pairing with the X chromosome.

Expression of X-linked genes in females
a. Males have one X chromosome: females have 2
b. Dosage compensation is needed
c. One female X chromosome is turned off early in development
d. One of the two Xs in each cell at that time is chosen randomly for inactivation
e. Females thus have patches of tissues with one or the other X chromosome active
Species must adjust the relative doses of the sex chromosomes in males and females (dosage
compensation). Humans and other mammals compensate by turning off one copy of the X
chromosome in females. One X chromosome is inactivated in each cell, randomly earlier than 6
weeks. Each cell chooses independently which cell gets turned off, but then it is set through
development and adulthood.
Almost all female mammals have patches of cells with different active X chromosomes. Calico
and tortoiseshell cats always are heterozygous for the X-chromosome locus O and have one O
allele (black) and one o allele (orange), are female. Patches of their fur express O or o,
depending on which X is inactivated.

Expression of X-linked genes in males
a. Males have one X chromosome; females have 2
b. Males are hemizygous for X-linked genes
c. In males, X-linked alleles always affect the phenotype
The X chromosome has many important genes. When the X has a defective gene, the male
doesnt have a second copy to produce any of the protein so the effects are more severe.

Males have only one X chromosome:
- Only one allele of each X-linked gene. They are hemizygous=haploid for all genes on
this chromosome
- Most defective alleles are recessive to their functional counterpart
- For autosomal genes and for X-linked genes in femailes, defective alleles are usually
heterozygous with the normal allele so the phenotype is normal
- For X-linked genes in males, one defective allele causes a defective phenotype


Can natural genetic variation explain natural phenotypic variation?
a. Genetic variation is intrinsically quantized
b. Natural phenotypic variation is continuous
c. What factors transform one into the other?
a. Small effects
b. One-to-many and many-to-one
c. Interaction effects
d. Environmental effects
e. Chance effects

Genetic variation is: discontinuous, quantized, atomized, discrete, digital
i.e. the base is either: A or G or C or T. There are no in-betweens. Same goes for the amino
acids.
In contrast, natural phenotypic variation is: continuous, smoothly varying, analog, gradual
Before 1850, people observed continuous variation within each species. They also observed
adaptation and diversity between species, so they assumed blending of parental characteristics in
offspring. Then Darwin (1859) came and realized that natural selection explains adaptation as a
consequence of continuous variation. But, Darwin assumed blending inheritance (this eliminates
variation!)
Mendel (in 1865) found the factors controlling heredity DO NOT blend. Discrete factors
(genes/alleles) are passed unchanged from parent to offspring through the generations.
Later naturalists rejected Darwin, and invoked inheritance of acquired characters (Lamarckism),
an innate drive for change or the sudden appearance of dramatic new variants. Mendel was also
rejected because it was too weird and going against the accepted ideas of the time.
But, in 1900, Mendels work was rediscovered and validated him, finding it explains inheritance
(but only of distinct phenotypes, not continuous variation).

The Modern Evolutionary Synthesis (1930s):
Genes are responsible for small, continuous phenotypic differences as well as dramatic discrete
ones. Natural selection acts by changing allele frequencies in populations.
So, how does the underlying discontinuous DNA variation cause the smooth phenotypic
variation we see?
- Most non-silent DNA variants cause only very small changes to phenotype
- Most non-silent DNA variatns affect many aspects of phenotypes
- The effects of most non-silent DNA variatns depend on what variants are present at many
other positions
- The environment also affects phenotype
- Chance also affects phenotype

Most Natural Genetic variation has small effects
a. The concept of heritability
b. Identifying the responsible genes
c. Genome-wide association studies (GWAS)
d. Many genes have small effects on height
e. What might we be missing?
We want to understand how natural genetic variation causes natural phenotypic variation
Components of the explanation:
- Most DNA differences have small effects on phenotype
Consider genes affecting height. How many genes for height are there?/how much of height is
controlled by genes?/how heritable is height? 80% of the observed differences in human height
are due to DNA sequence differences, so the heritability of human height is 80%
Heritability is the fraction of phenotypic difference due to genotypic differencesapplies to
continuously varying traits.
Heritable means it is transmitted genetically from parent to childapplies to discretely variable
traits.
How do we identify genes that affect a particular trait?
We use GWAS, analysis of SNPs to find places in genome associated with differences in the
trait of interest.
1. Find many thousands of people who differ for the trait of interest
2. Use a DNA chip to type their alleles at each of 10
6
SNP genome positions
3. Look for SNPs where the two populations have different allele frequencies
The computer then makes a Manhattan Plot, with chromosome number on the X axis and log of
allele frequencies on the Y axis, so any obviously out of range dots, show that there is a
significant difference in the allele frequency.
The missing heritability problem:
80% of the differences in human height are due to differences in genes. But, only 10% of
the differences in human height are explained by the 180 genes that have been found. Do many
contributions to phenotypic variations come from rare alleles? GWAS studies only consider
effects of SNPs (1+ % of the population), we each also have many variants that are rare in the
population. So maybe its due to gene interaction effects?

