topic 1_introduction to genetics

SBB 1054 Genetics

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Prepared by Pratheep Sandrasaigaran

Lecturer at Manipal International University

GENETICS TEXTBOOKS

1. Concepts of Genetics, Klug, Cummings, Spencer, Palladino, 2012

2. Human Genetics concepts and Application 9th ed.

3. Biology, 8th Edition, Campbell-Reece

4. Genetics for Dummies. Tara. R.R

5. The facts on file Illustrated guide to The human: body Cells and Genetics


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RATIONALE

1. The rationale to include this module in the academic programme is because this module is the core and major module in the academic programme.

2. The course is designed in developing an understanding of Genetics theory and practical.


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OBJECTIVES

This subject serves as a core for students to:

1. Understand the fundamental concepts in Genetics

2. Have in depth knowledge about chromosome structure and genetic code

3. To understand the knowledge and steps on crossing over during meiotic divisions, linkage

4. To understand the knowledge of genetic testing and able to analyse as well construct the family pedigree


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COURSE LEARNING OUTCOMES

• Demonstrate an understanding of fundamental concepts in Genetics and justify the concepts.

• Develop an understanding that enables to illustrate the chromosomal structure and genetic code.

• To know knowledge on crossing over during meiotic divisions and able to measure the linkage percentage.

• To comprehend the knowledge of genetic testing and to analyse as well to construct the family pedigree


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Getting Registered in www.edmodo.com

6 Prepared by Pratheep Sandrasaigaran

Group Code: te6gvr (Valid till 2nd March 2017 only!)

• Notes • Assignment • Lab manual • Useful tips • Guidance • Forums • Coursework marks • Important announcements

http://www.edmodo.com/

IMPORTANT DATES..!

1. Test 1- Week 6 (20th – 24th MAC 2017)

2. Test 2- Week 11 ( 24th – 28th APR 2017)

3. Assignment 2- 3rd May 2017 (Week 12)

4. Study Break- Week 15 (22nd – 26th MAY 2017)

5. Exam- Week 16 & 17 (29th MAY – 9th JUN 2017)


Figure taken from Internet

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Lecturer at Manipal International University

1.0 Introduction to genetics

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Figure taken from Internet

• Understand the concept of genetics in brief

• History of genetics

• Define chromosomes and genes

• Knowing the different branches of genetics

By the end of this chapter you should be able to:

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1.1 Introduction: What Is Genetics?


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Genetics?


TRAITS OF AN

ORGANISM

INHERITED- PARENTS VARIATIONS

BLUEPRINT

DNA CHROMOSOME

EVOLUTIONS MENDAL

AMAZING

UNIQ

UE

CODE CLONING

FUNDAMENTALS 11

Introduction to Genetics.mp4

What Is Genetics?

• Genetics is the field of science that examines how traits are passed from one generation to the next.

• Blueprint of life.

• An organism’s genes, snippets of DNA that are the fundamental units of heredity, control how it looks, behaves, and reproduces.


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The four major subdivisions Genetics


Classical genetics

Population genetics

Molecular genetics

Quantitative genetics

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Four major subdivisions Genetics

• Classical genetics: Describes how traits (physical characteristics) are passed along from one generation to another.

• Molecular genetics: The study of the chemical and physical structures of DNA, its cousin RNA, and proteins.


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Four major subdivisions Genetics

• Population genetics: Takes Mendelian genetics (that is, the genetics of individual families) and ramps it up to look at the genetic makeup of larger groups.

• Quantitative genetics: A highly mathematical field that examines the statistical relationships between genes and the traits they encode


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How different/similar are our DNA sequences?


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http://www.nature.com/scitable/knowledge/library/comparative-genomics-13239404

Organism Estimated size (bp)

Chromosome # Estimated

gene #

Human (Homo sapiens) 3 billion 46 ≈ 25000

Mouse (Mus musculus) 2.9 billion 40 ≈ 25000

Fruit fly (Drosophila melanogaster)

165 million 8 ≈ 13000

Plant (Arabidopsis thaliana) 157 million 10 ≈ 25000

Roundworm (Caenorhabdtis elegans)

97 million 12 ≈ 19000

Yeast (Saccharomyces cerevisiae)

12 million 32 ≈ 6000

Bacteria (Escherichia coli) 4.6 million 1 ≈ 3200







• How different/similar are you compared to your siblings?

