Biolove genetics part 1

M.I/ASASI/2013 Page 1

BIOLOVE

GENETICS


Genes

– Basic unit of inheritance or information about specific traits

– Located on chromosomes

– For example, the height of pea plant is determined by a gene

Locus

– Location in chromosomes where genes are located

Allele

– If the a gene give the height

characteristics,

– Allele determine either it is tall or short

– So, Allele is the variant of the same gene

Another example

– Gene: Hair colour

Allele: Black or blonde

– Gene: Fur colour

Allele: White or yellow

Dominant Allele

– Presented by capital letter. Example: (T, P, B, A)

– Will show the effects on organism

Recessive allele

– Presented by small letter.

– No effects on organism if paired with dominant allele

For example:

If P is for blue colour, and p is for red colour

Pp = blue colour

pp = red colour

Homozygous

– The same letter. Example: tt, YY, NN

– Can be either homozygous dominant or recessive

pp Pp


Homozygous dominant

– PP, YY, TT, MM

– Combination of two same capital letter

Homozygous recessive

– pp, tt, mm, nn

– combination of two same small letter

Heterozygous

– one small letter and one capital letter

– Example: Tt, Mn, Hh, Rr

Genotype

– Genetic composition of an organism which is not visible externally

– The genotype of plant is represented by the allele present

– Hence, if P is allele for tall plant, all tall plants will have the genotype of Pp or PP

Phenotype

– External appearance or observable features

– Example: Colour, size, structure

History of genetis

We have to know Mendel, the father of modern genetics

What he do?

– He study the inheritance of traits in pea plants

Who is he?

– An Austrian priest


Why he chose pea plant to study about inheritance of traits?

• Advantages of pea plants for genetic study:

– There are many varieties with distinct heritable features, or characters (such as

flower color); character variants (such as purple or white flowers) are called traits

– Mating of plants can be controlled

– Each pea plant has sperm-producing organs (stamens) and egg-producing organs

(carpels)

– Cross-pollination (fertilization between different plants) can be achieved by dusting

one plant with pollen from another

• Mendel chose to track only those characters that varied in an either-or manner

• He also used varieties that were true-breeding (plants that produce offspring of the same

variety when they self-pollinate)

Inheritance of single trait is called as monohybrid

• In a typical experiment, Mendel mated

two contrasting, true-breeding varieties, a

process called hybridization

• The true-breeding parents are the P1 or

parental generation

• The hybrid offspring of the P generation

are called the F1 generation or first filial

generation

• When F1 individuals self-pollinate, the

F2 generation or second filial generation is

produced


• When Mendel crossed contrasting, true-breeding white and purple flowered pea plants, all

of the F1 hybrids were purple

• When Mendel crossed the F1 hybrids, many of the F2 plants had purple flowers, but some

had white

• Mendel discovered a ratio of about three to one, purple to white flowers, in the F2

generation

Fertilized among F1

F1 x F1

If the dominant or

recessive trait is not

mentioned in the

question, please

refer to this table.


Law of segregation

Two alleles of a gene seperate or segregate from each other into different gametes during the

formation of gametes.

• Thus, an egg or a sperm gets only one of the two alleles that are present in the somatic cells

of an organism

• This segregation of alleles corresponds to the distribution of homologous chromosomes to

different gametes in meiosis

• The possible combinations of sperm and egg can be shown using a Punnett square, a

diagram for predicting the results of a genetic cross between individuals of known genetic

makeup

This is Monohybrid cross

Allele in a pair Separate/segregate Into different gamete

Gametes must

be circled


• Crossing two true-breeding parents differing in two characters produces dihybrids in the F1

generation, heterozygous for both characters (YyRr)

