Regulation of
Gene Expression

Prokaryotes

Lac Operon

always off
by default

disaccharide, its digestive,
lactose breaks down to glucose
and galactose

example of both
positive and negative
regulation

organization of
lac operon

DNA

regulatory sequences

promoter for regulatory
gene (pi)

regulatory gene (f)
codes for repressor
protein

promoter for structural genes (Plac)

Operator

RNA polymerase

when RNA can bind

lactose available, low glucose

if glucose is scarce, the high level of cAMP activated CPR, which binds to the promoter and increases RNA polymerase binding there. the lac operon produces large amounts of mRNA coding for the enzymes that the cell needs for use of lactose

when RNA cannot bind

lactose absent, repressor active, operon off

the lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator. the enzymes for using lactose are not made

lactose present, repressor inactive, operon on

allolactose, an isomer of lactose, binds to the repressor, inactivating it and depressing the operon. the inactive repressor cannot bind to the operator, and so the genes of the lac operon are transcribed, and the enzymes for using lactose are made

high glucose, lactose available

when glucose is present, cAMP is scarce, and CPR is unable to stimulate trancription at a significant rate, even though no repressor is bound

Lac I

located outside the lac operon. codes for an allosteric repressor protein that can switch off the lac operon by binding to the lac operator

structural genes

Lac Z

B-galactosidase

hydrolyzes lactose to glucose and galactose

Lac Y

Permease

the membrane protein that transports lactose into the cell

Lac A

Trans-acetylase

detoxifies other molecules entering the cell via permease

Trp Operon

always on

codes for tryptophan

requires 5 enzymes

essential amino acid

synthesis: always building something

trp R
(regulatory gene)

repressor

consists of:

promoter

RNA polymerase

operator

genes of operon

trp E

trp D

trp C

trp B

trp A

RNA binds here

when RNA cannot bind

tryptophan present, repressor active, operon off

as tryptophan accumulates, it inhibits its own production by activating the repressor protein, which binds to the operator, blocking transcription. enzymes for tryptophan synthesis are not made

when RNA can bind

tryptophan absent, repressor inactive, operon on

RNA polymerase attaches to the DNA at the operons promoter and transcribes the operon genes. enzymes for tryptophan synthesis are made

Eukaryotes

differential gene expression

the expression of different genes by cells
with the same genome

chromatin modifification

transcription

RNA processing

splicing

occurs when transcription
is still under way

addition of poly A tail

addition of 5' cap

added as soon as transcription is initiated

cap and tail added, introns removed and exons spliced together

created coding segments

what a DNA strand
consists of

distal control
elements (upstream)

enhancers, thousands of nucleotides
upstream or downstream of a gene
or even without an intron

proximal control
elements

located near the promoter

exon and introns

poly A signal
sequence

the last exon of the gene is transcribed into an RNA sequence that signals where the transcript is cleaved and the poly A tail is added

termination region
(downstream)

promoter

transcription start site

transcription factors

specific

activators- lead to increased expression

enhancer

repressor

bind to DNA sequences then go to a group of mediator proteins. these in turn bind to general transcription factors and then RNA polymerase II, thus assembling the transcription initiation complex.

general

leads to low(basal) levels of transcription

TATA box

production of a few RNA transcripts from genes that are not expressed all the time, but instead are regulated

chromatin: DNA + protein

histone: responsible for the first level of DNA packing in chromatin

different types of packaging

heterochromatin

highly compacted

no genes expressed

euchromatin

less compaction

genes expressed

histones used to form core:
H2A, H2B, H3, H4

Operon

a cluster of functionally
gene related genes can be
under coordinated control of a
single on-off "switch"

how is a "switch"
turned on or off?

on
(induced)

activator bound
to operator

off
(basal)

repressor bound
to operator

types of genes
associated with cancer

oncogenes

cancer causing genes

proto oncogenes

normal cellular genes that
code for proteins that stimulate
normal cell growth and division

if mutated, can turn
into cancer cells

encode components of growth factor signal transduction pathways

tumor supressor genes

encode proteins that inhibit
abnormal cell division

p53

protein it encodes is a specific transcription factor that promotes the synthesis of cell cycle- inhibiting proteins

defective or missing transcription factor, such as p53, cannot activate transcription

BRCA2

Ras gene

G protein that relays a signal from a growth factor receptor on the plasma membrane to a cascade of protein kinases

issues signal on its own

cancer cells

exhibit neither:

density dependent inhibition

anchorage dependence

do not respond normally to the body's control mechanisms

do not need growth factors to grow and divide

make their own growth factor

may convey a growth factor's signal without the presence of the growth factor

may have an abnormal cell cycle control system

repressor: binds to operator and blocks
attachment of RNA polymerase to promoter
preventing gene transcription repressor
protein encoded by regulatory gene

