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A level Proteins

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					Proteins (Talk about function, structure and bonding)

Primary:
Type, number, order, sequence, properties, 3d shape, biological functions

Secondary:
folds and coils, H bond, regular intervals, nearby amino acids, alpha helix,
axis, right handed, Hydrophobic R groups out, H parallel to axis,
stabilize helix, beta pleated, 2 or more regions, parallel, associate, h bonds
between adjacent chains

Tertiary:
Extensive folding, compact, globular, 3d shape, far away R groups, name
four bonds, soluble in water, hydrophobic in, hydrophilic out

Quaternary:
two or more polypeptide chains, hydrophobic, ionic, form functional
protein

Haemoglobin:
oxygen carrier, RBC, globular protein, quat structure, 2 alpha to beta tertiary
Four chain coil, hydrophobic in, hydrophobic out, aqueous blood
Fe2+, red color, oxy transport, reversible

Collagen:
Structural support for cells
Recurring polypetide subunits topocollagen, quaternary protein,
made up of 3 polypeptide chains, h bonds triple helix, stability
glycine proline, tropocollogen interacts with other running parallel
convalent bonds lysine, fibrils to fibres, staggered so no weak areas
stable due to triple helix and cross linkage
Enzyme

Effective collisions, correct orientation, active site, enzyme substrate complexes,
activation energy, highly specific,

Temperature:
Rate increases, optimum, max rate
K.E up, effective collisions, ESC, unit time, rate of reaction up

Beyond optimum, rate down, Increase in K.E disrupts intermolecular bonds (eg)
that stabilize 3d shape, unfold, active site lost, denature.

PH:
Narrow range, optimum ph, enzyme catalyzed reaction at maximum, current ph,
bonds that maintain 2nd 3rd most intact. Active site most ideal. Frequency of
effective collisions, most ESC formed per unit time, max rate.

Beyond optimum, affect tertiary. Changes in H+ concentration. Distrupt h bonds
maintaining active site, ionization of active site, changes charge, affect binding
 substrate less likely to bind to enzyme


Substrate concentration:
Low, a lot free active sites, immediate catalyse. Substrate up, effective collisions
up, more esc formed per unit time, ror increases

Medium, increase at slower rate, more active sites occupied, less free active
sites., competition, lower porbabilty, another factor becomes limiting

High, adding more, no increase, active sites fully occupied, max capacity, enzyme
conc limiting factor.

Competitive inhibition:
Close resemblance, competes for active site, binding prevents ESC’s, prevent
formation of products

Increasing conc of substrates decrease effect of competitive inhibitor, probability
of enzyme substrate collision increases. High substrate concentration, can reach
V max. inhibition overcome by high substrate concentration

Low conc of substrate, majority active sites occupied by CI, few ESC, ROR lower.
Substrate conc up, more compete with inhibitors for active sites. More ESC, ROR
up.
High substrate conc, most enzyme bind to substrate. V max achieved.

Non competitive inhibition:

No resemblance to substrate of enzymes. Binds to any other part other than
active site. Causes change in configuration of enzyme plus active site. Renders
proportion of enzyme molecules out of action. Original V max cannot me
reached.

Carbohydrates

Sucrose is not a reducing sugar

Sucrose= glucose + fructose
Lactose= glucose + galactose
Malaltose = glucose + glucose

Benedicts test:
2cm cube test solution in test tube
4cm Benedicts reagent excess
shake
heat in boiling water bath for two minutes
observe for colour change

For non reducing sugar, (if test negative):
Boil equal volume of test solution with dilute HCL for one minute to hydrolyze
disacharrides to monosacharrides.
Cool contents
Neutralize with NaHCO3 as benedicts reagent works only in alkaline condition
Carry out benedicts test again.


Starch:


Structure:                                   Function:

Many alpha glucose units                     Large molecule, insoluble, doesn’t affect
                                             osmotic potential. Large energy store


Amylose
(alpha 1,4 glycosidic linkages)              Helical, compact unbranched, little
coiling                                      space taken up


Amylopectin                                  Branchpoints to allow glucose to be
(alpha 1,4 1,6 glycosidic linkages)          hydrolysed faster, compact for storage
coiling and branching


Glycogen

Animal storage, 1000-1200 alpha glucose – large molecule, insoluble, storage,
little osmotic pressure.
Structure similar to amylocpectin, but more branched- helical and compact

More branched so more end for enzyme to work on to hydrolyze glycogen to
form glucose quickly


Cellulose

Structure:                                Function:

Many beta glucose residus,                Long fibre, exists as straight chain
Beta 1,4 glycosidic linkage

Alternate glucose units rotated 180      Allows straight chains to form
                                          Allow OH groups to project outwards
                                          to form H bonds, cross linkning


OH groups from H bonds with adjacent      Cellulose fibres from microfibrils =>
chains                                    macro => high tensile strength




                              Amylose vs Cellulose

Amylose
                                                 Cellulose

                                                 Beta glucose
Alpha glucose
                                                 Beta 1,4
Alpha 1,4
                                                 Straight chain
Helical
                                                 Alternate units 180
No rotation
                                                 OH groups cross link with adjacent cellulose
Cant form bonds with other amylose molecule
                                                 Cellulase
Hydrolysed by alpha amylase
                                                 Roughphage, structural funtion
Nutrient for humans and plants
                                                 Component of cell wall
Energy store
                                                 Cross link micro to macro fibrils
Cannot form fibrils
Lipids (structure than function)

Saturated fatty acids:
Maximum number of hydrogen bonds, no CC double bond, straight chain
 packed more closely, greater hydrophobic interactions, higher melting point

Unsaturated fatty acids:
Kinks, due to CC double bond, cant pack as compactly, hydrophobic interactions
weaker, lower melting point.

Fat test:

2cm cube of ethanol to 2cm cube of test sample
add equal amount of water
if cloudy white suspension, lipid is present
Cell Organelles (structure, function, where is it found, what does it
contain, significance)

Nucleus
Largest organelle, ovoid, nuclear envelop, double membrane, nuclear pores,
allow passage

Contains chromatin, thin threads when DNA not dividing. When cell divides
condense to form chromosomes.

Contains nucleolus, contain dna rna and proteins, place where ribosomal rna
synthesized.

Controls activities in cell, contains hereditary material

Ribosome
Protein synthesis, small and large subunit, found in cytosol or attached to ER

ER
Extensive network of membranous tubules and sacs called cisternae. Outer
membrane of nuclear envelope continuous with ER

rER
ribsomes attached
protein synthesis meant for secretion out of cell or to plasma membrane,
proteins fromed enter cisternal space, vesicles bud off ER, carried to Golgi

sER
lacks ribosomes, tubular
lipid stnthesis, detox of drugs

Golgi Apparatus

Stacked of membrane bound sacs called cisternae,
Forming and maturing face.

Receives proteins and lipids, final modifications take place, carbohydrate chains
may be attached, give different glycoprotein products.

Exit maturing face, form lysosomes.


Lysosome
Single membrane
Contains hydrolytic enzymes.
Enzymes synthesized in rER, transported to golgi for furthur processing.
Process enzymes bud of trans face form lysosomes.


Lysosome fuses with vesicles via endocytosis, release their enzymes, digest
contents.



Mitochondrion

Rod shaped, double membrane, outer inner membrane separated by
intermembrane space, inner membrane folded cristae, cristae projected into
matrix. Matrix has circular dna, ribosomes and various enzymes involved in
aerobic respiration to fom ATP

Chloroplasts

Lens shape, bound by double membrane
Innermembrane consists of flattened sacs with choloroplasts called thylakoids,
chlorophyll on thylakoid.

Cytoskeleton

Network of protein fibers throughout cytoplasm, structural support, controls cell
movement

Microtubules- tubulin, separate chromosomes during cell division

Centrioles

rod like structures positioned at right angles to each other
each contain nine triplets of microtubles arranged in a ring
found in centrosome
located close to nucleus
during cell division, centrioles replicate and move to opposite ends of cell
found in animal cells

important in nuclear division in animal cells, organizing of microtubles


Cell Fractionation

Break cells apart, separate organelles, homogenized in blender, centrifuge used
to separate based on density. Mixture spun in centrifuge high speed, centrifugal
force separate cell components based on size and densities. Largest organelles
sediment out first
Membranes


Fluid Mosiac Model

Plasma membrane 7.5nm thihc.

Phospholipid molecules occur in a bilayer

Charged groups of phospholipids face outwards and interact with aqueous
environment

Hydrocarbon chains of phospholipid face inwards and form the hydrophobic
interior

Interspersed among phospholipids are extrinsic and intrinsic proteins.

Some intrinsic proteins help regulate passage of substances in and outside cell.

