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BULLET BIOLOGY

CHAPTER 4

Glycolysis

• 2atp in forms unstable 6C intermediate

• Nad reduced

• 4 atp out, forms two pyruvates.

link reaction:

• pyruvate + coA and NAD

• reduces NAD, releases CO2 decarboxylation, produces acetyl-coA

Krebs:

• substrate level phosphorylation: acetylcoa(2c) onto 4c acceptor

• reduces 2 nad, 1 fad, releases 2CO2

electron transfer chain:(oxidative phosphorylation)

• hydrogen on NAD/FAD transferred from carrier to carrier

• by a series of redox reactions

• releases energy as electrons passed on

• ATP from ADP+P with ATPase

• (protons into intermembrane space, pass back through ATPase)

• oxygen last acceptor to produce water

Electron transfer chain: aerobic respiration • redNAD oxidised to NAD, electron passed along ETC by series of redox

reactions • oxygen final electron acceptor, with H ions, produces H2O • (energy used to transport H-ions across to intermembrane space) • (potential used by ATP synthase to phosphorylise ADP to ATP)



• neurotransmitter causes activation of charge activated membrane channels,

opening them • sodium ions diffuse in rapidly causing depolarisation

• potassium diffuses out to start recovery

Myelinated vs Not: • non-myelinated - next section of membrane depolarised

• myelinated – next node depolarised (which is a whole schwann cell

away) • impulse jumps from node to node

muscle contraction:

• ca2+ binds to tromysin • revealing binding site on actin (which was obstructed by troponin)

• myosin with atp bound to it attaches to the actin filament in the strong

state

• ADP and P released, causing power stroke

• Z bands pulled closer together

• ATP binds causing the release of the actin filament

• calcium ions activate ATPase Rigor mortis = no atp = actin not released = rigid

Trichromatic vision

• cones sensitive to different wavelengths

• absorb R, B, G

• combinations of stimulated cells interpreted to form colours Eye muscles:

• brain detects too much light/impulses on retina• radial muscles increase diameter via sympathetic system

• antagonistic circular muscle decrease via parasympathetic

Rods and Cones: • both on lamellae, both bleach/break down in light with the formation of trans-

retinal (from cis)



• rods = rhodopsin, highly sensitive to all wavelengths of light • cones = iodopsin, weakly sensitive to specific wavelengths (see above) • cones are one-to-one with bipolars and ganglions • rods are many-to-one, with an summation effect, where many activated

rods signal greater intensity.

Speciation:

• (geographically) isolated populations

• no interbreeding; no gene flow

• “in any population there is variation due to mutation (+random

assortment)”

• two populations experience different conditions = different selection

pressures •

natural selection = differential mortality/survival, adapting toenvironment

• different features/adaptations selected for between populations • changes allele frequency = genetically different populations • leading to reproductive isolation = speciation, when they can't produce

fertile offspring

Variation from meiosis:

• Formation of chiasmata/crossing over

• exchanges alleles between homologous chromosomes

• new combination of linked alleles

• random movement of homologous chromosomes

• each gamete is different = random fertilisation • independent assortment

what causes a range of phenotypes in a species

• phenotype depends on genotype and environment;

• different environments produce variation• due to different selection pressures = competition, predation, disease • which lead to differential survival • mutations produce new alleles

• meiosis produces new combinations of alleles

• random fusion of gametes + independent assortment



Insulin:

• increase in blood sugar detected by Bcells in Islets of langerhans

• insulin secreted, binds to specific receptors on liver/muscle cells

• leads to more glucose entering, lowering blood glucose levels

• glycogenesis in liver cells

ADH

• if water potential of blood falls, detected by osmoreceptors in hypothalamus;

• leads to ADH released from pituitary gland;

• ADH makes cells of collecting duct/distal convoluted tubule permeable

to water;

• water leaves filtrate by osmosis; smaller volume of urine produced;

Loop of Henle

• Sodium ions diffuse into descending limb • water osmoses out • sodium ions actively transported from ascending limb • which is impermeable to water • high sodium concentration in tissue fluid • water leaves collecting duct/distal tubule by osmoses due to water

potential difference

temperature responses:

• impulses to hypothalamus from skin+others/ detection of blood temperature

• sends impulses to hypothalamus heat gain/loss centre

• contraction/dilation of arterioles, divert blood away from/to skin (via

shunt vessels)

