Chapter 16 Notes pgs 333-348 10/14/14 4:28 PM

1. Eukaryotic cells exhibit both short-term and long-term differentiation,

whereas prokaryotic cells only have short-term responses.

2. Transcriptional regulation – determines which genes are

transcribed to mRNA =

a. Post-transcriptional regulation – affects the process of mRNA

b. Translational regulation – translation into proteins

c. Posttranslational regulation – life span and activity of proteins

REGULATION OF GENE EXPRESSION IN PROKARYOTES E. coli catabolizes sugars and molecules for C and energy – needs

lactose to trigger enzyme production for catabolizing sugar, won’t

do it if lactose isn’t present

o Three genes encode enzymes for catabolizing lactose by E.

coli, only transcribed when lactose present

Structural gene – gene that encodes a protein that has function

other than gene regulation

Regulatory gene – gene that encodes protein that regulates

expression of structural genes

Operon – cluster of prokaryotic genes and regulatory sequences

(DNA sequences involved in gene regulation)

o Operator – a short segment that regulatory protein binds to

Repressor – when active, prevents operon genes from

being expressed

Activator – when active, turns on gene expression

Promoter – site where RNA polymerase binds to begin transcription

Transcription unit – cluster of genes transcribed into single mRNA

THE LAC OPERON FOR LACTOSE METABOLISM IS TRANSCRIBED WHEN AN INDUCER INACTIVATES A REPRESSOR

LacZ, lacY, lacA involved in lactose catabolism (order: ZYA)

o lacZ encodes B-galactosidase – catalyzes hydrolysis of

disaccharide sugar, lactose, into monosaccharide sugars,

glucose, galactose

o lacY encodes permease enzyme that transports lactose into

cell

o lacA encodes transacetylase enzyme, unclear function

Lac Repressor – encoded by lacI gene, nearby but separate from lac

operon, ACTIVE

Negative gene regulation system - Lactose present

converted by B-galactosidase to allolactose, isomer of lactose

(inducer for lac-operon [inducible operon – inducer molecule

increases its expression] to transcribe genes, inactivates Lac

repressor)

Positive gene regulation system – two conditions: lactose

present + glucose low or absent (efficient transcription of lac

operon genes) OR lactose present + glucose present (very low level

of transcription of lac operon genes)

o CAP – regulatory molecule that acts an activator that

stimulates gene expression, synthesized in INACTIVE form.

When cAMP activates it, CAP binds to CAP site in promoter

and enables RNA polymerase to bind and transcribe the

operon’s genes

o Increase in glucose, cAMP levels low, inactive CAP

o Decrease in glucose, cAMP levels low, active CAP

TRANSCRIPTION OF THE TRP OPERON GENES FOR TRYPTOPHAN BIOSYNTHESIS IS REPRESSED WHEN TRYPTOPHAN ACTIVATES A REPRESSOR

Tryptophan – amino acid that is used in synthesis of proteins

Operation controlled by trpR (repressor INACTIVE), not located near

the genome (for lac operon it was nearby)

trpR activated when tryptophan levels are high

o operon is example of repressible operon, tryptophan is a

corepressor, activates the repressor to turn off expression of

the operon

LAC OPERON VS. TRP OPERON Lac operon – high levels of glucose: inactivation of adenylyl

cyclase so cAMP drops too low to activate CAP, so CAP can’t

bind to CAP site, RNA polymerase can’t bind to promoter

o Active form synthesized

o Inducer allolactose inactivates repressor

o Structural genes then transcribed

Trp operon – no tryptophan present already, then it goes

fwd, tryptophan binds to repressor to block at operon, RNA

polymerase binds to promoter, otherwise it doesn’t.

o inactive form synthesized

o corepressor (tryptophan) activates repressor

o activate repressor blocks transcription of the operon

REGULATION OF TRANSCRIPTION IN EUKARYOTES1. Transcription factors bind to TATA box and recruit DNA polymerase II

forming the transcription initiation complex

2. Polymerase unwinds DNA, begins transcription

3. upstream to promoter: promoter proximal region – contains regulatory

sequences called promoter proximal elements, regulatory proteins may

bind and either stimulate or inhibit rate of transcription initiation for this or

on the enhancer. (can be activators or repressors)

combinatorial gene regulation – by combining regulatory

proteins in certain ways to determine rate of transcription (works

because: use less regulatory proteins to control more gene

activity)