• How different/similar are you compared to your Gf/Bf?

• How different/similar are you compared to your neighbor?

• How different/similar are you compared to Donald Trump?

• How different/similar are you compared to your cat/ pet?

• How different/similar are you compared to Godzila/ Dinosaur?

• How different/similar are you compared to dust/ bacteria?


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• On average, you are 99.9% identical to another human…

• What does it mean?: About 1 base in 1000 is different

• 1/1000 x 100% = ?


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My hobby

My hobby is reading. I read story books, magazines, newspapers and any kind of material that I find interesting. This hobby got started when I was a little boy. I had always wanted my parents to read fairy tales and other stories to me. Soon they got fed up and tired of having to read to me continually. So as soon as I could, I learned to read. I started with simple ABC books. Soon read simple fairy tales and other stories. Now I can fast going about anything that is available. Reading enables me to learn about so many things that I would otherwise not know. I learned about how people lived in bygone days of magic and mystery. I learned about the wonders of the world, space travel, human achievements, gigantic whales, tiny viruses and other fascinating things of our world. The wonderful thing about reading is that I do not have to learn things the hard way. For example, I do not have to catch a disease to know that it can kill me. Also I have to go into the jungle to learn about tiger


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My hobby

My hobby is reading. I read story books, magazines, newspapers and any kind of material that I find interesting. This hobby got started when I was a little boy. I had always wanted my parents to read fairy tales and other stories to me. Soon they got fed up and tired of having to read to me continually. So as soon as I could, I learned to read. I started with simple ABC books. Soon read simple fairy tales and other stories. Now I can fast going about anything that is available. Reading enables me to learn about so many things that I would otherwise not know. I learned about how people lived in bygone days of magic and mystery. I learned about the wonders of the world, space travel, human achievements, gigantic whales, tiny viruses and other fascinating things of our world. The wonderful thing about reading is that I do not have to learn things the hard way. For example, I do not have to catch a disease to know that it can kill me. Also I have to go into the jungle to learn about tiger


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My hobby

My hobby is reading. I read story books, magazines, newspapers and any kind of material that I find interesting. This hobby got started when I was a little boy. I had always wanted my parents to read fairy tales and other stories to me. Soon they got fed up and tired of having to read to me continually. So as soon as I could, I learned to read. I started with simple ABC books. Soon read simple fairy tales and other stories. Now I can fart going about anything that is available. Reading enables me to learn about so many things that I would otherwise not know. I learned about how people lived in bygone days of magic and mystery. I learned about the wonders of the world, space travel, human achievements, gigantic whales, tiny viruses and other fascinating things of our world. The wonderful thing about reading is that I do not have to learn things the hard way. For example, I do not have to catch a disease to know that it can kill me. Also I have to go into the jungle to learn about tiger


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Chromosome 3- locus XM_019023187


