C.1.1  Explain the four levels of protein structure, indicating the significance of each levelPrimary (1°) Structure

The order / sequence of the amino acids of which the protein is composed Formed by covalent peptide bonds between adjacent amino acids Controls all subsequent levels of structure because it determines the

nature of the interactions between R groups of different amino acids

Secondary (2°) Structure The way the chains of amino acids fold or turn upon themselves Held together by hydrogen bonds between non-adjacent amine (N-H) and

carboxylic (C-O) groups May form an alpha helix, a beta-pleated sheet or a random coil Secondary structure provides a level of structural stability (due to H-bond

formation)

Tertiary (3°) Structure The way a polypeptide folds and coils to form a complex molecular shape

(e.g. 3D shape) Caused by interactions between R groups; including H-bonds, disulphide

bridges, ionic bonds and hydrophilic / hydrophobic interactions  Tertiary structure may be important for the function of the enzyme (e.g.

specificity of active site in enzymes)

Quaternary (4°) Structure The interaction between multiple polypeptides or prosthetic groups that

results in a single, larger, biologically active protein A prosthetic group is an inorganic compound involved in protein structure

or function (e.g. the heme group in haemoglobin) A protein containing a prosthetic group is called a conjugated protein Quaternary structure may be held together by a variety of bonds (similar to

tertiary structure)

C.1.2  Outline the difference between fibrous and globular proteins, with reference to two examples of each protein type

C.1.3  Explain the significance of polar and non-polar amino acids Polar amino acids have hydrophilic R groups, whereas non-polar amino acids

have hydrophobic R groups For water soluble proteins, non-polar amino acids tend to be found in the

centre of the protein (stabilising structure) while polar amino acids are found on the surface (capable of interacting with water molecules)

For membrane-bound proteins, non-polar amino acids tend to be localised on the surface in contact with the membrane, while polar amino acids line interior pores (to create hydrophilic channels)

For enzymes, the active site specifically depends on the location and distribution of polar and non-polar amino acids as hydrophobic and hydrophilic interactions can play a role in substrate binding to the activesite

C.1.4  State four functions of proteins, giving a named example of eachStructure:  Support for body tissue (e.g. collagen, elastin, keratin)Hormones:  Regulation of blood glucose (e.g. insulin, glucagon)Immunity:  Bind antigens (e.g. antibodies / immunoglobulins)Transport:  Oxygen transport (e.g. haemoglobin, myoglobin)Movement:  Muscle contraction (e.g. actin / myosin, troponin / tropomyosin)Enzymes:  Speeding up metabolic reactions (e.g. catalase, lipase, pepsin) 

C.2.1  State that metabolic pathways consist of chains and cycles of enzyme-catalysed reactions Most chemical changes in a cell results from chains and cycles of

reactions, with each step controlled by a separate specific enzyme This allows for a far greater level of control and regulation of metabolic

pathways (such as photosynthesis and cell respiration)

C.2.2  Describe the induced fit model When enzymes and substrates bind, the active site is not completely rigid

and may undergo a conformational change in shape to better fit the substrate

This conformational change may increase the reactivity of the substrate andbe necessary for the enzyme's catalytic activity

The induced fit model explains how an enzyme may be able to bind to, and catalyse, several different substrates (broad specificity)

The Induced Fit Model

C.2.3  Explain that enzymes lower the activation energy of the chemical reactions that they catalyse Every reaction requires a certain amount of energy to proceed - this is the

activation energy (Ea) Enzymes speed up the rate of a biochemical reaction by lowering the

activation energy If more energy is in the products than the reactants, energy is lost from

the system (endergonic) These reactions are usually anabolic (building things up), as the energy is

being used up in bond formation between two substrate molecules If more energy is in the reactants than the products, excess energy is

released into the system (exergonic)  These reactions are usually catabolic (breaking things down), as the energy

is released from the broken bonds within molecules 

Reaction Pathway of a Typical Exergonic / Exothermic Reaction

C.2.4  Explain the difference between competitive and non-competitive inhibition, with reference to one example of eachCompetitive Inhibition

A molecule (inhibitor) which is structurally / chemically similar to the substrate and binds to the active site of the enzyme

This serves to block the active site and thus prevent substrate binding (competes for the active site)

Its effect can be reduced by increasing substrate concentrationExample:  Relenza is a competitive inhibitor of neuraminidase (influenza virus enzyme), preventing the release of virions from infected cells

Non-competitive Inhibition A molecule (inhibitor) which is not structurally or chemically similar to

the substrate and binds to a site other than the active site (allosteric site)

This causes a conformational change in the active site, meaning the substrate cannot bind 

Its effect cannot be reduced by increasing substrate concentration as it is not competing for the active siteExample:  Cyanide (CN-) inhibits enzymes (cytochrome oxidase) in the electron transport chain by breaking disulphide bonds within the enzyme