Many natural genetic variants affect multiple traits (pleiotropy)
a. One phenotype is affected by alleles of many genes
b. Alleles of one gene affect many phenotypes
c. Interaction effects between alleles of different genes add complexity
We want to understand how natural genetic variation causes natural phenotypic variation
Components of the explanation:
1. Most phenotypes are affected by more than one gene
2. Most non-silent DNA variants affect more than one aspect of phenotype
3. Most DNA differences have small effects on phenotypes
4. The effects of differences at one locus depend on differences at another locus
Why do most genes affect more than one phenotype?
- Each phenotype is a human construct, not a discrete biological entity. The body evolves
as an integrated whole. Even a gene responsible for a single enzymatic step will have
consequences for many of the phenotypes we measure
- Most regulatory proteins directly affect multiple genes. Each DNA-binding protein can
bind to many sites in the genome, potentially regulating many different genes. A DNA-
binding protein will bind with different strengths to different sites in the DNA, depending
on their sequences.

Effects of natural genetic variation depend on chance
a. Small processes have big chance effects
b. Role of chance in gene expression
c. Role of chance in embryonic development
d. Chance events interact with genetic factors
Chance affects small things as well as large.
Chance events in the cell, chance is not important for very small molecules (ex: ions) because
these are usually present in very large numbers. The average cell contains about 10
11
Na
+
ions.
But, its very important in the activities of regulatory proteins, which may be present in only a
few molecules per cell or may rarely have an occasion to act

Chance effects in gene expression (molecules randomly bumping into each other)
- How many molecules of this specific regulatory protein are present in the cell?
- Does this regulatory protein bind to the gene now or later?
- Does this RNA polymerase bind the promoter now, or 30 seconds later?
- Does another polymerase bind as soon as the promoter becomes vacant? Or later?
- Did this RNA polymerase insert a wrong base? (RNA polymerase has no proofreading)
- Does this ribosome make an error?
- How many times does this mRNA get translated before its degraded?
- How long does this protein molecule take to be folded and transported to its site of
action?
- Did this protein molecule fold a bit incorrectly?
- How many times does this protein molecule act before it is degraded?
Chance genetic effects (somatic, not heritable):
- In females, which X chromosome is inactivated in which embryonic cell
- Somatic mutations, both small mutations and big chromosomal changes (origin and
progression of cancer, the semi-random changes used by the immune system to diversify
antibodies
Chance effects in embryonic and fetal development:
- Cell migration
- Response to extracellular signals (independent of the environmental variation we can
describe

How Natural genetic variation affects the risk of cancer
a. Examples: retinoblastoma, BRCA1 and 2, colorectal cancer-risk alleles with small effects
Retinoblastoma: rare tumor of young children, forms unpigmented tumor, reflects photo flash

The two-hit model of cancer initiation:
Retinoblastoma and many other cancers are initiated by mutations in genes whose normal
function is to prevent inappropriate cell growth. These mutant alleles are usually recessive to the
normal allele, so a tumor will only begin to grow when BOTH alleles are nonfunctional.
- Sporadic: new mutation in Rb (not heritable unless in germ line). Somatic RB- mutations
occur independently in both alleles in a retina cell. ~60% of cases, usually only occurs in
one eye, no increased risk of cancers in other tissues. Need two somatic mutations in the
same cell.
- Familial: parent had a germ-line mutation in Rb. Child inherits a Rb- allele. Somatic Rb-
mutation occurs in the other allele in a retina cell. ~40% of cases. Usually occurs in both
eyes. Cancer may develop in other tissues later. Only need one somatic mutation in any
given cell
Mutations in BRCA1 and BRCA2 raise the risk of breast cancer. The BRCA1 and 2 proteins are
both important in a particular form of DNA repair (homology-directed repair of DNA breaks).
Both proteins are part of a genome surveillance complex, along with many other proteins.
Women who inherit one BRCA- allele have lifetime breast cancer risk of 50-70%. Inheriting 2
BRCA1 mutations (one from each parent) has never been reported and is believed to be a lethal
birth defect.
Mutations in BRCA1 and 2:
The two-hit model is thought to apply to BRCA tumors. But it is hard to distinguish between the
mutation that initiated abnormal cell growth and all the other mutations that subsequently
accumulated because the BRCA complex was nonfunctional. More than 90% of breast cancer
occur in women with two normal alleles of each BRCA gene. So although having a BRCA
mutation dramatically increases your risk above that of the average woman, not having a BRCA
mutation doesnt dramatically lower your risk.

Cancer risk alleles with smaller effects:
Colorectal cancer:
~30% of cases are familial. 5% are specific high0risk syndromes (often mutations in DNA
repair genes). The other 25% are due to poorly understood genetic factors and 70% are sporadic
with GWAS showing SNPs associated with increased risk.

