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JULY 6_CORE CONCEPTS IN GENETICS

A. Analyze the major points of Mendel’s experiments

A.1 Introduction (notes adopted and modified after Gallant 2014)

1. Gregor Mendel (1822-1884) was an Augustinian monk in Austria who experimented with garden peas
and developed the foundation of modern genetics. He noticed that peas have several traits and always
showed only one pair (e.g. yellow and green pods) rather than blend which was previously believed.
He crossed garden peas with different traits to see what the offspring would look like.
2. In a typical breeding experiment, Mendel would cross-pollinate (hybridize) two contrasting, true-
breeding pea varieties (true breeding means that the offspring all have the same trait)
a) The true-breeding parents are the P generation, and their hybrid offspring are the F1
generation (F = filius, Latin for “son”)
b) Mendel would then allow the F1 hybrids to self-pollinate to produce an F2 generation
3. When Mendel crossed a purpled flower plant and a white-flowered plant, the F1 offspring were all
purple.
a) When Mendel allowed the F1 plants to self-fertilize, the F2 generation include both purple-
flowered and white-flowered plants. The white trait, absent in the F1, reappeared in the F2.
b) Mendel reasoned that the heritable factor for white flowers was present in the F1 plants, but
somehow did not affect flower color
c) Purple flower color is a dominant trait, and white flower color is a recessive trait.
d) The offspring were always present in a 3:1 ratio in F2. That is, three showed the dominant
trait for every one showing the recessive trait.
4. Mendel also found out that no matter what combinations he tried, one trait always dominated and
masked the other.
a) It didn’t matter if the trait came from the male or female parent
b) The traits were controlled by factors which later known as genes
5. Mendel worked out a hypothesis consisting of four (4) statements to explain the results he observed.
a) Alternative versions of genes account for variations in inherited traits
(i) These alternative versions are called alleles (short for allelomorph, allos Gk. other;
morph Gk. form). For example, the gene that controls the color of the flowers in Mendel’s
peas has two alleles – purple and white.
(ii) Each gene resides at a specific locus on a specific chromosome.
b) For each trait, an organism inherits two alleles, one from the mother and one from the father.
(i) In homozygous individuals, these two alleles are similar
(ii) In heterozygous individual, these two alleles are different
(iii) An organism’s trait are called its phenotype
(iv) An organism’s genetic make-up is called its genotype
c) If the two alleles for a trait are different, then one, the dominant allele, masks the presence of
the other, recessive allele, and determines the appearance of the organism
(i) It is important to remember that the term “dominant” does not mean that the allele is the
most common in the population. The recessive allele might be more common.
d) Mendel’s law of segregation states that the “two alleles for a trait separate during gamete
formation / production and end up in different gametes”. The law of independent
assortment says that the alleles segregate independently from one another.
(i) If an organism has two identical alleles for a particular trait, then that allele is present as
a single copy in all gametes.
(ii) If different alleles are present, then 50% of the gametes will receive one allele and 50% of
the gametes will receive the other.

A.2 Mendel’s first experiment considered only one (1) trait

1. An individual that is heterozygous for one trait is called a monohybrid and a cross between two
heterozygotes is called a monohybrid cross

e.g. round seed x wrinkled seed

P : RR x rr
Gametes: R , R r , r
F1 : Rr (all round)

use two F1 individuals as new parents (P)

P : Rr x Rr
Gametes: (2 types) R , r (2 types) R , r
F1genotypic ratio: 1:2:1
F2 : RR, Rr, Rr, rr F1 phenotypic ratio: 3:1

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2. A Punnet square can be used to show genotype, phenotype and probability

e.g. heterozygote purple (Pp) x white (pp)

p p F1genotypic ratio: 2:2 or 1:1

P Pp Pp F1 phenotypic ratio: 2:2 or 1:1
p pp pp

Result: F1 1 purple: 1 white

e.g. two heterozygous tall plants (Tt)

T t F1genotypic ratio: 1:2:1

T TT Tt F1 phenotypic ratio: 3:1
t Tt tt

Result: F1 3 tall: 1 short

3. Test cross
a) Imagine that you have an organism showing a dominant phenotype. Is the individual
homozygous or heterozygous? To be able to say for certain, a test cross is performed.
b) The unknown individual is crossed with a homozygous recessive individual
c) The genotype of the unknown parent can be deduced from the appearance of the offspring.

A.3 Mendel later wondered if traits always go together or if they were inherited separately

1. To answer the question, he considered two traits at once – and this is what we refer to as the
dihybrid cross
a) In one cross, he studied the inheritance of seed color and seed shape.
(i) The allele for yellow seeds (Y) is dominant to the allele for green seeds (y)
(ii) The allele for round seeds (R) is dominant to the allele for wrinkled seeds (r)
b) Mendel crossed true-breeding plants that had yellow, round seeds (YYRR) with true-breeding
plants that has green, wrinkled seeds (yyrr)
c) Case 1: If the two traits are transmitted from parents to offspring as a package, the F1
offspring would produce yellow, round seeds. The F2 offspring would produce two
phenotypes (yellow+round; green+wrinkled) in a 3:1 ratio, just like a monohybrid cross.
d) Case 2: If the alleles separated independently from one another, we should observe four
different combinations. The four different kinds of sperm and four different kinds of eggs
should give 16 different combinations in the offspring.
e) Mendel found a 9:3:3:1 ratio in the F2 generation