Competitive versus Non-competitive Inhibition

C.2.5  Explain the control of metabolic pathways by end-product inhibition, including the role of allosteric sitesEnd-product inhibition is a form of negative feedback in which increased levels of product decrease the rate of product formation 

Because metabolic pathways usually consist of chains (e.g. glycolysis) or cycles (e.g. Krebs cycle), the product can regulate the rate of its own production by inhibiting an earlier enzyme in the metabolic pathway

The product binds to an allosteric site of an enzyme, causing a conformational change in the active site (non-competitive inhibition)

As the enzyme can not currently function, the rate of product formation will decrease (and with less product there is less enzyme inhibition)An example of end-product inhibition is the regulation of ATP formation by phosphofructokinase (an enzyme in glycolysis)

ATP inhibits phosphofructokinase, so that when ATP levels are high, glucoseis not broken down (but instead can be stored as glycogen)

When ATP levels are low, phosphofructokinase is activated and glucose is broken down to make more ATP

C.3.1  State that oxidation involves the loss of electrons from an element, whereas reduction involves a gain of electrons and that oxidation frequently involves gaining oxygen or losing hydrogen, whereas reduction frequently involves losing oxygen or gaining hydrogen

Redox (reduction-oxidation) reactions are chemical reactions that involve the transfer of electrons (gain or loss) between species

Mnemonics for redox reactions include: OIL RIG:  Oxidation Is Loss (of electrons), Reduction Is Gain (of

electrons) ELMO:  Electron Loss Means Oxidation LEO goes GER:  Loss of Electrons is Oxidation, Gain of Electrons

is Reduction In metabolic reactions, a species that has been reduced has the ability to

reduce other species (this is the predominant role of hydrogen carriers)

The differences between oxidation and reduction can be summarised by the following table:

C.3.2  Outline the process of glycolysis, including phosphorylation, lysis, oxidation and ATP formation

Glycolysis is the first stage of cell respiration and involves the breakdown of glucose into two molecules of pyruvate

It is an anaerobic reaction (does not require the presence of oxygen) and occurs in the cytoplasm

There are four main parts in glycolysis (not including intermediary steps):1.  Phosphorylation:  A hexose sugar is phosphorylated by two ATP to becomehexose biphosphate2.  Lysis:  The hexose biphosphate splits into two triose phosphates (3C sugars)3.  Oxidation:  Hydrogen removed from the triose phosphates via oxidation (NAD is reduced to NADH + H+)4.  ATP Formation:  Four ATP molecules are released as the triose phosphates are converted into pyruvate 

Overall:  One molecule of glucose results in 2 pyruvate, 2 (NADH + H+) and 2 ATP (net gain)

C.3.3  Draw and label a diagram showing the structure of a mitochondrion as seen in electron micrographs

               C.3.4  Explain aerobic respiration, including the link reaction, the Krebs cycle, the role of NADH + H+, the electron transport chain and the role of oxygen

Aerobic respiration takes place in the mitochondria, using the pyruvate produced via glycolysis

It produces large amounts of ATP in the presence of oxygen via three main processes:C.4.1  Draw and label a diagram showing the structure of a chloroplast as seen in an electron micrograph

C.4.2  State that photosynthesis consists of the light-dependent and light-independent reactionsPhotosynthesis is a two-step process:1.  The light dependent reactions convert the light energy into chemical energy2.  The light independent reaction uses the chemical energy to make organicmolecules

Overview of Photosynthesis

C.4.3  Explain the light dependent reactions The light dependent reactions occur on the thylakoid membrane and may occur

by either cyclic or non-cyclic processes In both processes, light excites chlorophyll (clustered in photosystems)

which release electrons that pass through an electron transport chain, making ATP (photophosphorylation)

Non-Cyclic Photophosphorylation Chlorophyll in photosystems I and II absorbs light, which triggers the

release of high energy electrons (photoactivation) The electrons from photosystem II pass along a series of carriers (electron

transport chain), producing ATP via chemiosmosis  The electrons from photosystem I reduce NADP+ to generate NADPH + H+

Electrons lost from photosystem I are replaced by electrons from photsystemII

Electrons lost from photosystem II are replaced by electrons generated by the photolysis of water (oxygen is produced as a by-product)

Cyclic Photophosphorylation Only photosystem I is involved in cyclic photophosphorylation The high energy electrons released by photoactivation pass along an

electron transport chain (producing ATP) before returning to photosystem I Cyclic photophosphorylation does not produce NADPH + H+, which is needed

for the light independent reactions Thus while cyclic photophosphorylation can make chemical energy (ATP) from

light, it cannot be used to make organic molecules

Non-Cyclic versus Cyclic Photophosphorylation

C.4.4  Explain photophosphorylation in terms of chemiosmosis As the electrons (released from chlorophyll) cycle through the electron

transport chains located on the thylakoid membrane, they lose energy This free energy is used to pump H+ ions from the stroma into the thylakoid The build up of protons inside the thylakoid creates an electrochemical

gradient (or proton motive force) The H+ ions return to the stroma via the transmembrane enzyme ATP synthase,

which uses the potential energy from the proton motive force to convert ADPand an inorganic phosphate (Pi) into ATP

