WJEC Biology Unit 3

ATP

adenosine triphosphate

ATPase

Breaks down ATP into ADP and a phosphate ion

How is ATP formed?

By adding a phosphate group to ADP

Chemiosmosis

the flow of protons down an electrochemical gradient through atp synthetase coupled with the synthesis of atp from adp and a phosphate ion

The Electron Transport Chain

high energy electrons pass from electron carrier to electron carrier which provides energy for the proton pumps to pump protons from the intermembrane space into the matrix which generates an electrochemical gradient, providing the energy for the protons to flow down an electrochemical gradient through ATP synthetase, synthesising ATP from ADP and a phosphate ion

The names of the photosynthetic pigments

chlorophyll a, chlorophyll b, carotenoids, xanthophylls

Where in the leaf is chlorophyll found?

palisade mesophyll

How do you calculate an Rf value?

divide the distance the pigment has travelled by the distance the solvent has travelled

absorption spectrum

how much light is absorbed at different wavelengths of light

action spectrum

rate of photosynthesis at different wavelengths of light

What did Engelmann do in his experiment?

He placed spirogyra in a suspension of motile aerobic bacteria and used a prism to refract the white light. The aerobic bacteria migrated towards the regions that had the highest oxygen concentrations, which corresponded the regions of red and blue light, so he concluded that the red and blue wavelengths were responsible for photosynthesis

Where are the antenna complexes found?

in the plane of the thylakoid membrane

Which pigment is found in the reaction centre of the antenna complex?

chlorophyll a

What is light harvesting?

the absorption of light by the photosynthetic pigments

What are the 2 photosystems?

photosystem I and photosystem II

What happens in the light dependent stage of photosynthesis?

photons of light are passed to chlorophyll a and the electrons are raised to a higher energy level and passed to electron acceptors and used to synthesise ATP by phosphorylation or they are used to reduce NADP.

What happens in cyclic phosphorylation?

high energy electrons pass from PSI to an electron acceptor. The electron is donated to the electron transport chain, which generates a proton gradient for chemiosmosis and then the electron is passed back to PSI.

What happens in non-cyclic phosphorylation?

high energy electrons are passed to NADP and reduce it. PSI is an electron short, so PSII passes a high energy electron to the electron transport chain, generating a proton gradient which drives chemiosmosis and the electron is passed to PSI.

What is the photolysis of water?

The splitting of water by light producing protons, electrons and oxygen. The electrons replace those lost from PSII, the protons reduce NADP and oxygen diffuses out of the chloroplast as a waste product.

What happens in the Calvin Cycle?

Carbon Dioxide is taken up by 5C ribulose bisphosphate, forming an unstable 6C compound and then 2 molecule of glycerate 3 phosphate which is catalysed by rubisco. ATP and reduced NADP reduce G3P to triose phosphate, which is converted into glucose and then into starch. Most of the TP is converted into ribulose bisphosphate, which allows the calvin cycle to continue

How can triglycerides be generated from the calvin cycle?

Acetyl CoA can be synthesised from glycerate-3-phosphate and converted into fatty acids. Triose phosphate can be converted into glycerol and reactions between them form triglycerides.

How do limiting factors affect the rate of photosynthesis?

If they become too low, the rate of photosynthesis will decrease. If they increase, the rate of photosynthesis will also increase but beyond the saturation point it will level off.

What are the limiting factors of photosynthesis?

light intensity, carbon dioxide concentration and temperature

Macronutrients are

needed in substantial amounts

Micronutrients are

needed in tiny amounts

What is the symptom of nitrogen deficiency?

stunted growth

what is the symptom of magnesium deficiency?

chlorosis of the leaves

What happens in aerobic respiration?

the complete breakdown of glucose, releasing energy and ATP

What happens in anaerobic respiration?

The incomplete breakdown of glucose, releasing little energy and few ATP molecules

Where does glycolysis take place?

in the cytoplasm

What happens in glycolysis?