2. Thus, case 2 is accepted. Traits are indeed inherited independently.

Parent (Generation1): yellow, round seeds (YYRR) x green, wrinkled seeds (yyrr)
Gametes : only one type, YR x only one type, yr
FI : YyRr (all yellow, round seeds)

Parent (Generation2): (F1) YyRr x (F1) YyRr [self-cross]

Gametes : 4 types: YR, Yr, yR, yr x 4 types: YR, Yr, yR, yr
F2 :

YR Yr yR yr

YR YYRR YYRr YyRR YyRr

Yr YYRr YYrr YyRr Yyrr

yR YyRR YyRr yyRR yyRr

yr YyRr Yyrr yyRr yyrr

F2 genotypic ratio : 1:2:2:2:1:2:1:2:2:1

F2 phenotypic ratio : 9/16 yellow, round seeds

3/16 yellow, wrinkled seeds 9:3:3:1
3/16 green, round seeds
1/16 green, wrinkled seed

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A.4 Mendelian inheritance is governed by laws of probability (Campbell and Reece, 2005)

1. The probability scale ranges from 0 to 1, where 0 means that there is no chance the event will occur
and 1 means the event will occur every time.

a. Probability can be calculated using the equation:

no. of correct outcomes
P= _____________________________
no. of total outcomes
b. The probability of tossing heads with a coin is 1/2
c. The probability of rolling a 3 with a 6-sided die is 1/6, and the probability of rolling any other
number is 1- 1/6 = 5/6
2. If the outcome of one event has no effect on the outcome of future events, they are said to be
independent events, e.g. the chance of getting heads in a coin toss is 1/2 ; the chance of getting heads
a second time is still 1/2
3. The rule of multiplication can be used to determine the chance that two or more independent events
will occur together in some specific combination.
a. Calculate the probability of each independent event
b. Multiply the individual probabilities to obtain the overall probability of these events occurring
together
c. The probability that two coins tossed at the same time will land heads up is 1/2 x 1/2 = 1/4
d. Similarly, the probability that a heterozygous pea plant (Pp) will self-fertilize to produce a white
flowered offspring (pp) is the chance that a sperm with a white allele will fertilize an ovum with a
white allele
e. This probability is 1/2 p [sperm] x 1/2 p [ovum] = 1/4 pp [offspring]
f. The rule of multiplication also applies to dihybrid crosses
(i) For heterozygous parents (YyRr), the probability of producing a YR gamete is
1/2 x 1/2 = 1/4.
(ii) The probability that an F2 plant from heterozygous parents [YyRr x YyRr] will have a
YYRR genotype is 1/16. Why? The probability to produce a YR sperm is 1/4 and the
probability to produce a YR ovum is also 1/4. Note that there are 4 gametes for each
parent.
4. The rule of addition also applies to genetic problems.
a. The chance of either one of the two possible outcome occurring is the sum of the two individual
probabilities.
(i) Example 1, there are two ways that F1 gametes can combine to form a heterozygote [e.g.
YyRr]
(ii) The dominant allele could come from the sperm [YR] and the recessive allele [yr] from
the ovum [probability = ¼]
(iii) Or the dominant allele could come from the ovum [YR] and the recessive allele [yr] from
the sperm [probability of ¼]
(iv) The probability of obtaining a heterozygote is 1/4 + 1/4 = ½
(v) Example 2, from the same dihybrid cross presented above where both parents are
heterozygotes, what is the probability that a YYrr and yyrr offspring will come out in F2?
The probability of YYrr is 1/16 and yyrr is 1/16. Hence, by following the rule of addition,
we have 1/16 + 1/16 = 2/16 or 1/8 chance that both genotypes will come out in the F2
offspring. Note that each offspring represents an “individual probabilities”

A.5 Were garden peas (Pisum sativum) considered a true-breeding variety?

For his experiments, Mendel chose plants that were true-breeding. This means that when the
plant was self-fertilized (or cross-fertilized with others like it), the offspring always had the same
traits as the parent plant. (Finding these true-breeding plants took two years of experimentation and
an enormous amount of record keeping.) During his experiments, Mendel ensured that the plants he
was using would not self-fertilize, as would occur in nature, by removing their stamens (the pollen-
producing structures) before they produced pollen. In this way, he could control the matings among
the pea plant parents (the P generation or F0) by taking pollen from a flower from one plant and
using it to fertilize the flower of another plant. The resulting seeds were the offspring of those two
chosen plants. He carefully controlled these breeding events and tracked the traits of every parent
and each offspring through many generations (Nature Education 2014)

A.6 Pea plants were a very good choice as a model organism

Why did Mendel choose pea plants to investigate inheritance? It is likely that he knew these
plants well, and he had observed them for some time before setting out to do his controlled
experimental breeding. Some advantages of this species compared to some others he could have used
were that pea plants:
 were inexpensive;
 were easy to grow from seed;
 grew rapidly;
 produced many seeds in a short time;