Integrating new understanding into old concepts
a. Some terminological history
b. Definitions and explanations of some confusing terms used by geneticists

The first geneticists worked with the simplest situations (mutant allelenew phenotype).
Alleles with large, easy-to-score effects, that affected only a single phenotype with simple
dominance that gave consistent phenotypes. Everything else was treated as an exception with a
special name.
Terms describing how heterozygouos alleles of one gene affect phenotype:
- Carrier. An individual who is heterozygous for a normal allele and a recessive (usually
disease-causing) allele. Also, loosely, anyone who has a mutant allele but a normal
phenotype.
- Dominant lethal: an allele that is lethal when heterozygous with a normal allele. Most
dominant lethal alleles may not be truly dominant, since the phenotype of a homozygote
for the allele usually isnt considered.
- Dominant allele: the term dominant is often applied to rare mutant alleles that have
strong phenotypes when heterozygous with the normal allele. Usually the phenotype of a
mutant homozygote has not been examined or is not considered.
- Dominant risk factor: is an inherited RB- allele dominant to the normal allele? The
phenotype of high risk of retinoblastoma is seen in Rb+Rb- individuals. But the
homozygous phenotype is probably different (embryonic lethal) . most geneticists would
say that an Rb- allele acts as a dominant risk factor for retinoblastoma. But this usage
isnt in strit agreement with the definition of dominance.
- Incomplete dominance/semi-dominance: situations where the heterozygote has a
phenotype that is intermediate between the phenotypes of the two corresponding
homozygotes. Many allele pairs that appear dominant/recessive for an organism-level
phenotype show this for molecular and cellular aspects of phenotype
- Co-dominance: a situation where the phenotype of the heterozygote has features of the
phenotypes of both homozygotes. This is also commonly seen with some molecular and
cellular aspects of phenotype.
- Over-dominance: an allele combination where the heterozygote shows a phenotype not
seen in either homozygote, or a more extreme version of the phenotype than either
homozygote (ex: sickle cell anemia). Often used in evolutionary contexts
Terms describing more complex effects on phenotype:
- Pleiotropy: affecting more than one aspect of phenotype. This is how genes usually act,
not a special case. The view of genes as each affecting a single aspect of a phenotype is
just a convenient simplification
- Epistasis: phenotypic effects that depend on the interactions between alleles of different
loci. This is normal for real genetic variation. Sometimes used strictly for situations
where the effects of alleles at one locus completely mask the effects of alleles at another
locus.
- Penetrance and expressivity: the strength of the correlation between genotype at a
specific locus and the phenotype associated with that genotype.
o Incomplete penetrance: not all people with the genotype have the phenotype
o Variable expressivity: people with the same genotype differ in the strength of
their phenotype.

DNA fingerprinting
a. Why DNA makes good evidence
b. VNTR loci as identifiers
c. VNTR mutation rates
d. The CODIS set of VNTR loci
e. New combinations in each new person
We all leave DNA behind, wherever we go. We shed about 40,000 skin cells/minute each of
which has DNA. It is a very stable molecule, doesnt degrade easily. PCR can amplify DNA
reliably from tiny amounts and complex/dirty mixtures. Our DNAs differ at several million
places. Each person is unique. Fingerprinting identifies people by their genotypes at a set of loci
(markers), each marker has many different alleles, so this leads to trillions of combinations, so
we know each persons is unique

VNTR loci: variable number tandem repeat loci
Repeat: short sequence present in multiple copies
Tandem: the copies are next to each other
Variable number: different alleles have different numbers of copies
Easy to tell different alleles apart, and they are variable in number. Mutations frequently
change the repeat number of VNTR loci. Mutations occur when DNA polymerase slips at a
repeat. Occurs frequently, but not all the time which is why its good for fingerprinting/paternity
One study found that 95% of VNTR mutations were gains/losses of one repeat. 1E-3 mutations
for VNTR loci per gamete per generation. Repeats were more frequent than losses. Longer
alleles were more mutable. 4 times as many mutatioons occurred in males as in females, because
male germline gets replicated a lot more than females. Some differences between ethnic groups
present.

CODIS set of DNA markers (combined DNA Index System): highly polymorphic in most
population. On different chromosomes. 13 loci they check for DNA fingerprinting and stuff.
Only identical twins will have the same markers. Length differences are easy to detect, so most
of the time you dont even need to do sequencing, just put automated DNA analysis, compare the
lengths of the markers.

Analyzing a single gene or gene panel
a. Check for known or suspected mutations
b. One gene or a panel of genes
c. PCR or sequencing
d. Ordered and interpreted by a physician or geneticist
e. Expensive
f. High risk population
g. Pre-implantation screening
h. Tumor typing
This can answer straightforward questions. Whether you do or do not have mutations in a
specific gene/if you have a specific mutation. Useful when the person has a condition/syndrome
that often has a well characterized genetic cause, when the persons relative is known to have a
specific genetic condition or when choice of treatment depends on the genetic cause.
To do:
1. Check for common mutations in one or a few known genes. Often can use PCR or a
specially designed DNA typing chip.
2. Check for rare or unkown mutations
Usually done at clinical genetics labs (usually university) not direct to consumer. Ordered and
interpreted by DR> can be expensive if not covered by health insurance.
Concerns:
1. Will knowning the results change the outcome? Is there a way to prevent or mitigate the
effects of bad alleles? Will the results change therapy?
2. Do you want to know this information? Do family members? Children, parents, siblings,
aunts uncles, cousings?
3. What if the results are inconclusive? If no explanatory mutation is found?
Examples: jewish genetic screening, preiplantation genetic diagnosis (generate embryos by IVF,
screen one cell of each early-stage embryo, test for known harmful mutations and chromosomal
abnormalities and only implant the best embryos) tumor panel because knowing which genes are
mutated or amplified can help guide therapy, but tumors are genetically complex, so one
genotype may not predict response to treatement.
In 1997 myiad genetics was granted a US patent on the human BRCA1 and 2 genes, whose
sequences they had determined. Without the patent, it would be much cheaper and more widely
available. Patent has been thrown out as of June 2013.

