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Biology 321 Genetics Winter 2009Dr. Sandra Schulze

Office BI409

Office Hours: WF 4:00PM – 5:00PM

Grading

• Exam I: 25%• Exam II: 25%• Exam III: 25%• Problem sets 25%*• No specific grades for attendance or participation, BUT if your grade is border line and you were active in these categories I will bump you to a higher grade

• *QUIZ FRIDAY on mitosis and meiosis –this quiz will count as one problem set!

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Assignments• Seven problem sets (one quiz plus six take-home sets) throughout the quarter

• Reading assignments and MORE problems from the text/my fevered brain

• This course requires both LEARNING FACTS and SOLVING PROBLEMS

• Exams will be sometimes similar, sometimes quite different from the problem sets and text book, but the principles you use to solve them will be the same!

• At the end of the year I will grade ONE or TWO problems from each set – this will form 25% of your final grade.

How will we use the class time?

• 3 days a week, 1hr 20m per lecture

• Break in middle of lecture, or leave 5 minutes earlier? VOTE!

• Fridays: assigned problem sets due AT THE BEGINNING OF CLASS!!!

• Wednesdays: will include both lecture and tutorial.

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Course Goals

• Introduction to some new concepts (learning new facts)

• Problem solving (using lots of facts)

• Critical thinking (privileged knowledge)

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Course Overview• Mitosis! Meiosis!• Transmission Genetics

– Model organisms, Mendel, complications to Mendel, recombination, human pedigrees

• Prokaryotic Genetics– Mechanisms of DNA exchange in Bacteria, mapping in E.coli

• Molecular Genetics – DNA and information storage, molecular basis of mutation, molecular techniques, positional cloning

• Special topics – Surprise surprise?

Let’s dive right into the (gene) pool!

Lecture 1: Mitosis and Meiosis

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Cell division

Prokaryotic cell division

Eukaryoticcell division

chromosomes

Prokaryotes and Eukaryotes

US(and this course)

Bacteria ArchaeaEukarya

THEM (also this course (a bit))

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Prokaryotic vs eukaryotic cells

Prokaryotic vs. eukaryotic cell size

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Prokaryotic chromosome

Eukaryotic chromosomes

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Bacterial chromosome

Human chromosome

NOT to scale!!! replicated chromosome (can you see why?)

Chromosomes•• ChromosomesChromosomes are (usually) LONG pieces of double stranded DNA

• Can be linear (eukaryotic) or circular (prokaryotic)

• Can be complexed with proteins (chromatinchromatin) or almost naked nucleic acid

• Chromosome number can vary widely• Cells (and organisms) with two pairs of every chromosome in a set are diploiddiploid

• Cells (and organisms) with only one of each chromosome in a set are haploidhaploid

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Genomes

chromosomes, genomes and genes

• The genome is the total information content represented by a single set of chromosomeschromosomes

• Genome organization = the way in which this information is broken up and distributed over the chromosomes

• Information includes genesgenes which are sequences of DNA located at specific positions along the chromosomes

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Organism Genome Size

(n)

# of Genes Chromosomes

(n)

Human 3,000,000,000 35,000 23 linear

D.

melanogaster

140,000,000 13,600 4 linear

C. elegans 97,000,000 19,000 6 linear

A. thaliana 125,000,000 25,500 5 linear

S. cerevisiae 13,000,000 5,800 16 linear

E. coli 4,700,000 4,000 1 circular

Human mtDNA 17,000 37 1 circular

Prokaryotic vs. eukaryotic genomes

Prokaryotic vs. eukaryotic genome organization

Bacterial genome is organized into a single (usually) circular chromosome that is relatively small (~106bp)

Eukaryotic genome is arranged in a series of linear chromosomes that vary widely in size

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Chromosome number: haploid, diploid, polyploid

• Talking about the number of chromosome setsthat represent the genome information content of an organism

• The haploid set of chromosomes in an organism is a certain number = n

• In diploid organisms, where the chromosomes come in pairs, the total number of chromosomes is 2n

• Some organisms (some plants, some fish etc) are polyploid – they have multiple sets of chromosomes

Diploid vs. haploid life cycle

Animals – like us Plants etc.