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 had observable alternate forms of several traits that were heritable (such as purple
versus white flowers or round versus wrinkled seeds); and
 were easy to artificially fertilize.
Tracking the patterns in several generations of organisms is not easy, and this endeavor was well
served by Mendel's choice of the pea plant as his model organism. Much like scientists of today who
often choose a simple worm or fly for their laboratory experiments, Mendel used an organism he
knew well and whose characteristics were fairly simple to track with the techniques available to him
at that time (Nature Education 2014)

B. Describe the roles of chromosomes in heredity

1. Around 1900, cytologist and geneticists began to notice connections between the behavior of
chromosomes and the behavior of genes.
a. Chromosomes and genes are both present in pairs in diploid cells
b. Homologous chromosomes separate and alleles segregate during meiosis
c. These observations led to the development of the chromosome theory of inheritance
(i) Genes occupy specific loci on chromosomes
(ii) Chromosomes undergo segregation during meiosis
(iii) Chromosomes undergo independent assortment during meiosis
d. The behavior of homologous chromosomes during meiosis can account for the segregation of
the alleles at each genetic locus to different gametes
e. The behavior of non-homologous chromosomes can account for the independent assortment of
alleles for two or more genes located on different chromosomes
f. Fertilization restores chromosomes and genes to pairs

2. Duplicated vs. unduplicated chromosomes (Fig. 1)

Chromosomes are thread-like structures located inside the nucleus of living cells. Each
chromosome is made of protein and a single molecule of deoxyribonucleic acid (DNA). Passed from
parents to offspring, DNA contains the specific instructions that make each type of living creature
unique (http://www.genome.gov/26524120).
Chromosomes either have one or two molecules of DNA plus associated proteins. A chromosome
with one molecule of DNA (i.e. one copy) is called an unduplicated chromosome because it only
contains one molecule of DNA (i.e. single linear strand of DNA). On the other hand, a duplicated
chromosome contains two identical DNA molecules (i.e. two copies), one is the template and the
other is the daughter strand (review semi-conservative form of DNA replication). Some texts refer to
these as unreplicated vs replicated chromosomes, respectively. In the case of a duplicated
chromosome, each molecule of DNA and associated proteins is called a sister chromatid.

Fig. 1. Difference between unduplicated and duplicated chromosomes

showing the genes.

3. Chromatid vs. Chromosome

Remember that when two DNA molecules are joined together, each will represent a chromatid
and both chromatids (called sister chromatids) when joined at the centromere is now considered a
duplicated chromosome. When a DNA molecule (and proteins) is not attached to one another, the
single molecule of DNA will not represent a chromatid but an unduplicated chromosome.

4. Centromere
When a chromosome is examined during mitosis or meiosis there is a pinched in region
somewhere along the length of the chromosome called the centromere. The centromere is a region to
which the spindle fibers attach to the chromosome and it is in a characteristic position that is constant
for different types of chromosomes. Thus the centromere is important for studying and identifying
chromosomes.

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5. Homologous chromosomes
Homologous chromosomes are chromosome pairs, one from each parent, that are similar in
length, gene position and centromere location. However, alleles from each homologue may or may not
be similar for each gene locus considered.

Paternal
chromosome

Maternal
chromosome

Fig 2. Homologous chromosome showing a locus for

flower color gene (with two alleles, purple and white)

6. Autosomes vs Sex Chromosomes

a. Autosome refers to those chromosomes that are not involved in sex determination. Human
diploid cells have 22 pairs of autosomes and 1 pair of sex chromosomes.
b. Sex chromosomes are chromosomes involved in sex determination. Human females have XX sex
chromosome while human males have XY sex chromosomes. Male birds are typically ZZ and
female birds are ZW.
c. In humans, X and Y chromosomes are not strictly homologous. Normally, the X chromosome is
bigger than the Y chromosome and most of the genes on the X chromosome do not have
corresponding genes on the Y chromosome. However, in the XY sex chromosomes of human male,
though non-homologous, they still behave as homologue during meiosis.

C. Describe the effects of dominance and recessiveness in heredity

[ see section A]

D. Solve basic problems on heredity, sex-linked characters, incomplete dominance, codominance and
polygenic inheritance

1. Not all traits follow the simple rules of Mendelian inheritance (i.e. complete dominance). Some alleles
show different degrees of dominance and recessiveness in relation to each other.
a. In codominance, both alleles are expressed and affect the phenotype.
(i) The heterozygote phenotype appears to be a blend of the two homozygous phenotypes
(ii) An example is roan cattle. A cross between a red bull and a white cow yields roan calves.
The calves appear reddish in color but on closer inspection, they have both red and white hairs. In
other words, both alleles are expressed.
b. In incomplete dominance, the phenotype is also a blend of both alleles.
(i) The offspring of a cross between heterozygotes show three (3) phenotypes: each from the
parental phenotype and a blended phenotype.
(ii) An example is seen in flower color of snapdragons
- A cross between a white flowered plant and a red-flowered plant will produce all pink F1
offspring
- Self pollination of the F1 pink-flowered offspring produces 25% white, 25% red and 50%
pink F2 offspring
(iii) A 1:2:1 phenotypic ratio is a characteristic of incomplete dominance
c. Some traits, like the ABO blood group in humans, are controlled by genes for which more than
two alleles exist. This is called multiple alleles.
(i) Remember that, even if more than two alleles exist in the population, each individual only
possess two alleles – each inherited from both parents
(ii) Example: Type AB phenotype in human blood groups has a genotype of IAIB
d. In epistasis, one gene affects the phenotypic expression of a separate gene.
(i) For example, in mice and many other mammals, coat color depends on two genes.
(ii) One, the epistatic gene, determines whether pigments will be deposited in hair or not.
Presence of (C) is dominant to absence (c) of pigment
(iii) The second gene determines whether the pigment to be deposited is black (B) or brown
(b)
(iv) Thus, an individual that is cc has a white coat (albino), regardless of the genotype of the
second gene
e. Some traits appear to be distributed across a spectrum, like skin color or height. These are
examples of polygenic inheritance.
(i) Skin color in humans is controlled by a t least three independent genes
(ii) An AABBCC individual is very dark; an aabbcc individual is very light.