2ATP are broken down into 2ADP and glucose becomes 6C glucose diphosphate which is broken down into 2 3C Triose phosphate molecules. NADox loses 2H and is reduced. 2 molecules of ATP are synthesised from 2ADP + Pi and Pyruvate is formed.

How much ATP is produced in glycolysis?

2 directly, 6 indirectly . Total = 8

What happens in the link reaction?

Pyruvate is dehydrogenated which reduces NADox. It is also decarboxylated so loses a CO2 and becomes 2C Acetate, which combines with coenzyme A forming Acetyl Coenzyme A.

Where does the link reaction take place?

mitochondrial matrix

How much ATP is produced from the link reaction?

0 directly, 6 indirectly. Total = 6

What happens in the Krebs Cycle?

The 6C compound is dehydrogenated, reducing NAD. The decarboxylation reactions releases CO2 and forms a 5C Compound, which is dehydrogenated and decarboxylated, forming a 4C Compound. ATP is produced by substrate level phosphorylation and 2 further dehydrogenation reactions (FAD and NAD) take place, regenerating the the 4C Compound at the beginning of the cycle so it can continue.

Where does the krebs cycle take place?

mitochondrial matrix

How much ATP is produced in the Krebs cycle?

2 directly, 22 indirectly (6 NAD x 3 & 3 FAD x 2). Total = 24

Overall, how much ATP is produced in aerobic respiration?

38 molecules of ATP

Where is the ETC in aerobic respiration found?

On the cristae of the inner mitochondrial membranes

How many proton pumps is NAD associated with and how many molecules of ATP can it generate?

3

How many proton pumps is FAD associated with and how many molecules of ATP can it generate?

2

Which reaction takes place in anaerobic respiration?

Glycolysis

How much ATP is produced in anaerobic respiration?

2 molecules of ATP

What happens in anaerobic respiration in mammals?

Pyruvate gains 2H from NADred and becomes lactate/lactic acid

What happens in anerobic respiration in yeast?

Pyruvate is decarboxylated, forming ethanal and releasing CO2. Ethanal gains 2H from NADred and forms ethanol.

How are lipids used as an alternative respiratory substrate?

They are hydrolysed into fatty acids and glycerol by lipase. Glycerol is converted into triose phosphate and enters via glycolysis. Fatty acids are split into 2 acetate molecules and enter the krebs cycle as Acetyl CoA.

How are proteins used as an alternative respiratory substrate?

They are hydrolysed into amino acids and deaminated forming a-keto and ammonia. Some keto acids are fed into glycolysis via pyruvate and some are fed into the krebs cycle via acetyl CoA.

How can bacteria be classified?

Coccus, spirillum and bacillus

What happens in the gram stain test?

The bacteria is stained with crystal violet and then the stain is fixed using lugol's iodine. The bacteria are decolourised using acetone and then a counter stain is applied using safranin.

How do gram positive bacteria stain and why?

Gram positive bacteria stain purple and remain purple after decolourisation and the counter stain because they have a thick peptidogylcan cell wall and they do not have an outer lipopolysaccharide layer so the mordant and the stain is retained within the cell.

How do gram negative bacteria stain and why?

Initially gram negative bacteria stain purple but this is lost after the acetone is applied because they have an outer lipopolysaccharide layer which is dissolved by the alcohol, so the stain is washed away, so they appear red after the counterstain with safranin.

Why are Gram-negative bacteria resistant to penicillin?

because the peptioglycan is protected by the outer lipopolysaccharide layer

What do bacteria need in order to be cultured?

nutrients, growth factors, a suitable temperature and a suitable pH

Obligate Aerobes

Only grow and metabolise in the presence of oxygen

Obligate Anaerobes

Only grow and metabolise in the absence of oxygen

Facultative anaerobes

grow and metabolise best in the presence of oxygen but can survive without

Why is Aseptic technique used?

to prevent contamination of the environment by the microorganisms and to prevent contamination of the cultures by the environment

examples of aseptic technique

Pass metal tools through a flame until they glow red

Autoclave glass equipment, heating at 121'C, under pressure for 15 minutes

Open the culture bottle using little finger and do not place the lid on the work surface

Sterilise the inoculating loop in the bunsen flame

Flame the neck of the bottle in the bunsen flame

Work close to the flame, which provides an updraft

Close the lid of the petri dish immediately and seal with tape, but do not seal completely, as that would bring about anaerobic conditions which would encourage pathogenic growth

How can bacteria be counted?