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Humans are diploidtwo of each chromosome –homologous pairs

Homologous chromosomes

• Members of a chromosome pair that contain the same genes

• Each member is called a homolog

• One is inherited from each parent (so they are not identical)

• Chromosomes that contain different genes are non-homologous

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humans are diploidtwo of each chromosome –homologous pairs

Homologous pair of chromosomes

humans are diploidtwo of each chromosome –homologous pairs

Non-homologous pair of chromosomes

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Autosomes and sex chromosomes

• In many eukaryotes, the sexes differ with respect to a single chromosome pair – these are the sex chromosomes

• In one sex they match (are homologous), and in the other they do not

• All the other chromosome pairs are autosomes

Human males are diploid, with unmatched sex chromosomes (XY)

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chromosome number: euploidyeuploidy

• Multiples of basic chromosome set.

• Haploids, diploids are euploid.

• Polyploids are also euploid:– Triploids

– Tetrapoloids

– Pentaploids

– Hexaploids etc.

Wheat varieties are polyploidmultiples of whole chromosome sets

Hexaploid, 6n=42

Diploid, 2n=14

Tetraploid, 4n=28

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chromosome number: aneuploidyaneuploidy

• Changes in number of individual chromosomes, relative to the normal diploid number of two.

• Hyperploid, increase in chromosome number (trisomy, etc.)

• Hypoploid, decrease in chromosome number (monosomy, nullosomy)

Aneuploidy is not usually a good thingTrisomy 21 (Down’s Syndrome)

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The cell cycle and mitosis

Time for replication, transcription

Interphase

Time for cell division: no gene

expression

Cell division

MITOSIS

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Chromosomes and chromatids• After the chromosomes replicate during S phase, two sister chromatids are joined together by the centromere

• When sister chromatids separate during mitosis, they can still be called chromatids but more accurately they are daughter chromosomes

centromere

S phase

Non sister chromatids

So what is a chromosome???

• At the end of S phase, a cell has twice as many chromatids as there are chromosomes in the G1 phase– A human cell for example has:

• 46 distinct chromosomes in G1 phase• 46 pairs of sister chromatids in S phase

•• Therefore the term Therefore the term chromosomechromosome is is relativerelative– In G1 and late in the M phase, it refers to the equivalent of one chromatid

– In G2 and early in the M phase, it refers to a pair of sister chromatidsjoined at the centromere

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Prophase

• Chromosomes condense and become visible– Sister chromatids attached at centromere

• Spindle apparatus forms outside of nucleus– Microtubules (tubulin) parallel to the cell axis– Centrosomes, composed of centrioles and pericentriolar material, form the spindle poles

• Nucleoli disappear

In animal cells

Centromere

Chromosome

MicrotubulesCentrosome

Centriole

Sister chromatids

Nuclear envelope

Prometaphase

• Nuclear envelope breaks down, vesiculates• Microtubules extend into nucleus

– Kinetochore microtubules attach to kinetochores• Sister chromatids attach to opposite poles

Polarmicrotubules

Astral microtubules

Kinetochoremicrotubules

Kinetochore

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Metaphase

• Chromosomes form bipolar attachments and move to the metaphase plate (equatorial plane)

• Sister chromatids face opposite poles

(equatorial

plane)

Metaphaseplate

Anaphase

• Centromeres divide first and start to separate• Sister chromatids separate and move along microtubules to opposite spindle poles

• After migration of sister chromatids (now daughter chromosomes) to their respective poles, the spindle poles separate further

Separating sisterchromatids

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Telophase

• Nuclear envelope reforms around each set of chromosomes

• Chromosomes de-condense• Nucleoli reappear• Spindle disperses

Re-formingnuclear envelope

Chromatin Nucleoli reappear

cleavage

furrow

Cytokinesis

• Contractile ring forms around the equator of the cell, forms a cleavage furrow, then divides the cell into two halves (animal cells)

• Genetic material (chromosomes) and cytoplasm are divided equally into two daughter cells

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The cell cycle, ploidy, and DNA content during mitosis

Chromosomes and genomes

• How many chromosomes are here: 2n=?

• How many before DNA replication?

• How many after replication?

• Hint: count centromeres

Before replication

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4

4

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Chromosomes and genomes

Before replication • If before replication, there are two genomes in a diploid cell, how many genomes after replication but before cell division?

• 4 genomes

Chromosomes and genomes

Before replication

• If before replication, there are four chromosomes in a diploid cell, how many chromosomes after replication but before cell division?

• If the centromeres have separated, a temporary 4n stage (4n=8 chromosomes)

• And the number of chromosomes equals the number of chromatids

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Purpose of Mitosis? Parent cell is diploid (2n=2)

2n

Homologs don’t usually pair at mitosis

Chromatids separate (4n)

Daughter cells are diploid (2n=2)

•leads to daughter cells with the same DNA content (barring rare somatic mutations), same number of chromosomes as the parent cell

Summary of Mitosis for 2n=2

• Start with 1 cell (2 chromosomes, 2 chromatids)

• DNA replicates during S phase (2 chromosomes 4 chromatids)

• Sister chromatids separate at Anaphase (4 chromosomes, 4 chromatids)

• After Telophase and Cytokinesis, finish with 2 daughter cells (both 2 chromosomes, 2 chromatids)

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If everything was mitotic….