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CTCCTCCTGTTCGACAGTCAGCCGCATCTTCTTTTGCATCGCCAGCCAAGCCACATCGCTGAGACACCATGGGGAAGGTGAAGGTCGGAGTCAACGGATTTGGTCGTATTGGGCGCCTGGTCACCAGGGCTGCTTTTAACTCTGGTAAAGTGGATATTGTTGCCATCAATGACCCCTTCATTGACCTCAACTACATGGTTTACATGTTCCAATATGATTCCACCCATGGCAAATTCCATGGCACCGTCAAGGCTGAGAACGGGAAGCTTGTCATCAATGGAAATCCCATCACCATCTTCCAGGAGCGAGATCCCTCCAAAATCAAGTGGGGCGATGCTGGTGCTGAGTACGTCGTGGAGTCCACTGGTGTCTTCACCACCATGGAGAAGGCTGGGGCTCATTTGCAGGGGGGAGCCAAAAGGGTCATCATCTCTGCCCCCTCTGCTGACGCCCCCATGTTCGTCATGGGTGTGAACCATGAGAAGTATGACAACAGCCTCAAGATCATCAGCAATGCCTCCTGCACCACCAACTGCTTAGCACCCCTGGCCAAGGTCATCCATGACAACTTTGGTATCGTGGAAGGACTCATGACCACGGTCCATGCCATCACTGCCACCCAGAAGACTGTGGATGGCCCCTCCGGGAAACTGTGGCGTGATGGCCGCGGGGCTCTCCAGAACATCATCCCTGCCTCTACTGGCGCTGCCAAGGCTGTGGGCAAGGTCATCCCTGAGCTGAACGGGAAGCTTACTGGCATGGCCTTCCGTGTCCCCACTGCCAACGTGTCAGTGGTGGACCTGACCTGCCGTCTAGAAAAACCTGCCAAATATGATGACATCAAGAAGGTGGTGAAGCAGGCGTTGGAGGGCCCCCTCAAGGGCATCCTGGGCTACACTGAGCACCAGGTGGTCTCCTCTGACTTCAATAGCGACACCCACTCCTCCACCTTCGACACTGGGGCTGGCATTGCCCTCAACGACCACTTTGTCAAGCTCAT

Chromosome 3- locus XM_019023187


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CTCCTCCTGTTCGACAGTCAGCCGCATCTTCTTTTGCATCGCCAGCCAAGCCACATCGCTGAGACACCATGGGGAAGGTGAAGGTCGGAGTCAACGGATTTGGTCGTATTGGGCGCCTGGTCACCAGGGCTGCTTTTAACTCTGGTAAAGTGGATATTGTTGCCATCAATGACCCCTTCATTGACCTCAACTACATGGTTTACATGTTCCAATATGATTCCACCCATGGCAAATTCCATGGCACCGTCAAGGCTGAGAACGGGAAGCTTGTCATCAATGGAAATCCCATCACCATCTTCCAGGAGCGAGATCCCTCCAAAATCAAGTGGGGCGATGCTGGTGCTGAGTACGTCGTGGAGTCCACTGGTGTCTTCACCACCATGGAGAAGGCTGGGGCTCATTTGCAGGGGGGAGCCAAAAGGGTCATCATCTCTGCCCCCTCTGCTGACGCCCCCATGTTCGTCATGGGTGTGAACCATGAGAACTATGACAACAGCCTCAAGATCATCAGCAATGCCTCCTGCACCACCAACTGCTTAGCACCCCTGGCCAAGGTCATCCATGACAACTTTGGTATCGTGGAAGGACTCATGACCACGGTCCATGCCATCACTGCCACCCAGAAGACTGTGGATGGCCCCTCCGGGAAACTGTGGCGTGATGGCCGCGGGGCTCTCCAGAACATCATCCCTGCCTCTACTGGCGCTGCCAAGGCTGTGGGCAAGGTCATCCCTGAGCTGAACGGGAAGCTTACTGGCATGGCCTTCCGTGTCCCCACTGCCAACGTGTCAGTGGTGGACCTGACCTGCCGTCTAGAAAAACCTGCCAAATATGATGACATCAAGAAGGTGGTGAAGCAGGCGTTGGAGGGCCCCCTCAAGGGCATCCTGGGCTACACTGAGCACCAGGTGGTCTCCTCTGACTTCAATAGCGACACCCACTCCTCCACCTTCGACACTGGGGCTGGCATTGCCCTCAACGACCACTTTGTCAAGCTCAT


• How different/similar are you compared to your neighbor?

- 1 different per 1000 bases

- 3 000 000 000 bases per set

- 2 sets each person

- 6 000 000 differences


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How much phenotypic differences do these genotypic differences make?

• Most of 6 000 000 DNA differences don’t make any detectable differences to phenotype.

• But the rest cause all the heritable differences between people

• The same kinds of DNA differences cause the phenotypic differences in all other species too..!