It can either be counted directly by counting each cell or it can be counted indirectly by measuring turbidity

What is a total count?

Counting living and dead cells

What is a viable count?

only counting living cells

What happens if the dilution is too great?

there will be too few colonies on the plate for the count to be statistically sound

What happens if the dilution is insufficient?

The colonies merge which leads to an underestimate in numbers

1 in 10 dilution

1 in 10, 10 in 100, 1 in 1000, 1 in 10,000, 1 in 100,000

83 colonies in 1cm3 of a 10-3 dilution

83 x 103 = 83,000 in 1 cm3 of original sample

1 in 100 dilution

1 in 100, 1 in 10,000, 1 in 100,000

55 colonies in 1cm3 of a 10-2 dilution

55 x 102 = 5500 in 1cm3 of original sample

What is another method of measuring growth directly?

using a haemocytometer

How can growth be measured indirectly?

Using a colorimeter

What affects the size of a population?

Birth rate, death rate, immigration, emigration

How do fugitive species control their numbers?

They reproduce rapidly and they rapidly invade new environments

How do equilibrium species control their numbers?

through competition in a stable environment

What are the phases of the one step growth curve?

lag, log, stationary, death

What does the lag phase represent?

The time taken for the individuals in the environment to reach sexual maturity, find a mate and gestate their young

What happens in the log (exponential) phase?

The population increases logarithmically

What happens in the stationary phase?

The population has reached its carrying capacity and the birth rate is equal to the death rate

What does the death phase represent?

the population has decreased to such an extent that the death rate is greater than the birth rate

What are biotic factors?

Competiton, new diseases, parasitism, increase in predator numbers

What are abiotic factors?

temperature, light intensity, water availability

What is a population crash?

a sudden, dramatic decrease in population number that occurs when the population greatly exceeds its carrying capacity

Population growth =

(births + immigration) - (deaths + emigration)

Why do predator prey interactions cause both populations to oscillate?

due to negative feedback mechanisms

The rate of growth in the log phase =

(number of bacteria at day 9 - number of bacteria at day 4) divided by (9-4)

density dependent factors

competition, predation, parasitism, disease

What do density-dependent factors do?

their effect increases as the population increases. They determine the carrying capacity and weaken individuals.

Density independent factors

earthquake, tsunami, volcanic eruptions, extreme weather, wildfires

How can abundance be measured?

Capture-mark-recapture, kick sampling, random sampling, systematic sampling

What is an ecosystem?

a characteristic community of interdependent species and their habitat, which is comprised of abiotic and biotic factors and is dynamic so changes over time

What do producers do?

They are autotrophic and absorb light energy, converting simple inorganic compounds into more complex organic compounds

What do consumers do?

they are heterotrophic and they ingest or absorb organic carbon from other organisms

What do herbivores do?

they feed on organic matter produced by producers

What do carnivores do?

they feed on other animals at lower trophic levels

What do detritivores do?

they feed on dead organic matter

What do decomposers do?

they break down organic compounds into simple inorganic compounds which can be absorbed by plant roots

Why is not all of the energy that reaches producers absorbed?

light is reflected from the wrong leaf surface, wrong wavelengths of light cannot be absorbed by the pigments and light passes through the leaf but does not hit the photosynthetic pigments

Why is the length of food chains limited?

because there would be insufficient energy to support more trophic levels

photsynthetic efficiency =

the quantity of light energy incorporated into biomass divided by the quantity of light energy hitting the leaf multiplied by 100

Gross Primary Productivity (GPP)

the rate of production of chemical energy in biological molecules by photosynthesis per unit area and time (kJm-2y-1)

Net Primary Productivity (NPP)

the energy in the biomass of the plant which could pass to the primary consumers at trophic level 2 during feeding (kJm-2y-1)