IB BIo revision notes topic 3,7,8

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3.1.1 State that the most frequently occurring chemical elements in living things are carbon, hydrogen, oxygen and nitrogen The approximate proportions of the four main elements in living things are: • Carbon (19%) • Hydrogen (10%) • Oxygen (65%) • Nitrogen (3%) 3.1.2 State that a variety of other elements are needed by living organisms, including sulphur, calcium, phosphorus, iron and sodium Outside of the four main elements, living things may contain trace amounts of 20 or so other elements, including: • Sulphur (0.25%) • Calcium (1.5%) • Phosphorus (1%) • Iron (0.7%) • Sodium (0.15%) 3.1.3 State one role for each of the elements mentioned in 3.1.2

Transcript of IB BIo revision notes topic 3,7,8

Page 1: IB BIo revision notes topic 3,7,8

3.1.1  State that the most frequently occurring chemical elements in living things are carbon, hydrogen, oxygen and nitrogen

The approximate proportions of the four main elements in living things are:

• Carbon (19%)                      

• Hydrogen (10%)                        

• Oxygen (65%)                        

• Nitrogen (3%)

3.1.2  State that a variety of other elements are needed by living organisms, including sulphur, calcium, phosphorus, iron and sodium

Outside of the four main elements, living things may contain trace amounts of 20 or so other elements, including: 

• Sulphur (0.25%)                        

• Calcium (1.5%)                        

• Phosphorus (1%)                       

• Iron (0.7%)                        

• Sodium (0.15%)

3.1.3  State one role for each of the elements mentioned in 3.1.2

Sulphur (S):  Found in certain amino acids (cysteine and methionine), allowing proteins to form disulphide bonds

Calcium (Ca):  Found in bones and teeth, also involved

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in neurotransmitter release in synapses

Phosphorus (P):  Component of nucleic acids and cell membranes

Iron (Fe):  Found in haemoglobin (animals), allowing for oxygen transport

Sodium (Na):  Involved in the generation of nerve impulses in neurons

3.1.4  Draw and label a diagram showing the structure of water molecules to show their polarity and hydrogen bond formation

Structure of a Water Molecule:

▪ Water (H2O) is made up of two hydrogen atoms covalently bound to an oxygen atom

▪ While this bonding involves the sharing of electrons, they are not shared equally 

▪ The oxygen atom, having more protons (+ve), attract the electrons (-ve) more strongly (i.e. the oxygen has a higher electronegativity)

▪ Thus the oxygen atom becomes slightly negative and the hydrogen atoms become slightly positive

Hydrogen Bonding between Water Molecules▪ Covalently bonded molecules that have a slight potential

charge are said to be polar

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▪ The slightly charged regions of the water molecule can attract other polar or charged compounds

▪ Water molecules can associate via weak hydrogen bonds (F/O/N bonding with H)

Structure and Bonding of Water Molecules

3.1.5  Outline the thermal, cohesive and solvent properties of water

Thermal Properties▪ Water has a high specific heat capacity (the measure of

energy required to raise the temperature of 1 g of substance by 1°C)

▪ Water has a high heat of vaporisation (amount of energy absorbed per gram as it changes from a liquid to a gas / vapour)

▪ Water has a high heat of fusion (amount of energy required to be lost to change 1 g of liquid to 1 g of

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solid at 0°C)▪ These properties occur as a result of the extensive

hydrogen bonding between water molecules - this allows water to absorb considerable amounts of energy with little change in form (H-bonds need to be broken first)

Cohesive Properties▪ Water molecules are strongly cohesive (they tend to

stick to one another)▪ Water molecules will also tend to stick to other

molecules that are charged or polar (adhesion) ▪ These properties occur as a result of the polarity of a

water molecule and its ability to form hydrogen bonds with appropriate molecules

Solvent Properties▪ Water can dissolve many organic and inorganic

substances that contain electronegative atoms  (such as fluorine, oxygen and nitrogen)

▪ This occurs because the polar attraction of large quantities of water molecules can sufficiently weaken intramolecular forces (such as ionic bonds) and result in the dissociation of the atoms

Other Properties▪ Water is transparent, allowing light to pass through it

(important for photosynthesis)▪ Water expands when frozen, becoming less dense /

lighter (important for life on earth - oceans don't freeze)

3.1.6  Explain the relationship between the properties of

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water and its use in living organisms as a coolant, medium for metabolic reactions and transport medium

Coolant▪ Both plants and animals use the evaporation of water

from the surfaces of their bodies to facilitate cooling (sweating and panting in animals, transpiration from leaves in plants)

▪ Water can be used to carry heat to cooler places in our bodies (countercurrent exchange of thermal energy)

Medium for Metabolic Reactions

▪ Water can dissolve many organic and inorganic substances to facilitate chemical reactions

▪ Water can also absorb thermal energy released as a by-product of many chemical reactions

Transport Medium▪ The forces of attraction between water molecules help

facilitate the transport of water up the xylem of plants▪ Water is an effective transport medium for dissolved

substances (in plants, minerals from the soil and sugars from the leaves can be transported in water through the xylem and phloem respectively; while in animals, water in the blood is used to transport oxygen, glucose and urea)

