» Outline of course» Pedigrees (example: cystic fibrosis)» Mendel’s experiments with pea plants» Proteins» Cells

Today… Genome 351, 4 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

A larger familyTwo unaffected individuals have eight children, two of whom have cystic fibrosis

Another generation

Building pedigrees

= Deceased male

= Unaffected male

= Affected male

= Unaffected female

= Affected female

Horizontal line = matingVertical line = offspring

= Identical twins

= Unknown sex

Building pedigrees (cont’d)

=

Building pedigrees (cont’d)

I

II

III

• 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

Generation I:

Generation II:

Actual results:

Hybrid pea plants

x

The yellow trait returns in generation III

True-breeding yellow pea pod strain

True-breeding green pea pod strain

Hybrid pea plants

Generation I:

Generation II:

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

Generation III:

Identical findings seen with other traits…Parental Phenotypes1. Green X yellow pod

Gen IIGreen

Gen III428 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 pinched5474 Round1850 wrinkled651 axial207 terminal787 long277 short

2.95 : 1

2.96 : 1

3.14 : 1

2.84 : 1

Mendel’s interpretations

xTrue-breeding green pea pod strain

True-breeding yellow pea pod strain

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

Mendel’s interpretations

xTrue-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)

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

xTrue-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

mal

e ga

met

esx

-The Punnett Square

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 sameHeterozygote: The two copies of the gene are

differentGenotype: the information specifying a traitPhenotype: the manifestation of the trait itself

Genotypes?Phenotypes?

Information passes from one generation to the next!

Applying Mendel’s principles to CF

Two unaffected individuals have eight children, the two of whom have cystic fibrosisC = common allelec = cystic fibrosis allele

The Punnett Square

c

C

cC

Cc

Cc

Heterozygous parents

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

Cystic fibrosis is recessive

CFTR+

CFTR+

CFTR+

CFTR-

CFTR-

CFTR-

Homozygous (wild-type)

Homozygous (mutant)

Heterozygous

Cystic Fibrosis

NO

NO

YES

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)

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•most often has a globular (spherical) 3-D shape & is 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 contractionAntibodies ImmunityHemoglobin, myoglobin Oxygen transportInsulin, glucagon Blood glucose controlCollagen Tendons,dermisKinases Modulate protein activityDehydrogenases MetabolismThrombin, fibrinogen Blood clottingKeratin Hair and skinTrypsin, proteases DigestionPolymerases DNA, RNA synthesisNaATPases Ion pumps

Collagen

G6PDAlbumin

33

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