Topic 5

2. Describe the structure of chloroplasts in relation to their role in photosynthesis.

Grana- Arranged in stacks with discs known as thylakoids Thylakoids- Site of photosynthesis, site of green pigmentchlorophyll Chlorophyll- Captures energy from light, converts it to ATP Stroma- Where ATP is used to convert carbon dioxide into glucose, contains enzymes which can be used in cellular respiration, glucose converted to starch

3 Describe the overall reaction of photosynthesis as requiring energy from light to split apart the strong bonds in water molecules, storing the hydrogen in a fuel (glucose) by combining it with carbon dioxide and releasing oxygen into the atmosphere.

6CO2 + 6H20 + Energy C6H12O6 (glucose) + 6O2 Includes the light dependent reaction (including hydrolysis using light energy) and the light independent reaction (production of glucose by carbon fixation in the Calvin cycle).

4 Describe the light-dependent reactions of photosynthesis including how light energy is trapped by exciting electrons in chlorophyll and the role of these electrons in generating ATP, and reducing NADP in photophosphorylation and producing oxygen through photolysis of water.
Light dependent reaction takes place in thylakoid membrane of chloroplast Light energy excites electrons from PSII along the electron transfer chain (ETC) to PSI Photolysis of water makes H+ ions, electrons and oxygen Energy lost as the electron moves along the ETC is used to pump H+ ions to one side of the thylakoid membrane. H+ ions then travel back to the stroma via the enzyme ATP synthase. The enzyme uses energy from this process to make ATP from ADP + inorganic phosphate. Light energy excites electrons in PSI to even higher energy levels. The electrons and H+ ions are transferred to NADP to make reduced NADP. Cyclic photophosphorylation makes ATP only. Non-cyclic photophosphorylation makes ATP and reduced NADP.

5 Describe how phosphorylation of ADP requires energy and how hydrolysis of ATP provides an immediate supply of energy for biological processes.
Hydrolysis of ATP : Loss of phosphate molecule to release energy which is used by the cell. ATP is converted into ADP.

Photophosphorylation of ADP: Condensation reaction needing energy which comes from a catabolic reaction. Energy is needed to form the bond as energy was released when the bond was broken. ATP Adenosine triphosphate. ADP Adenosine diphosphate.

Jan 12

6. Describe the light-independent reactions as reduction of carbon dioxide using the products of the light-dependent reactions (carbon fixation in the Calvin cycle, the role of GP, GALP, RuBP and RUBISCO) and describe the products as simple sugars that are used by plants, animals and other organisms in respiration and the synthesis of new biological molecules (including polysaccharides, amino acids, lipids and nucleic acids). Also known as the Calvin cycle. Does not require light energy, (directly) however it does rely on products from the light dependent reaction. (ATP and Reduced NADP) Takes place in Stroma of the chloroplast. CO2 enters leaf through stomata diffuses in to stroma. Combined with RuBP, Produces 2 molecules GP RUBISCO catalyses the reaction between CO2 and RuBP. ATP and Reduced NAPD reduce GP to GALP, which is then converted into glucose and other organic compounds. 5/6 of TP molecules used to regenerate RuBP,using ATP.

7. Carry out calculations of net primary productivity and explain the relationship between gross primary productivity, net primary productivity and plant respiration.

NPP = GPP plant respiration The GPP of the grass is 19,000kJm-2 yr-1. The grass loses 8000kJm-2 yr-1 from respiration. NPP= 19,000 8000 = 11,000kJm-2 yr-1. Gross primary production (GPP) is the total amount of energy produced by vegetation; some of that energy is used for cellular respiration i.e. for the growth and development of the plant. What is left over is called net primary production (NPP) and that represents the total available energy in an ecosystem the form of dry plant biomass.

8 Calculate the efficiency of energy transfers between trophic levels.

% efficiency of energy transfer between trophic levels
=

Net productivity of a level

x 100

Net productivity of previous level

9. Discuss how understanding the carbon cycle can lead to methods to reduce atmospheric levels of carbon dioxide (including the use of biofuels and reforestation).