This process is called chemiosmosis

Photophosphorylation via Chemiosmosis

C.4.5  Explain the light independent reaction The light independent reaction occurs in the stroma and uses the ATP and

NADPH + H+ produced by the light dependent reaction (non-cyclic) The light independent reaction is also known as the Calvin cycle and occurs

via three main steps:

1.  Carbon Fixation The enzyme rubisco (RuBP carboxylase) catalyses the attachment of CO2 to

the 5C compound ribulose bisphosphate (RuBP) The unstable 6C compound that is formed immediately breaks down into two 3C

molecules called glycerate-3-phosphate (GP)

2.  Reduction Each GP molecule is then phosphorylated by ATP and reduced by NADPH + H+

This converts each GP molecule into a triose phosphate (TP) called glyceraldehyde phosphate

3.  Regeneration of RuBP For every six molecules of TP produced, only one may be used to form half a

sugar molecule (need two cycles to form a complete glucose) The remaining TP molecules are reorganised to regenerate stocks of RuBP in

a reaction that involves ATP With RuBP regenerated, this cycle will repeat many times and be used to

construct chains of sugars (e.g. sucrose) for use by the plant

The Light Independent Reaction (Calvin Cycle)

C.4.6  Explain the relationship between the structure of the chloroplast and its function Thylakoids:  Small lumen means small changes in proton concentration have a

large effect on the proton motive force Grana:  Thylakoids arranged in stacks to greatly increase surface area

available for light absorption (chlorophyll located in thylakoid membrane) Stroma:  Contains appropriate enzymes and suitable pH for the light

independent reaction to occur

C.4.7  Explain the relationship between the action spectrum and absorption spectrum of photosynthetic pigments in green plants

Pigments absorb light as a source of energy for photosynthesis The absorption spectrum indicates the wavelengths (frequency) of light

absorbed by each pigment The action spectrum indicates the rate of photosynthesis for each

wavelength / frequency There is a strong correlation between the cumulative absorption spectrum of

all photosynthetic pigments and the action spectrum Both display two main peaks - a larger peak at ~450 nm (blue) and a smaller

peak at ~670 nm (red) with a decrease in between (green)

Absorption Spectrum versus Action Spectrum

Chlorophyll and Photosystems

C.4.8  Explain the concept of limiting factors in photosynthesis, with reference to light intensity, temperature and concentration of carbon dioxide

The law of limiting factors states that when a chemical process depends on more than one essential condition being favourable, its rate will be limited by the factor that is nearest its minimum value

Photosynthesis is dependent on a number of favourable conditions, including:

Light Intensity Light is required for the light dependent reactions (photoactivation of

chlorophyll and photolysis of water molecules) Low light intensities results in insufficient production of ATP and NADPH +

H+ (both needed for the light independent reaction)

Temperature Primarily affects the light independent reaction (and to a lesser extent

the light dependent reactions) High temperatures will denature essential enzymes (e.g. rubisco), whereas

insufficient thermal energy will prohibit reactions from occurring

Concentration of Carbon Dioxide Carbon dioxide is required for the light independent reaction to occur

(carbon fixation of RuBP by rubisco) At low levels, carbon fixation will occur very slowly, whereas at higher

levels the rate will peak as all rubsico are being used

Factors Affecting the Rate of Photosynthesis

C.4.9  Analyse data relating to photosynthesis Remember the equation for photosynthesis and the different roles of the

light dependent and light independent reactions The law of limiting factors states that the rate of a reaction will be

determined by the substrate nearest its minimum value Remember the factors that can affect the substrates and identify how this

in turn can effect the amount of products

Also, remember that plants also undergo cell respiration, and that the amounts of photosynthetic products formed will be determined in part by theamounts used in cellular respirationD.1.1  Describe four processes needed for the spontaneous origin of life on Earth1.  The non-living synthesis of simple organic molecules (from primordial inorganic compounds)2.  The assembly of these organic molecules into polymers3.  The formation of polymers that can self-replicate (enabling inheritance)4.  Packaging of these molecules into membranes with an internal chemistry different from their surroundings

D.1.2  Outline the experiments of Miller and Urey into the origin of organic compoundsMiller and Urey recreated the conditions of pre-biotic Earth in a closed system consisting of a series of flasks and tubes

These conditions included a reducing atmosphere (low oxygen), high radiation levels, high temperatures and electrical storms

Water was boiled to form vapour and then was mixed with methane, ammonia and hydrogen

The mixture of gases was exposed to an electrical discharge (sparks) to simulate lightning