Surface Tension

The force of attraction between water molecules makes water sufficiently dense for some smaller organisms to move along its surface

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3.2.1  Distinguish between organic and inorganic compounds

▪ Organic compounds are compounds containing carbon that are found in living things - except hydrogen carbonates (HCO3

-), carbonates (CO32-) and oxides of

carbon (CO, CO2)▪ Inorganic compounds are all other compounds (there are

less different inorganic compounds than organic compounds)

Carbohydrates are organic compounds consisting of one or more simple sugars that as monomers follow the general basic formula of (CH2O)x

Note:  Exceptions to this basic formula and the inclusion of other atoms (e.g. N) can occur

3.2.2  Identify glucose and ribose from diagrams showing their structure

Glucose(first) (C6H12O6) Ribose(second) (C5H10O5)

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3.2.3  List three examples each of monosaccharides, disaccharides and polysaccharides

Monosaccharides:  Glucose, galactose, fructose

Disaccharides:  Lactose, maltose, sucrose

Polysaccharides:  Cellulose, glycogen, starch

3.2.4  State one function of glucose, lactose and glycogen in animals and of fructose, sucrose and cellulose in plants

Animals

Glucose:  A source of energy which can be broken down to form ATP via cellular respiration

Lactose:  A sugar found in the milk of mammals, providing energy for suckling infants

Glycogen:  Used by animals for short term energy storage (between meals) in the liver

Plants

Fructose:  Found in honey and onions, it is very sweet and a good source of energy

Sucrose:  Used primarily as a transportable energy form (e.g. sugar beets and sugar cane)

Cellulose:  Used by plant cells as a strengthening component of the cell wall

3.2.5  Outline the role of condensation and hydrolysis in the relationship between monosaccharides, disaccharides and polysaccharides

▪ Condensation (dehydration) reactions occur when molecules are covalently joined together and water is

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formed as a by-product▪ In carbohydrates, the bond that is formed is called a

glycosidic linkage▪ The opposite of a condensation reaction is a hydrolysis

reaction, which requires a water molecule to break a covalent bond between two subunits

▪ Monosaccharides are single monomers that are joined to form disaccharides, while sugars containing multiple subunits (more than 10) are called polysaccharides

A Condensation Reaction between Two Monosaccharides

Lipids are a group of organic molecules that are insoluble in water but soluble in non-polar organic solvents

Common lipids include triglycerides (fats and oils), phospholipids and steroids

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3.2.2  Identify fatty acids from diagrams showing their structure

   

Unsaturated (double bonds)

Saturated (no double bonds)  

General Structure                                                  

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3.2.5  Outline the role of condensation and hydrolysis in the relationship between fatty acids, glycerol and triglycerides

▪ A condensation reaction occurs between the three hydroxyl groups of glycerol and the carboxyl groups of three fatty acids

▪ This reaction forms a triglyceride (and three molecules of water)

▪ The bond between the glycerol and the fatty acids is an ester linkage

▪ When one of the fatty acids is replaced by a phosphate group and phospholipid is formed

▪ Hydrolysis reactions will, in the presence of water, break these molecules down into their constituent subunits

Formation of a Triglyceride

3.2.6  State three functions of lipids

Structure:  Phospholipids are a main component of cell membranes

Hormonal signalling:  Steroids are involved in hormonal

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signalling (e.g. estrogen, progesterone, testosterone)

Insulation:  Fats in animals can serve as heat insulators while sphingolipids in the myelin sheath (of neurons) can serve as electrical insulators 

Protection:  Triglycerides may form a tissue layer around many key internal organs and provide protection against physical injury

Storage of energy:  Triglycerides can be used as a long-term energy storage source

3.2.7  Compare the use of carbohydrates and lipids in energy storage

Similarities:

▪ Complex carbohydrates (e.g. polysaccharides) and lipids both contain a lot of chemical energy and can be used for energy storage

▪ Complex carbohydrates and lipids are both insoluble in water - they are not easily transported

▪ Carbohydrates and lipids both burn cleaner than proteins (they do not yield nitrogenous wastes)

Differences:

▪ Lipid molecules contain more energy per gram than carbohydrates (about twice as much)

▪ Carbohydrates are more readily digested than lipids and release their energy more rapidly

▪ Monosaccharides and disaccharides are water soluble and easier to transport to and from storage sites than lipids

▪ Animals tend to use carbohydrates primarily for short-term energy storage, while lipids are used more for long-term energy storage

▪ Carbohydrates are stored as glycogen in animals while

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lipids are stored as fats (in plants carbohydrates are stored as cellulose and lipids as oils)

▪ Lipids have less effect on osmotic pressure within a cell than complex carbohydrates

Proteins are large organic compounds made of amino acids arranged in a linear chain

The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code

3.2.2  Identify amino acids from diagrams showing their structure

Generalised Structure of an Amino Acid

Types of Amino Acids

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3.2.5  Outline the role of condensation and hydrolysis in the relationship between amino acids and polypeptides

▪ A condensation reaction occurs between the amino group (NH2) of one amino acid and the carboxylic acid group (COOH) of another amino acid

▪ This reaction forms a dipeptide (plus a molecule of water) that is held together by a peptide bond