SNP-typing the genomeHapMap
a. SNVs, polymorphisms and SNPs
b. Hisotyr of SNP analysis
c. HapMap
SNV: single nucleotide variant; the presence of different nucleotides at homologous positions in
2 DNA sequences
SNP: single-nucleotide polymorphism; a SNV present in more than 1% of the alleles
Haplotype: the genotype of a short segment of a chromosome
One product of the Human Genome project was tools for study of hyman genetic diversity.
There were more than 1.4 million SNPs in 2001. Now we think there are more than ten million
HapMap: to catalogue genetic diversity from around the world. Shows where genes, exons,
introns are, SNPs, allele frequencies in different populations and genotypes frequencies


SNP-typing the genome
a. SNP-map catalog and SNP-typing chips made GWAS (genome wide association studies)
possible
b. GWAS data creates phenotypic predictions useful for personal SNP analysis
c. SNP-typing chips made personal genome analysis affordable

GWAS: We want to find the genes whose differences cause the phenotypic differences we care
about, to find the places in the genome where these genes are. This became possible because of
HapMap (a sequence-map of the location of many differences) and SNP-typing chils (an
efficient way to genotype many differences at once.

SNP chips let us efficiently identify alleles at SNP positions. Personal DNA typing becomes
practical. ($99 for a millions SNPs). Odds ratio-risk compared to average person (average being
1.00). some phenoytpyic differences are directly caused by SNP alleles. Most phenotypic
differencesy are caused by non-SNP alleles closely linked to SNPs. The SNP-phenotype
connections identified by GWAS made SNP-typing useful for individuals. GWAS lets us use
alleles at SNP positions to predict phenotypes (as differences from the average).
How SNPs are chosen when the typing chip is designed:
- Even coverage of the genome
- Coverage of known important SNPs
- High coverage of coding regions
- Coverage of known structural variants (indels, rearrangements)

Exome Sequencing:
An exome is the expressed part of the genome. In this case, all the coding regions (exons) and
the sequences within 250 bp of them.
1. Obtain a DNA sample
2. Break into short fragments (~1kb)
3. Use a special DNA chip to separate all the fragments with sequences characteristic of the
exome
4. Sequence all those fragments many times over to get high accuracy
Why sequence an exome?
- Its a lot cheaper than sequencing a whole genome and gets almost the same information
- To find the cause of an unexplained disease that appears to be genetic
- Research benefits (causes of unexplained phenotypes, cases where mutations dont cause
the expected phenotype)

Haplotypes:
a. Whats a haplotype
b. Following haplotypes through the generations
c. Ancestral haplotypes
d. Very ancient haplotypes
e. Processes that degrade haplotypes
Haplotype=haploid genotype. A segment/sequence of DNA that has been inherited intact from
an ancestor.
The segments stay intact in a logarithmic decrease. i.e. if we assume 1 crossover per generation
within 5 years the average length of intact segment goes from 100 to 10, but after that it takes a
very long time to change. As the intact ancestral segments get shorter, they get more stable,
because being short makes them less likely to be sites of recombination. This means that we can
detect very ancient ancestral haplotypes.

Ancestry:
a. Underlying principles of ancestry:
a. Mitochondrial and y chromosome DNAs track maternal and paternal lineages
b. Segments of ancestral DNA are lost over the generations
c. Biological ancestors are not always genetic ancestors
d. We have many ancestors in common
Haplogroup=group of closely related sequences that are the descendants of a single haplotype

Mitochondria are the energy-generating organelles (substructures) in cells. They have their own
little DNA molecules, and theyre passed to offspring only from the mother via the egg, but not
the sperm. Maternal lineage inherits mitochondrial DNA.
Y-chromosome DNA. Because the Sry gene on the Y chromosome causes male development,
Y-chromosomes are passed only from father to son. Paternal lineage inherits Y-chromosome
DNA

The mitochondrial and Y-chromosome assays tell you only about one lineage of your ancestry-a
single person in each generation. Because mitochondrial and Y-chromosome DNA sequences
are not broken up by recombination, they are powerful tools for following a single lineage.
But the farther back you look, the less your single mtDNA and y-chromosome ancestors
contributed to the rest of your genome. If they lived a few hundred years ago, their contribution
to your autosomes and X-chromosome is only about 0.1% of your genome. There is a distinction
between biological and genetic ancestors.
- Many of our biological ancestors are not genetic ancestors. Our genomes dont
contain DNA segments from many of our ancestors. These are the biological not the
genetic ancestors.
In theory we have a million ancestors who lived about 500 years ago. But we have inherited
only about 2600 genomic segments from all of them. More than 99% of our biological ancestors
are not represented in our genome/our genomes contain segments from less than 1% of our
ancestors. In each generation, some ancestral segments dont get passed on, just by chance.
- Many of our biological ancestors were the same people. We have common ancestors on
both sides of the family.
Genetic diversity arises over the generations by random mutation and is shuffled by sexual
reproduction. Genetic diversity is lost over the generations when individuals do not reproduce
and when random ancestral blocks of DNA are not passed to descendants. This loss of genetic
diversity and of ancestral DNA segments is more likely if the population becomes very small
(bottleneck).