4. coactivator – multiprotein complex forming a bridge between activators

at enhancer and proteins at promoter – LOOP to stimulate transcription

5. motifs – helxix-turn-helix, zinc finger, leucine zipper

helix-turn-helix: loop region of protein connects to second to hold

first helix in place

zinc fingers: zinc fingers bind to specific base pairs or DNA grooves

leucine zipper: dimers, hydrophobic interaction between leucine

residues hold monomers together

METHYLATION OF DNA CAN CONTROL GENE TRANSCRIPTION

enzymes add methyl group to cytosine bases, can silence

genes, transcription turned off – example of epigenetics where

change in gene expression doesn’t involve change in DNA sequence

of gene or genome

o ex: X chromosome inactivation where one of two X

chromosomes pack into Barr body, turned off

heterochromatin – tighter DNA packing, only in eukaryotes, inactive

euchromatin – lighter DNA packing, active in transcription

differential gene expression – selectively expressing genes to produce a

variety of cells, because same genome

control elements – enhancers, silencers, operators, promoters, control gene

expression

Chapter 13 Notes pg.256-277 10/14/14 4:28 PM

Genes located on different chromosomes assort independently in gamete

formation because the two chromosomes behave independently during

meiosis

Linked genes – genes on the same chromosome

(+) – indicates wild type

chromosome recombination – two homologous chromosomes exchange

segments with each other by cross-over during meiosis, function of the

distance between linked genes -> closer, inherited together, lower chance of

recombination

genetic recombination – process by which the combinations of alleles for

different genes in two parental individuals become shuffled into new

combinations in offspring individuals

recombination frequency – the percentage of testcross progeny that are

recombinants

map unit – unit of a linkage map (mu or cM) is 1% = frequency, RELATIVE

measurement

sex-linked genes – genes that are inherited differently in males & females

homogametic sex – XX

heterogametic sex – XY

haploid – 1n

diploid – 2n

criss-cross inheritance – transmission of trait from male to female to male

etc.

reciprocal cross – switched phenotypes of parents

key to determining X-linked inheritance of recessive trait – all male

offspring of a cross between true breeding mutant female and wild-type male

have the mutant phenotype

INHERITANCE PATTERNS

Hemophilia – males are bleeders if they receive an X chromosome that

carries the recessive allele Xh. The disease also develops in females with the

recessive allele on both of their X chromsommes, genotype XhXh-rare.

(more common in males than females because males only need one

X to carry recessive trait Xh)

Dosage compensation mechanism – inactivates one of the two X

chromosomes in most body cells of female mammals, random chosen, Barr

body

orange and black patches of fur in calico cats result from

inactivation of one of the two X chromosomes in regions of the skin

of heterozygous females. Males, which only get one of the two

alleles, have either black or orange fur.

Red-green color blindness – X-linked recessive inheritance, cannot

distinguish between red or green colors

Duchenne muscular dystrophy – X-linked recessive inheritance, muscle

tissue degenerates in late childhood , unable to walk -> gene encodes

dystrophin, which anchors a particular glycoprotein complex in the plasma

membrane of a muscle fiber to the cytoskeleton in the cytosol – NOT

FUNCTIONAL IN PATIENTS, tearing leads to muscle destruction, live for 25

years

DETERMINATION OF HUMAN SEX

Based on Y chromosome which contains SRY gene, which

switches development toward maleness at an early point in

embryonic development

First month: structures are the same for XX and XY embryos

6-8 weeks: SRY gene activates in XY embryos, producing a protein

that regulates the expression of other genes, thereby stimulating

part of these structures to develop as testes, tissues degenerate

that would otherwise develop into female structures and go to penis

and scrotum.

Deletion – broken segment is lost from chromosome

Duplication – occurs if segment is broken from one chromosome and

inserted into its homolog.