▪ Multiple amino acids can be joined together to form a polypeptide chain

▪ In the presence of water, polypeptides can be broken down into individual amino acids via hydrolysis reactions

Formation of a Dipeptide

3.3.1  Outline DNA nucleotide structure in terms of a sugar (deoxyribose), base and phosphate

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3.3.2  State the names of the four bases in DNA

A-T (Uracil in RNA)

C-G

       

▪ Adenine and guanine are purines (double ring bases)▪ Thymine and cytosine are pyrimidines (single ring bases)

3.3.3  Outline how the DNA nucleotides are linked together by covalent bonds into a single strand

▪Nuc

leotides a linked into a single strand via a condensation reaction

▪ The phosphate group (attached to the 5'-C of the sugar) joins with the hydroxyl (OH) group attached to the 3'-C of the sugar

▪ This results in a phosphodiester bond between the two nucleotides and the formation of a water molecule

▪ Successive condensation reactions between nucleotides results in the formation of a long single strand

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3.3.4  Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds

Two polynucleotide chains of DNA are held together by hydrogen bonds between complementary base pairs

▪ Adenine pairs with thymine (A=T) via two hydrogen bonds

▪ Guanine pairs with cytosine (G=C) via three hydrogen bonds

In order for bases to be facing each other and thus able to pair, the two strands must run in opposite directions (i.e. they are anti-parallel)

As the polynucleotide chain lengthens, the atoms that make up the molecule will arrange themselves in an optimal energy configuration 

This position of least resistance results in the double-stranded DNA twisting to form a double helix with approximately 10 - 15 bases per twist

 

3.3.5  Draw and label a simple diagram of the molecular structure of DNA

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3.4.1  Explain DNA replication in terms of unwinding of the double helix and separation of the strands by helicase, followed by the formation of the new complementary strands by DNA polymerase

Helicase▪ Unwinds the DNA and separates the two polynucleotide

strands by breaking the hydrogen bonds between complementary base pairs

▪ The two separated polynucleotide strands act as templates for the synthesis of new polynucleotide strands

DNA Polymerase

▪ Synthesises new strands from the two parental template strands

▪ Free deoxynucleoside triphosphates (nucleotides with three phosphate groups) are aligned opposite their complementary base partner and are covalently bonded together by DNA polymerase to form a complementary nucleotide chain

▪ The energy for this reaction comes from the cleavage of the two extra phosphate groups

3.4.2  Explain the significance of complementary base pairing in the conservation of the base sequence of DNA

Each of the nitrogenous bases can only pair with its complementary partner (A=T ; G=C)

Consequently, when DNA is replicated by the combined action of helicase and DNA polymerase:

▪ The new strands formed will be identical to the original strands separated from the template

▪ The two DNA molecules formed will be identical to the original molecule

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DNA Replication is a Semi-Conservative Process

3.4.3  State that DNA replication is semi-conservative

DNA replication is a semi-conservative process because when a new double-stranded DNA molecule is formed:

▪ One strand will be from the original moleculeOne strand will be newly synthesised 

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3.5.1  Compare the structure of DNA and RNA

3.5.2  Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase

Transcription is the process by which an RNA sequence is produced from a DNA template:

▪ RNA polymerase separates the DNA strands and synthesises a complementary RNA copy from one of the DNA strands

▪ It does this by covalently bonding ribonucleoside triphosphates that align opposite their exposed complementary partner (using the energy from the cleavage of the additional phosphate groups to join them together)

▪ Once the RNA sequence has been synthesised, RNA polymerase will detach from the DNA molecule and the double helix will reform

▪ The sequence of DNA that is transcribed into RNA is called a gene

▪ Transcription occurs in the nucleus (where the DNA is) and, once made, the mRNA moves to the cytoplasm (where translation can occur)

Three main types of RNA are predominantly made:

▪ Messenger RNA (mRNA):  A transcript copy of a gene

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used to encode a polypeptide▪ Transfer RNA (tRNA):  A clover leaf shaped sequence

that carries an amino acid▪ Ribosomal RNA (rRNA):  A primary component of

ribosomes  

3.5.3  Describe the genetic code in terms of codons comprised of triplets of bases

The genetic code is the set of rules by which information encoded in mRNA sequences is converted into proteins (amino acid sequences) by living cells

▪ Codons are a triplet of bases which encodes a particular amino acid

▪ As there are four bases, there are 64 different codon combinations (4 x 4 x 4 = 64)

▪ The order of the codons determines the amino acid sequence for a protein 

▪ The coding region always starts with a START codon (AUG) and terminates with a STOP codon

                                                                                              The Genetic Code

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The genetic code has the following features:

▪ It is universal - every living thing uses the same code (there are only a few rare and minor exceptions)

▪ It is degenerate - there are only 20 amino acids but 64 codons, so more than one codon may code for the same amino acid (this allows for silent mutations whereby a change in the DNA sequence does not affect the polypeptide sequence)

3.5.4  Explain the process of translation, leading to polypeptide formation

Translation is the process of protein synthesis in which the genetic information encoded in mRNA is translated into a sequence of amino acids in a polypeptide chain

▪ Ribosomes bind to mRNA in the cell's cytoplasm and move along the mRNA molecule in a 5' - 3' direction until it reaches a start codon (AUG)