PART 2

Mitosis:
a. The role of cell division
b. The problem mitosis must solve
c. Components of the solution:
a. DNA replication makes 2 chromatids from 1 chromosome
b. Keep the paired chromatids together
c. Release them all at once

In asexual organisms all cell divisions are mitosis. Meiosis is only in sexual reproduction

Haploid: somatic cells have one set of chromosomes (gametes)
Diploid: somatic cells have 2 sets of chromosomes
N: number of different chromosomes in one set

How mitosis works:
1. Sister chromatids stay together after DNA replication
2. Each chromatid has a kinetochore at its centromere
3. Spindle fibers attach to each pair of kinetochores and pull the pairs of chromatids apart
4. The cell divides in two
Chromatid is one of the 2 DNA molecules and their associated proteins present after a
chromosome has replicated
Sister chromatids are the 2 DNA molecules from one replicated chromosome
A kinetochore is a protein structure
A centromere is the DNA sequence where the kinetochore is built. Each chromosome or
chromatid has one
How do the spindle fibers know which kinetochore to grab? They dont. they just grab randomly
and pull but if nothing pulls back they let go. By pulling in opposite directions, the opposing
fibers move the chromatid pairs to the middle of the cell.
Why dont the chromatids separate right away once they are being pulled by the spindle fibers?
Theyre tied together by loops of a protein called cohesin. Cohesion doesnt let go until fibers
have attached to the kinetochores of all the chromatids. Then, all the coheisn is cut by the
enzyme separase.

Sexual life cycles: what meiosis and mating accomplish
a. Ploidy changes in sexual life cycles
b. When and where meiosis and mating happen
c. New combinations of alleles
d. Homologous chromosomes
e. What is recombination good for?
Without meiosis (reductive division that takes a diploid cell and makes haploid daughter cells
with different combinations) there would be no sexual reproduction. Without meiosis, cells
would have way too many copies of chromosomes and no different combinations
1. Why do most protists, plants and animals reproduce sexually? It must be good to
randomize the combinations of alleles in different members of a species, although
researchers dont agree about why.

Meiosis: The Basics
a. The special problems meiosis has to solve
b. Meiosis is 2 division (1 and 2), but only meiosis 1 is interesting, 2 is basically the same as
mitosis
c. The homologous chromosomes must first be brought together, then meiosis 1 proceeds
like mitosis
Whats the gentic problem meiosis evolved to solve?
- Making haploid gametes from a diploid cell
o 3 new problems to solve:
o 1. Ensuring each haploid cell gets one complete set of chromosomes (solved by
pairing the homologs)
o 2. Making each haploid set a random mixture of the diploid cells two sets (solved
by random kinetochore orientation)
o 3. Randomizing alleles that are on homologous chromosomes (solved by crossing
over)

After DNA replication:
-keep sister chromatids together.
-bring homologs together and lock them side-by-side
The homologs find each other and hold together by base pairing
Spindle fibers attach to the kinetochores and pull the homologs apart

Meiosis 1:
Opposing spindle fibers push/pull the kinetochores of the paired homologs to the center of the
cell (align at the metaphase plate)
When all pairs of homologs are attached to fibers from both sides, the pairs are pulled apart, just
as in mitosis. Then the cell divides.

Female meiosis makes 1 ovum that is well stocked and 3 polar bodies that dont work. The cell
doesnt divide down the middle in meiosis one, it divides close to the edge to create the ovum
and the polar bodies. Same thing happens in meiosis 2. Males on the other hand, make 4 equal
spermatids from each round of meiosis.

How does base pairing happen?
Each chromatid is a double helix of DNA (plus chromatin protiens). At some places the DNA
breaks and a strand unzips from its partner. The free single strands feel around for another strand
they ca base pair with. But the new partner cant be in the sister chromatid, it must be in the
other member of the homologous pair.
Result: this is how homologous chromosomes align to each other. They are correctly paired for
metaphase, precisely aligned for crossing over and broken in a few places.
Why is crossing over important?
a. Crossovers make new combinations of the parental alleles
b. Crossovers tie the homologs together, so they align properly on the metaphase plates
How do crossovers happen?
The ends of the broken DNA strands rejoin with the wrong partners. Because the DNAs were
aligned by base pairing, no sequences are deleted or inserted. All genes are intact; only the
connection has changed. The crossover ties the homologs together.

