Populations

Gregor Mendel was a 19th century monk, who performed hybridization experiments
with pea plants.

He found that when he crossed purple flowered plants with white flowered plants, the
first filial, or F1 generation, produced purple flowers. He called the purple trait
dominant, and the white trait recessive.

When Mendel self-pollinated the F1 generation plants, the F2 generation expressed

both the dominant and recessive traits in a 3:1 ratio, now referred to as the Mendelian
ratio.

The expression of a trait is the phenotype and an individual’s genetic make up is the
genotype.
 Note: The phenotype is expressed through the action of enzymes and other
structural proteins. Which are encoded by genes.

A diploid individual (having homologous chromosomes) will have two chromosomes

each containing a separate gene that codes for that specific one trait. These two
chromosomes are homologous by definition.

Their corresponding genes are located at the same locus or position on the respective
chromosomes. Each gene contributes an allele to the genotype.

- An allele is an alternative form of a gene (one member of a pair) that is

located at a specific position on a specific chromosome

- Alleles are prominently represented in a Punnett square.

Note: The Punnett square is a diagram that is used to predict the outcome of a
particular cross or breeding experiment.
 A Punnett square showing a typical monohybrid cross

However, only the dominant allele is expressed if there is a dominant and a

recessive allele. If both alleles are dominant the dominant phenotype is expressed. If
both alleles are recessive the recessive phenotype is expressed.

An individual with a genotype having two dominant or two recessive alleles is said
to be homozygous for that trait

An individual with a genotype having one dominant or one recessive allele is said
to be heterozygous for that trait, and is called a hybrid.

Ex. F1 generation above is heterozygous

Mating relatives is called inbreeding.

- Inbreeding increases the frequency of individuals with deleterious

recessive genetic diseases!!

- It does NOT change the frequency of alleles!!

a) Each allele of a gene accounts for a percentage of the total

number of gene copies, and that percentage is known as the
allele frequency
 - It also does change genotype frequencies (it will increase the
number of homozygous individuals within a population)!!

Outbreeding, or outcrossing, is the mating of nonrelatives which produces hybrids or

heterozygotes!!

Anticipation is a phenomenon whereby the symptoms of a genetic disorder become

apparent at an earlier age as it is passed on to the next generation!!

Penetrance is the frequency that a genotype will show up in the phenotype.

- Highly penetrant alleles, and highly heritable symptoms, are easier to

demonstrate, because if the allele is present, the phenotype is generally
expressed. Mendelian genetic concepts such as recessiveness, dominance, and
co-dominance are fairly simple additions to this principle.

- Alleles which are highly penetrant are more likely to be noticed by clinicians
and geneticists, and alleles for symptoms which are highly heritable are more
likely to be inferred to exist, and then are more easily tracked down.

Expressivity is to what degree a penetrant gene is expressed!!

- This differs from penetrance in that penetrance refers to the likelihood of the
gene generating any phenotype at all, while expressivity refers to the
influence of an expressed gene in individuals!!

Genetic leakage is when genes flow from one species to another!!

- This is a concern for things like GM foods or antibiotic resistance, where

genes are able to cross species.

Law of Segregation
The Law of Segregation, also known as Mendel's First Law, essentially has three parts:

1. Alternative versions of genes account for variations in inherited

characteristics. This is the concept of alleles. Alleles are different versions of
genes that impart the same characteristic. For example, each human has genes that
control eye color, but there are variations among these genes in accordance with
the specific color for which the gene "codes".
2. For each characteristic, an organism inherits two alleles, one from each
parent. This means that when somatic cells are produced from two alleles, one
allele comes from the mother and one from the father. These alleles may be the
same (true-breeding organisms/homozygous e.g. ww and rr in the Fig. at the top
of the page), or different (hybrids/heterozygous, e.g. wr).
 3. The two alleles for each characteristic segregate during gamete
production. This means that each gamete (or germ cell) will contain only one
allele for each gene. This allows the maternal and paternal alleles to be combined
in the offspring, ensuring variation.
4. The phenotypic expression of the alleles is not a blend of the two,
but show complete dominance!!

In other words, Alleles segregate independently of each other when forming gametes.
When any individual produces gametes, the copies of a gene separate, so that each
gamete receives only one copy. A gamete will receive one allele or the other!!! So any
gamete is likely to possess any allele.

Since, according to the law of segregation, each gametic genotype is

equally likely, each offspring genotype is also equally likely!!!

When a heterozygous individual exhibits a phenotype that is an

intermediate between its two alleles, the alleles are referred to as partial
or incomplete dominance!!!