▪ Anticodons on tRNA molecules align opposite appropriate codons according to complementary base pairing (e.g. UAC will align with AUG)

▪ Each tRNA molecule carries a specific amino acid (according to the genetic code)

▪ Ribosomes catalyse the formation of peptide bonds between adjacent amino acids (via a condensation reaction)

▪ The ribosome moves along the mRNA molecule synthesising a polypeptide chain until it reaches a stop codon, at this point translation stops and the polypeptide chain is released

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The Process of Translation

3.5.5  Explain the relationship between one gene and one polypeptide

▪ A gene is a sequence of DNA which encodes a polypeptide sequence

▪ A gene sequence is converted into a polypeptide sequence via the processes of transcription (making an mRNA transcript) and translation (polypeptide synthesis)

▪ Translation uses tRNA molecules and ribosomes to join amino acids into a polypeptide chain according to the mRNA sequence (as read in codons) 

▪ The universality of the genetic code means all organisms show the same relationship between genes and polypeptides (indicating a common ancestry and allowing for transgenic techniques to be employed)

▪ Some proteins may consist of a number of polypeptide chains and thus need multiple genes (e.g.

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haemoglobin consists of four polypeptide subunits encoded by two different genes)

▪ When a gene is mutated it may lead to the synthesis of a defective polypeptide, hence affecting protein function

The 'One Gene - One Polypeptide' Rule

There are two exceptions to the 'one gene - one polypeptide' rule:

▪ Genes encoding for tRNA and rRNA do not code for polypeptide sequences (only mRNA sequences code for polypeptides)

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A single gene may code for multiple polypeptides if alternative splicing occurs (the removal of exons as well as introns)

3.6.1  Define enzyme and active site

Enzyme:  A globular protein that increases the rate of a biochemical reaction by lowering the activation energy threshold (i.e. a biological catalyst)

Active Site:  The site on the surface of an enzyme which binds to the substrate molecule

3.6.2  Explain enzyme-substrate specificity

Active site and substrate complement each other in terms of both shape and chemical properties (e.g. opposite charges)

Binding to the active site brings the substrate into close physical proximity, creating an enzyme-substrate complex

The enzyme catalyses the conversion of the substrate into a product (or products), creating an enzyme-product complex

As the enzyme is not consumed in the reaction, it can continue to work once the product dissociates (hence only low concentrations are needed)

Enzyme-Substrate Specificity

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Lock and Key ModelEnzymes and substrates share specificity (a given enzyme will only interact with a small number of specific substrates that complement the active site)

This explanation of enzyme-substrate interaction is described as the 'lock and key' model (a lock only opens in response to a specific key)

3.6.3  Explain the effects of temperature, pH and substrate concentration on enzyme activity

Temperature

▪ Low temperatures result in insufficient thermal energy for the activation of a given enzyme-catalysed reaction to be achieved

▪ Increasing the temperature will increase the speed and motion of both enzyme and substrate, resulting in higher enzyme activity 

▪ This is because a higher kinetic energy will result in more frequent collisions between enzyme and substrate

▪ At an optimal temperature (may differ for different enzymes), the rate of enzyme activity will be at its peak

▪ Higher temperatures will cause enzyme stability to decrease, as the thermal energy disrupts the hydrogen bonds holding the enzyme together

▪ This causes the enzyme (particularly the active site) to lose its shape, resulting in a loss of enzyme activity (denaturation)

pH▪ Changing the pH will alter the charge of the enzyme,

which in turn will protein solubility and may change the shape of the molecule

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▪ Changing the shape or charge of the active site will diminish its ability to bind to the substrate, abrogating enzyme function

▪ Enzymes have an optimum pH (may differ between enzymes) and moving outside of this range will always result in a diminished rate of reaction

Substrate Concentration▪ Increasing substrate concentration will increase the

activity of a particular enzyme▪ More substrate means there is an increased likelihood of

enzyme and substrate colliding and reacting, such that more reactions will occur and more products will be formed in a given time period

▪ After a certain point, the rate of reaction will cease to rise regardless of further increases to substrate concentration, as the environment has become saturated with substrate and all enzymes are bound and reacting (Vmax)

Factors Affecting Enzyme Activity

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3.6.4  Define denaturation

Denaturation is a structural change in a protein that results in the loss (usually permanent) of its biological properties

▪ Heat and pH are two agents which may cause denaturation of an enzyme

Denaturation

3.6.5  Explain the use of lactase in the production of lactose-free milk

Lactose is a disaccharide of glucose and galactose which can be broken down by the enzyme lactase

Historically, mammals exhibit a marked decrease in lactase production after weaning - leading to lactose intolerance (incidence is particularly high in Asian / African / Native American / Aboriginal populations)

Lactose-free milk can be produced by purifying lactase (e.g. from yeast or bacteria) and binding it to an inert substance (such as alginate beads)

Milk passed over this immobilised enzyme will become lactose-free

The generation of lactose-free milk can be used in a

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number of ways:

▪ As a source of milk for lactose-intolerant individuals▪ As a means to increase the sweetness of milk (glucose

and galactose are sweeter in flavour), thus negating the need for artificial sweeteners

▪ As a way of reducing the crystallisation of ice-creams (glucose and galactose are more soluble than lactose)