The phenotypes of offspring depend on:
- Genotype components and events. What happens when alleles pass from parents to
offspring?
o Meiosis in both parents
o Fertilization between random maternal and paternal gametes
- Phenotype components and events
o Which alleles or combinations of alleles cause which phenotypes?
One egg: genotype is a random outcome from the many possibilities for this womans meiosis.
Millions of sperm: genotypes are just some of the random outcomes possible for this mans
meiosis

Genetic analysis began with Mendel
a. Mendel used crosses to investigate the mechanism of inheritance (genetic analysis)
b. He was a serious and well trained scientist (he studied the whole population, not just
outstanding individuals)
c. His results were solid (good science)
d. His findings were unexpected:
a. Genotype and phenotype
b. Phenotypes dont blend
c. Traits disappear and reappear unchanged
d. Organisms have two versions
e. Parents each pass one version to progeny
What Mendel found out about peas:
1. One kind of element (one gene) controls each character. This created the concepts of
genotype and phenotype
2. Pea plants have 2 versions of each of these genes (2 alleles). Peas are diploid, as are most
plants and animals
3. Ovules and pollen grains each have only one allele of each gene, randomly chosen from
the two present in the organism that produced them. gametes are haploid
4. Genes and alleles are stable; they dont morph or change over the generations
5. When a plant has 2 different alleles of a gene, these alleles do not influence each other;
each passes unchanged into the gametesgenes arent changed by the process of
inheritance
6. Each seed, and thus each organism, results from one ovum being fertilized with one
pollen grain (not many, as previously thought)
7. The two parents make equal contributions to the character
8. The effect of an allele is independent of whether it comes from the ovule or the
pollenhaploid-diploid sexual cycle
9. When a plant has 2 different alleles of each of two genes, the alleles of each gene move
independently into the gametes.-->the mechanism of inheritance randomly recombines
the alleles of different genes

Mendels findings and what we now know
Mendels conclusions separated genotype and phenotype. What do we now know that explains
this?
- DNA sequences are inherited, proteins are not. Information is inherited
- DNA is physically very stable and sequence changes are rare
- DNA contains coded information specifying the sequences of proteins
What mendel didnt discover:
-linkage
-Multiple alleles
- Other genetic relationships besides dominance


Solving genetics problems usually requires inferring various combinations of the following:
- Genotype components:
o What happens when alleles pass from parents to offspring?
Meiosis in both parents what gamete genotypes and frequencies are
produced from what parental genotypes?
Fertilization between random maternal and paternal gameteswhat
offspring genotypes and frequencies are produced from what gamete
genotypes?
- Phenotype Components
o Which alleles or combinations of alleles cause which phenotypes?

True-breeding: when self-pollinated or crossed with the same strain, all offspring had the same
phenotype as the parents, i.e. homozygous

Hemizygous: only one allele. Example: men are hemizygous for genes on the X chromosomes



Testcross: a mating to individuals homozygous for recessive alleles of the genes in question.
- Much easier to infer genotypes from phenotypes
- Can read out gamete genotypes directly from progeny phenotypes
- Crossovers affect gamete genotypes in only one parent
- Much easier to predict or interpret frequencies

What does recombination frequency tell us? A measure of relative gene positions. With
physical maps, units are bp. For genetic maps, units are probabilities of crossover (map units).
A genetic map unit or centimorgan, is defined as the distance between genes for which one
product of meiosis in 100 is recombinant. The physical length of a map unit depends on the
length of the chromosome and on minor variations in the probability of a crossover in different
parts of chromosomes; in humans its usually about 700 kb.

Genetic linkage does not equal physical/covalent linkage. Genes on the same chromosome are
always physically linked by the covalent bonds of the DNA backbone. Genes far apart on the
same chromosome usually have at least one crossover between them, making them genetically
unlinked. The gametes with different allele combinations are produced in equal frequencies, as
if the genes were not on the same chromosome.

Complementation: if the mutations are in different genes they can still have wild-type phenotype
offspring. Crossed a set of homozygous recessive mutants defective in the same process with
each other. Wild type progeny phenotype means the mutations are in different genes. Mutant
progeny phenotype means the mutations are in the same gene.

Why heritability matters:
1. Natural selection requires heritable variation
2. It predicts the effects of breeding programs
3. It determines how we study human traits and what we can do about them
4. It raises many ethical and societal issues (nature vs. nurture)

Heritability:
- Property of a population, not individuals.
- It is always an estimate
- Depends on how the trait is defined
- Depends on the specific population
- Depends on the specific environment


Heritability: the fraction of phenotypic difference due to genotypic differences. Applies to
continuously varying traits.
Heritable: transmitted genetically from parent to child. Applies to discretely varying traits.
How to estimate heritability: find ways to separate the effects of genes and environment, when
you dont know which genes or which aspects of environment matter
- Compare the observed and expected resemblance between known relatives
- Measure the response to a single generation of defined artificial selection

GWAS works because:
- Short haplotype segments are rarely disrupted by crossovers and rarely changed by
mutation. So, alleles causing phenotypic differences remain associated with specific SNP
alleles. (Linkage persists between ancestral SNP alleles and nearby ancestral alleles
affecting phenotype).
Complicating factors for GWAS:
- Results are very sensitive to how the phenotypes are categorized.
Ex: sexual orientation, intelligence, mental illness are hard to quantify
- Results may be very sensitive to errors in assigning phenotypes.
- SNP-typing omits many alleles, including all the rare ones.
- Crossover hotspots disrupt linkage between some SNP alleles and causal alleles
- The studied group may be too small
- The studied group may not contain the important rare alleles
- The population may have genetically distinct sub-populations.
- Statistical analysis must correct for multiple comparisons
A GWAS examines 500,000-1 million SNPs for significant differences between the two
populations. Statistical correction for multiple tests is essential, but the best methodology is not
obvious.