- Alleles showing partial dominance are represented with the same

capital letter, and distinguished with a prime or superscript!!

- For instance, a cross between red flowered sweet peas and white flowered
sweet peas may produce pink flowers. The genotype of the pink flowered
individual would be expressed as either CC’ or C^rC^w.

If the heterozygote exhibits both phenotypes, the alleles are codominant!!

Note: Human blood type alleles are codominant because a heterozygote

exhibits A and B antigens on the blood cell membranes. Type
AB blood.

The term “polygenic inheritance” is used to refer to the inheritance of

quantitative traits, traits which are influenced by multiple genes, not just
one!!

- The genes in question are therefore said to be multifactoral

- In addition to involving multiple genes, polygenic inheritance also looks

at the role of environment in someone's development!!
One easily understood example of polygenic inheritance is height. People are not just
short or tall; they have a variety of heights which run along a spectrum. Furthermore,
height is also influenced by environment; someone born with tall genes could become
short due to malnutrition or illness, for example, while someone born with short genes
could become tall through genetic therapy. Basic genetics obviously wouldn't be enough
to explain the wide diversity of human heights, but polygenic inheritance shows how
multiple genes in combination with a person's environment can influence the expression
of the alleles.

Law of Independent Assortment

Mendel concluded that different traits are inherited independently of each other, so that
there is no relation, for example, between a cat's color and tail length.

Genes that code for DIFFERENT traits, when located on DIFFERENT

chromosomes, do not affect each other during gamete formation!!

- The law of independent assortment doesn’t work for genes on the same
chromosome!!

In independent assortment the chromosomes that end up in a newly-formed gamete are

randomly sorted from all possible combinations of maternal and paternal chromosomes.
Because gametes end up with a random mix instead of a pre-defined "set" from either
parent, gametes are therefore considered assorted independently. As such, the
gamete can end up with any combination of paternal or maternal chromosomes!!!

If two genes are located on the same chromosome, the likelihood that will remain
together during gamete formation is indirectly proportional to the distance separating
them. They are said to be linked. Thus, the closer they are on the chromosome, the
more likely they will remain together!!

Linkage mapping is critical for identifying the location of genes that cause genetic
diseases. In an ideal population, genetic traits and markers will occur in all possible
combinations with the frequencies of combinations determined by the frequencies of the
individual genes.

- For example, if alleles A and a occur with frequency 90% and 10%, and
alleles B and b at a different genetic locus occur with frequencies 70%
and 30%, the frequency of individuals having the combination AB would
be 63%, the product of the frequencies of A and B, regardless of how close
together the genes are
A linkage map is a genetic map of a species or experimental population that shows the
position of its known genes and/or genetic markers relative to each other in terms of
recombination frequency, rather than as specific physical distance along each
chromosome.

A genetic map is a map based on the frequencies of recombination between markers

during crossover of homologous chromosomes.

- The greater the frequency of recombination/crossover (segregating

independently) between two genetic markers, the farther apart they
are assumed to be. Conversely, the lower the frequency of
recombination between the markers, the smaller the physical
distance between them!!

If 4 genes A, B, C, D occur on same chromosome use the following crossover

frequencies to determine the order of the genes on the chromosome.

A+D= 5%
B+C= 15%
A+C= 30%
C+D= 35%
B+D= 50%

Answer: BCAD

A dihybrid cross is a cross between two F1 offspring of two individuals that differ in
two traits. For example: RRyy/rrYY or RRYY/rryy parents result in F1 offspring that are
heterozygous for both R & Y.

Parents: RYry x RYry

RY Ry rY ry
RY RRYY RRYy RrYY RrYy
Ry RRYy RRyy RrYy Rryy
rY RrYY RrYy rrYY rrYy
ry RrYy Rryy rrYy rryy

The phenotypic ratio of a dihybrid cross is 9:3:3:1

9 will express both dominant alleles (ex. Yellow and round)

-1 will be pure Dominants
-1 will be pure Recessive
 3 will express 1 dominant and 1 recessive allele (ex. Yellow and wrinkled)

3 will express the other 1 dominant allele and other 1 recessive allele (ex.
green and round)

1 will express both recessive alleles (ex. green and wrinkled)

In a dihybrid cross you also get:

- 4 dihybrids (heterozygous for both characteristics)

- 4 dihomozygous (homozygous for both characteristics)

- 8 monohybrids/monohomozygous children

** The parents of a dihybrid cross are identical at the genes of interest **

Here is a great problem set for dihybrid crosses:

http://www.biology.arizona.edu/mendelian_genetics/problem_sets/dihybrid_cross/
dihybrid_cross.html

Sex Chromosomes

The chromosomes of male and females differ. Humans have 46 chromosomes. In

humans, the 23rd pair of chromosomes establishes the sex of the individual, and
each partner is called a sex chromosome. One of the 23rd chromosomes of a male is
abbreviated. Instead of appearing as two Xs in a karyotype (a map of chromosomes),
the chromosome pair appears as an X and a Y.