Contain cholesterol that serves to regulate fluidity of membrane by retarining
movement of phospholipids in warm temps and prevent close packaging in cold
temps

Fluid as cell membranes are dynamic structures, proteins and phospholipids
exhibit lateral and transverse mobility.

Move about in the plane of membrane, proteins embedded in membrane
constantly change position, move in a sea of phospholips

Proteins are randomly spread throughout in a patchwork manner, hence the
mosaic arrangement.
Mitosis

Nuclues divides, two daughter nuclei, same number of chromosomes as parent,
genetically identitical, ensures diploid condition of parental cells maintained

Growth of organism, repair of worn out tissues, asexual reproduction.

Cell cycle

G1
Cell builds up store of energy, manufactures proteins for cell division, syntheises
organelles like mitochondria and ribsomes

S Phase
DNA replication occurs, DNA content doubles

G2
Cell continues to build large store of energy, manufactures proteins and
organelles.

Cell not dividing chromosome in form of chromatin. Replicates to produce two
identical sister chromatids, attached to centromere. First stage of mitosis, sister
chromtids condense and coil to form chromosomes.


Centrioles

Cytoplasm, close to nuclear envelop, located at centrosome, pairs and right
angles to each other, each consists of 9 groups of microtubles arranged in triples,
involved in spindle fibre formation during mitosis and meiosis.

Spindle fibres made of tubulin subunits, shortening of these fibres by removing
tubulin subunits accounts for sepration of chromosomes during nuclear division.

Process

Prophase
Condensation of chromatin to chromsomes. Chromosome consists of 2 sister
chromatids help by a centromere.

Centrioles move to opposite ends of the cell. Spindle fibre start to form

Nucleolus and nuclear envelop start to disintergrate

Chromosome start to move to equator of the cell

Metaphase
Chromosome align along spindles equator and spindle fibre attached to
chromosomes centromere.

Attached to kinetochore

Anaphase
Centromere of chromosome decides,
Sister chromatids separate, move to opposite poles of spindle, V shape

Telophase
Separated sister chromatids reach their respective poles of spindle, become
chromosomes of daughter cells
Decondense to chromatin
Spindle fibres disintergrate.
Nucleolus and nuclear envelop reform.

To ensure mitosis produce genetically identical cells,

Dna is replicated, semi conservative, when anaphase occurs, contain same dna as
that of parent. Arrangement of chromosomes along equator, spindle fibre
attached, ensure chromsomes spilt equally between two daugter nuclei.

Cytokineses
Furrow froms as plasma membrane pinches inwards between two nuclei, furrow
deepens till they separate to two daughter cells

In plants, golgi vesicles line in middle of parent cell, fuse to form cell plate,
extends across equator. Vesicles contain material for cell wall. Cell plate fuses
with parent cell wall and cell membrane separating the two daughter cells.

Abnormal events

Non disjuntion:
Failure of sister chromatids to separate during anaphase. Due to lack or
improper spindle fibre formation.

Polyploidy results in non disjunction of all chromosomes within diploid parent
while anueploidy occurs if its not all.
Meiosis

Nucleus divides to give four daughter cells, each containing half the number of
chromosomes from parent. Daughter cells genetically different, form gametes.

Homologous chromosomes

Diploid 2 sets of chromosomes. Each parent. 2n. chromosomes that determines
same characteristics are homologous.

Identical loci and pair with each other during meiosis

Same size, length, same position of centromeres.

Determine same characteristics but need not be the same, eg blue eyes and black
eyes

Prophase 1

Condenstation, homologous chromosomes pair up, undergo synapsis to from
bivalents, chiasmata formation, non sister chromatids break and rejoin, exchange
genetic material, via crossing over, new combination of alleles

Spindle fibres, centrioles move, Nucleolus and nuclear disintegrate

Metaphase 1

Homologous pairs arrange on equator of spindle
Spindle fibres attached to centromres via kinectochore
Independent assortment arrangement.

Anaphase 1

Homologous chromosomes sepeeerate and move to opposite poles due to
shortening of spindle fibres. Centromores remain intact.
Telophase 1

homologous chromosomes reach opposite poles of spindle. Fibres disintegrate,
nuclear envelope and nucleolus reform

Prophase 2 metaphase 2 anaphase 2 anaphase 2

Same as in mitosis

Subsequent cytokineses results in 4 daughter cells each being haploid and
genetically different from the parent cell and other daughter cells




Significance of meiosis

Sexual reproduction:
Haploid gametes fuse, zygote, restores diploid number of chromosomes,
prevents doubling of chromosomes in each successive generation.

Genetic variation:
New combination of alleles via:

Chiasmata formation and crossing over, enables exchange of genetic material
between homologous chromosomes.

Independent assortment. Orientation of pair of homologous chromosomes at
metaphase plate are random. Separation results in random assortment of
maternal and paternal chromosomes in gametes.

Random fertilization of gametes.

 result in genetic variation
DNA and Genomics

Structure of DNA

Double stranded, 2 polynucleotide strands, phophodiester bonds. Strands anti
parallel, base projected inwards so can interact via H bonds. Strands twisted,
helical. Nitrogenours bases form CBP. AT CG. Purines and pyramidines same
ration ensure with of dna constant throughout of width 2nm .

Function

Carry coded information to direct cell activity:
long polymer, store large amount of genetic info.

Stable:
H bonds, phophodiester bonds, less reactivity as no OH groups at carbon 2 of
deoxyribose.
Double helix, wrapped around histone protein


DNA replication

Origin of replication, helicase, break h bonds, unwinds seperates

ssDNA binding protein attach, stabalize, prevent recoiling, both act as templates
for daughter

separate, replication bubble, replication both directions

primase, catalyse short rna chain completmentary, polymerase cannot from
scratch
free dna nucleotides added to 3’ end of mucleotides 5’ to 3’

rna primers excised and replaced with correct nucleotides by dna poly 1

dna poly 3 add free nuceoltides to 5’ end, leading strand continous towards rep
fork,

lagging synthesis decontinously, short fragments of nucleotides0000000000000
okazaki fragments

rna primers removed, by dna polymerase 1 and fragments joined by dna ligase

overall replication towards rep fork


Semi conservative replication

E coli 14 generation, heavy isotope nitrogen, all have 15N in their bases, heavier
than normal dna

Bacteria transferred to light 14N of bacteria and allowed to divide just once.

DNA extracted and measured using caesium chloride density gradient.

DNA heavier than 14N bacteria but lighter than 15N bacteria, proves 15N and
14N incororated into dna bases. Hence proves semi conservative replication.

Structure of RNA

Single stranded, ribose sugar with OH on second carbon, uracil instead of
thymine

Trna:

Function- transfers amino acid to ribonsomes. Ranges them along mrna.
Single stranded RNA (80 nucleotides)
Clover leaeda shope, due to H bond between cbnp at certain regions.
5’G 3’ CCA for aa atachemnt site.
Opposite end of aa atcachement site is anti codon
Made of three base pairs complementary to codon on mrna
Each aa has a trana with specific anti codon.
Anticodon CBP with complemnatry codon in mrna.
Amino acid added to tran via trna synthethase



Central dogma
Uni directional flow of genetic info from dna to rna to protein via transcription
and tranlation

Rna used so prevent dna from damage due to exposure, more rna means more
copies of protein made simultaneously.
Each rna transcript can be translated more than once. Efficiency


Transcription.

Sequence of dna bases copied onto complementary sequence of bases in mRNA.
Dna template has promoter and terminator

Intiation:
3’ to 5’ dna template transcription. Sense strand
Rna polymerase, promoter, unwinds, break h bonds
Rna polymerase moves along 3’ to 5’, free ribonucletides added to dna via CBP
Catalyses phophodiesterbonds
AU GC TA CG
Transcription stops termination factor
Mrna relased, dissociates from dna, coils back
Prokaryote, hair poon loop, eukaryote, poly adenylation signal.

Rna procecessing

Eukaryotes- introns exons
Introns, dna not translated to proteins, exons dna translated to proteins
Pre mrna transcribed has introns and exons,
Introns removed and exons spliced
Poly a tail 5’ methyl guanosine residue cap stabilize out nucleus

Porkaryotes no introns, no mrna processing. No nuclear envelope, translation
and transcription take place simultaneously in cytoplasm.


Genetic code

Degenerate- more than one codon code for same aa,
Code is non overlapping
Code is punctuated.
Sequence of mrna read in three nucleotides called codon for particular aa
AUG start UAA UAG UGA stop codons


Translation

Prokaryotes:
30s ribosomal subunite binds to mrna via shine denalgro sequence at 5’ end of
mrna
shine dalgarno sequence is ribosomal binding site 8 basepairs upstream of start
codon aug.

