B3 OCR Gateway

Genes code for proteins.  The double stranded DNA helix is in the nucleus, and contains the base code which determines which proteins are made at the ribosomes. The DNA cannot leave the nucleus so it’s base pairs separate and the strand unzips to form two single DNA strands. A copy is made of part of one strand of the DNA, now called the messenger RNA. This single strand leaves the nucleus and goes to the ribosome. The order of bases found in a section of DNA is called the base code with each THREE bases code for an amino acid. At the ribosome the code is read and the correct amino acids are put together in the correct order.

The sequence of the amino acids in the protein chain determines the shape that the protein will fold up into.

 Proteins determine your characteristics- The fact that proteins are folded in a specific way giving them a specific shape, means that they have a particular function. Therefore the genes you inherit determine what types of proteins your body makes and thus control your characteristics

Structure and functions of a cheek cell:
Nucleus - contains DNA
Cell Membrane - controls when enters and leaves the cell
Mitochondrion - Aerobic respiration happens here. Energy is released from glucose in the presence of oxygen. 
Cytoplasm -  Where many of reactions happen
At certain magnification the ribosomes are too small to be seen

DNA is found in the nucleus.  Forms structures called chromosomes.  A section of a chromosome is called a gene.  Each gene is a code for making proteins.  Our bodies need proteins to grow and make proteins.  Everyone has his or her unique DNA code.

DNA – double helix; complimentary base pairs (adenine – thymine; cytosine – guanine)

Need proteins for:
Growth, repairing new cells, building structures such as muscle, bone, skin, hormones, enzymes

Genetic code controls how enzymes are made in your cells, enzymes control chemical reactions in the body, and will control your characteristics.

Different types of cell make different proteins- all our different types of cell have the same DNA but they make different proteins. This is because they only have the genes switched on which results in the production of specific enzymes (made of protein) e.g. pancreas cells only have genes swtiched on which result in the production of insulin. Some genes do not make proteins but control the switching on or off of other genes.

Watson and Crick used Rosalind Franklin's data (X-ray data which showed that a DNA molecule consisted of two chains wound in a double helix) and built their model of DNA, which included a double helix with pairs of bases forming cross-links. They publishes their paper before Franklin and so got all the credit.

Watson and Crick shared Nobel Prize with Maurice Wilkins, Franklins supervisor in 1962 as Frankin died in 1958 and Nobel Prizes can't be given posthumously. 

In 1968 Watson wrote a book and acknowledged the importance of Franklins contribution.

There is always a delay in scientific discoveries and its importance being recognised or awarded as other scientists have to verify and repeat the work. Also, it's not always clear how useful the discovery is. 

4 Examples:

Collagen - found in skin, bones, tendons, ligaments, and walls of blood vessels (structural)

Insulin- Is a protein hormone which is prodcued in the pancreas, travels to the liver and muscles where is cuases blood sugar levels to be lowered

Haemoglobin- Is a carrier protein in red blood cells which carries oxygen

Enzymes – protein catalysts which speed up reactions in the body.

Stem cells can divide to make more cells and these can become any one of the 220 different cell types. In any cell not all of the 20,000 genes are switched on and being used. Some genes do not actually control making proteins. They switch other genes on or off. 

Enzymes are biological catalysts – they speed up a biological reaction.

Involved in the following reaction: photosynthesis, respiration, protein synthesis

Each enzyme is specific to a substrate.Enzymes can join substrate molecules together to make a larger molecule, or can break substrates down into something smaller. 

The shape of an enzyme:
Active site - Substrate molecules need to fit into the active site. This brings them together so they can form a bond. This makes a bigger molecule.
In some cases - A big substrate molecule fits into the active site, A bond breaks and two smaller molecules are made

The lock and key hypothesis is a hypothesis about how enzymes work. The two sunstrate molecules fit side by side into the enzymes active site. A bond forms between them and one large product molecule is formed . The free enzyme (active site) is now able to catalyse andother reaction of this type.

How are two new molecules made?
The large substrate molecule fits into the enzymes active site and the bond in the substrate molecule breaks to form two smaller product molecules. The free enzyme is able to catalyse another reaction the same as this. 

Each enzyme is specific for its substrate molecules.

The lock and key hypothesis is a hypothesis about how enzymes work. The two sunstrate molecules fit side by side into the enzymes active site. A bond forms between them and one large product molecule is formed . The free enzyme (active site) is now able to catalyse andother reaction of this type.

How are two new molecules made?
The large substrate molecule fits into the enzymes active site and the bond in the substrate molecule breaks to form two smaller product molecules. The free enzyme is able to catalyse another reaction the same as this. 

Each enzyme is specific for its substrate molecules.

Low temperature:
Active site and substrate has less energy so they dont move very fast and so there are less successful collisions. The rate of reaction is low.

High Temperature:
As the temperature increases, there is more energy and so more more successful collisions. For most chemical reactions, the rate of reaction doubles qith a 10C rise in temperature.
However
If the temperature gets too high - the shape of the ezymes active site changes, the substrate molecule cannot fit into the active site and reactions slow down to a complete stop.This is because the enzyme has denatured.