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1.2 History of genetics


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What principles of inheritance did Gregor Mendel discover by breeding garden pea plants?

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Gregor Mendel - Mini Biography.mp4

Advantages of pea plants for genetic study

• There are many varieties with distinct heritable features, or characters (such as flower colour).

• Mating can be controlled

• Each flower has sperm-producing organs (stamens) and an egg-producing organ (carpel)

• Cross-pollination (fertilization between different plants) involves dusting one plant with pollen from another


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Parental generation (P) Stamens

Carpel

TECHNIQUE

2

1

3

4


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Figure 14.2b

First filial generation offspring (F1)

RESULTS

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• Mendel chose to track only those characters that occurred in two distinct alternative forms

• He also used varieties that were true-breeding (plants that produce offspring of the same variety when they self-pollinate)

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Mendal’s Experiment

• In a typical experiment, Mendel mated two contrasting, true-breeding varieties, a process called hybridization

• The true-breeding parents are the P generation

• The hybrid offspring of the P generation are called the F1 generation

• When F1 individuals self-pollinate or cross- pollinate with other F1 hybrids, the F2 generation is produced


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Mendal’s Experiment


The Law of Segregation

The Law of Independent Assortment

1 2

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Mendal’s Experiment: The Law of Segregation

• Mendel identified his first law of inheritance by following one characters at one time

• Crossing two true-breeding parents differing in one characters produces monohybrid in the F1 generation, heterozygous for both characters

• A dihybrid cross, a cross between F1 dihybrids, can determine whether two characters are transmitted to offspring as a package or independently


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• Mendel observed the pattern six pea plant characters, each represented by two traits

• What Mendel called a “heritable factor” is what we now call a gene

Mendal’s Experiment: The Law of Segregation

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Figure 14.4

Allele for purple flowers

Locus for flower-color gene

Allele for white flowers

Pair of homologous chromosomes


• A capital letter represents a dominant allele, and a lowercase letter represents a recessive allele

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Phenotype

Purple

Purple

Purple

White

3

1

1

1

2

Ratio 3:1 Ratio 1:2:1

Genotype

PP (homozygous)

Pp (heterozygous)

Pp (heterozygous)

pp (homozygous)

Figure 14.6

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Mendal’s Experiment: The law of independent assortment

• Mendel identified his second law of inheritance by following two characters at the same time

• Crossing two true-breeding parents differing in two characters produces dihybrids in the F1 generation, heterozygous for both characters

• A dihybrid cross, a cross between F1 dihybrids, can determine whether two characters are transmitted to offspring as a package or independently


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Figure 14.8

P Generation

F1 Generation

Predictions

Gametes

EXPERIMENT

RESULTS

YYRR yyrr

yr YR

YyRr

Hypothesis of dependent assortment

Hypothesis of independent assortment

Predicted offspring of F2 generation

Sperm

Sperm or

Eggs

Eggs

Phenotypic ratio 3:1

Phenotypic ratio 9:3:3:1

Phenotypic ratio approximately 9:3:3:1 315 108 101 32

1/2 1/2

1/2

1/2

1/4 1/4

1/4 1/4

1/4

1/4

1/4

1/4

9/16 3/16

3/16 1/16

YR

YR

YR

YR

yr

yr

yr

yr

1/4 3/4

Yr

Yr

yR

yR

YYRR YyRr

YyRr yyrr

YYRR YYRr YyRR YyRr

YYRr YYrr YyRr Yyrr

YyRR YyRr yyRR yyRr

YyRr Yyrr yyRr yyrr

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Mendal’s Experiment: 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 or those far apart on the same chromosome

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


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Inheritance patterns are often more complex than predicted by simple

Mendelian genetics

• The relationship between genotype and phenotype is rarely as simple as in the pea plant characters Mendel studied

• Many heritable characters are not determined by only one gene with two alleles

• However, the basic principles of segregation and independent assortment apply even to more complex patterns of inheritance


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Extending Mendelian Genetics for a Single Gene

• Inheritance of characters by a single gene may deviate from simple Mendelian patterns in the following situations:

- When alleles are not completely dominant or recessive

- When a gene has more than two alleles

- When a gene produces multiple phenotypes


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Degrees of Dominance

• Complete dominance occurs when phenotypes of the heterozygote and dominant homozygote are identical

• In incomplete dominance, the phenotype of F1 hybrids is somewhere between the phenotypes of the two parental varieties

• In codominance, two dominant alleles affect the phenotype in separate, distinguishable ways


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P Generation

Red White

Gametes

CWCW CRCR

CR CW

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P Generation

F1 Generation

1/2 1/2

Red White

Gametes

Pink

Gametes

CWCW CRCR

CR CW

CRCW

CR CW

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P Generation

F1 Generation

F2 Generation

1/2 1/2

1/2 1/2

1/2

1/2

Red White

Gametes

Pink

Gametes

Sperm

Eggs

CWCW CRCR

CR CW

CRCW

CR CW

CW CR

CR

CW

CRCR CRCW

CRCW CWCW

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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


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Carbohydrate

Allele

(a) The three alleles for the ABO blood groups and their carbohydrates

(b) Blood group genotypes and phenotypes

Genotype

Red blood cell appearance

Phenotype (blood group)

A

A

B

B AB

none

O

IA IB i

ii IAIB IAIA or IAi IBIB or IBi


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Is she having an affair? Think!

• A man divorced his wife immediately after the blood group result of his son was revealed by the doctor in HKL.

• The man is blood group A+ while his wife is blood group B+.

• His newborn son is tested blood group O+. Possible?

• The doctors were puzzled by the man’s impulsive act!!!

48 Prepared by Pratheep Sandrasaigaran

Test Your Knowledge 1


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1. There are 4 subdivision of genetics that you will be studying for SBB 1054 Genetics.

2. Gregor Mandal is the father of genetics and DNA.

3. Two law introduced by Gregor Mandal is known as Mendelian law.

4. Mendelian law can explain every phenotypes and genotypes.

5. The secret of success of Gregor Mandal is the pea plant itself.


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http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCLD_qsHP0MgCFZcHjgodLkkC4w&url=http%3A%2F%2Fwww.notaio.org%2Fconcorso_notarile2.htm&psig=AFQjCNF2sitVXDq8A_X_k11kNST3Sp4PyQ&ust=1445415730506564

1.3 Introductions to Chromosomes and Genes


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The Chromosome Theory of Inheritance

• Mendel conducted his experiments before the structure and role of chromosomes were known.

• About 20 years after his work was published, advances in microscopy allowed researchers to identify chromosomes.

• What is chromosome?

• Chromosomes in diploid cells exist in pairs, called homologous chromosomes (identical in size and location of the centromere).


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• In mitosis, chromosomes are copied and distributed so that each daughter cell receives a diploid (2n) set of chromosomes.

• Meiosis is associated with gamete formation.

• How many chromosome human have in general?

• How many chromosome do you see in human gamete?


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• The chromosome theory of inheritance states:

- Mendelian genes have specific loci (positions) on chromosomes

- Chromosomes undergo segregation and independent assortment


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P Generation Yellow-round seeds (YYRR)

Green-wrinkled seeds (yyrr)

Meiosis

Fertilization

Gametes

Y

Y R R

Y R

y

y r

y r

r


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F1 Generation

All F1 plants produce yellow-round seeds (YyRr).

Meiosis

Metaphase I

Anaphase I

Metaphase II

R R

R R

R R

R R

R R R R

r r

r r

r r

r r

r r r r

Y Y

Y Y

Y Y

Y Y

Y Y Y Y

y y

y y

y y

y y

y y y y

Gametes

LAW OF SEGREGATION The two alleles for each gene separate during gamete formation.

LAW OF INDEPENDENT ASSORTMENT Alleles of genes on nonhomologous chromosomes assort independently during gamete formation.

1

2 2

1

1/4 1/4

1/4 1/4 YR yr Yr yR


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F2 Generation

3 Fertilization recombines the R and r alleles at random.

Fertilization results in the 9:3:3:1 phenotypic ratio in the F2 generation.