Rrna has complemantary anti shine dalgarno sequence at 3’ end.

Mrna binds, positioned at P site,

Start codon aug establishes codon reading frame for mrna, attracts trna carrying
formly methionine trna

50s subunit ribosome binds, using energy of hydrolysis of gtp to form TIC

Eukaryotes:

Initiator trna comples carrying formyl methionine binds to the small subunit of
ribosome at the P site.

Mrna contains a finder sequence in the 5’ end which binds to a complementary
anti finder sequence of rrna.

Subunit moves downstream till it reaches start codon.

Initiaion factors bring components together, energy relased from hydrolysis of
gtp is expanded to form TIC.

Elongation

Amino acid trna complex of formly methionine binds to complementary start
codon aug at P site

Another trna carrying another amino acid recognizes next codon binds to A site

Peptide bond formation between AA occupying a site and p site by peptidyl
transferase,

Trna at P site loses its amino acid in process.

Ribosome moves a distance of one codon in 5’ to 3’ direction,

Trna without amino acide orgiannly at P site now shifted to E site, where it is
released.

Trna at A site that has dipeptide is translocated to P site,

Empty a site is ready to receive the third trna comlex which is anticodon is
complemenrtaary to thir codon of mrna.

Elongation till reaches stop codon.
A site accepts relasease factor, addition of water molecule to polypetptide chain.

Hydrolyses bond between polypeptide chain and trna at P site, release
polypeptide

Ribosomal subunits disassemble,
Polypeptide chain folds to assume tertiary and quat structure



Sickle Cell Anaemia

Single base substitution of dna that codes for beta globin chain
Adenine replaces thymine
Codon changes from CTT to CAT
Result in mrna being translated to change from GAA to GUA
Results in valine instead of glutamine in polypeptide chain.
Forms sickle cell haemoglobin
Valine is non polar and hydrophobic whereas glutamine is polar and hydrophilic
In low oxy levels, haemoglobin less soluble in water RBC crystallize due to
hydrophobic r group of valine
Result in rbc having distinct sickle shape




Genetics of Viruses

Viruses (what is it, what is has, structure)

Obligate intracellular parasites
Infect host cells of pro and eu
Cant reproduce on its own
Use host cell machinery

Have nucleic acid and protein encodes genetic information, viral proteins
Dna or rna
Nucleic acid surrounded by nucleocapsid

Nuclecapsid

Protect, digestion, enzymes
Sites that allow virion to host cell
Proteins to allow virion penetrate host cell

Membrane envelope

Phospholipids and glycoprotein
Aquire them through budding from cell membrane
Incorporates own protein such as glycoprotein spikes into envelope
Spikes help attach virus to receptors on susceptible host cell

Are viruses living.

Proliferate in cell.
Not in cell, never carry out functions of living thing
When affect host cell, use cellular machinery.

Living
reproduce fast rate in host cells, has genes, can mutate

non living
no cytoplasm or organelles, never metabolise, no generation of atp


Lytic cycle

Bacteriophage infects bacteria, multiplies inside using host cell machinery
Result in death of host cell when bacterium lyses and release phages produced in
lytic cycle

Structure of phage
Head structure, capcid, nucleic dna inside
In t4 tail hollow tube where nucleic acid passes through
surrounded by contractile sheath
end of tail, tail fibres, involved in biding of fage to bacteria cell receptors

Lytic cycle

Attachment:
Tail fibres attached to receptor, surface

Pentration:
T4 penetrates bacterium by contracting is contractile sheath of tail
Drives hollow tube into bacterium, facilitate entry of viral dna into cytoplasm of
host cell
Empty cpasid outside
Eclipse period

Replication
Enzymes encoded by phage genome shits down bateriums protein and dna
synthesis,
Replicates own genome, use bacterium cellular machinery to synthesize pahge
enzymes and structural components.
First genes express in enzyme that degrades host cell dna

Maturation
T4 phage components assemble around the replicated genomes to form mature
phage particle

Release
Phage directs production on enzyme lysosome breaks bacterial cell wall causing
cell lysis

The lysogenic cycle
Replicates phage genome without destroying host cell, lamda phage, one tail
fibre

Phage adsorbs to surface receptor of host cell, inject linear dna into the host cell

Host, lambda phage dna forms a circle,

Lysogenic cycle, dna integrates into specific region of host bacterium
chromosome,
Viral dna known as lambda prophage, cell is lysogen

Prophage gene codes for a repressor protein that prevents transcription of most
prophage genes

Phage genome mostly slient in bacterium

Everytime e coli divides, replicates phage dna along with its own dna. Allows
virus to propogate without killing host cells

External simulation uv light cuase prophafe to generate active phages that lyse
host cells.



Influenza

Envelop virus
Genome, 8 ssRNA code for viral proteins such as haemagluttinin and
neuraminidase

Hamagllutinin 80%, glycoprotein facitlitates binding on virus and entry of viral
genome into target cells

Neuraminidase 20%, enzyme involved in release of progeny virus from infected
cells

Attachement
Spread by aerolized viral particles,
Influenza virus, receptor sites, hemaggglutinin

Penetration
Endocytosis, host cell surface membrane invaginates and pinches off, virus in
endocytiv vesicle.
Vesicle, heaemagglutinin fuses the viral envelope with the membrane of the
vesicle
Viral capsid is released, viral dna released into cytoplasm

Replication
Rna transported to nucleus
Rna dependent polymerase replicates ssRNA use as template, synthesis of viral
proteins

Maturation
Viral rna transported from nucleus to cytoplasm
Undergo translation,
Synthesis viral particles

Release
Envelops, budding,
Viral proteins and glycoproteins incorporated into host cell membranes
Budding, host cell membrane evanginates and pinches off to form viral envelope


HIV (retrovirues)

Make dna from RNA, genome single stranded RNA, Reverse transcriptase

Structure:
2rna molecures, reverse trancriptase, proteins packed around them
Lipid membrane round capsid and glycoprotein

Attachment
Affects host immune cells, hiv gp120 binds to specific receptors like CD4 present
on many immune cells

Penetration
Virus fuses with plasma membrane
Protein capsid coat removed, released viral proteins, RT and integrase
Viral rna transcribed into DS DNA using reverse transcriptase

Replication
Integrates genetic material into host cell uclues via integrase
Provirus
Everytime host cel divdies, provirus replicates along with cellular DNA
After dormancy viral genes expressed.
Activation- transcribe viral dna into mrna, leave nucleus
Mrna translated to viral proteins in host cell

Maturation
Capsid around viral genome,
Viral proteins and glycoproteins incorporated dinto host cel membrane, form
envelope




Bacteria

Not bound within nuclear envelope, found in nucleoid. One orig, few thousand
genes organized into operons, folded into loop domains bound to central protein
scaffold, supercoiling.


Porkaryotic gene expression and regulation

Structural gene
Regions of dna code for product that has enzymatic function or structural
function
Regulatory gene
Regions of dna that code for protein products that rugulate expression of
structural gens

Opeeron concept
Structure of genes with related function
Structural genes code for specific products
Genes expressed as polycistroninc mrna

All genes under control of single promoter and transcription terminatror
Operator acts as a switch, positioned between promoter and structural genes
control acess of rna polymerase.

Outside operon is regulatory gene that codes for repressor protein


Trp operon, repressible operon

Promoter, operator 5 structural genes for enzymes.