• pili erector muscles trap air around hairs, sweat production altered,

shivering triggered by hypothalamus

nasty little brain questions:

• touch etc:



• impulses to brain

• to sensory areas in cerebral hemispheres

• interpreted by association areas

• visual

• cone/rod stimulated, (bp cell, ganglion)

• impulses to brain via optic nerve, cross over

• to visual cortex in cerebellum

• to visual association areas

• speech

• association area sends impulses to association area for speech

(wernickes)

• words from memory

• which sends impulses to motor area for speech (broccas)

• impulses to muscles of face and larynx

Definitions: Allele: variant of a gene

homologous pair: two copies of a chromosome formed from mitosis sex linked gene: not present on Y, present only on X,

separate species: can't produce fertile offspring

codominance: both alleles presented when both present polygenic traits: many genes control one factor, results in continuousdistribution

epistasis: where one gene modifies the effect of another

chiasmata: crossing over of chromosomes refractory period: time between impulses

Binary fission: the way prokaryotes reproduce asexually (different frommitosis) Bivalent: Pair of homologous chromosomes recessive allele: only expressed if homozygous

mitochondrial crista: Infoldings of the inner membrane



fungi: chitin cell wall, hyphae, Mycelium

myosin: thick strand, heads for ATP binding and powerstroke (likeoars) actin: thin filament, binding sites, Z lines pulled together in

powerstroke

reflex: response to a stimulus which isn't under conscious control Independent assortment: the lining up on the equator, random which of thechromosomes end up on each side. significant difference: a difference which has a less than 5% chance of happening, therefore must be due to an external factor.

Chapter 5

pH of mud:

• take a sample and dilute with water

• test with universal indicator

Salty mud kills plants:

• more negative water potential

• water passes out of roots

passage of energy in food chain:

• respired by producers & their consumers

• dead matter + waste respired by detritovores

• lost as heat

• fossilised remains combusted by filfy yumans



Any population graph, consider these points:

• rise and fall/variation/cycles

• peaks/troughs lag behind that of the prey species

• include a couple figures

• slower rate/sudden rate of increase, decrease?

• plateau rather than sharp peak?

trophic levels:

• heat loss from respiration, catching prey, digestive inefficiency

• only some of the biomass converted to predator biomass

• after many trophic levels simply too much biomass/energy lost

Eutrophication:

• nitrate is limiting factor for plant growth

• algal bloom/rapid increase in plant growth

• as it is needed for protein synthesis

• competition for light with surface plants outcompeting deeper plants

• plants die providing food for decomposers

• respire aerobically using all the oxygen increasing BOD

• invertebrates/fish die which are also decomposed.

related to farming?

• removing hedges etc increases soil erosion

• increased runoff carries more fertilisers/more blown into lake

• less absorbed by hedges = more in lake

Monoculture:

• hedgerows lost as impractical for large machines

• deep rooted plants and wind exposure increase soil erosion• large number of same species grow closer together

• smaller variety of plants so smaller variety of niches

• increased disease spread due to proximity

• increased need for fertilisers = eutrophication



succession (clearings - secondary succession)

• short lived plants, (foxgloves) change soil conditions allowing other plants to

colonise

• shrubs/small trees move in and outcompete them for light/water etc

• eventually large trees dominate again

succession (bare land - primary succession)

• plants (like lichens and mosses) begin to grow, increasing organic matter

around themselves

• eventually results in soil, with moisture, colonised (by grasses)

• soil conditions change making them suitable for larger plants which

outcompete them for light/etc

succession (aquatic - primary/secondary)

• build up of organic matter, small aquatic plants grow

• stabilise the silt, hold in organic matter, more suitable for plants which

breach the surface

• further stabilise the soil with large root systems, reeds with Vlarge rootscreate soil

• terrestrial plants colonise the rich soil making it appropriate for large

trees like oaks

• climax community

Bioaccumulation:

• pesticide not broken down

• stored in tissues/fat

• bioaccumulation occurs

• because animals higher up eat many organisms lower down

Carbon cycle:

• leaves + dead matter digested by secretion of extracellular enzymes

• by decomposers = fungi + bacteria (or animals which then die and are

decomposed)

• absorb soluble products to produce proteins and carbohydrates ie

chitin, murein, protease

• respire to release CO2



• absorbed by plants for photosynthesis, glucose used to make cell walls

etc

Random sampling:

• grid up area, use random numbers to choose (transects can be appropriate)

• place large numbers of transects ( >10)

• count number of X, divide by area

Nitrogen:

Secretion by animals:

• proteins digested to aminos, deamminated to urea• excreted from kidneys in urine.