The mixture was then allowed to cool and after one week was found to contain some simple amino acids and complex oily hydrocarbons

Based on these findings, it was concluded that under the hypothesised conditions of pre-biotic Earth, organic molecules could be formed

The Miller-Urey Experiment

D.1.3  State that comets may have delivered organic compounds to EarthComets contain a variety of organic molecules (~20% of a comet's tail is comprised of organic material)Heavy bombardment about 4,000 million years ago may have delivered both organic compounds and water to early Earth

D.1.4  Discuss possible locations where conditions would have allowed for the synthesis of organic compoundsOrganic synthesis requires the presence of a range of inorganic molecules and an energy source to combine them into organic formsLocations where such conditions may have existed in the past include:

Hydrothermal vents:  Regions of the ocean floor where superheated water is released from the Earth's crust

Volcanoes:  Intensive volcanic activity could provide sufficient thermal activity either on land or under the seabed

Extraterrestrial locations:  Other planets (e.g. Mars) may have been subjected to appropriate conditions (compound transfer via meteorites)

D.1.5  Outline two properties of RNA that would have allowed it to play a role in the origin of lifeThe RNA world hypothesis proposes that a world filled with RNA-based life predates current DNA-based organismsRNA has two key properties that would have allowed it to function in this manner:

1.  RNA can self-replicate

RNA is able to store information in a sequence of four nucleotides (similarto DNA)

Short sequences of RNA have been able to duplicate other molecules of RNA accurately

2.  RNA can act as a catalyst Modern cells use RNA catalysts (called ribozymes) to remove introns from

mRNA and help synthesise new RNA molecules In ribosomes, rRNA is found in the catalytic site and plays a role in

peptide bond formation

RNA is the only molecule capable of both these properties but has since been superceded:

DNA, through its greater chemical stability (double helical structure) has taken over as the data storage form

Protein, through its greater variability (20 amino acids as opposed to 4 nucleotides) has taken over as the catalytic form

The RNA World Hypothesis

D.1.6  State that living cells may have been preceded by protobionts, with an internal chemical environment different to their surroundingsProtobionts are aggregates of abiotically produced organic molecules surrounded by a membrane or membrane-like structureExamples include coacervates and microspheres

A membrane creates an internal chemical environment different to the surroundings, which could lead to optimal conditions for life activities

D.1.7  Outline the contribution of prokaryotes to the creation of an oxygen-rich atmospherePrimordial Earth had a reducing atmosphere that contained very low levels of oxygen gasAfter about ~2 billion years of prokaryotic life, a form of chlorophyll evolved in prokaryotes (forming cyanobacteria)This allowed for the process of photosynthesis to occur, creating oxygen gas as a by-product via the photolysis of waterThe increase in oxygen in the atmosphere lead to: 

The breakdown of chemicals in the atmosphere and oceans to produce oxidisedcompounds (e.g. CO2)

The evolution of organisms capable of breaking down oxygen-rich oxidising agents

The formation of an ozone layer which restricted UV radiation to allow for the proliferation of a wider range of life forms

D.1.8  Discuss the endosymbiotic theory for the origin of eukaryotesAn endosymbiont is a cell which lives inside another cell with mutual benefitEukaryotic cells are believed to have evolved from aerobic prokaryotes thatwere engulfed by endocytosisMitochondria and chloroplasts are suggested to have originated by endosymbiosis

Evidence supporting the theory of endosymbiosis: Mitochondria and chloroplasts have their own DNA (which is naked and

circular) Mitochondria and chloroplasts have ribosomes that are similar to

prokaryotes (70S) Mitochondria and chloroplasts have a double membrane and the inner membrane

has proteins similar to prokaryotes

Mitochondria and chloroplasts are roughly the same size as bacteria and aresusceptible to the antibiotic chloramphenicol

D.2.1  Define allele frequency and gene poolAllele Frequency:  The proportion of an allele within a populationGene Pool:  The sum total of alleles present in a sexually reproducing population

D.2.2  State that evolution involves a change in allele frequency in a population's gene pool over a number of generationsBy natural selection, alleles encoding for beneficial adaptations will confer a survival advantage and lead to improved reproductionThese alleles are more consequently more likely to be inherited and thus the population's gene pool will change over generations

D.2.3  Discuss the definition of the term speciesA species is a population whose members have the potential to interbreed toproduce fertile, viable offspring

They are therefore unable to produce fertile offspring with members of a different species

Hybrids are individuals produced by cross-breeding between two different species, and are reproductively sterile (e.g. ligers, mules)

There are a number of caveats to this biological explanation of species: Certain organisms (e.g. bacteria) do not reproduce sexually (although may

transfer genetic information via conjugation) Some organisms are only known through fossil records, making it impossible

to ascertain breeding capacity Geographically isolated organisms may never come into contact, meaning

there is no information regarding their ability to interbreed It may be physically impossible for some members of the same species to

mate (e.g. different dog breeds) Some species spread around an area to form interlinked breeding populations

whereby the population 'ends' cannot interbreed (ring species)