Translocation – broken segment is attached to a different, non-homologous

chromosome

Inversion – broken segment reattaches to the same chromosome from

which it was lost, but in reversed orientation, so that the order of genes is

reversed

Duplication less harmful than deletion and can promote evolutionary change

without destroying important genetic information

SOME CHROMOSOME MUTATIONS INVOLVE CHANGES IN THE NUMBER OF

ENTIRE CHROMOSOMES

occur through nondisjunction – the failure of homologous pairs to

separate during first meiotic division or of chromatids to separate

during the second meiotic division

aneuploids – individuals with extra or missing chromosomes

euploids – normal set of chromosomes

monoploids – individuals with one set of chromosomes

polyploids – individuals with more than the normal number of

chromosomes

o triploids – three copies of each chromosome

o tetraploids – have four copies

trisomy – trisomy-13 produces Patau syndrome with characteristics

including cleft lip and palate, small eyes, extra fingers & toes,

mental developmental retardation, cardiac anomalies, trisomy-18

produces Edwards syndrome with characteristics including small

size at bith and multiple congenital malformations

polyploids – failure of spindle to function normally during mitosis,

spindle fails to separate duplicated chromosomes—twice the

usual number of chromosomes, can also occur when single egg

is fertilized by more than one sperm, humans – 99% die from this

triploidy – three chromosomes instead of 2, fertilization by two

sperm instead of one, rare – cultivated bananas are triploid

Boys are more likely to get sex diseases because a girl needs two copies to

display a recessive trait whereas boys only get one

Chapter 11 Notes: pgs 219-229 10/14/14 4:28 PM

Meiosis only occurs in eukaryotes that reproduce sexually and only in diploid

organisms

Homologous pair – have the same genes, arranged in the same order in

the DNA of the chromosomes

Gonads – primary reproductive organs

Diploid – 2n

Haploid – 1n, only as sperms or eggs

Somatic cells – body cells of a species

Gamete – sperm or ova

Autosome – chromosomes other than the sex chromosomes

Sex chromosome – X or Y

Synapsis – happens during prophase I where the two chromosomes of each

homologous pair come together and line up side-by-side in a zipperlike way

How does genetic recombination occur?

Crossing over, where the enzymes brek and rejoin DNA molecules of

chromatids with great precision – visible under microscope when

the chromosomes condense and thicken further

Crossovers/chiasmata – show that two of the four chromatids

have exchanged segments

MEIOSIS OVERVIEW

- PREMIOTIC INTERPHASE: DNA replicates & chromosomal proteins are

duplicated – two copies are identical sister chromatids produced

-MEIOSIS I: homologous chromosomes pair & non-sister chromatids cross-

over -> two cells with haploid number chromosomes produced

- MEIOSIS II: sister chromatids separate -> now daughter chromosomes,

forming only half of DNA strand in each molecule -> 4 cells produced

PROPHASE I:

replicated chromosomes fold and condense into threadlike

structures in nucleus

pairing/synapsis occurs -> tetrad (fully paired homologs), the

homologous chromosomes pair in a protein framework called the

synaptonemal complex

crossing over forms chiasmata AKA the enzymes break and

rejoin DNA molecules of chromatids

PROMETAPHASE I – getting everything ready for alignment/splitting

Nuclear envelope breaks down

Spindle enters former nuclear area

Two chromosomes of each pair attach to kinetochore microtubules

leading to opposite spindle poles

METAPHASE I – actual aligning

Movements of spindle microtubules align the tetrads on equatorial

plane – the metaphase plate – between the two spindle poles

ANAPHASE I:

Two chromosomes of homolog separate and move to opposite

spindle poles

TELOPHASE I:

New nuclear envelopes form in some species but not others

INTERKINESIS:

Single spindle of the first meiotic division disassembles and

microtubules reassemble into two new spindles for second division

No DNA replication occurs

PROPHASE II:

Chromosomes condense and spindle forms

PROMETAPHASE II:

Nuclear envelope breaks down, spindle enters the former nuclear

area, and spindle microtubules leading to opposite spindle poles

attach to the two kinetochores of each chromosome

METAPHASE II:

Movements of the spindle microtubules align the chromosomes on

the metaphase plate

ANAPHASE II:

Spindles separate the two chromatids of each chromosome and pull

them to opposite poles

NOW CALLED CHROMOSOMES INSTEAD OF CHROMATIDS

TELOPHASE II:

Chromatids decondense to extended interphase state, spindles

deassemble, nuclear envelope forms around masses of chromatin -

> 4 haploid cells

SEX CHROMOSOMES IN MEIOSIS

XX is fully homologous

XY is partially homologous

GENETIC VARIABILITY COMES FROM….