Nitrogen cycle:

• nitrogen fixing bacteria convert N2 to NH3

• urea converted to NH3 in ammonification

•NH3 converted to NO2 then NO3 by nitrifying bacteria

• NO3 taken up by plants by active transport

• converted to aminos to proteins

• decomposed/eaten and excreted/eaten and decomposed

• releasing NH3 or urea again.

• denitrifying bacteria turn nitrates to N2 again in anaerobic conditions.

piss of your teacher by writing two lines:

decomposers break down proteins to amino acids, ammonified to ammonia which isconverted by nitrifying bacteria to nitrites to nitrates which is absorbed actively byplants using ATP against concentration gradient (9 marks)



5: population: all the members of a species in one area

standard deviation: spread of the results about the mean

climax community: when succession is done = stable, many niches, largevariety of plants=more food sources succession: an area is colonised by plants, one type after another,generally increasing stability.

Chapter 7: microbes and disease

Immune system:

• macrophages ingest bacteria, process them, attach to them by antigens

• display bacterial peptides (from their antigens) on the MHC proteins

• moves in blood and binds to a (helper)T-lymphocyte

• activates it and causes it to produce cytokines, which increases

complement production + attracts more macrophages. • Helper-T binds to a matching B lymphocyte causing it to undergo clonal

expansion • which produces antibodies, which increases complement binding(opsenisation), and agglutination

Immunological memory:

• some activated T/(B)lymphocytes remain in the lymph nodes after infection

• once activated by binding with the original antigen type, they undergo

clonal expansion

• producing millions of antibodies

• faster because it doesn't need t-helpers = direct activation

Stages of microbial growth:



• LAG phase: active, no increase in numbers. Cells are respiring and producing

enzymes and ribosomes. • GROWTH phase: binary fission occurring rapidly. No intraspecific

competition for resources, no limiting factors. Maximum rate of reproduction • STATIONARY phase: carrying capacity reached. Intraspecific

competition, rate of reproduction falls and death rate increases, so the

turbidity may remain roughly constant. Viable count falls. • DEATH phase: nutrients exhausted, toxicity due to metabolic products/

secondary metabolites increases, number of viable cells falls to zero. Turbidity drops due to cell lysis

Viral replication: • virus binds using antigens that are complimentary in shape to specific

receptors on the cell surface. • Inserts its genome into the cell or joins into the cell membrane to

release its genome • DNA genomes can incorporate into the host genome and be exhibited

later or form mRNA immediately • RNA genomes are typically converted by reverse transcriptase that was

present in the virus itself • at some point mRNA is produced which codes for the production of the

virus's genome, surface proteins and capsids. • Cell lysis releases the viruses. Sometimes the virus genome includes a

gene for cell lysis that is activated after the production of many viruses • some viruses use the host cell membrane for themselves, in which casethey have self antigens aswell so will most likely be undetected by the hostimmune system. = enveloped

Viral damage: • The virus can digest host genetic material, disrupt genes by inserting its

genome into them • use up all the host cells amino acids and ATP for viral protein synthesis • lyse the cell, sometimes releasing toxins or causing the cells to produce

them.

Antibiotics prevent bacterial growth by: • inhibiting protein/ribosome production



• creating pores in the cell membrane/wall/capsule • prevent cell wall synthesis • prevent binary fission by preventing DNA replication

Antibodies:

• Y shaped: 2 light chain pairs which are variable and specific in shape to the

unique antigen presented • Heavy chain, which may be bound to other heavy chains depending on

the immunoglobulin type • when multiple cells with that antigen are bound to the light chains they

agglutinate and can be removed from the blood more easily by macrophagesor other mechanisms.