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f. Sex-linked traits (http://biology.about.com/od/genetics/ss/sex-linked-traits.htm)

(i) Genes that are found on the sex chromosomes are called sex-linked genes. These genes
can be on the X chromosome or on the Y chromosome. If a gene is located on the Y
chromosome, it is a Y-linked gene. These genes are only inherited by males because, in
most instances, males have a genotype of (XY). Females do not have the Y sex
chromosome. Genes that are found on the X chromosome are called X-linked genes.
These genes can be inherited by both males and females. Since genes for a trait may have
two forms or alleles, one allele is usually dominant and the other is recessive. Dominant
traits mask recessive traits in that the recessive trait is not expressed in the phenotype.
(ii) In X-linked recessive traits, the phenotype is expressed in males because they only
contain one X chromosome. The phenotype may be masked in females if the second X
chromosome contains a normal gene for that same trait. An example of this can be seen in
hemophilia. Hemophilia is a blood disorder in which certain blood clotting factors are
not produced. This result in excessive bleeding that can damage organs and tissues.
Hemophilia is an X-linked recessive trait caused by a gene mutation. It is more often seen
in men than women. For instance, when the mother is a carrier and the father does not
have the trait, the following will be produced: the sons have a 50/50 chance of inheriting
the trait and the daughters have a 50/50 chance of being carriers of the trait. If a son
inherits an X chromosome with the hemophilia gene, the trait will be expressed and he
will have the disorder. If a daughter inherits the mutated X chromosome, her normal X
chromosome will compensate for the abnormal chromosome and the disease will not be
expressed.

Parent: (Father, normal) XHY x (Mother, carrier) XHXh

Gametes: XH , Y XH , Xh
F1:
Mother
Father
XH Xh

XH XHXH XHXh

Y XHY XhY

F1 genotypic ratio for sons:

25% normal (XHY); 25% hemophilic, expressed (XhY)

F1 genotypic ratio for daughters:

50% normal (XHXH) & (XHXh) but XHXh is a carrier

(iii) In X-linked dominant traits, the phenotype is expressed in both males and females who
have an X chromosome that contains the abnormal gene. If the mother has one mutated X
gene (she has the disease) and the father does not, the sons and daughters have a 50/50
chance of inheriting the disease. If the father has the disease and the mother does not, all
of the daughters will inherit the disease and none of the sons will inherit the disease.
(iv) There are several disorders that are caused by abnormal sex-linked traits. In addition to
hemophilia, color blindness, Duchenne muscular dystrophy, and fragile-X syndrome
are examples of X-linked recessive disorders. A common Y chromosome linked disorder
is male infertility.

2. Mendelian Crosses Made Easy - A step-by-step guide

a. Determine the traits to be used.
b. Know how the alleles are expressed, which is dominant, which is recessive, etc.
c. Establish a letter symbol for each trait. Use upper case and lower case letters for the
dominant and recessive alleles, respectively. You may have to use an alternative method
for incomplete dominance or codominance.
d. Determine the genotypes of the parents. Keep alleles for each gene together and always
write dominant alleles first.
e. Determine the gametes that are produced by the parents. Remember that each parent
makes their own gametes. Also, each gamete has to get one allele of each gene (i.e. one
letter from each trait).
f. Use random fertilization to combine the gametes in all possible combinations. A Punnett
square can be used.
g. Determine the genotypes and phenotypes of the offspring.

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3. How to Solve Genetics Problems - things to keep in mind

a. If an individual shows the recessive trait, you know s/he is homozygous recessive.
b. If an individual expresses a dominant trait that individual has at least one dominant
allele.
c. If an intermediate phenotype or blending of phenotypes is observed, expect incomplete
dominance or codominance.
d. If a trait expresses itself disproportionately in males or females, suspect sex-linkage.
e. Monohybrid heterozygous crosses result in 3:1 phenotypic ratios.
f. Dihybrid heterozygous crosses result in 9:3:3:1 phenotypic ratios.
g. Incomplete dominance and codominance result in 1:2:1 phenotypic ratio.