10 Explain that the numbers and distribution of organisms in a habitat are controlled by biotic and abiotic factors.
Abiotic factors E.g. temperature, light availability, and water/space availability. Ideal abiotic factors allow organisms to grow fast and reproduce successfully Therefore, ideal abiotic factors cause increased population size and wide distribution. Abiotic factors that arent ideal can cause an organism to be unable to live successfully in an area Biotic factors E.g. predation, interspecific competition, and intraspecific competition If an organism is out-competed, it has to move away from the better-adapted organism. This affects distribution. Ideal biotic factors allow organisms to grow fast and reproduce successfully

11 Describe how to carry out a study on the ecology of a habitat to produce valid and reliable data (including the use of quadrats and transects to assess abundance and distribution of organisms and the measurement of abiotic factors, eg solar energy input, climate, topography, oxygen availability and edaphic factors).

Chose a location eg. sea shore, search the habitat and compose a hypothesis. Mark out an area to collect data (transect). Use either random, systematic or stratified sampling. Measure abiotic factors at each 1m point along the line. Sample organism along transect using chosen sampling method with a 1m2 quadrat and collect required data.

12. Explain how the concept of niche accounts for distribution and abundance of organisms in a habitat.
Niche- The role an organism plays within its environment. Abundance -Two organisms cannot occupy the same niche, if this does occur the species will compete until only one remains. Distribution Organisms can only exist in habitats where all the conditions that make up their role exist.

13. Describe the concept of succession to a climax community.

Succession is the process by which communities colonise an ecosystem and are then replaced over time by other communities after being out-competed. Primary succession starts when pioneer species (e.g. lichen) colonise new land surface. Abiotic conditions are harsh and there is no soil. These pioneer species die and the decomposed material forms a basic soil. New organisms (e.g. grass) move in and the process repeats making the soil develop. Secondary succession begins with a soil layer and the pioneer species are larger plants (e.g. shrubs, small trees). Competition occurs and dominant species out-compete less adapted plants (e.g. grass). More species move in and create species diversity. The final stage climax community eco system supports largest, complex community of plants unlikely to change: steady state.

14 Outline the causes of global warming including the role of greenhouse gases (carbon dioxide and methane, CH4) in the greenhouse effect.
Causes of global warming: human activity, increase of greenhouse gases (causes the greenhouse effect), burning of fossil fuels, farming, deforestation, carbon sinks, Greenhouse effect- incoming short infrared wavelength, earth radiates longer infrared wavelength, excess amount greenhouse gases cause large amounts re-radiated infrared wavelength to be reflected back- warming of earth surface Co2- concentration increasing- human activity and carbon sinks Methane- concentration increasing- produced by extraction of fossil fuels and more decaying waste and more cows, thawing of frozen ground

15 Describe the effects of global warming (rising temperature, changing rainfall patterns and seasonal cycles) on plants and animals (distribution of species, development and life cycles). Rising Temperature affects metabolism because of enzyme optimum temperatures = affects distribution and decrease in rate of growth. Changing Rainfall Patterns = affects life cycles and distribution Seasonal Cycles = affects life cycles and distribution (because of availability of food and reproduction).

16 Explain the effect of increasing temperature on the rate of enzyme activity in plants, animals and micro-organisms.
Higher temperature = higher kinetic energy Higher energy = more collisions More collisions = more efficient chemical reactions in enzymes Temperature too high = enzymes denature and chemical reactions cannot occur efficiently Optimum temperature = Temperature too low enzymes do not work and chemical reactions cannot occur efficiently Therefore, increase in temperature increases growth in plants, animals and microoragnisms. They are

17 Describe how to investigate the effects of temperature on the development of organisms (eg seedling growth rate, brine shrimp hatch rates).