Ring Species

D.2.4  Describe three examples of barriers to gene poolsThere are two main categories of reproductive isolation barriers:

Prezygotic isolation - before fertilisation occurs (no offspring are produced)

Postzygotic isolation - after fertilisation occurs (offspring is either notviable or infertile)

D.2.5  Explain how polyploidy can contribute to speciationPolyploidy is a condition in which an organism has more than two complete sets of chromosomes in all somatic cells (i.e. > diploid)It is far more common in plant species as they lack separate sexes and are capable of asexual reproduction (self-pollination)It may occur as a result of the failure of a meiotic cell to undergo cytokinesis (so chromosome replication occurs minus cell division)Consequently gametes are diploid (2n) and resulting offspring are tetraploid (4n) Because tetraploid offspring can no longer mate with diploid organisms (triploid offspring tend to be infertile), speciation has occurred

Polyploidy

D.2.6  Compare allopatric and sympatric speciationSimilarities:

Both involve the formation of a new species via isolation of the genetic pool from an existing species

Both occur when natural selection creates genetic divergence between the new and ancestral populations

Differences:

Allopatric Speciation versus Sympatric Speciation

D.2.7  Outline the process of adaptive radiationAdaptive radiation describes a rapid evolutionary diversification of a single ancestral lineage

It occurs when members of a single species occupy a variety of niches with different environmental selection pressuresConsequently, members evolve different morphological adaptations as a result of natural selectionAdaptive radiation results in speciation (many species from an ancestral line) and may be further enhanced by reproductive isolationAn example of adaptive radiation can be seen in the variety of beaks seen in the Galapagos finches

D.2.8  Compare convergent and divergent evolutionSimilarities:

Both explain the presence of similar structures in different organisms

Differences:

D.2.9  Discuss ideas on the pace of evolution, including gradualism and punctuated equilibriumGradualism

Continuous change at a constant pace over a long period of time Arises as a result of the gradual accumulation of mutations / variations Examples in the fossil record of gradual change with intermediate forms

support this theory An example is the evolution of the modern horse (gradual change in size and

foot structure with changing habitat)

Punctuated equilibrium Evolution proceeds rapidly in bursts for short periods of time, intermittent

with long periods of stability In periods of stability organisms become well suited to the environment,

with natural selection acting to maintain characteristics Equilibrium is punctuated by a rapid environmental change (e.g. volcanic

eruption, meteor impact) which leads to directional selection Gaps in the fossil record and the lack of intermediate forms for many

species support this theory Strata in the fossil record that show the appearance of many new species

following a mass extinction support this theory

Different Theories on the Pace of Evolution

D.2.10  Describe one example of transient polymorphismA polymorphism is the occurrence of two or more clearly different phenotypes within the same population of a species - it reflects the effects of more than one allele in the gene pool

Transient Polymorphism A situation when there are two alleles in a gene pool (polymorphic) and one

allele is gradually replacing another This is due to a strong environmental selective pressure causing

directional selection to eliminate one allele Example: Industrial melanism or antibiotic resistance in bacteria (refer to

dot point 5.4.8 for more detail)

D.2.11  Describe sickle cell anaemia as an example of balanced polymorphismBalanced Polymorphism

A situation when there are two alleles in a gene pool (polymorphic) and thefrequency of the two alleles in not changing

Occurs when selective pressures promote the coexistence of the two alleles (i.e. heterozygous advantage) causing a stabilising selection

Example: Sickle Cell Anaemia Sickle cell anaemia is controlled by a single gene mutation (refer to dot

point 4.1.4 for more detail) Individuals homozygous for the sickle cell allele have abnormally shaped

red blood cells that lead to pronounced health complications Individuals homozygous for the normal blood cell allele are highly

susceptible to malarial infection In areas where malaria is common, heterozygous individuals experience an

advantage over either form of homozygote

These individuals are more likely to survive and reproduce, leading to a balance in the frequency of the two alleles (heterozygous advantage)

The Link Reaction Pyruvate is transported from the cytosol to the mitochondrial matrix in a

reaction that produces (one) NADH + H+ via oxidation The pyuvate loses a carbon (as CO2) and the remaining two carbons are

complexed with coenzyme A (CoA) to form acetyl CoA

The Krebs Cycle In the matrix, acetyl CoA combines with a 4C compound to form a 6C compound Over a series of reactions the 6C compound is broken back down into the

original 4C compound These reactions result in the formation of 2 CO2 molecules, 1 ATP molecule

and multiple hydrogen carriers, specifically 3 (NADH + H+) and 1 FADH2 

The Electron Transport Chain The hydrogen carriers (NADH + H+ and FADH2) provide electrons to the

electron transport chain on the inner mitochondrial membrane As the electrons cycle through the chain they lose energy, which is used to

translocate H+ ions to the intermembrane space (creating a gradient) The hydrogen ions return to the matrix through the transmembrane enzyme ATP

synthase, producing multiple ATP molecules (via chemiosmosis)