5. A pedigree chart a diagram that shows the occurrence and appearance or phenotypes of a particular
gene or organism and its ancestors from one generation to the next.
a. In a pedigree, squares represent males and circles represent females. Horizontal lines
connecting a male and female represent mating. Vertical lines extending downward from
a couple represent their children. Subsequent generations are therefore written
underneath the parental generations and the oldest individuals are found at the top of
the pedigree.
b. If the purpose of a pedigree is to analyze the pattern of inheritance of a particular trait, it
is customary to shade in the symbol of all individuals that possess the trait.

E. Explain the role of environment on inheritance (see J. Evolution)

1. Genotype + Environment = Phenotype
2. Physical characteristics and other aspects of health, growth and development are due to the
interaction of genetic and environmental factors.

F. Describe the nature, expression and regulation of gene action.

Reference: Lectures adopted from University of Leicester Virtual Genetics Education Center
1. Gene expression is the process by which the genetic code, i.e. the nucleotide sequence of a gene is
used to direct protein synthesis and produce the structures of the cell. Genes that code for amino acid
sequences are known as structural genes.
2. The process of gene expression involves two main stages:
a. Transcription: the production of messenger RNA (mRNA) by the enzyme RNA polymerase, and
the processing of the resulting mRNA molecule.
b. Translation: the use of mRNA to direct protein synthesis, and the subsequent post-translational
processing of the protein molecule
3. Some genes are responsible for the production of other forms of RNA that play a role in translation,
including transfer RNA (tRNA) and ribosomal RNA (rRNA).
4. A structural gene involves a number of different components:
a. Exons. Exons code for amino acids and collectively determine the amino acid sequence of the
protein product. It is these portions of the gene that are represented in final mature mRNA
molecule.
b. Introns. Introns are portions of the gene that do not code for amino acids, and are removed
(spliced) from the mRNA molecule before translation

Fig. 3 Structural genes and

components

5. Gene control regions

a. Start site. A start site for transcription.
b. A promoter. A region a few hundred nucleotides 'upstream' of the gene (toward the 5' end). It is
not transcribed into mRNA, but plays a role in controlling the transcription of the gene.
Transcription factors bind to specific nucleotide sequences in the promoter region and assist in
the binding of RNA polymerases.

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c. Enhancers. Some transcription factors (called activators) bind to regions called 'enhancers' that
increase the rate of transcription. These sites may be thousands of nucleotides from the coding
sequences or within an intron. Some enhancers are conditional and only work in the presence of
other factors as well as transcription factors.
d. Silencers. Some transcription factors (called repressors) bind to regions called 'silencers' that
depress the rate of transcription.

Fig. 4 Central Dogma of Molecular Genetics

6. Transcription is the process of RNA synthesis, controlled by the interaction of promoters and
enhancers. Several types of RNA are produced, including messenger RNA (mRNA) which specifies the
sequence of amino acids in the protein product, as well as transfer RNA (tRNA) and ribosomal RNA (r
RNA), which play a role in the translation process. It involves 4 steps:
a. Initiation. The DNA molecule unwinds and separates to form a small open complex. RNA
polymerase binds to the promoter of the template strand (also known as the 'sense strand' or
'coding strand'). The synthesis of RNA proceeds in a 5' to 3' direction, so the template strand must be
3' to 5'.
b. Elongation. RNA polymerase moves along the template strand, synthesizing an mRNA molecule.
In prokaryotes RNA polymerase is a holoenzyme consisting of a number of subunits, including
a sigma factor (transcription factor) that recognizes the promoter. In eukaryotes there are three RNA
polymerases: I, II and III. The process includes a proofreading mechanism.
c. Termination. In prokaryotes there are two ways in which transcription is terminated. InRho-
dependent termination, a protein factor called "Rho" is responsible for disrupting the complex
involving the template strand, RNA polymerase and RNA molecule. In Rho-independent
termination, a loop forms at the end of the RNA molecule, causing it to detach itself. Termination in
eukaryotes is more complicated, involving the addition of additional adenine nucleotides at the 3' of
the RNA transcript (a process referred to as polyadenylation).
d. Processing. After transcription the RNA molecule is processed in a number of ways: introns are
removed and the exons are spliced together to form a mature mRNA molecule consisting of a single
protein-coding sequence. RNA synthesis involves the normal base pairing rules, but the base thymine
is replaced with the base uracil.

Image source: http://biomoocnews.blogspot.com/2013_11_01_archive.html

Fig. 5 Comparison of transcription process in (a) prokaryote and (b) eukaryote

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7. In translation, the mature mRNA molecule is used as a template to assemble a series of amino acids
to produce a polypeptide with a specific amino acid sequence. The complex in the cytoplasm at which
this occurs is called a ribosome. Ribosomes are a mixture of ribosomal proteins and ribosomal RNA (r
RNA). Translation process has 4 steps:
a. Initiation. The small subunit of the ribosome binds at the 5' end of the mRNA molecule and moves
in a 3' direction until it meets a start codon (AUG). It then forms a complex with the large unit of
the ribosome complex and an initiation tRNA molecule.
b. Elongation. Subsequent codons on the mRNA molecule determine which tRNA molecule linked to
an amino acid binds to the mRNA. An enzyme peptidyl transferase links the amino acids together
using peptide bonds. The process continues, producing a chain of amino acids as the ribosome
moves along the mRNA molecule.
c. Termination. Translation in terminated when the ribosomal complex reached one or more stop
codons (UAA, UAG, UGA). The ribosomal complex in eukaryotes is larger and more complicated
than in prokaryotes. In addition, the processes of transcription and translation are divided in
eukaryotes between the nucleus (transcription) and the cytoplasm (translation), which provides
more opportunities for the regulation of gene expression.
d. Post-translation processing of the protein