Inducer: inactivates repressor

repressor: binds to operator and blocks
attachment of RNA polymerase to promoter
preventing gene transcription repressor
protein encoded by regulatory gene

polypeptide subunits that make up enzymes for tryptophan synthesis

Cell Cycle

interphase

G1 phase

cell growth, accumulates materials
for DNA synthesis

S phase

DNA synthesis occurs, and
DNA replication results in duplicated
chromosomes

chromosome: consists of
one chromotid

2 chromatid= 1 chromosome

duplicated to make one chromosome

called sister chromatids

one of the multiple chromosomes in a eukaryotic cell is represented here, not yet duplicated. normally it would be a long, thin chromatin fiber containing one DNA molecule and associated proteins

once duplicated, a chromosome consists of two sister chromatids connected along their entire lengths by sister chromatid cohesion. each chromatid contains a copy of the DNA molecule

molecular and mechanical processes seperate the sister chromatids into two chromosomes and distribute them to two daughter cells

G2 phase

cell synthesizes proteins needed
for cell division

centrosome: microtubule organizing center

centrioles: pair present with in centrosome

a nuclear envelope encloses the nucleus

the nuleus contains one or more nucleoli

two centrosomes have formed by the duplication of a single centrosome. centrosomes are regions in animal cells that organize the microtubules of the spindle. each centrosome contains two centrioles

chromosomes, duplicated during S phase, cannot be seen individually because they have not been condensed

mitotic cell

also called M phase
consisting of:

mitosis

division of cell material

cytokinesis

division of cytoplasm

prophase

chromatin fibers become more tightly coiled, condensing into discrete chromosomes observable with a light microscope

nucleoli disappear

each duplicated chromosome appears as two identical sister chromatids joined at their centromeres and, in some species, all along their arms by cohesins (sister chromatid cohesion)

mitotic spindle begins to form. it is composed of the centrosomes and the microtubules that extend from them. the radial arrays of shorter michrotubles that extend from the centrosomes are called asters

centrosomes move away from each other, propelled partly by the lenthening microtubules between them

prometaphase

nuclear envelope fragments

microtubules extending from each chromosome can now invade the nuclear area

chromosomes have now become even more condensed

kitetochore, speacialized protein structure, has now formed at the centromere of each chromatid

two sister chromatids oriented- opposite poles (stable arrangement)

metaphase

the centrosomes are now at opposite poles of the cell

the chromosomes have all arrived at the metaphase plate, a plane that is equidistant between the spindles two poles. the chromosomes' centromeres lie at the methaphase plate

for each chromosome, the kinetochores of the sister chromatids are attached to kinetochore microtubules coming from opposite poles

anaphase

begins when the cohesin proteins are cleaved. this allows the two sister chromatids of each pair to part suddenly. each chromatid thus becomes an independent chromosome

the two new daughter chromosomes begin moving toward their opposite ends of the cell as their kinetochore microtubules shorten. because these microtubules are attached at the centromere region, the centromeres are pulled ahead of the arms.

the cell elongates as the nonkinetochore microtubules lenghten

by the end of anaphase, the two ends of the cell have equivalent- and complete- collections of chromosomes

telophase

two daughter nuclei form in the cell. nuclear envelopes arise from the fragments of the parents cells nuclear envelope and other portions of the endomembrane system

nucleoli reappear

the chromosomes become less condensed

any remaining spindle
microtubules are
depolymerized

mitosis, the division of one nucleus into two genetically identical nuclei, is now complete

cytokinesis

the division of the cytoplasm is usually well under way by late telophase, so the two daughter cells appear shortly at the end of mitosis

in animal cells, cytokinesis involves the formation of a cleavage furrow, which pinches the cell in two

in plant cells, the cell plate forms dividing the two cells

2 daughter cells total

karyotype

arrangement of chromosomes in pairs starting with the longest chromosome

different type of cells

somatic cells

all body cells except the reproductive cells

mitotically dividing and G0-arrested cells

make up vast majority of individuals tissues

diploid in nature(2N)

has two sets of chromosomes

in humans, its 46

germ cells

pockets of specialized cells

produce games (egg/sperm)

incorporated into ovaries and testis

undergo meiosis

haploid gametes

single set of chromosomes

in humans, its 23

reproductive/sex cells

sex chromosome is X

in a sperm cell, the sex
chromosome may be either
X or Y

genome

genetic information

Allele: alternate forms of
genes located on homologous
chromosomes

homologous chromosomes: two chromosomes with genes for the same traits one from each parent

BRCA1

Carbohydrates

Monosaccharide

simplest carbohydrate, simple sugars, these are monomers from which more complex carbohydrates are built. glucose C6H12O6

Gycosidic Linkage

a covalent bond between two monosaccharides by dehydration reaction

Disaccharide

are double sugars consisting of two monosaccharides joined by a covalent bond. they consist of two monosaccharides joined by a glycosidic linkage.