Genetic recombination – chiasmata shit

The differing combinations of maternal and paternal chromosomes

segregated to the poles during anaphase I – how they split on the

metaphase plate

The particular sets of male and female gametes that unite during

fertilization – who has sex with who

Chapter 15 pgs. 305-326 10/14/14 4:28 PM

blending theory of inheritance – hereditary traits blend evenly in

offspring through mixing of the parents’ blood

Mendel’s work with peas:

Studied a variety of characters – specific heritable attribute or

property of organism (seed color, shape, flower color)

Character differences or traits – alternate forms of these characters

Garden pea – easily grown in monastery garden

Plants typically self-fertilize but prevented this by removing

anthers and encouraging cross-pollination

Mandel first worked with crosses of plants differing in one character

Crosses

o P generation

o F1 generation

o F2 generation

HYPOTHESIS

o The adult plants carry a pair of factors [genes] that

govern the inheritance of each trait (alleles)

o if an individual’s pair of genes consists of different alleles, one

allele is dominant over the other, which is recessive

o the pair of alleles that control a character segregate as

gametes are formed; half the gametes carry one allele, and

the other half carry the other allele

now known as Principle of Segregation

o needed to have added one further hypothesis: Independent

assortment because alleles of genes assort independently

product rule – multiply individual probabilities to get the probability of

them happening in succession

sum rule – when there are two or more ways of obtaining the same

outcome

MENDEL USED A TESTCROSS TO CHECK THE VALIDITY OF HIS HYPOTHESIS

Test cross – cross between individual with dominant phenotype

and a homozygous recessive individual to determine if dominance is

hetero or homozygous

Dihybrid – an F1 that is produced from a cross that involves two characters

and is heterozygous for each of the pairs of alleles of the two genes involved

(Aa Bb)

Dihybrid cross – a cross between two individuals that are each

heterozygous for the pairs of alleles of two genes

Chromosome theory of inheritance – genes and their alleles are carried

on the chromosome

Locus – site on the chromosome where gene is

Incomplete dominance – one allee is not completely dominant over

another allele of the same gene

F1 phenotype is intermediate between the phenotypes of the two

parents

Phenotypes of F2 individuals are directly determined by the

different genotypes of the individuals, giving a 1:2:1 ratio instead of

3:1 ratio

Example of incomplete dominance:

FLOWER COLORS

o CR allele encodes an enzyme that produces a red pigment,

but two alleles CRCR are needed to produce the active form of

the enzyme to fully produce the red flowers, enzyme

completely inactive in CWCW form – colorless that appear

white. CRCW produce pink color.

o Sickle-cell disease

Homozygous for a recessive allele means YOU HAVE IT

Heterozygous: carrier, milder form of disease

CODOMINANCE:

Alleles have equal effects in individuals

ABO blood system

o IA and IB are co-dominant alleles that are each dominant to

the recessive i allele

o iAiA – iA

o iAiB – AB

o iAi – A

o iBi – B

o ii – O

EPISTASIS:

Genes interact with one or more alleles of a gene at one locus

inhibiting or masking the effects of one or more alleles of a gene at

a different locus

Labrador retriever colors – black, brown, golden

o Bb or Bb – black fur

o bb – chocolate brown

o EE/Ee – allows deposition of color

o ee – no color – golden

o true breeding black x true breeding yellw: BbEe black

heterozygous, BbEe x BbEe – 9/16 black, 3/16 chocolate, 4/16

yellow

polygenic inheritance – several to many genes contribute to the same

character

pleiotropy – single genes affect more than one character of an organism

example: sickle cells: recessive allele of a single gene that affects

hemoglobin structure and function… but causes many other

symptoms like blood vessel blockage, fatigue, abdominal pain,

heart failure, paralysis, etc… pleiotropic effects

true breeding – when self-fertilized they passed traits without change from

one generation to the next

hybridization – breeding of genetically diverse species

monohybrid cross – a cross between two individuals that are each

heterozygous for the same pair of alleles