Image source: http://biosiva.50webs.org/translation.htm

Fig. 6 Stages of translation (protein synthesis)

7. Gene regulation is a label for cellular processes that control the rate and manner of gene expression. A
complex set of interactions between genes, RNA molecules, proteins (including transcription factors) and
other components of the expression system determine when and where specific genes are activated and
the amount of protein or RNA product are produced.
a. Some genes are expressed continuously, as they produce proteins involved in basic metabolic
functions; some genes are expressed as part of the process of cell differentiation; and some genes are
expressed as a result of cell differentiation.
b. Mechanisms of gene regulation include:
 Regulating the rate of transcription. This is the most economical method of regulation.
 Regulating the processing of RNA molecules, including alternative splicing to produce more than
one protein product from a single gene.
 Regulating the stability of mRNA molecules.
 Regulating the rate of translation.
8. Transcription factors are proteins that play a role in regulating the transcription of genes by binding
to specific regulatory nucleotide sequences.

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G. Identify some genetic disorders

Reference: http://www.zo.utexas.edu/faculty/sjasper/images/t11.3.jpg

H. Identify the causes of mutations (Campbell and Reece, 2005; Freeman 2005; Hartl and Jones 2005)

http://www.biologyisfun.com/genetics/mutations http://www.pleasanton.k12.ca.us/avhsweb/thiel/apbio/labs/non_mendel.html

http://monag9a.files.wordpress.com/2013/12/mutation-dna-sequence.gif
http://www.cancer.gov/PublishedContent/Images/cancertopics/understandingcancer/estrogenreceptors/slide10.gif

1. What is mutation? A heritable alteration in a gene or chromosome; and it is the process by which
such an alteration happens.
2. Causes of Mutation
a. Spontaneous mutation occurs without exposure to any obvious mutagenic agent.
Sometimes, DNA nucleotides shift to a different chemical form (know as an isomer)
which in turn will form a different series of hydrogen bonds with its partner. This leads
to mistakes at the time of DNA replication
b. UV light
c. X-rays and ionizing radiation

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d. Benzene, formaldehyde, carbon tetrachloride

e. Viruses and microoganism
3. Mutagens and their effect
a. Ionising radiation – Nuclear radiation, X-rays, gamma rays (e.g. medical treatment)
associated with development of cancers (e.g. leukaemia, thyroid cancer and skin cancer).
High energy radiation from a radioactive material or from X-rays is absorbed by the
atoms in water molecules surrounding the DNA. This energy is transferred to the
electrons which then move away from the atom. Left behind is a free radical, which is a
highly dangerous and highly reactive molecule that attacks the DNA molecule and alters
it in many ways. Radiation can also cause double strand breaks in the DNA molecule,
which the cell's repair mechanisms cannot correct.
b. Viruses and microorganisms – once integrated into human chromosome, it can upset
genes and can trigger cancer (e.g. Aspergillus spp)
c. Environmental poisons – organic solvents such as formaldehyde, tobacco, coal tars,
benzene, asbestos, some dyes which eventually causes developmental anomalies in
embryos
d. Chemical mutagens - change the sequence of bases in a DNA gene in a number of ways:
 mimic the correct nucleotide bases in a DNA molecule, but fail to base pair
correctly during DNA replication.
 remove parts of the nucleotide (such as the amino group on adenine), again
causing improper base pairing during DNA replication.
 add hydrocarbon groups to various nucleotides, also causing incorrect base
pairing during DNA replication.
e. Sunlight - contains ultraviolet radiation (the component that causes a suntan) which,
when absorbed by the DNA causes a cross link to form between certain adjacent bases. In
most normal cases the cells can repair this damage, but unrepaired dimers of this sort
cause the replicating system to skip over the mistake leaving a gap, which is supposed to
be filled in later. Unprotected exposure to UV radiation by the human skin can cause
serious damage and may lead to skin cancer and extensive skin tumors
4. The effect of mutation
a. Not all are harmful, some possess selective advantage especially if it’s related to
adaptation and increased survival (e.g. mutation of a gene towards antibiotic resistance
in bacteria)
b. Survival advantage
c. Most common among bacteria and viruses but also seen in insects
d. If no selective pressure, it may remain in the population
 Harmful mutations
e. Cystic fibrosis and sickle cell anaemia
f. Dysfunctional proteins
g. Albinism – caused by mutation in gene of enzyme pathway of melanin
 “Beneficial” mutation
h. Bacteria – antibiotic resistance through mutation, transfer between bacterial species
e.g: Superbugs such as MRSA have arisen this way
b. RNA viruses – such as HIV – mutates its protein coat so that the host human is unable to
make antibodies quick enough against it
5. Neutral mutation
a. Neither harmful or beneficial to the organism but may be important in an evolutionary
sense
b. Silent mutations
c. Virtually impossible to detect because no observable effect