- Human cells are diploid and have 22 different types of autosomes, each
present as two copies, and two sex chromosomes. This gives 46 chromosomes
in total
- An autosome is a non-sex chromosome!!!

- Male: XY Female:XX

When a gene is found on the sex chromosome, it is called sex-linked. Generally, the
Y chromosome does not carry the allele for the sex-linked trait!!!
Thus, the allele that is carried by the X chromosome in the male is expressed
whether it is dominant or recessive.

Since the female has two X chromosomes, her genotype is found through the rules of
dominance.

But for the hundreds of other genes on the X, are males at a disadvantage in the amount
of gene product their cells produce? The answer is no, because females have only a
single active X chromosome in each cell!!!

During interphase, chromosomes are too tenuous to be stained and seen by light
microscopy. However, a dense, stainable structure, called a Barr body is seen in the
interphase nuclei of female mammals. The Barr body is one of the X chromosomes. Its
compact appearance reflects its inactivity!!!

- So, the cells of females have only one functioning copy of each X-linked
gene….the same as males.
 Recall:

Schematic of the cell cycle. outer ring: I=Interphase, M=Mitosis; inner ring: M=Mitosis,
G1=Gap 1, G2=Gap 2, S=Synthesis; not in ring: G0=Gap 0/Resting.

X-inactivation occurs very early in embryonic development. In a given cell, which of a

female's X chromosomes becomes inactivated and converted into a Barr body
is a matter of chance, Nevertheless, in most cases, the recessive phenotype is
only displayed in homozygous recessive individuals!!

If a female carries a recessive trait on her 23rd pair of chromosome without expressing it
she is called a carrier and has a good chance (50%) of it being expressed in her sons.

Pedigree chart tips

 - The dominants don’t skip generations and the recessives skip generations
- The recessives can skip generations
- The autosomals can appear in either sex
- The X linked dominants appear more in females and the X linked recessives
appear more in males

autosomal dominant inheritance

- A trait can appear in either sex (at least one parent has trait if a child has
trait as well)

- Does not skip generations

autosomal recessive inheritance

- Can appear in either sex

- Homozygous recessive genotype

- Heterozygotes, or carriers, wild type allele masks expression of the mutant

allele

- From the mating of 2 heterozygotes carrying an autosomal recessive disease

gene
a) 25% will have a homozygous normal child
b) 25% risk of having a homozygous affected child
 c) 50% chance of having a heterozygous child who is a carrier.

- ¾ of all children appear phenotypically normal

- Can skip generations

- If both parents affected, then we will see all kids affected as well!!!

X-linked recessive

- Much more common in males, skips generations

- An affected male does not pass the trait to his sons, but produces all
carrier daughters.

X-linked dominant
- Much more common in females because they are twice as likely to be
affected

- Affected father will have all daughters affected!!!

Y-linked inheritance

All sons affected and no daughters affected

Mitochondrial inheritance

Mother passes on disease to all children and males don't pass it on!!!

Evolution
In population genetics, a gene pool is the complete set of unique alleles in a
species or population!!

- A large gene pool indicates extensive genetic diversity, which is associated

with robust populations that can survive bouts of intense selection.

- Meanwhile, low genetic diversity (due to inbreeding and population

bottlenecks) can cause reduced biological fitness and an increased chance
of extinction.

Evolution is a change in the gene pool and NOT the ratio of what genes
are expressed in the phenotype!!
Animals and plants are grouped into several categories which indicate their degree of
relationship, one to another.

These, starting from the general to the specific, are:

 Kingdom
 Phylum
 Class
 Order
 Family
 Genus
 Species

Note: Plants and Fungi use divisions instead of phyla!!!

Within each group there are subgroups, which are unimportant for the MCAT (except for
the subphylum Vertebrate, which is in the phylum Chordata.

Since organisms within the same group have similar genetic structures, they
probably share similar phylogenies (evolutionary history)!!!

- For instance, all mammals belong to the class Mammalia and the phylum
Chordata; thus, all mammals probably share a common ancestor that
they do not share with birds, which are in a different class.

The course of development of an organism from embryo to adult reflects its

evolutionary history!!

The taxonomy is changing, for now we have superkingdoms called domains. There are
three domains: Bacteria, Archaea, and Eukarya.