Low tryp conc:
repressor moleculre inactive, not bound to operator region

High trp:
acts as co repressor, turn off transcription, tryptophan binds to repressor
molecule
active repressor, bind to operator region
transcription of 5 genes blocked as rna polymerase cannot bind to promoter


lac operon inducible operon

regulates metabolism of lactose, lactose metabolized if glucose is absent

operator, promoter, 3 structural genes lacZ lacy lax A

lac repressor coded by laclgene

lactose absent:
repressor molecule binds to operator region to prevent transcription of genes
that encode for lactose metabolism, rna polymerase cant transcribe
no resource wasted

lactose present:
allolactose acts as inducer, bind to repressor moleculre,
change configuration of inducer, cant bind to operator, allow mrna to attached to
rna polymerase to transcribe 3 genes.
Preferred substrate of bacteria is glucose, glucose present, inhibits enzyme
adenylyl cyclase, which converts ATP to cyclic AMP, camp low,

camp and needed to activate CAP so as to enhance binding of rna polymerase to
promoter to increase trancription

at low glucose concentration, camp high, as adenylyl cyclase not inhibited. camp
bind to CAP to form complex, enhaces binding, translate enzyme.
                        Prokaryote             Eukaryote
Organization




Genome Size             Smaller (0.6to10MB)    Larger, 10MB to 100000MB



                        Circular chromosome    Linear chromosomes
Form                    Plasmids




Packing of DNA          Looped domains by      More extensive than porkaryote
                        Protein scaffold
                                               Coiling dna 8 histone protein,
                        Supercoiling looped    nucleosome, joined by linker DNA
                        Domains with dna
                        binding proteins.      30nm solenoid fibre, form looped
                                               domains anchored by non histone
                                               scaffolding protein

                                               coiled further folded to form
                                               mitotic chromosome




Organization of genes   Operons concepts,      No operon, each gene controlled by
                        cluster of genes       individual promoter to code for
                        regulated by single    protein product
                        promoter

Dnal location           Nucleoid no            Chromosomes found in nucleus
                        membrane bound
                        nuclues

Orig                    One                    Many

Gene Length             Shorter                Longer

Introns and exons       Not interrupted by     Coding sequences interrupted by
                        non coding             non coding sequences introns
                        sequences introns      located in between exon sections


Non coding DNA          Small amount.          90% of genome does not code for
                        Consisting mainly of   protein or RNA.
                        regulatory sequences
Euakaryotic chromatin

Euchromatin region
Less condensed
genes actively or to be transcribed. Depleted of nucleosomes

Heterochromatin region
Condensed
Transcriptionally inactive, genes not expressed
Usually centromeres and telomeres, repetitive

Degree of condensation through chemical modification of dna and histone
proteins, methlylation.

Organization of eukaryotic chrmosome

First level of packing, wrapping negatively charge dna around groups of eight
positively charged proteins called histones, to form nucleosomes.

Joined by linker dna

Coiling of nuclesomes in 30nm solenoid fibre

Solenoid fibre forming looped domains anchored by non histone scaffolding
proteins forming a 30nm fibre

Centromeres (role and structure)

Sister chromatid adhesion, kinectochore formation, protein, serves as
attachment point for spindle fibres, anaphase

220 nucleotides, highly repititve
non coding dna


Telmeres

Ends of linear dna molecules
Many repeats 5’TTAGGG3’ non coding

End replication problem
Leading strand continuously 5’ 3’
Lagging discontinuously 3’5’ short okazaki frangments.
Each okazaki fragment has rna primer in front of it to provide 3’ OH end so it can
add deoxyribonucleotides for synthesis of new daughter strand.
To change rna to dna, there must be dna strand in from of primer to provide 3’
oh group so it can excise the primer to add deoxyribonucleotides to 3’ OH end
However it doesn’t happen when last rna primer attached to 3’ end of dna
template.

In the end rna primer destroyed by enzymes and newly formed daughter strand
is shorter than parental strand.

Process continuous critical genes may be lost.

1)Telomeres protect genes from being eroded, act as buffers to prevent loss of
crucial genes.
Potect linear ends of dna from degradation by deoxyribonucleases.

2) maintain integrity of chromosomal end with ends of other chromosmes,
prevents fusion.

3)limit life span of cells
undergo apotosis after few rounds of replication so limit extent of accumulated
mutation, prevet development of cancer cells.

Telomerase
Entended by telomerase. Contain short rna molecule complementary to repeast.
Allow extension of parental strand.

Telmoratse rna sequence pairs with telomrer sequence and enzyme uses rna
template to extend telomrer length by rna template dna synthesis

Dna polymerase makes all but the end double stranded.

Active in germ/sex cells.

1.5% coding

unique sequence of dna codding for protein or rna. Exons regions.

Moderatively repetitive dna (coding sequence) tandem gene clusters, multiple
repeats. Code for products required in large quantities.

98.5 non coding

introns, play role in alternative splcing. Allow one gene code for more than one
polypeptide. Tend to 5’GTXXXXAG3’

control elements, non coding dna that help regulate transcription. Promoter- rna
polymerase attach initiate transcription. Enhancer, 1000bp upregulate
transcription activate. Sinlencer, 1000bp, suppress transcription, downregulate.

Highly repetitive DNA
Centromere, sister chromatids attached, condensed regions. Kinecthocore,
spindle fibre fformation
Telomere, caps the end of chromosome
Microsatellites anlinkage mapping. Minisatellites VNTR dna fingerprinting.

Gene amplification.

increase in copies of gene from repeated replication of region of dna.
Cell high copy n umber od gene. increased expression of gene. transcription rate
increased. Amplification for products required in large quantities

1)development
amphibian eggs, large, high requirements for protein synthesis. Requires huge
number of ribosome. Need high rate of transcription for ribosomal rna. Hence
must amplifiy ribosomal rna genes

2) cancer

cells acquire resistance to growth inhibiting drugs.
Cells may respond to chemotherapeutic drugs by amplifying genes that prevent
drug from being effective

Amplification of multiple drug resistant genes.
More pumps on membrane of cells to eject molecules from cell including
chemotherapy drugs, make drugs ineefective. Hence tumour can spread.

Proto oncogenes to oncogenes

Cancer cells, oncogene included in amplified region, over expression of gene,
unregulated cell growth and division

3) evolution and diversity

genes in extra set accumulate random mutation,
increase variation of alleles in gene pool
evolution of new gene with new function,
evolution of new species via natural selection selected by environment

Process of gene amplification

   1) gene duplication due to unequal crossing of segments of non sister
      chromatids
   2) slippage, template shifts with respect to new complementary strand.
      Result in one region of template copied twice




Eukaryotic processing of pre mrna
Eukaryotic genes, non coding dna introns within coding regions exons

Rna polymerase 2 transcribes the gene, synthesizing pre mrna

Before undergoing translation must undergo processing


Capping

7’ methylguanosine 5’ cap added to 5’ end of dna, shield mrna from 5’
exonucleases. Signal for selection of start AUG codon of complex during
translation. Export out of nucleus

polyadenylayion

poly a tail added to 3’ end. 200 consecutive adenosine residues. Stabilizes mrna
protect from 3’ exonucleases. Export of out nucleus

splicing

in nucleus. 5’GU and 3’AG splice sites
five snRNP particles bind to splice site, rna form CBP with splice sites
spliceosome formed, bring upstream and downstream exons close together, fold
premrna at correct orientation for splicing

introns excised and exons brought together.  mature mrna

biological functions of introns and rna splicing

introns in nucleus serve as feedback mechanism, control production of rna
introns and exons enable genes to code for more than one polypeptide,
alternative splicing.

More protein products than number of genes, can carry fewer genes.

Alternative splcing

Conversion of pre mrna into more than one type of mature mrna by retaining or
removing certain exons




Need for gene regulation in eukaryotic genome.

Organisms do not need to express their genes all the time.

Controlling rate of transcription
Control elements: sequence of non coding dna that binds to regulatory protein
and influences gene expression (promoters, enhancers and silencers)

Rna polymerase plus protein complexes, general transcription factors, assemble
into complex on promoter form TIC, transcripte at low rate.

High rates require specific transcription factors with other control elements.

Promoters

Non coding DNA, recognition sites for genral transcription factor, bind and
recruit rna polymerase to nearby promoter.

Portoter 25-35bp upstream of start site tata box, which is recognition site by rna
poly to initiate transcription. Promoters located next to genes they regulate.


Enhancers

Distal control elements. Recog site for activators. Looping mechanism brings
bound activator protein, interact rna polymerase and other TF, enhances rna
polymerase, upregulate transcription of a gene


Silencers,

Distal control elements, thousand base pairs, TF bind, expression of gene they
control is repressed

Block dna binding site for activator protein
Masking activation domain of activator, preventing TIC
Interact with TF, blocking assembly or release of rna polymerase
Pack regions into heterochromatin



Activators and repressor proteins in each cell determine type of genes expressed


Histone Modification (acetylation)

Eukaryotic DNA packaged into highly organized and densely packed structures
known as chromatin

Histones can be modified to increase or decrease transcription
Unraveling of chromation regulated by acetylayion
Decreased net positive charge or histone
Lower affinity for negatively charged dna
Allow greater accesibiloity to d na,
Facilitates assembly of general TF and rna polymerase at promoter.

Deacytylation, converse is true


DNA methlyation

Changes structure of DNA, transcription factors require CpG rich sites to bind to
dna
Methylation interferes with their binding.
Eukaryotes found on transcriptionally silent regions of the genome, gene
silencing
Methylation complimented with deacetylation to silence gene



Control of gene expression at translational and levels.

Prevent translation:
Mask mrna with proteins so it cant be translated
Repressors bind to 5’ UTR, prevents ribosome binding

Control mRNA stability:
More stable, (longer half life) more times it can serve as template for assembly of
polypeptide.