▪ As a means of shortening the production time for yogurts or cheese (bacteria ferment glucose and galactose more readily than lactose)

 

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3.7.1  Define cell respiration

Cell respiration is the controlled release of energy from organic compounds in cells to form ATP (adenosine triphosphate)

3.7.2  State that, in cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate, with a small yield of ATP

Glycolysis is the breakdown of one molecule of glucose (6C) into two molecules of pyruvate (2 x 3C) with a small net yield of ATP (2 molecules of ATP)

▪ This process also results in the reduction of two hydrogen acceptors (NAD+) to form 2 molecules of NADH + H+

3.7.3  Explain that, during anaerobic cell respiration, pyruvate can be converted in the cytoplasm into lactate, or ethanol and carbon dioxide, with no further yield of ATP

Anaerobic respiration occurs in the absence of a ready supply of oxygen (e.g. during intense physical activity, when oxygen reserves are depleted)

In order to generate the small amounts of energy provided by glycolysis, the end product (pyruvate) must be converted into another substance before more glucose can be used

▪ This is because the conversion of pyruvate replenishes the levels of the hydrogen acceptor (NAD+) needed for glycolysis to occur

Anaerobic Respiration

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The conversion of pyruvate occurs in the cytoplasm of the cell and the products are:

▪ Lactate (3C) in animal cells▪ Ethanol (2C) and carbon dioxide (CO2) in plants, fungi

(e.g. yeast) and bacteria▪ The conversion of pyruvate into ethanol and CO2 is also

known as fermentation

3.7.4  Explain that, during aerobic cell respiration, pyuvate can be broken down in the mitochondrion into carbon dioxide and water with a large yield of ATP

Aerobic respiration occurs in the presence of oxygen and takes place in the mitochondrion

Pyruvate is broken down into carbon dioxide and water and a large amount of ATP is formed (34 - 36 molecules)

Although this process begins with glycolysis (to break down glucose into pyruvate), glycolysis does not require oxygen and is an anaerobic process

Anaerobic versus Aerobic Respiration

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3.8.1  State that photosynthesis involves the conversion of light energy into chemical energy

Photosynthesis is the process by which plants synthesise organic compounds (e.g. glucose) from inorganic compounds (CO2 and H2O) in the presence of sunlight

Photosynthesis is a two step process: 

1.  The light dependent reactions convert the light energy into chemical energy (ATP)

2.  The light independent reactions use the chemical energy to synthesise organic compounds (e.g. glucose)

The organic molecules produced in photosynthesis can be used in cellular respiration to provide the energy needed

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by the organism

3.8.2  State that light from the Sun is composed of a range of wavelengths (colours)

Sunlight is white light, made up of all the colours of the visible spectrum

Colours are different wavelengths of light and range from ~ 400 nm - 700 nm

The colours of the visible spectrum are (from longer to shorter wavelength):

Red    Orange    Yellow    Green    Blue    Indigo  Violet    (R.O.Y.G.B.I.V)

3.8.3  State that chlorophyll is the main photosynthetic pigment

Chlorophyll is the main site of light absorption in the light dependent stage of photosynthesis

There are a number of different chlorophyll molecules, each with their own distinct absorption spectra (the spectrum of light absorbed by a substance)

When chlorophyll absorbs light energy, they release electrons which are used to make ATP (chemical energy)

3.8.4  Outline the difference in absorption of red, green

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and blue light by chlorophyll

The main colours of light absorbed by chlorophyll are red and blue light

The main colour of light not absorbed (it is reflected) by chlorophyll is green light

▪ This explains why leaves are green - excepting when the presence of other pigmented substances (e.g. anthocyanins) produces a different colour

▪ Deciduous trees stop producing high amounts of chlorophyll in the winter (due to insufficient sunlight), allowing other photosynthetic pigments (e.g. xanthophylls, carotenoids) to come to the fore, which changes the colour of the leaf

3.8.5  State that light energy is used to produce ATP, and to split water molecules (photolysis) to form oxygen and hydrogen

The first part of photosynthesis is the light dependent reaction, which uses light energy to make ATP

Light Dependent Reaction▪ Light stimulates chlorophyll to release electrons, which

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results in the production of ATP▪ Light energy also splits water molecules (photolysis),

producing oxygen and hydrogen▪ The hydrogen is taken up by a hydrogen carrier (NADP+)

to form NADPH▪ The splitting of water also releases electrons, which

replace those lost by the chlorophyll▪ The ATP and hydrogen (NADPH) are taken to the site of

the light independent reactions

3.8.6  State that ATP and hydrogen (derived from the photolysis of water) are used to fix carbon molecules to make organic molecules

The second part of photosynthesis is the light independent reaction, which makes organic compounds from the products of the light dependent reactions

Light Independent Reaction

▪ ATP and hydrogen (carried by NADPH) are products of the light dependent reactions

▪ They are used to fix carbon molecules together (add CO2

to basic carbon compounds)▪ This allows for the production of more complex organic

molecules (e.g. sugars)▪ These organic molecules can then be stored to use in

cellular respiration as required 

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3.8.7  Explain that the rate of photosynthesis can be measured directly by the production of oxygen or the uptake of carbon dioxide, or indirectly by an increase in biomass