• A dihybrid cross, a cross between F1 dihybrids, can determine whether two characters are

transmitted to offspring as a package or independently

This is not valid

for dihybrid

cross


• Using a dihybrid cross, Mendel developed the law of independent assortment

• The law of independent assortment states that each pair of alleles segregates

independently of each other pair of alleles during gamete formation

• Strictly speaking, this law applies only to genes on different, nonhomologous

chromosomes

• Genes located near each other on the same chromosome tend to be inherited

together

• Mendel’s laws of segregation and independent assortment reflect the rules of

probability

• When tossing a coin, the outcome of one toss has no impact on the outcome of the

next toss

• In the same way, the alleles of one gene segregate into gametes independently of

another gene’s alleles

• The multiplication rule states that the probability that two or more independent

events will occur together is the product of their individual probabilities

• Probability in an F1 monohybrid cross can be determined using the multiplication rule

• Segregation in a heterozygous plant is like flipping a coin: Each gamete has a chance

of carrying the dominant allele and a chance of carrying the recessive allele


Extension to Mendel’s Genetics

• Complete dominance occurs when phenotypes of the heterozygote and dominant

homozygote are identical

Heterozygote = Pp

Homozygote dominant = PP

• In incomplete dominance, the phenotype of F1 hybrids is somewhere between the

phenotypes of the two parental varieties

– For example:

– The third organism display both

appearance from parents

• In codominance, two dominant

alleles affect the phenotype in separate,

distinguishable ways

- Example provided in the

summary table of degree of dominance

at page 11

GG HH x

GH

OR

TT YY

TY

x

It is not necessary to write the capital

letter C when writing the genetic

diagram

Both has identical

phenotype which is

purple colour


Multiple Alleles

• Most genes exist in populations in more

than two allelic forms

• For example, the four phenotypes of

the ABO blood group in humans are

determined by three alleles for the

enzyme (I) that attaches A or B

carbohydrates to red blood cells: IA, IB,

and i.

• The enzyme encoded by the IA allele

adds the A carbohydrate, whereas the

enzyme encoded by the IB allele adds

the B carbohydrate; the enzyme

encoded by the i allele adds neither

Epistasis

– In Epistasis, a gene at one locus alters the phenotypic expression of a gene at a second locus

– For example, in mice and many other mammals, coat color depends on two genes

– One gene determines the pigment color (with alleles B for black and b for brown)

– The other gene (with alleles C for color and c for no color) determines whether the pigment

will be deposited in the hair

If at least one allele C is exist,

the fur will have either black

or brown colour

If no allele C exist but only

allele c is exist, for example

BBcc, the fur will have no

colour. Fur will be white.

Briefly, if no dominant allele

for colour, the fur will have

no colour


Polygenic Inheritance

• Quantitative characters are

those that vary in the population

along a continuum

• Quantitative variation usually

indicates polygenic inheritance,

an additive effect of two or more

genes on a single phenotype

• Skin color in humans is an

example of polygenic inheritance

• More than two genes will affect

the skin colour

Testcross

– Crossing an unkown genotype with a homozygous recessive

________ x rr

Summary of Extension to Mendelian Genetics

unknown

Homozygous recessive


Useful Diagram To help you



Steps to write genetic diagram

Step 1: Cross the parents

BbCc x BbCc

Step 2: Obtain the gamete

– From BbCc, we make the gamete by using the arrows

– OR we can use numbering system

Number the letter as shown above

Then, combine the letter

+ = BC

BbCc

BC

bc bC

Bc

BbCc 1

3

2 4

+

2 3

2 4

1 4

+

+

=

=

=

Gamete

Note that number 1 and 2

cannot cross together.

Same goes to number 3

and 4

1 3

bC

bc

Bc

BC


If the genotype exist as BBCC,

Then the gamete will be BC and BC. But we will take one only out of two which we’ll write BC only

instead of BC and BC because it is the same.

Step 3: Draw a punnet square to obtain the F1

Step 4: Write the Genotypic ratio and phenotypic ratio

Genotypic ratio: ________________________________________

Phenotypic ratio: _______________________________________

DNA

– Is a polymer of nucleotides, each consisting of three components: a nitrogenous base, a

sugar, and a phosphate group

BBCC BBCc BbCC BbCc

BBCc BBcc BbCc Bbcc

BbCc BbCc bbCC bbCc

BbCc Bbcc bbCc bbcc

bC

bc

Bc

BC

bC bc Bc BC


• The nitrogenous bases

– Are paired in specific combinations: adenine with thymine, and cytosine with

guanine

• Each base pair forms a different number of hydrogen bonds

– Adenine and thymine form two bonds, cytosine and guanine form three bonds

• DNA

– Was composed of two antiparallel sugar-phosphate backbones, with the nitrogenous