Inbreeding
Raises similar issues for all plants and animals (including humans): harmful recessive alleles,
reserves of genetic variation, strains with reproducible genotypes and phenotypes.
In relatives, alleles are often identical by descent
Offspring of matings between relatives (consanguineous matings) are often homozygous for
harmful recessive alleles that, although rare in the population, were present in an ancestor. We
each carry about 400 deleterious alleles, about 2 of which cause serious disease when
homozygous. Most of these alleles are rare in the general population.

Relatedness coefficient: fraction of genes expected to be identical by descent between two
individuals
Inbreeding coefficient: fraction of alleles expected to be identical by descent in one individual

Inbreeding in animals is good for:
1. Breed for a more useful or attractive phenotype:
Breeding is very slow and expensive work. Speed up byy using very strong selection-
only let the very best individuals breed. Soon all members of the breed are descended from the
same small group of ancestors.
2. Breed for a uniform phenotype: medical research needs experimental animals with very
reproducible phenotypes, so results of experiments in different laboratories can be
compared. This usually requires fully homozygous strains. Inbred mouse strains are
obtained by deliberate severe inbreeding (ex: 20 generations of sibling mating).
Inbreeding depression is the reduced viability caused by harmful recessive alleles
becoming homozygous.
Some plant species naturally self-pollinate (ex: Mendels peas) harmful recessive mutations are
quickly eliminated by natural selection, so these species dont suffer inbreeding depression

Inbreeding and genetic variation in evolution and conservation
Most sexual species are outbred: dont really mate with close relatives. They have evolved
mechanisms that reduce inbreeding:
- Genetic: mating type alleles must be different
- Dispersal of gametes: wind or insect pollination, fertilization in open water
- Behavioral: one sex leaves the natal territory to find mates
Some species are naturally inbred:
Many plant species naturally self-pollinate. Harmful recessive mutations are quickly eliminated
by natural selection, so these species dont suffer inbreeding depression. Each plant is
homozygous, but the species as a whole contains plenty of genetic variation.
But why dont these species need variation for coping with pathogens, parasites and
environmental changes?
Some species have ibreeding thrust upon them by near-extinction:
1. Offspring are often homozygous for recessive harmful alleles, reducing fitness
(inbreeding depression)
2. Some recessive harmful alleles become fixed in the population
3. Population has little variation for coping with pathogens, parasites and environmental
changes.
-->extinction crisis worsens
Conservation and captive-breeding programs pay special attention to minimizing inbreeding.

Intraspecific hybrids (between members of the same species):
Common in plant and animal breeding. The effects are the inverse of inbreeding (cross of two
independently inbred strains):
- High vigor (heterosis)
- Harmful recessive alleles are complemented
- Normal or better than normal fertility and seed production
- Genetically and phenotypically uniform
- All these things take only one generation, but hybrids dont breed true.

Interspecific hybrids (between different species): only viable between some closely related
species. Best cases have high vigor, but are infertile. Hybrids with different chromosomes are
usually infertile: even if they have the same genes, the genes arent in the same arrangements on
the chromosomes. This leads to incorrect pairing in meiosis 1 and gametes with incomplete sets
of chromosomes (aneuploidy). In plants, infertility of hybrids is sometimes rescued by a
second error, duplication of all the chromosomes (by failure of a mitosis in a germ line cell).
This produces a tetraploid with normal fertility because now all the chromosomes have pairing
partners.

Hybrids rarely form between distantly related species. Mate-recognition mechanisms are
incompatible. If gametes do meet, the offspring are not viable because the genes are too
divergent.

Hybrids between populations that might become different species. Speciation: the series of
events by which a single ancestral species has become two distinct descendant species.

Hybridization is important in conservation genetics:
- If several small populations exist in nature, should they be interbred?
- Captive breeding programs in zoos: are the animals members of the same species?
important to clarify species relationships before beginning breeding programs
- Are the species actually species or hybrids?

FROM HERE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Polyploidy
Rare in animals, mainly in plants. Arises by failure of mitosis or meiosis. Polyploid
human zygotes are not viable, whereas plants are generally robust and healthy

Polyploidy: having more complete sets of chromosomes than an ancestor
- Triploid (3n), tetraploid (4n)
Euploid: having the normal number of complete sets of chromosomes
For plants and animals, usually 2 sets (diploid, 2n) for gametes, 1 set (haploid, n)

Aneuploid: having an incomplete or overcomplete set of chromosomes
- Monosomy (2n-1), trisomy (2n+1)

Polyploidy can arise by:
1. Mitotic failure: gives a tetraploid cell
2. Meiotic failure: gives a diploid gamete (+haploid gamete triploid zygote)
3. Fertilization of ovum by 2 sperm (gives a triploid zygote)
Polyploidy is rare in animals but common in plant, but animal somatic cells are often polyploidy,
especially terminally differentiated cells, i.e. in muscle tissue, or other tissue that is never
going to divide again

Cells can become tetraploid if something is going wrong in mitosis after the DNA has doubled,
so the cell aborts mitosis, but it has already doubled the DNA so next time it goes into the
mitosis cycle, it is starting out with double the amount of DNA even before the S phase.
Tetraploid plants are usually large and robust. Cells are larger. Absolute gene dosage is
doubled, but relative gene dosage is normal.
So because the plants are usually bigger, farmers often induce mitotic failure with colchicine,
which disrupts spindle microtubules.
Tetraploidization can restore fertility to an infertile diploid hybrid plant through mitotic abortion
and reset as described above.