▪ The rate of photosynthesis can be measured by changes in the amounts of inputs (CO2) or outputs (O2 or glucose) of the photosynthesis equation

▪ Water cannot be measured as it is involved in a number of essential processes besides photosynthesis (e.g. condensation and hydrolysis reactions)

Measuring CO2 Uptake▪ CO2 uptake can be measured by placing a plant in an

enclosed space with water▪ Carbon dioxide interacts with the water molecules,

producing bicarbonate and hydrogen ions, which increases the acidity of the resulting solution

▪ The change in pH can therefore provide a measure of CO2 uptake by a plant (increased CO2 uptake = more alkaline pH)

Measuring O2 Production

▪ O2 production can be measured by submerging a plant in an enclosed space with water attached to a sealed gas syringe

▪ Any oxygen gas produced will bubble out of solution and can be measured by a change in water level (via the position of the meniscus)

Measuring Biomass (Indirect)▪ Glucose production can be indirectly measured by a

change in a plant's biomass (weight)▪ This requires the plant to be completely dehydrated prior

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to weighing to ensure the change in biomass reflects a change in organic matter and not water content

▪ An alternative method for measuring glucose production is to determine the change in starch levels in a plant (glucose is stored as starch)

▪ Starch can be identified via iodine staining (resulting solution turns purple) and quantitated using a colorimeter

3.8.8  Outline the effect of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis

Temperature▪ Photosynthesis is controlled by enzymes, which are

sensitive to temperature▪ As temperature increases, the rate of photosynthesis will

increase as reagents have greater kinetic energy and are more likely to react

▪ Above a certain temperature, the rate of photosynthesis will decrease as essential enzymes begin to denature

Light Intensity▪ As light intensity increases, the rate of photosynthesis

will increase up until a certain point, when photosynthesis is proceeding at its maximum rate

▪ Further increases to light intensity will have no effect on photosynthesis (the rate will plateau), as chlorophyll are saturated by light

▪ Different wavelengths of light will have different effects on the rate of photosynthesis (e.g. green light will not be used)

CO2 Concentration▪ As the concentration of carbon dioxide increases, the

rate of photosynthesis will increase up until a certain

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point, when photosynthesis is proceeding at its maximum rate

▪ Further increases to carbon dioxide concentration will have no effect on photosynthesis (the rate will plateau), as the enzymes responsible for carbon fixation become saturated

Factors Affecting the Rate of Photosynthesis

7.1.1  Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines

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▪ The carbon atoms in deoxyribose are numbered, with the nitrogenous bases attach to C1 and the phosphate group is attached to C5

▪ Nucleotides are joined by a covalent phosphodiester bond between the C5 phosphate group and the C3 hydroxyl group

▪ Hence one nucleotide strand runs 5' - 3'▪ The nitrogenous bases interact via hydrogen bonding

(complementary base pairing)Adenine (A) and thymine (T) share 2 hydrogen

bondsGuanine (G) and cytosine (C) share 3 hydrogen

bonds▪ In order for the bases to associate (i.e. face each other),

one strand must run antiparallel to the other (this antiparallel strand runs 3' - 5') 

▪ Double stranded DNA forms a double helix, with 10 nucleotides per turn and the structure containing both major and minor grooves

Structural Organisation of DNA

7.1.2  Outline the structure of nucleosomes

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▪ The DNA double helix contains major and minor grooves on its outer diameter, which expose                   chemical groups that can form hydrogen bonds

▪ The DNA of eukaryotes associates with proteins called histones

▪ DNA is wound around an octamer of histones (146 bases and 1.65 turns of the helix per octamer)

▪ The octamer and DNA combination is secured to a H1 histone, forming a nucleosome 

7.1.3  State that nucleosomes help to supercoil DNA and help to regulate transcription

▪ Nucleosomes serve two main functions:They protect DNA from damageThey allow long lengths of DNA to be packaged

(supercoiled) for mobility during mitosis / meiosis

▪ When supercoiled, DNA is not accessible for transcription

▪ Cells will have some segments of DNA permanently supercoiled (heterochromatin) and these segments will differ between different cell types

7.1.4  Distinguish between unique or single copy genes and highly repetitive sequences in nuclear DNA

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7.1.5  State that eukaryotic genes contain introns and exons

Intron:  A non-coding sequence of DNA within a gene (intervening sequence) that is cut out by enzymes when RNA is made into mature mRNA

Exon:  The part of the gene which codes for a protein (expressing sequence)

Eukaryotic DNA contains introns but prokaryotic DNA does not

7.2.1  State that DNA replication occurs in a 5' - 3' direction

▪ DNA replication is semi-conservative, meaning that a new strand is synthesised from an original template strand

▪ DNA replication occurs in a 5' - 3' direction, in that new nucleotides are added to the C3 hydroxyl group such that the strand grows from the 3' end

▪ This means that the DNA polymerase enzyme responsible for adding new nucleotides moves along the original template strand in a 3' - 5' direction

Direction of DNA Replication

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7.2.2  Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates

▪ DNA replication is semi-conservative and occurs during the S phase of interphase

▪ Helicase unwinds and separates the double stranded DNA by breaking the hydrogen bonds between base pairs