Stability affected by
Length of poly a tail
Presence of 5’ cap,
Specific proeins that bind to 3’ utr to mark mrna for rapid degradation
Hormanes that stimulate or retard rate of degradation of mrna, decreasing or
increasing availability for translation to protein

Post translational controls

Glycosylation, add carbs
Phophorylation
Acetylation methylation
Hydroxylation

(degradation of proteins)
Half life of proteins, destabilized by chemical modigication of N terminus by
ubiquitinylation. Addition of conserved protein ubiquitin covalently to a protein
targets it for degradation.

Post translational regulation in prokayotes:

Prevent ribosome access to ribosome binding sites on mrna
Alter rate of translation via formation of stems and loops that inhibit nucleases
from degrading parts of polycistronic mrna, give longer time for translation

Postranslatioon regulation in prokaryotes
Feedback inhibition, final product in metabolic pathway can inhibit enzyme early
in the pathway
Modifying protein structure




Cancer

Unrestrainied cell proliferation caused by mutations in genes, loss of cell cycle
regulation

Mutations in tumour suppressor genes or proto oncogenes cause cancer. Also
dna repair genes.

Activation onco, inactivate TS genes  result in cancer

Conversion of proto oncogenes to oncogenes

Normal cells, code protein products promote normal growth and divisin,
products part of cell growth signaling pathway.

Ras Oncogene

Gain of function mutation, change bsae, produce hyper active protein or protein
overproduction.

Chromosome 11, codes for G protein, involved in kinase signaling pathways that
control transcription of genes that regulate cell growth and differentiation.

Normal condition, signaling pathway will not operate unless triggered by growth
factor bound to receptor,. Triggers gtp molecule to bind to ras protein, make it
active. Passes signal to series of cytoplasmic kinases, activate transcription
factors that turn on genes for proteins that stimulate cell cycle.

Has intrisnsic gtpase gunction to hydrolyse gtp molecule, revert to inactive state

Point mutation substituition, G to T, cancer, glycine at AA #12 sub for Valine,
change function of G protein.
Does not allow release of GTP, ras oncoprotein continuously active, signaling
pathway always on, uncontrolled and excessive cell growth and proliferation
Dominant mutation, single copy of oncogene is sufficient for overexpresssion of
growth trait. GOF mutation as protein gained new function not present in cells
with normal gene.

Caused by gene amplification, extra copies lead to overproduction of protein

Insertional mutagenesis, retrovirus in dna causes over expression of proto
oncogene as gene under control of retroviral poromoter and enhancer sequence.

Chromosomal rearrangement, dnaa break and rejoin, hyperactive fusion protein


Tumour surprressor genes.

Code products that inhibit growth and division for cells if not met, cell’s breaks.
Loss of function, recessive mutation. Both copies normal gene mutated.

How TS lose funtion

Point mutation, misfolded protein, loss of heterozygosity

P53

P53 protein intergrate signals that sense dna damage in G1 and G2 phases of cell
cycle. Single base sub.

Damage to cell dna, signal for expression of p53 gene. p53 functions as
transctiption factor for genes such as p21, dna repair protein, whose product
stops cell cycle at g1 phase. Allowing dna repair before dna replication.
More p53, more p21 express. If damage too great, apoptasis. Prevent cell passing
damage to daughter. Prevent tumour formation

Mutated p53 allow dna damage to accumulate

Develpotment of cancer is a multi step process.

Multi step process, accumnulation of 4 to 6 independent mutations in key
regulatory genes.
Take decades, need time for accumulation to occur.
Activation of at least one oncogene, suppression of several tumour suppressor
genes
Mutation of dna repair genes.

Cells become immortalized
Evade apoptosis, evade immune system, induce formation of blood vessels.
Metastasis, invade normal tissues
Respiration

Control supply of energy released, efficiently capture, heat produced controlled,
direct cellular activites

1)Glycolysis (location, steps, conditions and products)
Break gluscose to 2 pyruvate, 2 net ATP, 2 reduced NAD
With o2 or no 02, cytoplasm

-Phosphorylalted twice to hexose 6C biphosphate (phosphorylation rate
determining step by phophofructokinase)

Phophote group added by 1 atp, make sugar more reactive, so more energy
extracted later, charge of phosphote group trap glucose in cell, membrane
impermeable to ions

-Hoxose 6C biphophote lysed to produced 2 triose phophote

-Each triose phophate oxiddised via NAD, 2reduced nad produced
Phosphorylated to form 3C molecule with 2 Pi attached.

-Dephosphorylated twice to form pyrubate

-Phosphate removed transferred to adp to form atp.


3)link reaction

pyruvate ransported to matrix of mitochondira, occurs when there is o2

pyruvate, decarboxylation, remove c02 form 2C fragment

reacts with coenzyme A to form acetyl coA
fragment oxidized via dehydrogenation, one reduced NAD formed

overall 2 acetyl coA, 2 co2 and 2 reduced nad


4)krebs cycle

matrix, aerobic conditions, one glucose molecule, kreb cycle turn twice as 2
acetyl coA produced

acetyl coA fed into krebs cycle, undergo condensation reaction with oxaloacetate
form citrate

decarboxylation twice to form 4c intermediate, 2 moles of c02 produced

1ATP formed per acetyl coA via substrate level phosphorylation

produced 3 reduced nad, 1 reduced fad bia dehydrogenation

oxaloacetate regenerated so cycle can continue

overall, 6 reduced nad, 2 reduced fad, 4 CO2, 2ATP

4)oxidative phosphorylation

poroduce atp, regenrate nad+ and fad so glucose can oxidation can continue

inner mitochondrial membrane, aerobic, electrons carriers of progressively
lower energy levels, final acceptor oxygen.

Nadh molecules donate electrons to first electron carrier,
Electrons are passed down from one electron carriers progressively to lower
energy lebels. Electrons come from reduced nad and fad

Energy from transfer of electrons power proton pump, transport h+ ions into
intermembrane space of mitochondrial membrane against conc grandient.

Membrane impermeable to ions, build up of electrochemical gradient in
intermembrane space, potential energy known as proton motive force.

When enough h+ accumulated, h+ flow back into matrix via atp synthase due to
proton motive force. As protons flow down, provide energy for inorganic
phophote molecules added to adp forming atp.

Final acceptor of electrons is oxygen, which is reduced to h20, if no 02 elextrons
can’t pass their electrons or receive, accumulation of products, nad+ fad not
regenerated.
How structure of mitochondia facilitate repsiearion

Thin membrane 1 micrometer, facilitate rapid diffusion intermediate btwn
cytoplasm and mito

Membrane regulates passage of substances in and out

Inner membrane has cristae, infoldings, increased surface area.
Increase space for electron carrier complexes of etc.
Presence of stalked particles, atpase,
Impermeable to h+ allow h+ ions to accumulate in intermembrane space,

Matrix has required enzymes


Anaerobic repiration
OP cant occur as no oxygen as last electron acceptor. Need to regenretrate nad+
and fad+ hence need alternative hydrogen acceptor.

Ethanal in plants, pyruvate in mammals.
Plants form ethanol, humans lactate
Photosynthesis

Structure of chloroplast

Large organelle (4un to 7um in length)
Double membrane, thylakoid membrane system enclosing thylakoid space
Filled with stroma, contain photosynthethic pigments, stacked to form grana,
joined by lamellae


Structure of chrolplast to function

Envelope, double membrane, spererates organelle from cell, allow
compartmentalization. Inner membrane form lemallae system increases SA

Lamellae system, consitssts of thylakoids, flattend fluid like stacs stacked up,
intergral lamaellae links granum together. For light reaction to accour, large SA
to attach pigments. Allows max avsorbtion of light

Stroma, water matrix, enzymes, chemicals, starch, lipids dna
Dark reaction occurs here, storage for stratch, associated with lamellae system
so products of light reaction channeled to dark

Thylakoid membranes right angles to light source for max absorbtion

Chrolrophyll absorbs red and blue violet light reflects green light
Chlorophyll structure to function
Tail hydrophobic to anchor to thylakoid membrane,
Head hydrophilic, next to aqueous stroma,
Has flat head, parallel to membrane surface, max light absorbtion
Absorbtion of light causes emission of electrons necessary for light reactions

Photosystem

Ps1 contains ps700 – special chlorophyll molecule at ps1 reactions centre that
absorb wavelength light at 700nm

Ps2 contains ps680- special chlorphyll a molecule at ps2 reaction centres absorb
wavelength at 680nm




Non cyclic photophosphorylation (what it involves and steps)

Ps1 PS2, nadp final e acceptor, produce atp and nadp. Photolysis of water

Photon of light strikes pigment molecule of light harvesting complex of ps2.
Energy relayed to other pigment molecules till reaches p680 special chlorophyll
a molecules in ps2 reaction centre

Energy excites P680 electorns to higher energy state, capture by primary
electron acceptor

Replace electrons lost, photolysis of water, enzyme splits water molecule into 2
electrons 2 h+ and oxygen. H20 -> 2e 2h+ 0.5 o2

Oxgen combines with other atom, o2 released as by product. H+ in thylakoid
space

Electron passes primary electron acceptor of ps2 to ps1 via ETC
Increasing electronegativity, electron travel downhill energy lost used to form
atp

Light strike pigment of light harvesting complex of ps1, energy relate to other
pigment molecules till in reaches p700 special chlorophyll a molecules in ps2
reaction centre
Excites electron in one of two p700 chlorophyy molecules to higher energy state,
electron captured by ps1 primary electron acceptor. Electron delpeted from psl
replaced by electron from ps2

Photoexcited electrons passed from ps1 epri electron acceptor to second
electron transport chain. Nadp+ acts as final electron accettpotr by nadp+
reductase,

Two e’s toghterh with h+ to nadph

High energy elctrons in nadph provide reducing power for synthesis of sugar in
light independent raction.