Triploidy can arise by an error in meiosis 1, if the chromosomes all go to one daughter cell,
giving two n+1 (should be n) and two empty cells, or during meiosis 2 with 2 normal gametes,
one diploid and one empty gamete.
Can also arise by double fertilization, common in plants.
Can also arise by mating of a tetraploid to a diploid.

In triploid meiosis chromosomes are unpaired or mispaired which leads to aneuploidy gametes,
even plants dont do well with that. Plants generally do well with even numbers of ploidy, so
that they always have paired chromosomes. Triploid fruits are often seedless (example: bananas,
watermelon). Bananas propagate asexually, but watermelons are created each generation by
crossing diploid with tetraploid. Bananas are a problem, because they are sterile

Triploid trout are also viable and large, but infertile. They can be used to stock lakes for sports
fishing with fish that are desirable but unable to breed. These are good because we dont have to
worry that they will escape and breed in the wild and take over.

Aneuploidy: incomplete/overcomplete sets of chromosomes, which happen from errors in
meiosis. the leading cause of reproductive failure and congenital birth defects in humans.
Happens from error in meiosis (very rarely, through mitosis in the germline)
In meiosis 1:
When the chrommosomes are paired, a single one accidentally goes to the wrong
daughter cell when splitting. If in meiosis 2, will have 2 normal gametes, one n+1 and one n-1

Why are most aneuploidies not viable (with exceptions for the trisomies for the smallest and sex
chromosomes)?
-genes whose products interact are usually on different chromosomes. Chromosome number and
organization is not very stable over evolutionary time and genes are not gathered into operons as
in bacteria. So, aneuploidy unbalances gene dosage. Natural selection has optimized gene
regulation, so that the products of different genes will be present in the best proportions for their
functions. But this only works if cells always have the same number of copies of the genes.

Viable human aneuploids:
- Down syndrome (trisomy 21): moderate and variable physical defects and mental
retardation
- Patau syndrome (trisomy 13): many severe physical defects
- Edwards syndrome (trisomy 18): many severe physical defects

Meiotic errors creating autosomal aneuploidies arise more often in the mother than the father and
the frequency increases with maternal age. Why? Prolonged meiotic arrest (in meiosis 1) in
females from before birth to when the oocyte matures (ovulation) and is fertilized (15-50 years
later).

Risk of down syndrome increases proportionally with mothers age, especially after age 35
Other risk factor for aneuploidy: failure of the chromosomes to cross over in meiosis, also
increased risk with increased age. The crossover ties the homologs together. Why dont they
come apart when the spindle fibers first pull on the kinetochores? The sister chromatids are still
held together by cohesion.

NOTES FROM 9C ON

Properties of LUCA:
- DNA genome
- Cellular, with a lipid bilayer membrane
- Protein synthesis
o rRNA ribosome machinery
o mRNA template
o tRNA adapters
o standard genetic code
- catalysis by proteins
- many modern biochemical pathways

Essential properties of living things:
- reproduction
- heredity
- heritable variation (affecting survival or reproduction
Natural selection!

Fundamental paradox: protein synthesis requires ribosomes-complex protein/RNA machines.
How could proteins evolve before there were proteins to synthesize them?
Catalytic RNAs resolve the paradox. RNAs can be enzymes and they are simple enough that
they can arise by chance.

Mitochondria:
- Structurally: membrane-bound organelles inside our cells (like tiny cells within cells).
Usually many per cell
- functionally: contain the proteins that generate cellular energy molecules by combining
break-down products of food with oxygen
- Evolutionarily: reduced forms of bacterial endosymbionts that live and replicate within
our cells. Many eukaryote organisms have endosymbiotic bacteria living in their cells (as
well as those bacteria living on their surfaces). In an eraly ancestor cell (more than 1
billion years ago) one endosymbiont was domesticated and became essential for energy
metabolism. Since then it gradually lost almost all genes from its DNA-some because
they werent necessary in the new environment, others because copies were picked up by
the host cells chromosomes
- genetically: DNA molecules inherited when the mitochondrion replicates eroding a few
of the proteins needed for mitochondrial function
a typical human cell has about 100 mitochondria, with about 500 mtDNA

The problem of heteroplasmy
- complete loss of mitochondrial function is lethal
- the mtDNAs of a cell with a itochondrial mutation are always a mixture of normal and
mutant molecules. The proportions vary widely
- so the severity of mtDNA mutant phenotypes is hard to predict

Solutions:
1. Pre-implantation genetic diagnosis (implant only healthy embryos) but, cant produce
embryos free of the mutations, just ones with a relatively high fraction of normal
mtDNA. Also, different embryo cells have different fractions of mutant mtDNA
2. egg with mutant mt from mother, take nucleus put in enucleated donor egg and fertilize
with fathers sperm

Epigenetics: mechanisms of gene regulation that can be stably inherited through mitosis and
(sometimes) meiosis, but can be established and released without changing the DNA sequence.

Functions of epigenetic regulation
- all our cells contain the same genes
- different cells and tissues differ in which genes they express
- these differences are created and maintained by gene regulation, not by changes in DNA
sequence
-