This occurs at specific regions (replication origins), creating a replication fork of two polynucleotide strands in antiparallel directions

▪ RNA primase synthesises a short RNA primer on each template strand to provide an attachment and initiation point for DNA polymerase III

▪ DNA polymerase III adds deoxynucleoside triphosphates (dNTPs) to the 3' end of the polynucleotide chain, synthesising in a 5' - 3' direction

The dNTPs pair up opposite their complementary base partner (adenine pairs with thymine ; guanine pairs with cytosine)

As the dNTPs join with the DNA chain, two phosphates are broken off, releasing the energy needed to form a phosphodiester bond

Synthesis is continuous on the strand moving towards the replication fork (leading strand) 

Synthesis is discontinuous on the strand moving away from the replication fork (lagging strand)

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leading to the formation of Okazaki fragments▪ DNA polymerase I removes the RNA primers and

replaces them with DNA▪ DNA ligase joins the Okazaki fragments together to

create a continuous strand

Overview of DNA Replication

7.2.3  State that DNA replication is initiated at many points in eukaryotic chromosomes

▪ Because eukaryotic genomes are (typically) much larger than prokaryotic genomes, DNA replication is initiated at many points simultaneously in order to limit the time required for DNA replication to occur

▪ The specific sites at which DNA unwinding and initiation of replication occurs are called origins of replication and form replication bubbles

As replication bubbles expand in both directions, they eventually fuse together; two generate two separate semi-conservative double strands of DNA

7.3.1  State that transcription is carried out in a 5' - 3' direction

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Transcription is carried out in a 5' - 3' direction (of the new RNA strand)

7.3.2  Distinguish between the sense and antisense strands of DNA

DNA consists of two polynucleotide strands, only one of which is transcribed into RNA

▪ The antisense strand is transcribed into RNAIts sequence will be complementary to the RNA

sequence and will be the "DNA version" of the tRNA anticodon sequence 

▪ The sense strand is not transcribed into RNAIts sequence will be the "DNA version" of the RNA

sequence (identical except for T instead of U)

7.3.3  Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator

A gene is a sequence of DNA which is transcribed into RNA and contain three main parts:

▪ Promoter:  Responsible for the initiation of transcription (in prokaryotes, a number of genes may be regulated by a single promoter - this is an operon)

▪ Coding Sequence:  The sequence of DNA that is actually transcribed (may contain introns in eukaryotes)

▪ Terminator:  Sequence that serves to terminate transcription (mechanism of termination differs between prokaryotes and eukaryotes)

Transcription is the process by which a DNA sequence (gene) is copied into a complementary RNA sequence and involves a number of steps:

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▪ RNA polymerase binds to the promoter and causes the unwinding and separation of the DNA strands

▪ Nucleoside triphosphates (NTPs) bind to their complementary bases on the antisense strand (uracil pairs with adenine, cytosine pairs with guanine)

▪ RNA polymerase covalently binds the NTPs together in a reaction that involves the release of two phosphates to gain the required energy

▪ RNA polymerase synthesises an RNA strand in a 5' - 3' direction until it reaches the terminator

▪ At the terminator, RNA polymerase and the newly formed RNA strand both detach from the antisense template, and the DNA rewinds

▪ Many RNA polymerase enzymes can transcribe a DNA sequence sequentially, producing a large number of transcripts

▪ Post-transcriptional modification is necessary in eukaryotes

Overview of Transcription

7.3.4  State that eukaryotic RNA needs the removal of

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introns to form mature mRNA

▪ Eukaryotic genes may contain non-coding sequences called introns that need to be removed before mature mRNA is formed

▪ The process by which introns are removed is called splicing

The removal of exons (alternative splicing) can generate different mRNA transcripts (and different polypeptides) from a single gene

7.4.1  Explain that each tRNA molecule is recognised by a tRNA-activating enzyme that binds a specific amino acid to the tRNA using ATP for energy

▪ Each different tRNA molecule has a unique shape and chemical composition that is recognised by a specific tRNA-activating enzyme

▪ The enzyme (aminoacyl-tRNA synthetase) first binds the amino acid to a molecule of ATP (to form an  amino acid-AMP complex linked by a high energy bond)

▪ The amino acid is then transferred to the 3'-end of the appropriate tRNA, attaching to a terminal CCA sequence on the acceptor stem and releasing the

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AMP molecule▪ The tRNA molecule with an amino acid attached is thus

said to be 'charged' and is now capable of participating in translation

▪ The energy in the bond linking the tRNA molecule to the amino acid will be used in translation to form a peptide bond between adjacent amino acids

7.4.2  Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three tRNA binding sites and mRNA binding sites

▪ Ribosomes are made of protein (for stability) and ribosomal RNA (rRNA - for catalytic activity)

▪ They consist of two subunits:The small subunit contains an mRNA binding siteThe large subunit contains three tRNA binding sites

- an aminacyl (A) site, a peptidyl (P) site and an exit (E) site

▪ Ribosomes can be either found freely in the cytosol or bound to the rough ER (in eukaryotes)

▪ Ribosomes differ in size in eukaryotes and prokaryotes (eukaryotes = 80S ; prokaryotes = 70S)

