Chapter 16 Notes pgs 333-348

10/14/2014

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, wont
do it if lactose isnt 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
operons 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 cant
bind to CAP site, RNA polymerase cant 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 doesnt.
o inactive form synthesized
o corepressor (tryptophan) activates repressor
o activate repressor blocks transcription of the operon

REGULATION OF TRANSCRIPTION IN EUKARYOTES

1. 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 doesnt 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
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, nonhomologous 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 chromosomestwice 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
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

blending theory of inheritance hereditary traits blend evenly in

offspring through mixing of the parents blood
Mendels 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 individuals 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
o
o
o

iAiB AB
iAi A
iBi B
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