Cyclic photophosphorylation

Involves photosystem 1 only, synthesis of atp

Photon of light strikes pigment molecule of light harvesting complex of ps1m
ebergy relayed to other pigment molecules till in reaches one of the p700 special
chlorophyy a molecules in ps1 reaction centre

Energy transferred excites one of the p700 electrons into a higher energy state
and electron is captured by pri electron accpetor which passes electrons to
middle of 1st elctron transport chain.

Loss of excitation energy is coupled to atp production as electrons move down
progreesively lower energy levels back to ps1

No nadph or o2 produced. Produce only atp, calvin cycle require more atp than
nadph, cyclic light dependent reaction makes up the difference


Atp synthesis by chemiosmosis

Splitting of h20 occurs in thylakoid space. Generates h+ ions
Electrons travelling down series of electron carriers used to pump H+ ions from
stroma to thylakoid membrane,

Accumulation of h+, proton motive force due to h+ gradient across membrane

Atp synthesis occurs when H+ flow down conc gradient through ATPase back to
stroma, adp to atp.

Light independent reaction (calvin cycle)

Stroma, make carbohydrates from co2,
Require atp, reducing power of nadph in light reactions, with or without light

   1) Co2 fixation
In stroma of chloroplast, co2 combines with 5 carbon ribulose biphosphate,
catalysed by rubp carboxylase
Result in unstable 6 c compound which splits to form two molecules of gycerate
3 phosphate

    2) reduction
3C clycerate 3 phosphote (GP_ phosphoglyceric acid reduced by naph to form
triouse phosphate
atp and nadph needed

triose phophate first carb produced in photosynthesis. Combine to form glucose
phosphate via condensation

3)
regeneration of co2 accpetor rubp
not all triose phophate used to synthesize glucose, some used to regenerate co2
acceptor molecule RUBP to accept co2 so carbon fixation can continue. Atp
needed for regenration
3 molecules of rubp generated form 5 molecules of triose phophate




Limiting factors

Rate limiting step, rate of a biochemical process which involves a series of
reactions will be limited by slowest reaction in the seres

Light, co2 concentration and temperature

Principal of limiting factors state that when a chemical process is affected by
more than one factor, rate is limited by that factor which is nearest its minimum
value.
Changing the quantity of the limiting factor directly affects rate of reaction

Light
No light rate 0, low light shortage of chemical products of light reaction like atp
and nadph.
Rate limiting step is point of calvin cycle when gp converted to tp via nadph.
Rate increases linearly till light saturation is reached,.

Low light intensities, co2 evolved as not used up in photosynthesis, when co2
given out during repiration used completely for co2 fixation, compensation point
is reached. Rate of photosynthesis = rate of repiration.

CO2
Low conc, rate limiting step in calvin cycle in when co2 fixation with rubp to
form 2 glycerate 3 phophate. Causes rubp and nadph to accumulate

Temperature.
Dark stage affected as involve enzymes.
Low temperatures, enzymes that catalyze reactions of calvin cycle work slowly,
nadph accumulates.

Water,
No water, stomata of plant close, decrease entry of c02, c02 becomes limiting
factor,
Source of protons and electrons through photlysis




Homeostatsis

Processes, constant internal environment
Cells function optimally
Maintain ph, temp, glucose level,

Deviation from set point acts as a stimulus
Detected by receptors which switches control mechanism,
Send signals to effector which initiate series of corrective mechanism to remove
stimulus
Bring system back to set point, response turned off by negative feedback loop.

Principles,
Self regulatingm corrective mechanism triggered by entity that needs to be
regulated
Negative feedback, disturbance in system sets in motion a sequence of events
which counteracts the disturbance, oppose stimulus to restore normal state.
Stimulus detected by receptor, switches on controller, send signal to effector
Appropriate response bring condition to normal limits


Homeostatic control of blood glucose level by insulin and glucagon

Blood flows to alpha and beta cells of islets of langerhans of pancreas. Detect
changes in blood glucose levels, react by secreted hormones

Stimulus: blood glucose level
Detector: alpha beta cells
Hormone: glucagon from aplph, insulin from beta
Effector: liver and musclce cells

Increase in blood glucose level

Detected beta cells, secrete insulin, insulin transport circulatory target tissues,
bind to receptor, trigger cacscade of intracellular events so tissues respond to
reduce blood glucose level.

Cause vesicles containing glucose carrier proteins to fuse to cell membrane,
increase glucose uptake, more permeability,

Increase intracellular enzyme activity to convert glucose to glycogen

As blood glucose level decrease, serves as negative feedback to beta cells to
decrease insulin secretion.

Insulin secretions return to normal when set point restored


Decrease in blood glucose level

Alpha cells
Glucagon secretion by alpha cells increase
Transported to target tissues, bind to receptor to trigger cascade of intracellular
signaling events to raise glucose level

Effects: glucagon increases through activation of enzymes that break gycogen to
glucose, formation of glucose from amino acid.

Glucose level increases, serves as negative feedback for alpha cells to decrease
glucagon secretion.

Normal when set point restored
Cell signaling

Reception

Formation of ligand recptor complex
Cell detects signaling molecule, change in shape of receptor protein, initiate
transduction

Transduction
Converts external signal to internal to bring specific cellular responses
Requires different series of molecules known as “relay molecules”

Cellular responses
G protein linked reeptor (glucagon)

Ligand binds to extracellular side of receptor,
Activated, changes shape,
Cytoplasmic side of receptor binds to inactive g protein, causing gtp to displace
the GDP
G protein active
Dissociates, move along membrane
Binds to enzyme adenylyl cyclase and activates it
Activated enzymes triggers next step in signal transduction pathway, initiating
signaling cascade that leads to cellular response.

Activation of adenylyl cyclase converts ATP to form cyclic AMP
camp is second messenger within target cells, duffuses to cytoplasm
camp activates protein alpha kinase which phophorylates and activates enzymes
like glycogen phosphorylase needed for breakdown of glycogen to glucose for
respiration
enzymes needed for formation of glycogen inhibited by alpha kianse through
phophorylation


Receptor tyrosine kinase (receptor for insulin)

Before signal molecule bind, receptor exists as individual polypeptides on
membrane
Binding of 2 signal molecules causes 2 of them to associate, form dimmer
Dimerization activates tyrosine kinase region at each polypeptide
In turn phosphorylates tyronsines on tail of other polypeptides
Receptor protein fully activated, recognized by specific relay molecules inside
cell
Each protein binds to phophorylated tyrosine, result in structural change lead to
activation
Activated protein triggers signal transduction pathway, lead to cellular response.
One receptor rtk may activate ten or more different transduction pathways and
cellular responses

Causes vesicles, glucose carrier proteins move fuse to cell membrane, increase
glucose uptake,
Activate enzymes that synthesis glycogen from glucose, glycogen snthethase,

Increase rate of protein fat synhesis



How increased blood sugar levels cause pancreatic cells to release insulin.
Increase blood glucose, increase atp production, glucose detected by beta cells.
Atp block KATP channels, closes, depolarization, activates voltage gated Ca2+
channels to open, influx of Ca2+
Stimulates exocytosis of vesicles containing insulin,
Released to blood

As blood glucose levels decrease, Katp channels open, cell hyperpolarize, no
influx of Ca2+, no exocytosis of vesicles containing insulin


To stop this reaction, g protein has gtpase enzyme to hydrolyze its bound GTP to
GDP
G protein inactive, leaves enzyme, return to original state
Allows pathway to shut down when signaling molecule not present




Neurone

Cell body
Dentrites receive signals
Axon transmit signals, ends are synaptic knobs, contain neurotransmitter
acetylcholine
Myelinated neurons:
Myelin sheath, wrap around axon => insulation, prevent loss of charges

Nodes of ranvier: gaps where myelin sheath absent, allows salutatory conduction
of impulses.


