Welcome to Genome 351!Human Genetics

April 1, 2013

There is still space available in this course; if you are not registered and wish to take this course, see me during the break, or immediately after class

Welcome to Genome 351!Human Genetics

March 28, 2011

There is still space available in this course; if you are not registered and wish to take this course, see me during the break, or immediately after class

Course goals

-Basic understanding of the concepts of (human) genetics

-Be able to critically read the science section of the New York Times

-Informed citizen, voter, health consumer

Discussion Section (AA) Wednesday 10:30-11:20 AM S110 Discussion Section (AB) Wednesday 1:30-2:20 PM S110

NO DISCUSSION SECTION THIS WEEK

Instructors: Leo Pallanck (4/1-5/3) Evan Eichler (5/6-6/7)

Office hours (by appointment): Fridays 1:00-2:00PM

Teaching Assistants:Adam Gordon; Office hours: Thursdays 4:00PM - 5:00PM S-110Blake Hovde; Office hours: Wednesdays 2:30PM – 3:30 PM S-110

Genome 351 – Human Genetics

Evan Eichler on 4/5

Suggested Textbook:The Human Genome -- A User’s Guide, Julia E. Richards & R. Scott Hawley Elsevier Science in Society Series, 3rd ed.2010

Course website:http://courses.washington.edu/gen351/

Will use course website to post:-announcements (e.g., room changes)-suggested reading-lectures; problem sets; answer keys

General course information

This week:Chapters 1 & 2

Course content

4/1-5/3: Basic Genetics/Molecular Biology (Leo Pallanck)-Mendel’s Laws & Segregation -Cell Cycle, Mitosis & Meiosis-DNA Replication -Recombination & Aneuploidy-Transcription, Splicing & Translation -Mutations

5/6-6/7: Human Genetics/Disease (Evan Eichler)-Human Genome -Disease Mechanisms-Human Molecular Evolution -Cancer Genetics-Population Genetics -Stem Cells & Gene Therapy-Mapping Genetic Traits

•Midterm exam (125 points)

•Final exam (125 points) – not cumulative, but…

• Six problem sets (60 total points) – handed out on Fridays, due the following Friday

• 2-3 Discussion section debates (40 points)

Grading on curve; mean = 2.8

To pass the course you must receive a minimum of 175 points

No make-up Exams!

Grading

» Attend class (lecture and discussion section)

» If you don’t understand something, don’t wait… ask for help! Can you explain today’s lecture to your non-scientist parents/friends without referring to the notes?

» Use the book as a resource to understand the lectures

» Work the problem sets/make sure you understand the answers

» Form study/discussion groups

» Make use of help time!

How to succeed in this course

» Outline of course

» Pedigrees (example: cystic fibrosis)

» Mendel’s experiments with pea plants

» Proteins

» Cells

Today…Genome 351, 1 April 2013, Lecture 1

-Inherited disease that affects the lungs and digestive system-Affects ~30,000 children and adults in the United States (~70,000 worldwide).-A defective gene and its corresponding protein product cause the body to produce unusually thick, sticky mucus that:

* clogs the lungs and leads to life-threatening lung infections; and * obstructs the pancreas and stops natural enzymes from helping the body break down and absorb food.

Cystic fibrosis

Two unaffected individuals have three children, the youngest of whom has cystic fibrosis (CF)

A simple pedigree

= Normal

= cystic fibrosis

How can you tell if CF is a genetic disorder?

A larger family

Two unaffected individuals have eight children, two of whom have cystic fibrosis

Does this tell you that CF is a genetic disorder?

What else might you want to know?

Another generation

Building pedigrees

= Deceased male

= Unaffected male

= Affected male

= Unaffected female

= Affected female

Horizontal line = matingVertical line = offspring

= Identical twins

= sex unspecified

=

Building pedigrees (cont’d)

=

Building pedigrees (cont’d)

I

II

III

Proband: affected individual who first brings attention to the trait

• Blending of traits

• Vital spark (paternal or maternal)

• Sperm carries preformed individual

(homunculus)

Some early theories on heredity

Gregor Mendel (1822–1884) introduces a more systematic approach

• Choice of a good model organism—garden pea- relatively short generation time—one per year- lots of progeny per cross- self-pollination and out-crossing possible- true-breeding strains readily available from

local merchant

• Choice of clear character differences to track- Yellow vs. green seed pods, round vs. wrinkled

seeds, purple vs. white flowers, etc.