Polysaccharide

are macromolecules polymers with a few hundred to a few thounsand monosaccharides joined by glycosidic linkage. serve as storage /structure

Lipids

highly nonpolar,hydrophobic, soluable in organic solvent

Ester Linkage

Bonds created when fats form

Fats

Saturated

Unsaturated

Proteins

Functional molecules consisting of one or more polypeptides

polypeptides

Amino Acid

molecules with carboxyl and amino groups

Denaturation

Loss of proteins native structure; usually irreversible

Nucleic Acids

Amino Acid sequence of polypeptides programed into a unit of inheritence

Nucleotide

monomer of nucleic acids
Formed by 5 carbon sugar covalently bonded to nitrogenous base and phosphate group

a reaction in which two molecules are covalently bonded to each other with the loss of a water molecule. removes water forms new bond

Hydrolysis

meosis and sexual
life cycles

special form of cell division that produces gametes

occurs in reproductive organs- ovaries and testes- produces egg or sperm

each gamete has one set of autosomes (22) and a single sex chromosome

meiosis I

homologous chromosomes
seperate

haploid cells with
duplicated chromosomes

prophase I

metaphase I

anaphase I

Telophase I

Cytokinesis I

pair of duplicated homologs held together by chiasma and sister chromatid cohesion

synapsis and crossing over

alignment of homologous pairs at the metaphase plate

seperation of homologs

Meiosis II

sister chromatids
seperate

haploid cells with
unduplicated chromosomes

prophase II

metaphase II

anaphase II

telophase II

Cytokinesis II

chiasmata occurs

4 daughter cells total

these protein- protein interactions lead to correct positioning of the complex on the promoter and the initation or RNA synthesis. many enhancers act at different times or in different cell types

Interphase

pair of homologous chromosomes
in diploid parent cell

pair of duplicated homologous chromosomes

sister chromatids

diploid cell with
duplicated chromosomes

Eukaryotic cell structures

Ribosomes

Process RNA to synthesize proteins

Free

suspended in cytosol and synthesize proteins that function within the cytosol

Bound

attached to outside of the ER or nuclear envelope synthesize proteins that are either included in membranes or exported from cell

Nucleus

Membrane enclosed; control center of cell; directs protein synthesis by synthesizing mRNA

All cells have

DNA or genetic code

Membrane

Prokaryotes

Non membrane bound nucleoid

70S ribosomes

Cell Wall

Flagella

Presence of peptidoglycan

Eukaryotes

Membrane bound nucleus

80S ribosomes

Cell Wall in plants only

Flagella and cillia

Cell Wall

protects the cell, maintains shape and prevents excessive uptake of water

Junctions

Tight

membranes of adjacent cells are fused, forming continuous belts around cells. Prevents leakage of extracellular fluid

Desmosomes

Fastens cells together and anchors to the cytoplasm

Gap

They directly connect the cytoplasm of two cells, which allows various molecules, ions and electrical impulses to directly pass through a regulated gate between cells.

channels between adjacent cells that perforate plant cell walls

Smooth ER

Has no ribosomes and is not involved in protein synthesis. Contains enzymes that synthesize the lipid membranes

Rough Er

Proteins that include ones that'll be released or secreted from the cell, such as proteins made into lysosomes, and also released from other locatons with in the cell,

Mitochondria

sites of cellular respiration, generating ATP from catabolizing sugars, fats, and other fuels in the presence of oxygen

Chloroplast

contain the green pigment chlorophyll and enzymes/molecules that function in the phosphosynthetic production of sugar

Lysosomes

membrane-bound sac of hydrolytic enzymes that an animal uses to digest macromolecules

Flagella

SAME AS MITOSIS AND MEIOOSIS TWO BUT DIFFERENT IN THE SISTER CHROMOSOMES STAY PAIRED UNTIL THE END OF MEIOSIS I

Cell Respiration

Goal

To produce ATP

Redox Reactions

When there is a transfer of one or more electrons from one reactant to another.

OIL RIG

oxidation is loss, reduction is gain

C6H12O6 + 6O2 -> 6CO2 + 6H2O. What is getting oxidied and what is getting reduced

Glucose (C6H12O6) is getting oxidized and Oxygen is getting reduced

Glycolysis

the breakdown of glucose by enzymes, releasing energy and pyruvic acid.

Starts with

1 Glucose, 2 NAD+, and uses 2 ATP

Energy Investment phase

Input: glucose, 2 ATP
Output: pyruvate, 2 net ATP, 2 NADH

NAD+

electron carrier involved in glycolysis

Oxidized and reduced form

oxidized

FAD

reduced

FADH2

Types of ATP formation

Substrate-level phosphorylation

When an enzyme transfers a phosphate group from a substrate molecule.

Oxidative phsophorylation

The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.

Mitochondria

powerhouse of the cell, converts food into energy

Inner membrane space

Mitochondrial part where the ETC pumps protons

Matrix

Innermost compartment of the mitochondrion

Respiration

The process by which cells break down simple food molecules to release the energy they contain.

Lactic acid fermentation

pyruvate gets reduced; hydrogen from NADH goes into pyruvate goes to forms Lactate. HADH gets recycled, glycolysis continued

causes soreness after physical exertion

Alcoholic fermentation

the anaerobic process by which yeasts and other microorganisms break down sugars to form carbon dioxide and ethanol