bases paired in the molecule’s interior

– Twisted into helical shape

Differences between DNA and RNA

Aspect DNA RNA

Sugar Deoxyribose Ribose

Bases A-T, C-G U-A, C-G

– The base thymine, T is replaced by Uracil, U

Strand Double Single

DNA Replication

– Copying the double strand DNA

– Genetic material is passed down to daughter cells

– Happens before cell division

In prokaryotes happen through the interval between cell divisions

Eukaryotes happens during the S phase


• In DNA replication

– The parent molecule unwinds, and two new daughter strands are built based on

base-pairing rules

Model of DNA replication

The Semiconservative model was then accepted when Meselson and Stahl carried out an experiment

to prove it.

• Experiments performed by Meselson and Stahl

– Supported the semiconservative model of DNA replication


• The copying of DNA

– Is remarkable in its speed and accuracy

• More than a dozen enzymes and other proteins

– Participate in DNA replication


• The replication of a DNA molecule

– Begins at special sites called origins of replication, where the two strands are

separated

• A eukaryotic chromosome

– May have hundreds or even thousands of replication origins

Replication occurs in the direction from 5’ to 3’

– Continuous repliation on 3’ to 5’ template

– Discontinuous on 5’ to 3’ template. Replication form short segments

DNA replication starts when the DNA is unwind by DNA Helicase at area known as replication

fork

More replication bubbles – faster the process of copying the DNA strand

Once Helicase has unwind the strand, single strand binding protein will bind to the single

strand DNA and stabilize it.

Here are the summary of action by the molecules


Primase will synthesize RNA primer

RNAase H removes the RNA primer

DNA polymerase I replace the RNA primer with DNA nucleotides

RNA primer is the start point for DNA polymerase

• Elongation of new DNA at a replication fork

– Is catalyzed by enzymes called DNA polymerases, which add nucleotides to the 3

end of a growing strand

• DNA polymerase I add nucleotides

– Only to the free 3 end of a growing strand

• Along one template strand of DNA, the leading strand

– DNA polymerase III can synthesize a complementary strand continuously, moving

toward the replication fork

• To elongate the other new strand of DNA, the lagging strand

– DNA polymerase III must work in the direction away from the replication fork

• The lagging strand

– Is synthesized as a series of segments called Okazaki fragments, which are then

joined together by DNA ligase

DNA polymerase I


Synthesis of leading and lagging strands during DNA replication

• DNA polymerases cannot initiate the synthesis of a polynucleotide

– They can only add nucleotides to the 3 end

Figure 16.15 showing Replication in Lagging strands

RNAase H remove

the RNA primer


6. RNAase H removes the primer

from 5’ end of second fragment. DNA

polymerase I replace the primer with

DNA nucleotides that it adds one by

one to the 3’ end of the 3rd fragment.

The replacement of the last RNA

nucleotide with DNA leaves the sugar

phosphate backbone with a free 3’

end


Protein Synthesis

The two stgaes of protein synthesis is Transcription and Translation

• Transcription

– Is the synthesis of RNA under the direction of DNA

– Produces messenger RNA (mRNA)

• Translation

– Is the actual synthesis of a polypeptide, which occurs under the direction of mRNA

– Occurs on ribosomes

• In prokaryotes

– Transcription and translation occur together

• In eukaryotes

– RNA transcripts are modified before becoming true mRNA


• Genetic information

– Is encoded as a sequence of nonoverlapping base triplets, or codons

• How many bases correspond to an amino acid?