• Careful mathematical analysis of the results- allowed him to develop and test specific models

Reasons why Mendel was successful:

Establish true-breeding strains, each of which exhibit clear character differences

Make crosses between different true-breeding strains

Identify and count the progeny traits (phenotypes)

…are the progeny traits (phenotypes) like one parent or the other? How many of each class are there?

??Make crosses between the progeny…

Mendel’s experimentscrosses within the true-breeding population yield progeny that show the same trait as the parent

xx

x

x

Results of Mendel’s experiments:

True-breeding yellow pea pod strain

True-breeding green pea pod strain

Predictions of:Blending

HypothesisVital spark Hypothesis

Homunculus Hypothesis

Greenish/yellow

All Green or yellowAll Green or yellow

Generation I:

Reciprocal cross gave same result

Generation II:

Actual results:

Hybrid pea plants

What happened to the yellow seed pod trait?

x

The yellow trait returns in generation III

True-breeding yellow pea pod strain

True-breeding green pea pod strain

Hybrid pea plants

was this just a peculiarity of the seed pod color trait?

Generation I:

Generation II:

Cross hybrid plants to one another (or self-cross)

Generation III:

in 3:1 ratio (green:yellow)

Identical findings seen with other traits…

Parental Phenotypes

1. Green X yellow pod

Gen II

Green

Gen III

428 Green152 yellow

Ratio (gen III)

2.82 : 1

2. Yellow X green seed Yellow 6022 yellow2001 green

3.01 : 1

3. Purple X white petal Purple 705 purple224 white

3.15 : 1

4. Inflated X pinched pod

5. Round X wrinkled seed

6. Axial X terminal flowers

7. Long X short stem

Inflated

Round

Axial

Long

882 inflated299 pinched

5474 Round1850 wrinkled

651 axial207 terminal

787 long277 short

2.95 : 1

2.96 : 1

3.14 : 1

2.84 : 1

How did Mendel interpret these findings?

Mendel’s interpretations

Both parents contribute a “determinant” (gene) that influences the seed pod color trait

x

True-breeding green pea pod strain

True-breeding yellow pea pod strain

The “G” or “g” gene

Each parent randomly donates only one of their two genes for any given trait to their offspring

Mendel’s interpretations

x

True-breeding green pea pod strain

True-breeding yellow pea pod strain

The g allele (which confers yellow seed pods) is recessive to the dominant G allele (which confers green seed pods).

There are two forms of a gene (alleles) for the seed pod color trait; the trait conferred by one allele (recessive) can be masked by the trait conferred by the other allele (dominant)

alleles: variants of a gene

recessive

dominant

Cross hybrid plants to one another (or self-cross)

Mendel’s interpretationsGenes are particulate (i.e., do not mix); recessive traits that are not evident in heterozygotes can be unmasked in progeny

Hybrid (heterozygous) pea plants

x

True-breeding (homozygous) yellow pea pod strain

True-breeding (homozygous) green pea pod strain

Generation I:

Generation II:

Generation III:The recessive trait reappears intact in generation III

How did Mendel explain the 3:1 ratio?

G g

G

g

female gametes

male

gam

ete

s

Explains the 3:1 ratio in the Generation III offspring from Mendel’s crosses

x

-The Punnett Squaregametes = sperm or eggs

General conclusions of Mendel’s work1. Many traits (phenotypes) are determined by

genes

2. Gene variants (alleles) can confer dominant or recessive traits (phenotypes)

3. There are two copies of each gene

4. Each parent randomly transmits only one of their two alleles of a given gene to their offspring

Some vocabulary

Gene: unit of information passed from one

generation to the next.

Alleles : variants of a gene (e.g., yellow vs. green)

Homozygote: both copies of the gene are the same

Heterozygote: the two copies of the gene are

different

Genotype: the information specifying a trait

Phenotype: the manifestation of the trait itself

Genotypes? GG Gg gg Gg

Phenotypes? greengreen greenyellow

Information passes from one generation to the next!

Applying Mendel’s principles to CF

Two unaffected individuals have eight children, two of whom have cystic fibrosis

cc cc

CcCc

C? C? C?C? C? C?