7.4.3  State that translation consists of initiation, elongation, translocation and termination

Translation occurs in four main steps:

▪ Initiation:  Involves the assembly of an active ribosomal complex

▪ Elongation:  New amino acids are brought to the ribosome according to the codon sequence

▪ Translocation:  Amino acids are translocated to a growing polypeptide chain

▪ Termination:  At certain "stop" codons, translation is ended and the polypeptide is released

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7.4.4  State that translation occurs in a 5' - 3' direction

▪ The start codon (AUG) is located at the 5' end of the mRNA sequence and the ribosome moves along it in the 3' direction

▪ Hence translation occurs in a 5' - 3' direction

7.4.5  Draw and label a diagram showing the structure of a peptide bond between two amino acids

7.4.6  Explain the process of translation, including ribosomes, polysomes, start codons and stop codons

Pre-Initiation:

▪ Specific tRNA-activating enzymes catalyse the attachment of amino acids to tRNA molecules, using ATP for energy

Initiation: 

▪ The small ribosomal subunit binds to the 5' end of mRNA and moves along it until it reaches the start codon (AUG)

▪ Next, the appropriate tRNA molecule binds to the codon via its anticodon (according to complementary base pairing)

▪ Finally, the large ribosomal subunit aligns itself to the tRNA molecule at its P-site and forms a complex with the small ribosomal subunit

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Elongation:▪ A second tRNA molecule pairs with the next codon in the

ribosomal A-site▪ The amino acid in the P-site is covalently attached via a

peptide bond to the amino acid in the A-site

Translocation:

▪ The ribosome moves along one codon position, the deacylated tRNA moves into the E-site and is released, while the tRNA bearing the dipeptide moves into the P-site

▪ Another tRNA molecules attaches to the next codon in the newly emptied A-site and the process is repeated

▪ The ribosome moves along the mRNA sequence in a 5' - 3' direction, synthesising a polypeptide chain

▪ Multiple ribosomes can translate a single mRNA sequence simultaneously (forming polysomes)

Termination: ▪ Elongation and translocation continue until the ribosome

reaches a stop codon▪ These codons do not code for any amino acids and

instead signal for translation to stop▪ The polypeptide is released and the ribosome

disassembles back into subunits▪ The polypeptide may undergo post-translational

modification prior to becoming a functional protein

Overview of the Process of Translation

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7.4.7  State that free ribosomes synthesise proteins for use primarily within the cell, and that bound ribosomes synthesise proteins primarily for secretion or for lysosomes

▪ Ribosomes floating freely in the cytosol produce proteins for use within the cell

▪ Ribosomes attached to the rough ER are primarily involved in producing proteins to be exported from the cell or used in the lysosome

▪ These proteins contain a signal recognition peptide on their nascent polypeptide chains which direct the associated ribosome to the rough ER

7.5.1  Explain the four levels of protein structure, indicating the significance of each level

Primary (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

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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)

Levels of Protein Organisation

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

7.5.3  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 active site

7.5.4  State four functions of proteins, giving a named example of each

Structure:  Support for body tissue (e.g. collagen, elastin, keratin)

Hormones:  Regulation of blood glucose (e.g. insulin,

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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) 

7.6.1  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)

7.6.2  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 and be 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

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7.6.3  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 

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Reaction Pathway of a Typical Exergonic / Exothermic Reaction

7.6.4  Explain the difference between competitive and non-competitive inhibition, with reference to one example of each

Competitive 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 concentration

Example:  Relenza is a competitive inhibitor of neuraminidase (influenza virus enzyme), preventing the release of virions from infected cells

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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 site

Example:  Cyanide (CN-) inhibits enzymes (cytochrome oxidase) in the electron transport chain by breaking disulphide bonds within the enzyme

Competitive versus Non-competitive Inhibition

7.6.5  Explain the control of metabolic pathways by end-product inhibition, including the role of allosteric sites

End-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

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product formation will decrease (and with less product there is less enzyme inhibition)

End-Product 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, glucose is 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

8.1.1  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

▪Re

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dox (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 OxidationLEO 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:

8.1.2  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

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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 become hexose biphosphate

2.  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)

8.1.3  Draw and label a diagram showing the structure of a mitochondrion as seen in electron micrographs

           

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8.1.4  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:

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

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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)

8.1.5 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

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▪ 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

8.1.6  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 cycle to occur

Outer membrane:  Contains appropriate transport

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proteins for shuttling pyruvate into the mitochondria

8.2.1  Draw and label a diagram showing the structure of a chloroplast as seen in an electron micrograph

8.2.2  State that photosynthesis consists of the light-dependent and light-independent reactions

Photosynthesis is a two-step process:

1.  The light dependent reactions convert the light energy into chemical energy

2.  The light independent reaction uses the chemical energy to make organic molecules

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Overview of Photosynthesis

8.2.3 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+

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▪ Electrons lost from photosystem I are replaced by electrons from photsystem II

▪ 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

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8.2.4  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 ADP and an inorganic phosphate (Pi) into ATP

▪ This process is called chemiosmosisPhotophosphorylation via Chemiosmosis

8.2.5  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

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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

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The Light Independent Reaction (Calvin Cycle)

8.2.6  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

8.2.7  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

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▪ 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 A ction Spectrum