- Archea is more closely related to Eukarya than Bacteria.

Recall: Archaea do have histones and don’t have peptidoglycan in their

cell walls

Dear King Phylum Came Over For Great Sex - DKPCOFGS

When naming an organism, the genus and species name are given in order. Typically,
they are both written in italics, and the genus is capitalized while the species isn’t.

Species is loosely limited to, but not inclusive of all organisms which can reproduce
fertile offspring with each other!!!
 - In other words if two organisms can reproduce fertile offspring, they
might be the same species!!!

- Another guideline for species is all organisms which can reproduce

selectively fit offspring in the wild!!!

- Organisms of different species may be prevented from producing fit offspring

by such things as:
a) geographic isolation – different geographic locations
b) habitat isolation – same location different habitat
c) seasonal isolation – different mating seasons
d) behavioral isolation – different mating rituals
e) mechanical isolation – physically impossible to mate

The way in which a species exploits its environment is called its niche. No two species
can occupy the same niche indefinitely. The theory of survival of the fittest predicts
that one species will be exploit the environment more efficiently, eventually leading
to the extinction of the other with the same niche!!

The definition of the “fittest” organism in this theory is the organism which can best
survive to reproduce offspring, which will, in turn reproduce offspring and so on
generation after generation.

A trait that is "selected against" is one that is unfavorable for reproductive

success, while one that is "selected for" allows for greater reproductive
success!!

There are two opposing reproductive strategies:

1) r-selection
a) involves producing a large number of offspring that mature rapidly
with little parental care

b) brood mortality is high

c) population growth curves are exponential!!

d) Generally found in unpredictable/rapidly changing environments

affected by density independent factors such as harsh environments
floods, drastic temp changes, short seasons etc.

2) k-selection
a) involves producing a small number of offspring that mature slowly
with parental care
b) population growth curves are sigmoidal!!! Which levels off at a
carrying capacity!!!
 i) Carrying capacity refers to the number of individuals who
can be supported in a given area within natural resource
limits, and without degrading the natural social, cultural and
economic environment for present and future generations.
j) Carrying capacity is a density dependent factor.

c) Generally found where the environment doesn’t change much

Note: A density dependent factor is a factor that depends on population size.

Note: A Density-independent factor affects all populations in similar ways,

regardless of the population size.

Speciation is the process by which new species are formed!!!

- When gene flow ceases between two sections of population,

speciation begins!!! Factors that bring about speciation include geographic,
seasonal, and behavioral isolation

Recall: I thought this was similar. As the embryo develops past the eight cell
stage, the cells become different from each other due to cell-
cell interactions. This process where a cell becomes committed
to a specialized development path is called determination. Cells
become determined to give rise to a particular tissue early on.
The specialization that occurs at the end of development forming
a specialized tissue cell is called differentiation. The fate of a
cell is typically determined early on, but that same cell usually
doesn’t differentiate into a specialized tissue cell until much
later at the end of the development process.

Adaptive radiation occurs when several separate species arise from a single
ancestral species, such as 14 species of Galapagos finches that all evolved
from one ancestor!!!

A species may face a crisis so severe as to cause a shift in allelic frequencie4s of the
survivors of the crisis. This is called an evolutionary bottleneck.

Divergent evolution exists when two or more species evolving from the same
group maintain a similar structure from the common ancestor!!!

- Called a homologous structure!!!

However, two species may independently evolve similar structures in
convergent evolution.

- Such similar structures are said to be analogous or homoplastic!!!

- An example of homoplasticity is the wings evolved by bats and birds; the two
do not share a common ancestor from which they received their wings.

Some phenotypic forms vary gradually within a species, such as height. Other forms are
distinct, like a flower color, either red or white. The occurrence of distinct forms is
called polymorphism!!!

Polymorphism in biology occurs when two or more clearly different

phenotypes exist in the same population of a species — in other words, the
occurrence of more than one form or morph

- Ex. Black or white

Symbiosis
A symbiosis is a relationship between two species.

The relationship can be one of 3 types of symbiotic relationships:

1) Mutualism – benefits both parties involved
2) Commensalism – benefits 1 party but doesn’t harm the other party
3) Parasitism – benefits 1 party at the expense of the others health

There is even a symbiosis called enslavement where one species enslaves another.

Hardy-Weinberg Equilibrium
Describes how less frequent alleles might be maintained in a population!!!

A population in Hardy-Weinberg Equilibrium has 5 properties:

1) Large population
2) mutational equilibrium
3) immigration or emigration must not change the gene pool
4) random mating
5) no selection of the fittest organism

and a population with these characteristics has no change in the gene pool/genetic drift

Genetic drift is where one allele may be permanently lost due to death of all
members having that allele!!!
Genetic drift is not caused by selective pressure!!!