Resting potential

Cells have charge difference across plasma membrane, unequal distribution of
K+ and Na+
Resting condition, inside axon negaticely charge than outside tissue fluid
Difference casues membrane potential.
-65 to -70mv
higher K+ and lower Na+ compared to outside

How PD maintained

Gradient maintained by:

1) Sodium potassium pump
transport Na+ out and K+ in, energy, active transport, 3Na+ out, two K+ in.

2) Selective permeability of membrane
ions leave enter cell through transmembrane protein molecules, facilitated
diffusion via leak channels

20-25x more permeable to K+ than Na+, more potassium leak channels in
membrane, K+ tend to difuse out, more positive ions outside axon.

Therefore membrane is polarized, net positive charge outside


Action potential

Depolarization

Stimulus changes permeability of membrane to Na+ and K+
Start of AP, permeability of membrane to Na+ increases due to opening of
voltage gated sodium ion channels
More depolarization, more Na+ channels open, positive feedback
Na+ diffuse into neurone down electrochemical gradient
Inside of axon increasingly positive -70mv to +40mv
Membrane depolarized

Repolarization

Peak of AP, Na+ gated channels close,
K+ gates, Permeability of membrane to K+ increases
K+ diffuse out of neuron and membrane repolarises

Hyperpolarisation

Brief period when potential becomes more negative at resting potential
Due to slight delay in closing of voltage gated K+ channels
Resting potential of -70v achieved by closure of gated channels and pump.


All or nothing law

Nerve will respond if stimulus exceed threshold potential, usually exceed -55mv
Ap generated, all have same peak of +40mv
Frequency of AP determine strength of stimulus



Propagation of nerve impulses.

One direction, regenerated anew at nodes of ranvier
Action potential at point of application creates area of positve charge
Adjacent region along axon at resting potential
Difference in potential between two regions creates local electrical circuit
Circuit changes membrane potential at next point in direction of impulse
transmission
Na+ influx, depolarized, more voltage faded Na+ channels open, more Na+ influx,
positve feedback.
Membrane potential reaches threshold value, action potential generated.
Slight depolarization of next node lead to sodium influx, positive feedback,
further depolarization and formation of another action potential at this node

As new action potential occurs at one region, previous region undergoing
repolarisation and hyperpolarisation. Na+ gates temporarily inactive, hence
nerve impulses do not get transmitted backwards due to regractory period

Myelinated neuron, local electrical circuits formed between nodes of ranvier, AP
jumps from one node to another, increasing speed of transmission. Salutatory
conduction.

Factors affecting speed of transmission

Diameter of axon
Larger, less resistance, faster rate

Myelin sheath
Myelinated axons, AP jumps from one node to another, salutatory conduction,
speeds up transmission

Temperature,
Affect movement of ions and fluidity of phospholipids. Temp up, KE up, speed
transmission up.

Refractory period

Time after AP where neurone cannot respond to another stimulus
Ensures unidirectionality of impulse, no over stimulation of nerves

Absolute refractory period. Na+ channels fully opened or inactivated

Relative refractory period. Cannot transmit another AP unless stimulus is
stronger than normally required. AP hyperpolarized, more difficult for stimulus
to exceed threshold value


Synapse


Structure
Point where axon of one neuron joins the dendrite or cell body of another
Gap of 20 nm, synaptic cleft
Neurone before synapse is presynaptic neurone, after is post synaptic
Presynaptic expanded to form synaptic knobb, contain many mitochondria, atp,
active transport, synthesis of neuro transmitter. And synaptic vesicles that
contain acetyl choline
Post synaptic membrane possesses protein receptor molecules that
neurotransmitters can bind after they difuse across synaptic cleft.

Transmission across membrane

Impulse at synaptic knob depolarizes the presynaptic membrane
Opens up calcium ion channels on presynaptic membrane briefly
Calcium ions diffuse to synaptic knob
Influx of calcium ions induce few synaptic vesicles containing acetylcholine to
fuse to prersynaptic membrane and release their contents via exocytosis
Acetylcholine molecules diffuse across synaptic cleft to post synaptic membrane
Acetylcholine binds with receptor protein on membrane. Receptor has shape
complementary to acetyl choline molecule so it can bind.
Binding changes receptor protein, opening channels so sodium ions can pass
through
Causes depolarization at postsynaptic membrane, EPSP,
Ap generated at postsynaptic neurone if threshold exceeded, impulse propagated
Removal of acetyl choline done by acetylchoinerase on post synaptic membrane,
hydrolyzes it to choline and ethanoic acid
Taken back to presynaptic knob, recombined to acetylcholine and repackaged
into synaptic vesicles.
Causes membrane to repolarise
Excitatory vs inhibitory synapses

EPSP

Change in conformation of receptor sites causes ion channel to open, allow Na+
to enter,
Lead to depolarization of post synaptic membrane.
Summation of a few EPSP to exceed threshold

Inhibitory

Released neurotransmitter substance increases permeability of membrane to Cl-
and K+. Cl- rush in, K+ rush out. Neurone more negative than resting potential,
More difficult to exceed threshold to form AP.




Evolution
Definition:
Decent with modification, development of new orms of organisms from pre
existing forms

Darwin

Species produce more offspring than environment can support
Lack of food or resources, many offsring don’t survive
Population members vary greatly in traits
Traits inherited from parents to offspring

Inference: individuals inherited traits that give them higher probability of
surviving and producing in a given environment rend to leave more offspring
than other individuals

Inference: unequal ability of individuals to survive and reproduce lead to
accumulation of favourable traits in population over generation


Natural selection:

Over production of offspring

Constancy in number, as tiny fraction completes development

Struggle for existence, individuals compete with each other for limited resources,
selective agent, determining survivability of offspring, selective agent keeps
numbers constant

Variation among offspring, gene mutations, chromosomal mutations, meisis
random fusion, can allow them to adapt better

Survival of fittest by natural selection, selective agent allow organisms with
favorable characteristics to survive longer, more chances of reproducing and
pass heritable traits to offspring. Converse for those with unfavorable traits that
will be selected against environment,

Like produce like. Pass theres characteristics to offspring, favorable traits appear
at higher frequency in next generation

Formation of new species. Advantageous variations gradually accumulate, less
facvorable variations diminish. New species form if they do not interbreed.

Which traits are favoured depends on environment context.

Smallest unit of evolution
Population, interbreeding individuals, particular species shatring common
geographical area

Natural selection acts on individuals, population evolves with time

Variation

Difference in characteristics

Continuous, exhibits gradation from one extreme to the other without breaks,
Polygenes and environment factors

Discontinuos, discrete differences in characteristics, one or two major genes, not
affected by environment.


Causes of variations

Environment- provides space and nutrients for growth and expression of traits
coded by genes

Genes- reshuffling by mating, meiosis, random fusion,

Mutation in evolution

Gene or point mutation, makes new alleles, increase gene pool for natural
selection to work on
Only mutations that occur in gametes can be passed on to next generation

Modes of selection
Survive and reproduce at a higher rate, directional selection, disruptive selection
and stabilizing selection

Selection favors extreme end of phenotypic range (directional) when
environment changes

Stabalizing favours imtermediate variants, reduces variation

Disruptive, favorours both ectremes of phenotypic range


Effect of environment on phenotype

Natural selection in peppered moth
Black vs white, black from mutation, before industrial revolution, after, walls
blackened, camouflage, removal of predator, white selected against. Increase in
allele frequency of dominant allele
Homology
study of similar characeteristics in various aspects such as anatomy, embryology
and molecular resulting from common ancestry.

Characteristics present in ancestral organism altered by natural selection as face
different environmental pressures.

Homologous trait is characteristic derived from common ancestor

Homolohgous structures

Same basic plan, same relative positions, same embryonic development, may or
may not serve same function

Divergent evoloution
Trait by common ancestor evolves into different variations over time due to
different environmental pressures.
Vertebrate limb, whale flippers, frog forelimbs, different function

Convergent evolution
Distantly related organisms resemble one another. Similar environmental
pressures and natural selection produce ANALOHOUS adatptions from different
ancestral lineages.

Analogous structures
Serve same function, bare superficial resemblace, DO NOT have same basics plan,
egs wings of bats and birds. Analogous to birds wing, but they did not inherit
wings from common ancestor



Embryology

Compare early stages of development in different animal species reveals
ADDITIONAL ANOTOMICAL HOMOLOGIES not visivle in adult organisms.