1. Place equal volumes of salt water into 6 containers 2. Place each container in different temperature water baths, ranging from 0-60 degrees 3. Control other variables (eg. Light intensity) 4. Leave containers in water baths until water has reached appropriate temperature. 5. Add equal quantities of brine shrimp eggs (40) to each container. 6. Check every 10 hours over a 72 hour periods for the presence of tiny swimming larvae. 7. Record time at which hatching begins.

18. Analyse and interpret different types of evidence for global warming and its causes (including records of carbon dioxide levels, temperature records, pollen in peat bogs and dendrochronology) recognising correlations and causal relationships.

Temperature The general trend of increasing global temperature over the last century is evidence for global warming. Dendrochronology A method for figuring out the age of a tree, the thickness of the ring depends on the climate when ring is formed, when its warmer the rings are thicker. Pollen in Peat Bogs Pollen is preserved in peat bogs, they accumulate in layers so the age of preserved pollen increases with depth. More pollen show an increase in temp.

19. Describe that data can be extrapolated to make predictions, that these are used in models of future global warming, and that these models have limitations.

Data on greenhouse gases can be extrapolated and to be used in models to make predictions about what will happen to temperature in the future and the long term effects of the environment. Limitations: Impossible to predict the exact impacts of CO2 or on aspects of the world climate. Extrapolations from past data cannot take into account unknown factors in the future.

20 Discuss the way in which scientific conclusions about controversial issues, such as what actions should be taken to reduce global warming or the degree to which humans are affecting global warming, can sometimes depend on who is reaching the conclusions.

Depends on what company the person is working for Bias

21 Describe how evolution (a change in the allele frequency) can come about through gene mutation and natural selection.
Allele frequency the proportion of an allele in the gene pool of a population. There are different alleles due to mutations some of these are advantageous and others arent. Therefore different individuals are better adapted to their environment so are more likely to survive and reproduce to pass on their genes (including the beneficial allele). This also then increases the offsprings chances of survival and reproduction. Overtime this increases allele frequency. This leads to evolution.

22 Explain how reproductive isolation can lead to speciation.

No crossover of gene pool Adaptations differ because of different circumstances/environments Different adaptations lead to difficulties in reproduction to produce fertile offspring = Different species Boom! Speciation. Can be caused by geographical barriers (allopatric speciation) and sympatric speciation

23 Describe the role of the scientific community in validating new evidence (including molecular biology, eg DNA, proteomics) supporting the accepted scientific theory of evolution (scientific journals, the peer review process, scientific conferences).

Topic 6

2.Explain the nature of the genetic code (triplet code, non-overlapping and degenerate)

A codon(or triplet code) is 3 bases, that code for an amino acid. These Codons are non-overlapping Degenerate- there are more possible combinations of triplets then there are available amino acids. (20 amino acids but 64 possible combinations)

3. Explain the process of protein synthesis and explain the roles of the template (antisense) DNA strand in transcription, codons on messenger RNA, anticodons on transfer RNA. Transcription : RNA polymerase attaches to the DNA at the beginning of a gene causing the hydrogen bonds to break and the DNA strands to separate. The anti-sense (template) strand is used to make mRNA RNA nucleotides line up alongside the template strand and pair up with their complementary bases. Joined together to form mRNA. mRNA leaves the nucleus through a nuclear pore.

 mRNA modification During transcription (in the nucleus), introns (sections of DNA that dont code for amino acid) are removed by splicing and exons (the sections that do code) are joined to form mRNA strands. Exons can be joined in different orders to form different mRNA strands, meaning more than one amino acid sequence and so more than one protein can be produced from one gene.

 Translation mRNA attaches to a ribosome and tRNA carry amino acids to the ribosome. The anti-codon on tRNA thats complementary to the first codon on mRNA attaches itself to mRNA by complementary base pairing. A second tRNA attaches itself to the next codon on mRNA. The amino acids are joined by a peptide bond. The first tRNA molecule moves away leaving its amino acid behind. This process continues until there is a stop codon on the mRNA molecule and there is a chain of amino acids (polypeptide chain).