I. Cite contributions of genetics to the field of medicine and agriculture

1. DNA technology and genomics

a. DNA technology has launched a revolution in the area of biotechnology (the
manipulation of organisms or their genetic components to make useful products)
b. DNA cloning permits production of multiple copies of a specific gene or other DNA
segment. To work directly with specific genes, scientists have developed methods for
preparing well-defined, gene-sized pieces of DNA in multiple identical copies, a process
called gene cloning. Through this technology, it was made possible to use the cloned gene
of interest in a wide array of agricultural or biomedical applications such as:
(i) introducing pest-resistance gene in plants,
(ii) alteration of bacterial DNA to be able to use them in cleaning toxic waste,
(iii) protein that dissolves blood clot in the heart [assist in therapy] and
(iv) human growth hormone development which minimizes stunted growth in
young adolescents.

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2. Contribution of genetics to the field of medicine (Campbell and Reece, 2005)

a. Post-genomic genetics has enormous promise for tracking down the genes involved in
common complex diseases
b. One of the greatest achievements of modern science has been the sequencing of the human
genome, which was largely completed by 2003. Scientists have also sequenced genomes of
other organisms and it has provided important insights of general biological significance
c. The practical applications of DNA technology affect our lives in many ways. One obvious
medical benefit of DNA technology is the identification of human genes whose mutation plays
a role in genetic diseases
(i) Medical scientists can now diagnose hundreds of human genetic disorders by using PCR
and primers corresponding to cloned disease genes, then sequencing the amplified
product to look for the disease-causing mutation
d. Application of gene therapy
(i) Gene therapy is the alteration of an afflicted individual’s gene. It holds great potential for
treating disorders traceable to a single defective gene
e. In pharmaceutical products
(i) Application of DNA technology include large-scale production of human hormones and
other proteins with therapeutic uses
(ii) Production of safer vaccines
f. In forensic science and solving crimes
(i) DNA “fingerprints” obtained by analysis of tissue or body fluids found at crime scenes
which can provide definitive evidence that a suspect is guilty or not
(ii) DNA “fingerprints” can also be used in establishing paternity
g. Genetic engineering can be used to modify the metabolism of microorganisms
(i) They can be used to extract minerals from the environment or degrade various types of
potentially toxic waste materials (phytomining and phytoremediation)

3. Contribution of genetics to agriculture (Campbell and Reece, 2005; Freeman 2005)

a. Agricultural Biotechnology includes a range of tools that scientists employ to understand
and manipulate the genetic make-up of organisms for use in the production or processing of
agricultural products
b. Why is AgriBiotech important? In a world where 800 million people, living mostly in rural
areas, go hungry every day, food demand is set to double in the next thirty years and arable
land is limited, advances in agriculture are critical if we are to reduce hunger and promote
growth and development in a socially acceptable and environmentally sustainable way.
c. Current areas of research in AgriBiotech:
i. Crop improvement research / transgenic plants
-Artificial selection: Based on basic Mendelian genetics where two plant types of the same
species are crossed to produce a better plant type, e.g. crossing a plant that has a high
tolerance to disease with a plant that has a high fruit yield gives you a disease resistant
plant with a high fruit yield.
ii. Creating gene banks
- A gene bank is large holding of plant types with their given traits and now with the genes
for these traits genetically marked.
- Crop scientists can now select a variety known to hold a specific characteristic, mark the
gene responsible for the trait and cross it with another variety known to hold a second
desirable characteristic.
- These techniques are simply traditional breeding techniques made more efficient by new
information about genes and new technologies.
- e.g. The United Nations’ gene bank holds over 530,000 samples of wild and domesticated
crops in public trust
iii. Genetic modification / transgenic animals
- Inserted genes from other species into plants/animals in order to increase yields or
protect against pests or environmental conditions.
- They are tested to ensure no adverse environmental or health effects.

J. Explain the mechanisms of evolution

1. Introduction
a. In modern times, we can define evolution as a change over time in the genetic composition of
a population. Evolution also refers to the gradual appearance of all biological diversity.
b. Evolution theory began major steps forward because of the publication of the book “On the
Origin of Species by Natural Selection” by Charles Darwin. Darwin made two major points in
the book:
(i) The basic idea of natural selection is that a population can change over time if individuals
that possess certain heritable traits leave more offspring than other individuals; and

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(ii) Natural selection results in evolutionary adaptation, an accumulation of inherited

characteristics that increase the ability of an organism to survive and reproduce in the
environment.