Oxygen acts as a final electron acceptor for the electron transport chain, allowing further electrons to enter the chain

Oxygen combines the electrons with H+ ions to form water molecules The electron transport chain produces the majority of the ATP molecules

produced via aerobic respiration (~32 out of 36 ATP molecules)Overview of Aerobic Respiration

C.3.5  Explain oxidative phosphorylation in terms of chemiosmosis Oxidative phosphorylation describes the production of ATP from oxidised

hydrogen carriers (as opposed to substrate level phosphorylation) When electrons are donated to the electron transport chain, they lose

energy as they are passed between successive carrier molecules This energy is used to translocate H+ ions from the matrix to the

intermembrane space against the concentration gradient The build up of H+ ions creates an electrochemical gradient, or proton

motive force (PMF) The protons return to the matrix via a transmembran enzyme called ATP

synthase As they return they release energy which is used to produce ATP (from ADP

and Pi) This process is called chemiosmosis and occurs in the cristae The H+ ions and electrons are combined with oxygen to form water, allowing

the process to be repeated anew

Overview of Chemiosmosis

C.3.6  Explain the relationship between the structure of the mitochondria and its function Inner membrane:  Folded into cristae to increase surface area for electron

transport chain Intermembrane space:  Small space between inner and outer membranes for

accumulation of protons (increases PMF)

Matrix:  Contains appropriate enzymes and a suitable pH for the Krebs cycleto occur

Outer membrane:  Contains appropriate transport proteins for shuttling pyruvate into the mitochondria

C.3.7  Analyse data relating to respiration Remember the equations for cellular respiration (aerobic and anaerobic) The law of limiting factors states that the rate of a reaction will be

determined by the substrate nearest its minimum value Remember the factors that can affect the substrates and identify how this

in turn can effect the amount of products In particular, be aware of the role of oxygen in aerobic respiration and

the alternate metabolic pathways that occur in anaerobic respiration Also, remember that glucose is not the only source of energy for use in

respiration Triglycerides can be broken down into glycerol and fatty acids (which can

be converted into acetyl CoA) Proteins can be deaminated (N-containing amine group removed) and used

D.3.1  Outline the method for dating rocks and fossils using radioisotopes, with reference to 14C and 40KRadiocarbon Dating

All living things are built from carbon-based organic matter While alive, this carbon content exists as a mixture of two isotopes

- 12C (stable) and 14C (radioactive) - maintained in constant proportions  When an organism dies, the proportion of radioactive 14C begins to decrease

as it is no longer being replaced from the environment The proportion of 14C remaining can be used to identify the age of a sample Carbon-14 analysis is only an effective means of dating for sample up to

~60,000 years of age as it has a half life of only 5,730 years

Potassium-Argon Dating Longer range dating can be accomplished by dating the rocks around a fossil

to determine an age range (i.e. relative dating) These dating techniques can only be undertaken on igneous rocks, not on the

fossils themselves or the sedimentary rock in which they are found 40K is released in lava from active volcanos and decays into 40Ar with a

half life of 1,300 million years Using the time of the volcanic eruption as a zero time point, the age of

the strata in which the fossil was found can be determined As any 40Ar would have been released during the eruption as a gas, levels

of 40Ar in the strata provide an indication of relative age

D.3.2  Define half-life

The half life of a radioisotope is a measure of the time taken for the radioactivity to fall to half its original level

In other words, it is a measure of the time taken for half the atoms in a radioactive sample to decay

D.3.3  Deduce the approximate age of materials based on a simple decay curve for a radioisotope

D.3.4  Describe the major anatomical features that define humans as primatesPrimates are adapted for an arboreal (tree-dwelling) life in a forest environment and possess the following features:

Forward facing eyes (binocular vision) Larger brains (improved cognition) Opposable thumbs (capable of power grip and precision grip) Finger pads with nails instead of claws (improved tactile sensitivity) Skull adapted for upright posture (downward facing foramen magnum) Rotating hand / forelimb (capable of pronation) Flexible shoulder joints (shoulder blades on dorsal side of the thorax)

D.3.5  Outline the trends illustrated by the fossils of Ardipithecus radius, Australopithecus including A.afarensis and A. africanus, and Homo including H. habilis, H. erectus, H. neanderthalensis and H. sapiens

Evolutionary TrendsBy comparing the different types of hominin fossils, we can identify key evolutionary trends:

More downward facing foramen magnum (caused by a transition to bipedalism) S-shaped curvature of the spine (an artifact of an increasingly erect

posture) Lower and broader pelvis (bipedalism has changed the hominin birthing

patterns and behaviours) Change in relative lengths of arm and leg bones (arms have become

relatively shorter and legs longer due to walking upright) Increased size of heel bone and alignment of big toe (changes in feet to

become greater weight-bearing structures) Flatter faces, with reduced brow ridges and jaw protrusion (head is no

longer the most anterior part of the body) Larger cranial capacity with increased brain size and greater

encephalisation (greater intellectual prowess) Smaller teeth and jaws more V-shaped (reflecting changing dietary

requirements with less emphasis on tough vegetation) Marked reduction in body hair (improved hunting and cultural practices have

lead to the development of warm clothing) Shift in muscle groups (particularly the gluteal and hamstring groups, in

order to accommodate new mode of locomotion)

Comparison of Early and Recent Hominin Skeletons

D.3.6  State that, at various stages in hominid evolution, several species may have coexistedSeveral species of hominid may have co-existed at the same time:

Homo habilis may have co-existed with various species of Australopithicus Homo neanderthalensis likely co-existed with Homo sapiens

D.3.7  Discuss the incompleteness of the fossil record and the resulting uncertainties about human evolutionIncompleteness of the Fossil Record

Fossilisation is an exceptionally rare occurrence that requires an unusual combination of special conditions

Most living things tend to decompose rapidly (or be scavenged) following death

Fossilisation tends to favour hard body parts (bone, teeth, shells, etc.) and exposed fossils will soon be weathered / destroyed

Only a small percentage of fossils have been discovered - fossilisation favours species that were long-lived and widespread

Significance of Incompleteness of the Fossil Record Individual fossils may not be representative of species (e.g. Homo

floresiensis - 'Hobbit' man) Very few complete skeletons have been discovered, and so paleoanthropology

is an inductive (data-poor) science Many conclusions have been drawn on limited data and are frequently re-

interpreted in the light of new discoveries

D.3.8  Discuss the correlation between the change in diet and increase in brain size during hominid evolution

A change in habitat in Africa ~2.5 million years ago may have prompted the emergence of Homo species from forest to savannah

This necessitated a change of diet to include meat (more protein), which increased the skull capacity and brain size of hominids

Improved diet quality provided energy to support greater brain function andlearning capacity (positive correlation)

Activities resulting from improved cognition (such as group hunting and cooking food) enabled hominids to eat a wider variety of food

Hominid Skull Development

D.3.9  Distinguish between genetic and cultural evolutionGenetic evolution involves physical changes in the human genome which become inherited (passed on through reproduction)

It involves the transfer of genes from one generation to the next (slow transfer)

Cultural evolution involves changes in human thinking and can be passed on by communication / social interaction

It involves the transfer of ideas / information either within or across many generations (fast transfer)

D.3.10  Discuss the relative importance of genetic and cultural evolution in the recent evolution of humans

Changes in genotype (genetic evolution via natural selection) have lead to cultural evolution in humans by promoting intelligent behaviour

Larger brain sizes have promoted increased learning capacity / greater cognitive ability

Prolonged gestations have promoted social interaction / familiy networks Bipedalism has promoted extensive migration and improved socialisation

tendencies Shorter finger bones and reduced reliance on forelimbs for locomation have

promoted increased tool manipulation Evolution of culture (e.g. art, science, language) has been more rapid and

recent than genetic evolution (which requires many generations) Further cultural evolution (through genetic engineering) may hasten changes

in our genetic evolution Certain products of cultural evolution (e.g. medicines) may reduce genetic

evolution via natural selection Other products of cultural evolution (e.g. pollution) may increase genetic

evolution (increased mutagenic rate)

D.4.1  Explain how the Hardy-Weinberg equation is derivedThe Hardy-Weinberg equation predicts the frequency of two alternate allelesin a populationIt is used for traits that show classical Mendelian inheritance:

Only two alleles for a gene (one dominant and one recessive allele) Follows autosomal inheritance (not sex-linked traits)

For two alleles of a given genetic characteristic, three genotypes will exist:  AA, Aa and aa

Dominant allele is A, with a frequency of p Recessive allele is a, with a frequency of q

The total frequency of both alleles will be 1 (i.e. p + q = 1) Because genotype frequencies consist of two alleles, the equation must be

squared: (p + q)2 = 1

This gives the expanded form of the Hardy-Weinberg equation: p2 + 2pq + q2 = 1

Deriving the Hardy-Weinberg Equation

D.4.2  Calculate allele, genotype and phenotype frequencies for two alleles of a gene, using the Hardy-Weinberg equationSuppose we had a population of 500 individuals, in which 9% of individuals were albino (albinism is a recessive characteristic  aa)Using the equations:   p + q = 1   and   p2 + 2pq + q2 =1•  If q2 = 0.09      q = 0.3  (√0.9)•  If q = 0.3      p = 0.7  (p + 0.3 = 1)•  If p = 0.7      p2 = 0.49  (0.7 × 0.7)•  Therefore 2pq = 0.42  (2 × 0.7 × 0.3)