C = common allelec = cystic fibrosis allele

What are the odds that this child is a carrier?

The Punnett Square

c

C

cC

CC Cc

Cc cc

Cc

Cc

Heterozygous parents

Applying Mendel’s principles to CF

Two unaffected individuals have eight children, two of whom have cystic fibrosis

cc cc

CcCc

C? C? C?C? C? C?

C = common allelec = cystic fibrosis allele

What are the odds that this child is a carrier?

The cystic fibrosis gene specifies a membrane protein

Proteins are the workhorses of the cell

• Many sizes and shapes– Rod-like, globular– Single subunit, multimeric

• Many distinct properties– Water soluble, lipid loving

• Many functions– Structure, catalysts, motors, signals, pumps

• Mutations often alter proteins

Including cystic fibrosis

Cystic fibrosis is recessive

CFTR+

CFTR+

CFTR+

CFTR-

CFTR-

CFTR-

Homozygous (wild-type)

Homozygous (mutant)

Heterozygous

Cystic Fibrosis

NO

NO

YES

One wild-type version of the gene is sufficient

A rare allele in the population

The allele that predominates in the population

But what are proteins (chemically)?

Polymers of 20 different amino acids(only 11 can be made by humans, others must be obtained from the diet)

Have a repeating backbone structure

Distinguished by their side chains (R groups)

The 20 amino acids

•Average protein = 300 to 400 aa’s

•Variety of linear amino acid sequences is almost infinite...

e.g., a protein of 100 amino acids made with the 20 different known amino acids can have 20100 different linear sequences

•Frequently have globular (spherical) 3-D shapes & are negatively charged

•E. coli (human intestinal bacteria) makes about 3,000 proteins

•humans make about 100,000 different proteins with 25,000 genes (WOW!)

Proteins adopt a variety of structures

Distinct proteins are different length chains of different amino

acids

Insulin -- Met-ala-leu-trp-met … glu-gln-tyr-cys-gln (110 aa)

Collagen -- Met-his-pro-gly-leu … cys-met-lys-ser-leu (1678 aa)

ß-Hemoglobin -- Met-val-his-leu … ala-his-lys-tyr-his (147 aa)

Protein FunctionActin, myosin Muscle contraction

Antibodies Immunity

Hemoglobin, myoglobin Oxygen transport

Insulin, glucagon Blood glucose control

Collagen Tendons,dermis

Kinases Modulate protein activity

Dehydrogenases Metabolism

Thrombin, fibrinogen Blood clotting

Keratin Hair and skin

Trypsin, proteases Digestion

Polymerases DNA, RNA synthesis

NaATPases Ion pumps

Collagen

G6PDAlbumin

42

Cells -- the basic unit of life

The Basic Unit of Life

• Organisms can be single cells (e.g., bacteria, yeast) or collections of many cells

• Prokaryotes (bacteria) lack a nucleus

• Eukaryotes have a nucleus and other

compartments

An animal cell

• Surrounded by the plasma membrane

• Contains a nucleus (where >99% of the genes are located) and cytoplasm with specialized organelles

•Come in many different shapes

The plasma membrane

The cystic fibrosis gene specifies a membrane protein

Mitochondria

• Site of ATP (energy) production

• Has its own circular DNA (<1% of the cellular genes located here)

• Mitochondrial genes are inherited from the mother

Human Cells

• Hundreds of cell types• Several categories– Epithelial (skin, intestinal, lung, but also pancreas, liver, kidney)

– Muscle– Nerve– Connective– Blood

Levels of Organization

• Organism• Organ systems• Organs• Tissues• Cells

Next time…

DNA is the genetic material

Structure of DNA reveals a digital code

Replication of DNA

CFTR regulates Cl- transport across membranes

Gene responsible for Cystic Fibrosis

Cystic Fibrosis

Affected persons can have unaffected parents

Disease can skip generations

Both sexes equally affected

Genetics of Cystic Fibrosis (CF)

* Autosomal recessive trait * ~1/25 Caucasians is a carrier* ~1/65 Africans is a carrier* ~1/90 Asians is a carrier

* Gene lies chromosome 7q31.2* Gene encodes a chloride channel expressed

in lung, skin and pancreas* DNA diagnosis in utero