– 3 base will form codon which will specify amino acid

Each codon consist of three nucleotides (base)

During transcription

– The gene determines the sequence of bases along the length of an mRNA molecule

4 characteristics of Genetic code

1. Triplet:

– 3 nucleotides(codon) will specify one amino acid

Each amino acid may have more than one codon. But one codon only specify for an

amino acid

– Overall 61 codons + 3 stop codons

– AUG is the start codon (AUG codes for methionine) for transcription

Stop codons

– UAA, UAG, UGA


2. Redundant:

– More than one codon for an amino acids

3. Unambigous

– One codon can only specify an amino acid only

– Which means if AAA is for Lysine, it is strictly for Lysine and cannot form other amino acid

4. No spaces or punctuation

Transcription

- Happens when the DNA strands separate

- One strand of DNA is used as the pattern to produce RNA using specific base pairing

- Catalyze by RNA polymerase

- Takes place in nucleus

Flow of transcription

Start: promotercoding regionterminator:End

• RNA synthesis

– Is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks

together the RNA nucleotides

– Follows the same base-pairing rules as DNA, except that in RNA, uracil(U) substitutes

for thymine(T)

• The stages of transcription are

– Initiation

– Elongation

– Termination


Initiation

- RNA polymerase bind to promoter

- DNA double helix unwind

- RNA polymerase transcribe the coding region

- No primer is needed for transcription because starts at the promoter

What is promoter?

- TATA box

TATA box is recognize by transcription factors

Transcription factors(TF) are proteins involve in the regulation of gene expression

TF has two domains(base)

At TATA box

For RNA polymerase to bind


- TF binds to DNA strand

- RNA polymerase II bind to DNA at TF

- TF + RNA polymerase + TATA box = transcription initiation complex

Elongation


- RNA polymerase elongate transcription from 5’ to 3’

- Transcribed DNA will reform the double helix

- New RNA dissociate from template

Termination

- RNA polymerase transcribes a terminator

- Terminator is one of the three stop codons (UAA, UAG, UGA)

- RNA strands released

- RNA polymerase dissociates from the template strand

• The mechanisms of termination

– Are different in prokaryotes and eukaryotes

• Eukaryotic cells modify RNA after transcription

• Enzymes in the eukaryotic nucleus

– Modify pre-mRNA in specific ways before the genetic messages are dispatched to the

cytoplasm

• Each end of a pre-mRNA molecule is modified in a particular way

– The 5 end receives a modified nucleotide cap (capped with Guanine, G)

– The 3 end gets a poly-A tail (Adenine, A)


Why mRNA ends need to be altered?

- Protects the RNA from degradation

- Helps the ribosome to attach to the mRNA

- Facilitates the transport out of the RNA from the nucleus

RNA splicing

– Pre-mRNA contains Introns (non coding region) and Exons (coding region)

– Removes introns and joins exons

• RNA splicing Is carried out by spliceosomes in some cases

• Ribozymes

– Are catalytic RNA molecules that function as enzymes and can splice RNA

• The presence of introns

– Allows for alternative RNA splicing


Translation

• A cell translates an mRNA message into protein

– With the help of transfer RNA (tRNA) and ribosomes

• Consist of three stages

- Initiation, elongation and termination

Translation: the basic concept

• Molecules of tRNA are not all identical

– Each carries a specific amino acid

on one end

– Each has an anticodon on the

other end

• Which means it has two attachment sites

- Amino acids

- Anticodon


• Ribosomes

– Facilitate the specific coupling

of tRNA anticodons with mRNA

codons during protein

synthesis

• The ribosomal subunits

– Are constructed of proteins

and RNA molecules named

ribosomal RNA or rRNA

• The ribosome has three binding sites for tRNA at the large subunit

– The P site

– The A site

– The E site

Small subunit is for mRNA binding site

E site – hold discharged amino acid

P site – holds the tRNA growing polypeptide chain

A site – holds the tRNA carrying the next amino acid


Initiation of Translation

Elongation

• In the elongation stage of translation

– Amino acids are added one by one to the preceding amino acid


Termination

• The final stage of translation is termination

– When the ribosome reaches a stop codon in the mRNA

• A number of ribosomes can translate a single mRNA molecule simultaneously

- Forming a polyribosome

Summary of transcription and translation

Biolove genetics part 1

Education

f1 generation

f1 f1 x f1

f1 individuals

different plants

f1 dihybrids

f1 monohybrid cross

f1 hybrids

white mendel