- Its results are random in evolutionary terms.

- when only 1 allele is present in a population, genetic drift cannot alter the
allele frequency because it has no place to drift to

The binomial theorem:

p^2 +2pq + q^2 = 100% or 1

Predicts the genotype frequency of a gene with only two alleles in a population in
Hardy-Weinberg equilibrium. Imagine that ‘A’ is the dominant allele and ‘a’ is the
recessive allele, and they are the only alleles for a specific gene. Now imagine that 80%
of the alleles are ‘A’. This means that 80% of the gametes will be ‘A’ and 20% will be
‘a’. The probability that the two ‘A’s come together is simply .8^2=0.64. The
probability that two ‘a’s come together is .2^2 = 0.04. Any remaining zygotes will be
heterozygous, leaving 32% heterozygotes. (2 x 0.8 x 0.2 = 0.32).

The final three possible genotypic frequencies in the offspring become:





Using the formula, we represent ‘A’ as p and ‘a’ as q. Since there are only two alleles:

p+q=1

Origin of Life

Our solar system is 4.6 billion years old. The earth itself is about 4.5 billion years old;
however, due to the volatile nature of early earth, there are no rocks on earth older than
3.9 billion years old.

Early earth probably had an atmosphere made mainly from nitrogen and hydrogen gas,
and very little oxygen gas. One theory holds the atmosphere contained clouds of
H2S, NH3, and CH4 creating a reducing environment. The Urey-Miller
experiments attempted to recreate the atmosphere of early earth and resulted in the
autosynthesis of molecules such as urea, amino acids, and even adenine.
The first cells are thought to have evolved from coacervates, lipid or protein bilayer
bubbles. Coacervates spontaneously form and grow from fat molecules suspended in
water.

Organisms may have initially assimilated carbon from methane and CO2!!

Recall:
1) Autotrophs are organisms that are capable of using CO2, as their sole source
of carbon
2) Heterotrophs use preformed, organic molecules as their source of carbon.

Organisms can be classified as well according to how they get their energy:

1) Phototrophs use light as their energy source.

a) Ex. Cyanobacteria – blue/green algae that uses photosynthesis.

Note: Only prokaryotes can acquire energy from an inorganic

source other than light.

2) Chemotrophs use the oxidation of organic and inorganic matter as their

energy source

Electrons or hydrogens can be acquired from inorganic matter by lithotrophs, or organic

matter by organotrophs.

Note: Humans are chemoheterotrophs

Note: All known chemoautotrophs are prokaryotes.

The earliest organisms were probably heterotrophs subsisting on preformed organic

compounds in their immediate surroundings. As preformed molecules became scarce,
some of these organisms developed chemosynthetic autotrophy followed by
photosynthetic autotrophy.

Around 2.3 billion years ago, the ancestors of cyanobacteria evolved. They were able
to use sunlight and water to reduce carbon dioxide. These were the first oxygen
producing, photosynthetic bacteria. The atmosphere began to fill up with oxygen.

Chordate Features

Chordata is the phylum containing humans!!!

Chordata doesn’t mean backbone.

- Vertebrate is a subphylum of Chordata
Chordates are defined as organisms that possess a structure called a notochord, at
least during some part of their development. The notochord is a rod that extends most
of the length of the body when it is fully developed. Lying dorsal to the gut but ventral to
the central nervous system, it stiffens the body and acts as support during locomotion.
Other characteristics shared by chordates include the following:

 bilateral symmetry
 segmented body, including segmented muscles
 three germ layers and a well-developed coelom.
 single, dorsal, hollow nerve cord, usually with an enlarged anterior end (brain)
 tail projecting beyond (posterior to) the anus at some stage of development
 pharyngeal pouches (gills) present at some stage of development
 ventral heart, with dorsal and ventral blood vessels and a closed blood system
 complete digestive system
 bony or cartilaginous endoskeleton usually present

They are deuterostomes, meaning their anus develops from or near the blastopore.
(Compare protostomes, where the mouth develops from or near the blastopore).

Chordates have a coelom (a body cavity within mesodermal tissue)!! At some stage
of their development they possess a notochord (an embryonic axial support, not the back
bone), pharyngeal slits (gills), a dorsal, hollow nerve cord, and a tail.

Members of the subphylum Vertebrata have their notochord replaced by a segmented

cartilage or bone structure. They have a distinct brain enclosed in a skull. Most
chordates are vertebrates.