…life would be pretty dull….

FORTUNATELY! THERE IS MEIOSIS!!!

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• Like mitosis, meiosis begins after a cell has progressed through interphase of the cell cycle

• Unlike mitosis, meiosis involves two successive divisions– These are called Meiosis I and II– Each of these is subdivided into

• Prophase• Metaphase• Anaphase• Telophase

Homologs pair on metaphase

plate (each homolog consists of

two sister chromatids)

Daughter cells

have one

homolog from

each pair. But

each homolog

still consists of

two sister

chromatids.

MEIOSIS

Reductive division

Mitotic division

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Meiosis is a reductivereductive division

• Daughter cells have half the chromosome complement of parent cells

• Daughter cells become gametes (the only truly immortal cells…)

Meiosis is a reductivereductive division• Daughter cells have half the chromosome complement of parent cells

• Daughter cells become gametes (the only truly immortal cells…)

YOU

MOM

DAD

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Homologous chromosome pairs

undergoing crossing over at the

sites of chiasmata. These pairs are

also called “bivalents” or “tetrads”

Prophase I of meiosis

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What is the consequence of crossing over?

Metaphase I of meiosis

• Bivalents are organized along the metaphase plate

• Pairs of sister chromatidsare aligned in a double rowdouble row, rather than a single row (as in mitosis)

• The arrangement is random with regards to the (blueand red) homologues

• A pair of sister chromatidsis linked to one of the pole

• And the homologous pair is linked to the opposite pole

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Metaphase, Anaphase and Telophase of Meiosis I

How many chromosomes? How many genomes?What is the DNA content?

Meiosis II: in fact a mitosis

• Meiosis I is followed by cytokinesis and then meiosis II

• The sorting events that occur during meiosis II are similar to those that occur during mitosis

•• However the starting point is differenHowever the starting point is different• For a diploid organism with six chromosomes (2n=6)– Mitosis begins with 12 chromatids joined as six pairs of sister chromatids. i.e. 3 pairs of chromosomes (2n); each chromosome containing 2 chromatids.

– Meiosis II begins with 6 chromatids joined as three pairs of sister chromatids. i.e. 3 chromosomes (1n); each chromosome containing 2 chromatids.

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Meiosis II

Meiosis summary for 2n=2• Start with 1 cell (2 chromosomes,

2 chromatids (not shown))

• DNA replicates during S phase (2 chromosomes, 4 chromatids)

• Homologous pairs line up at metaphase (2 chromosomes, 4 chromatids)

• Homologous pairs separate at Anaphase I (2 chromosomes, 4 chromatids)

• After Telophase I and Cytokinesis, 2 daughter cells (1 chromosome, 2 chromatids)

• After Telophase II and Cytokinesis, 4 daughter cells (1 chromosome, 1 chromatid)

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What is consequence of independent assortment of chromosomes?

So why are YOU so different from mom and dad???

• Two meiotic reasons• Crossing over at Prophase I• Independent assortment of chromosomes at anaphase I

• BOTH are forms of recombinationrecombination

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Crossing over and independent assortment are happening in

the same meiosis…

• Crossing over happens because homologs pair in meiosis I

• Independent assortment happens because the chromosomes segregate randomly at anaphase I after their random alignment at metaphase I

…and when you put them together in, say, a human context?

• 23 pairs of chromosomes, aligning on the metaphase plate independently of each other and segregating during the subsequent anaphase…well there’s a formula:

�2n where n = # chromosome pairs• Plug in the numbers and you get…well…millions of possible combinations

• Add in recombination and, well….is it any wonder you’re different from mom and dad?

• What’s another ENORMOUS consequence of this variability?

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Differences between meiosis and mitosis

1) Mitosis forms two identical daughters; meiosis forms four gametes that are notidentical.

2) Meiotic Prophase I: Crossing over occurs, forming recombinant chromosomes.

3) Meiotic Interphase II: No DNA replication.

4) Prophase is considerably lengthened, relative to mitosis. In mammalian females, prophase begins in gestation and continues until the oocyte grows during an estrous or menstrual cycle.

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http://www.pbs.org/wgbh/nova/baby/divi_flash.html