2. A brief summary of modern genetics and evolution – this highlights the key features of our
current understanding of genetics and evolution (Barton et al., 2007)
a. DNA interacts with the cell and environment to determine the phenotype.
- The DNA sequence alone is meaningless. It must be transcribed into messenger RNA,
tRNA and mRNA. The mRNA is then translated into proteins by the ribosomes. These
proteins must interact with each other, various RNA molecules and the DNA to determine
the timing of gene expression within the cell, the response to the outside world, and the
development of morphology and behavior. This sequence of interactions determines all
the characteristics that we observe – that is, the phenotype.
b. It is the populations that evolve.
- A species is not a single homogenous unit: It is a population of diverse individuals. A
species evolves as the proportions of different kinds of individuals within it change,
rather than in abrupt, discontinuous transitions.
c. Evolution is like a branching tree.
- Populations change, split into separate species and often become extinct. Tracing
forward, most individuals leave no descendants and most species go extinct. Tracing
backward, closely-related species merge in a recent common ancestor, and more
distantly related species share ancestry further back in time.
d. Evolution does not progress towards a goal.
- Populations evolve in response to chance variations and to their changing environment.
This leads to erratic change and to diversification, rather than progress toward any
particular end point.
e. All adaptation is caused by natural selection
- Although there are many causes of evolutionary change, only natural selection can lead to
adaptation – that is, to the complex and finely tuned structures that allow organisms to
survive and reproduce in diverse environments. Organisms are not designed for their
present way of life; rather, their ancestors accumulated variations that were favorable for
reproduction.

3. Evolution by Natural Selection (Freeman , 2005; Campbell and Reece 2005)

a. Populations and species evolve, meaning that their characteristics change through time. More
precisely, evolution is defined as changes in allele frequencies over time (recall p2+2pq+q2=1)
b. Natural selection occurs when individuals with certain alleles and traits produce the most
offspring in a population. An adaptation is a genetically-based trait that increases an
individual’s ability to produce offspring in a particular environment.
c. Evolution by natural selection is not progressive, and it does not change the characteristics of
the individuals that are selected – it changes only the characteristics of the population. Not all
traits are adaptive. All adaptations are constrained by genetic and historical factors.

4. Evolutionary processes (Freeman, 2005)

a. A population is a group of individuals from the same species that live in the same area and
regularly interbreed. There are other four mechanisms that cause evolutionary change via
shifting of allele frequency in a population:
(i) Natural selection – increases the frequency of certain alleles – the ones that
contribute to improved reproductive success.
(ii) Genetic drift – causes allele frequencies to change randomly. In some cases, drift may
even cause alleles that decrease fitness to increase in frequency.
(iii) Gene flow – occurs when individuals immigrate into (enter) or emigrate from (leave)
a population. Allele frequencies may change when gene flow occurs, because arriving
individuals introduce alleles to their new population and emigrating individuals
remove alleles from their old population.
(iv) Mutation – modifies allele frequencies by continually introducing new alleles. The
alleles created by mutation may be beneficial, detrimental or have no effect on fitness.
b. The Hardy-Weinberg principle acts as a null hypothesis when researchers want to test
whether evolution or non-random mating is occurring at a particular gene.
c. Inbreeding changes genotype frequencies but does not change allele frequencies.

5. Speciation (Freeman, 2005)

a. Speciation occurs when populations of the same species become genetically isolated by lack of
gene flow and then diverge from each other due to selection, genetic drift or mutation.
b. Populations can become genetically isolated from each other if they occupy different
geographic areas, if they use the same habitat within the same area, or if one population is
polyploidy and cannot breed with the other.

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c. Populations can be recognized as distinct species if they are reproductively isolated from each
other, if they have distinct morphological characteristics, or if they form independent branches
in the phylogenetic tree.
d. When populations that have diverged come back into contact, several outcomes are possible.

References:

Hartl DL and Jones EW. (2005). Genetics: Analysis of Genes and Genomes. 6th Ed. Jones and
Bartlett Publishers, MA USA. 854 pp
Cummings MR and Spencer CA. (2012). Concepts of Genetics. Pearson Education, Inc. NJ USA.
742 pp.
Klug WS and Cummings MR. (2000). Essentials of Genetics. Prentice Hall, PTR. USA. 816 pp.
Robinson TR. (2010). Genetics for Dummies. 2nd Ed. Wiley Publishing Inc., NJ USA. 369 pp.
Barton NH, Briggs DEG, Eisen JA, Goldstein DB and Patel NH. (2007). Evolution. Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, NY, USA. 833 pp.
Campbell N and Reece JB. (2005). Biology. 7th Ed. Pearson Education, Inc. NJ USA. 1231 pp.
Raven PH and Johnson GB. (2002). Biology. 6th Ed. [Online Learning Center]. McGraw-Hill
Companies. Available at http://www.mhhe.com/biosci/genbio/raven6tour/home.html.
Accessed May 30, 2014.
Freeman S. (2005). Biological Science. 2nd Ed. Pearson Education, Inc., NJ USA. 1283 pp.
Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P. (2008). Molecular Biology of the
Cell. 5th Ed. Garland Science, Taylor and Francis Group, NY USA. 1725 pp.

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Nature Education. (2014). Principles of Biology: An Online Textbook. Available as

http://www.nature.com/principles . Accessed June 13, 2014

National Institutes of Health - National Human Genome Research Institute. Available as

http://www.genome.gov/26524120 . Accessed June 14, 2014

University of Leicester Virtual Genetics Education Center. Available as

http://www2.le.ac.uk/departments/genetics/vgec/schoolscolleges/topics/geneexpression-regulation
Accessed June 15, 2014

Biology at the University of Texas. Lecture on Genetics. Available as

http://www.zo.utexas.edu/faculty/sjasper/images/t11.3.jpg. Accessed June 15 2014

Prepared by: Jay P. Picardal, MSc, PhD Biology candidate