Ways to immobilise enzymes: • entrapment – trapped on a mesh or fabric

• adsorbtion – stuck to the surface of something, like a bead • encapsulation – in alginate balls (time for reactants to diffuse in, only

surface enzymes are rapid) • Cross-linking with glucuraldehyde bonds (which damages some, but the

rest are very effective)

Sterile procedure hints: • Keep a bunsen burner nearby to create air currents to carry bacteria away

• sterilise things!: flame in a bunsen as appropriate, use an autoclave • minimise time that tubes, petris and bottles are open + exposed

Definitions:

Total count: number of live and dead cells – measured by turbidity/haemocytometry



Viable count: number of live cells – measured by dilution plating.<30 colonies not statistically reliable!! secondary metabolite: a product produced only in the death phase whenthere are severe limiting factors, ie penicilliumproduction by penicillin. Requires batch processes. Endotoxin: a toxin produced inside a bacteria which is onlyreleased upon cell lysis Exotoxin: a toxin produced and excreted by the bacteria that canbe converted to toxoids with heat. Plasmid: in bacteria, circular section of DNA separate from themain genome. Used to gain new genes and gainresistance. Passed around via sex pili Capsule another layer on top of the cell wall, protects againstphagocytosis etc. Herd immunity: enough people are immune so that transfer between thenon-immune is unlikely mesosome: Infoldings of the bacterial cell membrane for increasedsurface area.

Capsid: Viral protein, monomer of its protein shell. Shell is anicosahedron, or helical, possibly with additions, like

bacteriophages with their legs, or envelopes.

Immunological type: single means that only one kind of surface proteinexists, only one strain of it. Highly infectious: number of virus/bacteria required to cause infection isvery low. Invasiveness: how much and how fast the pathogen spreadsthrough the body, ie by blood and to internal organs isvery invasive. Spectrum antibiotics: narrow affects only a few specific bacteria, broadaffects all bacteria of a type.

Extras

Abiotic factors list:



NOT: "amount of sunlight" or anything wishywashy like this whole stupid subject

light intensity, nitrate concentration, soil moisture content, soil/air temperature, soilpH,

other mineral concentrations,

tests: temp:electronic thermometer

soil moisture: dry until it achieves constant mass, measure difference

ion concentration: use chemical test strip

fussy little locations:

light dependent: thylakoid membranes

independent: stroma

glycolysis: cytosol

krebs: matrix

ETC; mitochondrial inner membrane

speech – left brain!

niggly little figures

5/6ths or 83.3% of TP --> RBP

38 ATP produced in respiration (profit) more than 10 samples in any scientific test (or say “large number”) less than 0.05 critical p value for significant results

King = kingdom

Phillip = phylum



Came = class

Out =order

For =Family

Gay =Group

Sex =species

Synoptic

Mutation: • Change in the base sequence of DNA:

• Alteration(point mutation)- or insertion or deletion of one or morenucleotides,which may cause a frame shift resulting in the completemalfunction of the gene, unless multiples of 3 added/removed (codons) • may result in different mRNA being transcribed, resulting in different

aminos incorporated

•

can affect the active site, making it fit poorly (lowering rate). Can resultin the ability to break down poisons if the active site now fits those. DNA replication:

• semi-conservative as both strands used • DNA helicas breaks H-bonds to separate strands • complimentary nucleotides align and H-bond A-T, C-G • DNA polymerase joins phosphodiester backbone.

Genetic manipulation • gene removed from genome using restriction endonuclease or formed from

mRNA sequence using reverse transcriptase • PCR used to replicate it • Plasmid cut using the same endonuclease to create complimentary

sticky ends • the two are mixed and DNA ligase rejoins the Sections to form a

recombinant plasmid



• Introduced to a harmless bacteria for culturing, using heat shock or

CaCl solution etc. Protein production:

• DNA unzipped by DNA Helicase breaking the H-Bonds between strands • Complimentary RNA nucleotides bind to H-bonds, C<-->G, A-->U, T-->A• RNA polymerase joins phosphodiester backbone (up till now =

transcription) • mRNA migrates to ribosome, read in codons (3 bases). tRNA with

complimentary anticodon binds to sequence and is bound to appropriateAmino acid • amino acids joined with condensation bonds,

Haemoglobin

• has a high affinity for oxygen + acts as an oxygen store

• O2 + Hb => oxyhaemoglobin

• releases at low ppO2

• maintains diffusion gradient between blood and water

Standard enzymes:

• low rate at low temp• less energy = fewer collisions, less activation energy

• denatured at high temp

• breaking Hbons/ionic bonds

causes changes to tertiary structure, changing active siteDIAGRAMS:

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