Substituting these numbers for frequencies and applying them to our original population, we find that:

49% are homozygous dominant (AA), which is 245 individuals  (0.49 × 500)

42% are heterozygous (Aa), which is 210 individuals  (0.42 × 500) 9% are homozygous recessive (aa), which is 45 individuals  (0.09 × 500)

D.4.3  State the assumptions made when the Hardy-Weinberg equation is used When the Hardy-Weinberg equation is used in population genetics, it is

assumed that a constant allele frequency will be maintained over time For this to occur it is implied that: The population is large There is random mating There is no mutation There is no gene flow (immigration or emigration) There is no natural selection or allele-specific mortality

Graphical Representation of the Hardy-Weinberg Equation

D.5.1  Outline the value of classifying organismsClassification systems for living organisms are of value because they:

Allow us to distinguish between and compare organisms based on characteristics

Makes it easier to identify organisms according to a globally recognised scheme

Makes it easier to collect, sort and store information about organisms Shows how closely organisms are related and suggests evolutionary links Allows predictions to be made (about characteristics of members of a group)

D.5.2  Explain the biochemical evidence provided by the universality of DNA and protein structures forthe common ancestry of living organisms

All organisms use DNA and RNA as their genetic material Four bases (adenine, guanine, thymine, cytosine) form the basis of this

code and undergo the same complementary pairing (A = T ; G = C) Conserved genes have similar functions Common mechanisms for DNA replication and protein synthesis are used by all

organisms (including similar enzymes for these processes) The genetic code is (almost) universal – the same codons code for the same

amino acids  All living organisms use the same 20 amino acids for protein synthesis These amino acids are all L-isomers and not D-isomers Large groups of organisms share certain proteins and metabolic pathways

(e.g. haemoglobin, cytochrome c) The degree of difference between organisms in DNA / protein sequence

demonstrates the level of relationship between organisms The more similar the base / amino acid sequences are, the more closely

related two species are likely to be

Comparing DNA Sequences using DNA-DNA Hybridisation

 D.5.3  Explain how variation in specific molecules can indicate phylogeny

Phylogeny refers to an evolutionary line of descent and can be determined by comparing similar molecules in different species (e.g. haemoglobin)

Variations in these molecules (either base or amino acid sequence) will occur due to mutations

The greater the differences between the common molecules, the longer the time span since the two species had a common ancestor

Mitochondrial DNA is useful for tracing phylogeny as it is inherited via the maternal line, lacks recombination and has a known mutation rateD.5.4  Discuss how biochemical variation can be used as an evolutionary clock

Some genes or protein sequences may accumulate mutations at a relatively constant rate (e.g. a 1% change per million years)

If this rate of change is reliable, scientists can calculate the time of divergence based on the number of differences between two species

This concept is called the evolutionary clock (or 'molecular clock'), and is limited by a number of factors:

The rate of change can differ for different groups of organisms (e.g. animals and plants)

The rate of change can vary between different genes and different proteins Over long periods, earlier changes may be reversed by later changes

D.5.5  Define clade and cladisticsClade:  A group of organisms consisting of a single common ancestor and alldescendants of that ancestorCladistics:  A method of classification of living organisms based on the construction and analysis of cladograms

D.5.6  Distinguish, with examples, between analogous and homologous characteristics

Analogous versus Homologous Structures

D.5.7  Outline the methods used to construct cladograms and the conclusions that can be drawn from themConstructing Cladograms

A cladogram is a tree-like diagram where nodes represent the splitting of two new groups from a common ancestor

Members of a clade typically share a set of features not found in more distant relatives

Cladistics are most commonly based on molecular differences (base or amino acid sequences)

Cladograms are calculated by software that depicts the cladogram with the fewest number of brances

For rooting the cladogram, an outgroup (most distantly related species) is used

Conclusions from Cladograms The more nodes between two groups the less closely related they are

expected to be Cladograms are based on probability, but improbable events (e.g. certain

mutations) can occur, so relationships may be wrong

D.5.8  Construct a simple cladogramStep 1:  Organise organisms according to defined characteristics

Step 2:  Represent this information as a cladogram by ordering organisms byshared characteristics (nodes)

D.5.9  Analyse cladograms in terms of phylogenetic relationshipsThe more nodes between two groups, the less closely related they are expected to beAccording to the cladogram above:

The chimpanzee is most similar to the bear The lizard is equally similar to the bear and chimpanzee

D.5.10  Discuss the relationship between cladograms and the classification of living organisms Classification was traditionally based on morphology (structural

characteristics) Methods used to construct cladograms typically utilise a different approach

(e.g. molecular data - more objective) Cladograms can show ancestral relationships and reflect how recently two

groups shared a common ancestry As such they should be considered a good complement to traditional

classification schemes In some cases, cladograms have lead to revisions in scientific

classifications