4 Explain how one gene can give rise to more than one protein through post-transcriptional changes to messenger RNA.
During transcription introns and exons are copied into mRNA Introns- sections of gene which dont code for amino acids, exons do code for amino acids Depending on what introns are removed by splicing, and which exons are joined to form new mRNA strand this can lead to different proteins being formed as exons can be joined in different orders More than one amino acid sequence and so more than one protein can be produced from one gene

5 Describe how DNA profiling is used for identification and determining genetic relationships between organisms (plants and animals).

The more bands on 2 DNA profiles that match, the more closely related those two people are

6 Describe how DNA can be amplified using the polymerase chain reaction (PCR)
Mix DNA sample, free nucleotides, primers and DNA polymerase Primers = short pieces of DNA complementary to the bases at the start of the DNA fragment desired Heat to 95C to break hydrogen bonds between DNA strands Cool to 50-65C so the primers anneal (bind) to the separated strands Heat to 72C so DNA polymerase can work DNA polymerase lines up free nucleotides along the DNA template strands to form complementary strands Repeat Each PCR cycle doubles the amount of DNA present, amplifying the DNA.

7 Describe how gel electrophoresis can be used to separate DNA fragments of different length

8. Distinguish between the structure of bacteria and viruses.

Bacteria
Ribosomes Cell Wall Flagellum Slime Capsule Plasmids Plasma Membrane Nucleic Acid

Virus
Protein Coat(Caspid) Nucleic Acid(either DNA or RNA) Smaller than Bacteria Not cells

9. Describe the role of micro-organisms in the decomposition of organic matter and the recycling of carbon.

10 Describe the major routes pathogens may take when entering the body and explain the role of barriers in protecting the body from infection, including the roles of skin, stomach acid, gut and skin flora.

Pathogens can enter the body:

Cuts in the skin Through digestive system via contaminated food and drink Through respiratory system Mucosal surfaces Barriers . Stomach acid . Skin (physical barrier) . Gut and Skin flora (compete with pathogens) . Lysozyme (enzyme in mucosal layers, kills bacteria by damaging their cell walls)

11 Explain how bacterial and viral infectious diseases have a sequence of symptoms that may result in death, including the diseases caused by Mycobacterium tuberculosis (TB) and Human Immunodeficiency Virus (HIV). Pathogens are viruses, some fungi, some bacteria (anything that causes disease) As infectious diseases develop, they cause a sequence of symptoms, which could lead your ultimate annihilation. HIV infects and destroys immune system cells. Eventually progresses to AIDS when immune system deteriorates and fails.
Initial AIDS symptoms: reduction in no. of T-helper cells (with CD4 receptors), minor infections of mucus membranes, recurring respiratory infections As AIDS progresses: no. of T-helper cells decreases further, susceptible to more serious infections Late stages: very low no. of T-helper cells, serious infections that can kill.

12 Describe the non-specific responses of the body to infection, including inflammation, lysozyme action, interferon and phagocytosis
PHAGOCYTOSIS BY PHAGOCYTES e.g. macrophages. During phagocytosis, a pathogen is engulfed A lysosome full of lysozyme enzymes fuses with the phagocytic vacuole holding the pathogen The lysozyme break down the pathogen INTERFERONS Produced by cells infected with viruses Prevent viruses spreading to uninfected cells by inhibiting the production of viral proteins INFLAMMATION AT SITE OF INFECTION (s.o.i.) Vasodilation increases blood flow to s.o.i. which increases immune system cell concentration at s.o.i. Increases permeability of blood vessels at s.o.i. which allows immune system cells to move out of the blood and to the affected areas to destroy the pathogens.