An F1 F1 cross-fertilization

9 : 3 : 3 : 1

LAW OF SEGREGATION LAW OF INDEPENDENT ASSORTMENT

3


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• Walter Sutton and Theodor Boveri noticed that genes and chromosomes exist in pairs.

• They also notice that members of a gene pair and members of a chromosome pair separate from each other during gamete formation.

• Based on these parallels, Sutton and Boveri independently proposed that genes are carried on chromosomes


A drawing of chromosome X of D. melanogaster

Adapted from Concepts of Genetics, Klug, Cummings, Spencer, Palladino, 2012 . 58

Phenotype and Genotype

• Different alleles may produce differences in the observable features, or phenotype, of an organism.

• The set of alleles for a given trait carried by an organism is called the genotype.

• Knowing gene control the phenotype and genotype, what is the chemical nature of Genes?

• By the 1920s, scientists were aware that proteins and DNA were the major chemical components of chromosomes.


DNA

Protein

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DNA is carrier of genetic: heritable factor

• When T. H. Morgan’s group showed that genes are located on chromosomes, the two components of chromosomes; DNA or protein?

• The key factor in determining the genetic material was choosing appropriate experimental organisms

• The role of DNA in heredity was first discovered by studying bacteria and the viruses that infect them


An electron micrograph showing T phage infecting a cell of the bacterium E. coli

Adapted from Concepts of Genetics, Klug, Cummings, Spencer, Palladino, 2012

.

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DNA is carrier of genetic: heritable factor

• In 1952, Alfred Hershey and Martha Chase performed experiments showing that DNA is the genetic material of a phage known as T2

• To determine this, they designed an experiment showing that only one of the two components of T2 (DNA or protein) enters an E. coli cell during infection

• They concluded that the injected DNA of the phage provides the genetic information


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Bacterial cell

Phage

Batch 1: Radioactive sulfur (35S)

DNA

Batch 2: Radioactive phosphorus (32P)

Radioactive DNA

EXPERIMENT

Radioactive protein


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Bacterial cell

Phage


Radioactive protein

DNA


Radioactive DNA

Empty protein shell

Phage DNA

EXPERIMENT


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Bacterial cell

Phage


Radioactive protein

DNA


Radioactive DNA

Empty protein shell

Phage DNA

Centrifuge

Centrifuge

Radioactivity (phage protein) in liquid

Pellet (bacterial cells and contents)

Pellet Radioactivity (phage DNA) in pellet

EXPERIMENT


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Protein control the biological functions

• Lets do Maths..!

• Proteins are made from combinations of 20 different amino acids.

• Presume a protein is made of 3 bases of amino acid polypeptide. How many different type of protein can be derived?

• Now, if a Protein is made of 100 bases of amino acid polypeptide. How many different type of protein can be derived?


203 = 8000

20100 = ????

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Timeline of genetics


timeline showing the development of genetics from Gregor Mendel’s work on pea plants to the current era of genomics and its many applications in research, medicine, and society.

Adapted from Concepts of Genetics, Klug, Cummings, Spencer, Palladino, 2012 .

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Central dogma of genetics/

Molecular biology


Gene expression consists of transcription of DNA into mRNA (top) and the translation (center) of mRNA (with the help of a ribosome) into a protein (bottom).


1.4 Different branches of genetics


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Branches of genetics • Behavioural genetics

• Developmental genetics

• Conservation genetics

• Ecological genetics

• Evolutionary genetics

• Genetic engineering

• Genomics

• Human genetics

• Microbial genetics

• Molecular genetics

• Population genetics

• Quantitative genetics


Dolly, a Finn Dorset sheep cloned from the genetic material of an adult mammary cell, shown next to her

first-born lamb, Bonnie.



Diagram of the human chromosome set, showing the location of some genes whose mutant forms cause hereditary diseases. Conditions that can be diagnosed using DNA analysis are indicated by a red dot

Adapted from Concepts of Genetics, Klug, Cummings, Spencer, Palladino, 2012 .

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topic 1_introduction to genetics

Science