All vertebrate embryos during development have post anal tail, internal gill
pouches

Similarities in embryo development support view that all vertebrates decended
from common ancestor.


Molecular homology

Sharing ancestry based in molecular makeup, DNA and AA sequences.

Species descended from common ancestors that used this code,
Ancestral species decendants exhibit high overall similarity in DNA of ancestor,
as they evolve, accumulate more differences. Two species closely related would
share greater portion of DNA.

Difference could be mutation, mutations indicate how close they related.


Biogeography

Related forms evolved in one locale, diversified as they spread out into other
accessible areas.

Geographic distribution of species, closely related species tend to be
geographically close as well. Common origin, radiate out


Island biogeography
Most island species closely related to species found in nearest mainland
Mainland species that succeeded in adapting to new environments of the island
could evolve to give variety of new species when population spread to other
islands

If can adapt, adaptive radiation.

Other continents, more advanced placental mammals out compete marsupials
from ecological niches

Australia geographically isolated, provide opportunity for marsupials to undergo
adaptive radiation to fill deifferent ecological niche available.


Fossil records.

Reveal evolutionary changes, succession of life forms from simple to more
complex. Fossils in younger layers of rock reveal evolution of various groups of
eukaryotic organisms,

Molecular methods in classifying organisms

Sequences of dna are inherited, determine seuqnce of AA and proteins
Species diverge as changes occur in nucleotide bases, each acquiring own set of
genetic mutations.
Species phylogeneticlly closer have more similar sequences compared to
distantly retalred. Fewer differences in AA.

Advatages:
Objective, molecular characters are unambiguous, morphological features shapes
and structures difficult to distinguish.
Use to compare species that cannot be distinguished morphogicallly.
Electronic databanks for easy compartive study and classification



Neutral theory

Gene flow
Movement of alleles between populations due to migration or transfer of
gametes.

Prevent population from fully adapting to environment, or widespread of
beneficial alleles that arises in one pop to other pops.

Gene flow can introduce new alleles to population, could be due to result in
mutation that occurred in another population. Gene flow occurs at higher rate
than mutation, can alter allele frequencies directly

May cause new allele to increase in frequency due to natural selection or
decrease in frequency.

Genetic drift sped up by founder effect and bottleneck effect

Genetic drift

Chance events cause allele frequencies to fluctuate unpredictably, especially in
small populations


Founder effect
Few individuals isolated from larger population, establish new population, small
population, reduce genetic variation, smaller gene pool, alleles carried by
founders from original population by chance.

Bottleneck effect
Change in environment, flood, drastic reduction in size of pop, remaining
individuals carry small portion of alleles of original gene pool. Lost of alleles.
Certain alleles may be over represented among survivors


Genetic drift is significant in small populations. Alter allele frequencies
substantially. Causes allele frequencies to change at rondom.
Unlike natural selection, does not favour alleles, allele frequency subject to
change randomly.
Lead to loss in genetic variation.
Evolution depends on genetic variation, gentic drift, remove certain alleles in
gene pool, can affect how organism service in the environent.

Molecular clocks
Dna differences in certain parts of genome occur at fairly constant rate, not tied
to natural selection
Used as a yardstick to measure evolutionary changes, can tell how closely related
they are
Assumption is change in nucleotide substitutions in genes is is proportional to
tme elapsed.
Rate, one change per 25 million years.

However, gene may evolve at different rates in different groups, within genes,
different genes have different rates

Neutral theory of molecular evolution

Change at molecular level, selectively neutral, due to genetic drift
Change at molecular level selectively neutral
Changes do not influence fitness of organism

Act on neutral alleles

Preservation of genetic variation.

Ensure natural selection does not entirely reduce genetic variation by removing
all unfavorable genotypes
Mechanisms to preserve genetic variation:

Diploidy
Alleles expressed (phenotype) subject to natural selection
Eukaryotes diplkoaid, considerable amount of genetic variation hidden from
selection in form of recessive alleles.
Recessive alleles less favourable than dominant alleles, but can persist by
propagation in HETEROZYGOUS individuals.
Two recessive alleles than selected against, when two copies end up in zygote,
but its rare. Chance low
Heterozygote protection maintains huge pool of alleles which might not be
favored now but become more favorable when environment changes.

Balancing selection
Natural selection maintains two or more forms in a population
Includes heterozygote advantage and frequency dependent selection.

Heterozygot advantage
If heterozygous at particular locus and have greater fitness. Have the advantage.
Natural to maintain two alleles at that locus. Sickle cell anemia

Freuquency dependent selection

Phenotype declines if too common in population.
Scale eating fish. Selection favours whichever phenotype is lelast common.
Frequency of species ocilates over time.

Neutral variation
Dna variation, little or no impact on reproductive success. Non coding sequences
appear to confer no selcective advantage or disadvantage.
Mutations in changes to proteins can be neutral, little affect on protein function
and reproductive fitness.

Classification

Two part format,
First is genus, second is species
Panthera pardus

Why name it so
Common names for organism, cause confusion, each name may refer to more
than one species. Eg monkey

Do not reflect kind of organism they signify. Jellyfish vs crayfish
Different language have different words for various organisms.
Avoid ambiguity when communicating about research

Hierarchical Classsification
Taxonomy: naming and classifying diverse forms of life

King Philip came over for gene special
Kingdom Phylum Class order family genus species

Linking classification and phylogeny
Systematics: classification determining evolutionary relationships
Classification: Characteristics, do not take into account evolutionary
relationships

Phylogeny: organization of species that takes into account evolutionary
relationships and characteristics

Classifications OUGHT to reflect phylogeny but need to be hypothsised.
Use phylogentic tree to represent evolutionary history of organisms

Shows divergence of two evolutionary lineages from common ancestor.


Reconstructing phylogenies, Distinguish homologous features from analogous
features as former reflect evolutionary relationships. Use cladistics.

Clade has ancestors and decendents, share characteristics, but differ from each
other
Vetebrates share ancestral character.
Tree has branch lengths. Indicative relative amounts of genetic change.
Proportional to amount of genetic change in each lineage. Indicate time of
evolution.




Concept of species

Biological species concept
Species, group of population, members potential interbreed and produce fertile
offspring. Do not produce fertile offspring with other groups.

Members of species resemble each other due to gene flow, alleles transferred
between populations.

Formation of new species hinges on reproductive isolation, barriers block gene
flow, limit hybrids. Several barriers can isolate a species gene pool.

Barriers contribute to reproductive isoation can be prezygotic barriers or post
zygotic barriers.

Prezygotic Barriers:

Habitat isolation, occupy different habitats, wont meet, wont mate

Temporal Isolation, different times or seasons of mating

Behavorial isolation, different courtship rituals

Mechanical isolation, genitals cannot fit

Gametic Isolation, sperm cannot fertilize eggs of other species

Postzygotic barriers

Reduced hybrid viability, interactions of genes interact in ways impair hybrid
development

Reduced hybrid fertility, sterile, different chromosome number from bothe
parents, meiosis, cant produce normal gametes, infertile hybrid, cannot produce
offspring, gene cannot flow freely
Limitations of biological species concept.

No way to evaluate reproductive isolation of fossils, do not apply to organisms
that reproduce asexually, prokaryotes.


Other theories, morphological species concept

Characterizes species by body shape, structural features
Applied to asexual and sexual organism
But it is subjective

Ecological species concept
Ecological niche, see their behaviour, how they interact with environment, what
type of different food they eat although they look similar.

Phylogentic species concept

Species smallest group of individual share common ancestor. Compare
chaaracteriestics of morphology and molecular sequences with other orfanism.
Distinguish groups of individuals that are sufficiently different to be considered
separate species.
Degree of didfference is subjective.

Process of which new species arise from existing species

Allopatric speciation

Gene flow interrupted when population divided into geographically isolated
subpopulations

Separated gene pools may diverge.
Different mutations arise, different env, diff selection pressure natural selection
acts on the separated organism and genetic drift alters allele frequencies
Reproductive isolation may arise as by product
Gene pools of highly associated populations experience LITTLE GENE FLOW,
undergo allopatric speciation
Unable to form variable offspring from parental population if come back to
contact


Sympatric speciation

Occurs in populations in same geographical area.
Gene flow reduced by polyploidy, habitat differentiation and sexual selection

Polyploidy
Cell div, extra set of chromosomes
Autopolyploid 2 chromosome sets arrived from single species, failure of cell
division,
Allopolyploid two different species intervreed and produce hybrid offspring

Habitat differentiation
Subpopulation exploit habitat or resource not used by parent population.

Sexual selection
Choose who to mate with

				
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