13 Explain the roles of antigens and antibodies in the bodys immune response including the involvement of plasma cells, macrophages and antigen-presenting cells.
Antigen A protein or glycoprotein on invading pathogens that triggers a B-cell to engulf it. Plasma cell B cells are stimulated by cytokines to become B effector cells which differentiate into plasmas cells to produce antibodies. Antibody Binds to antigens, becoming an antitoxin to disable the pathogens toxins chemical actions and signals to be englufed by a macrophage. Macrophage Englufs a pathogen through phagocytosis forming a phagocytic vacuole which fuses to the organelle lysosome containing the digestive enzyme lysozyme. This breaks down the pathogen and for the antigens to be processed. Antigen-presenting cell A macrophage that has processed the antigens from the surface of a pathogen and presented them in its own cell surface membrane for B-cell recognition.

14. Distinguish between the roles of B cells (including B memory and B effector cells) and T cells (T helper, T killer and T memory cells) in the bodys immune response.

B Cells- WBC covered in proteins(antibodies) T-Cells WBC covered with receptors Plasma Cells produce antibodies during infection. Memory Cells-produces antibodies during second infection T-killer Cells- target infected cells and kill them by lysis (bursting/cutting the cells) T-helper Cells- Activate B-cells

15. Explain how individuals may develop immunity (natural, artificial, active, passive).

16 Discuss how the theory of an evolutionary race between pathogens and their hosts is supported by the evasion mechanisms as shown by Human Immunodeficiency Virus (HIV) and Mycobacterium tuberculosis (TB). Antibiotics HIV
AS HIV kills immune cells it infects, reduces overall number which reduces the chances of it being detected High rate of mutation in genes that code for antigen proteins Means memory cells that recognised original strain wont recognise mutated strain

TB
When engulfed by phagocytes, produce substances that prevent lysosome from fusing with phagocytic vacuole Bacteria cant be broken down and can multiply undetected Disrupts antigen presentation in infected cells which mean it can not be detected and killed Shows pathogens have evolved batter ways to avoid detection while reproducing which means they will be able to survive without being detected and killed, spreading to other cells and so can spread throughout the body.

17 Distinguish between bacteriostatic and bactericidal antibiotics. Bacteriostatic inhibits growth of the bacteria. Bactericidal destroys the bacteria.

18 Describe how to investigate the effect of different antibiotics on bacteria.

Use an agar plate Bacteria to be tested are spread on an agar plate under aseptic conditions, like using a Bunsen burner to sterilise equipment. Place four paper discs soaked in antibiotics, and one soaked in water to act as a control, on the agar plate. Do this under aseptic conditions. Use two different antibiotics and two different concentrations (e.g. 150mg and 250mg). So one paper disc at 150 mg of antibiotic one, one paper disc at 250 mg of antibiotic one, one paper disc at 150mg of antibiotic two etc. Incubate the plate at 25-30C for 24-36 hours, with the plate sealed in a way that allows oxygen in. Measure the zones of inhibition around each plate. The bigger the zone, the better the concentration/type of antibiotic.

19 Describe how an understanding of the contributory causes of hospital acquired infections have led to codes of practice relating to antibiotic prescription and hospital practice relating to infection prevention and control.

MRSA Causes boils and abscesses, regularly mutating to form antibiotic resistance. C.Diff Causes diarrhoea. Prevention:
Controlling of Antibiotics to decrease antibiotic resistant bacteria mutating. Hygiene to prevent transmission by washing hands using alcohol and chlorine foam. Isolation to contain infections and reduce spreading. Prevention Enter to Hospitals by screening patients and visitors and encouraging hygiene.

20. Describe how to determine the time of death of a mammal by examining the extent of decomposition, stage of succession, forensic entomology, body temperature and degree of muscle contraction
Temperature Bodies cool at 2c/phour, therefore a body at 35c would have been dead for an hour. Muscle Contraction Rigor mortis 4-6 hours after to death, muscle contract and become stiff. Entymology Appearance of insects and larvae. Demcoposition Enzymes and bacteria, decompose the body.

Sucession Types of organisms found on carrion change over time. Bacteria flies + larvae Beetles Nothing (No tissue)