Q10 = rate at high temperature / rate at low temperature
(rate of reaction per 10C increase)

pH
If the pH changes too much then the shape of the active site canges, the substrate molecules canot fit into it so the enzyme has been denatured. 

Gene mutation- is a change in a gene which can occur spontaneously (error in DNA replication) or by chemicals such as tar in cigarettes, x-rays or UV light (ionising radiation)

A mutation in a gene (a change in a base pair) results in a different protein being made which cannot do its normal job.

Harmful mutations- cause cells to keep dividing (cancer), different shaped haemoglobin (disease called sickle cell anaemia)

Useful mutations – pale skin is a mutation (people all used to have dark skin) and pale skin lets more light to make vitamin D (prevents rickets- soft bone disease) which is useful for people who live in countries where the sun is not strong

Neutral mutations (not good or bad)- Tongue rolling is due to a gene mutations.

Mutations lead to different proteins being made - Each protein has its own number and sequence of amino acids. As a result, each protein then folds into a particular shape to carry out its function. If one of the bases changes, a new protein could potentially be made.

How do plants and animals get energy?
Plants - trap sunlight energy and use it to make large molecules (proteins fats, carbohydrates), these molecules contain stored energy.
Animals - by eating plants or other animals that have eaten plants

Why do they need energy?
Building large molecules from smaller ones:
Plants use sugars, nitrates and other nutrients to make amino acids. These are joined together in long chains due to protein synthesis and join sugar molecules to make starch.
Animals joins sugar molecules together to make glycogen, which is similar to starch. 
Living organisms join fatty acids and glycerol together to make lipids.
Muscle contraction:
Animals need to move, find food/mate, muscle contraction uses energy and causes movement
Controlling body temperature: 
Some organisms, such as snakes,lizards etc. move into shade or sun and are slow at night or in winter. Birds and mammels can be active at night and in winter because a lot of energy from the food they eat is released as heat energy. This keeps their body temperature steady regardless of external temperature. However, this means they need to eat more fish/snakes/lizards

Aerobic Respiration:
Aerobic respiration uses oxygen. It happens continuously in the cells of plants and animals.

Anaerobic Respiration:
Anaerobic respiration takes palce without oxygen and doesn't happen continuously. It only happens when cells are not getting enough energy. 

ATP:
Energy released from glucose during respiration is used to make molecules of Adenosine Triphosphate. ATP is used as the energy source for all processes in cells that need energy. 

Aerobic Respiration:
Chemical reactions that use glucose and oxygen to release energy.
OXYGEN + GLUCOSE à CARBON DIOXIDE + WATER (+ ENERGY)
C₆H₁₂O₆ + 6O₂  à6CO₂ + 6H₂O 
Takes place in the mitochondria. Liver cells have many mitochondria as it carries out many reactions. Similarly muscle cells have lots of mitochondria as it requires lots of ATP for contraction.
Respiratory quotient is calculated

RQ = volume of carbon dioxide produced

       volume of oxygen consumed
If the amount of carbon dioxide produced is the same as oxygen used, the RQ value =1.  If the cell is not getting enough oxygen, the RQ value will be greater than 1.

Metabolic Rate - Measure of how quickly all the chemical reactions are going on in the organisms body. How much CO₂ it produces is also an indication of the organisms rate of respiration.
So you use more oxygen/min and produce more CO2/min, your heart rate increases to deliver more oxygen and glucose per minute. Breathing rate increases to remove extra CO2.

Anaerobic Respiration:
When you start hard exercise, your heart rate doesn't increase quickly enough to supply the extra oxygen. To make up for this, muscle cells use anaerobic and aerobic respiration.
Glucose --> lactic acid (+energy)
This releases much less energy per molecule of glucose than aerobic respiration. However, as this incomplete breakdown happens quickly, many molecule of glucose can be broken down.This cannot go on for long as lactic acid builds up and is toxic, casing pain and fatigue.

Enzymes and Respiration:
Temperature - when people warm up, their muscles warm up so respiration reactions go more quickly. When they start exercising hard, their respiration is faster and can release more energy
pH - increased lactic acid from anaerobic respiration lowers the pH. This reduces enzyme activity and so reduces rate of respiration. Muscles get fatigued. This is painful and your muscles stop contracting.
Fatigue and oxygen debt - During hard exercise, muscles become fatigued due to lack of oxygen. When you stop exercising your heart rate stays high so blood can quickly carry lactic acid to the liver and you continue to pant so extra oxygen can help deal with lactic acid in liver.
The oxygen needed to do this is called oxygen debt.

• Plasma – a yellow liquid, adapted to transport dissolved substances such as water, hormones, antibodies and waste products
• Red blood cells – transport oxygen around the body.  Red colour comes from haemoglobin.  Oxygen joins to the haemoglobin to form oxyhaemoglobin, which allows it to be transported around the body where it breaks down to oxygen and haemoglobin.The oxygen is delivered to the respiring cells.They do not have a nucleus – this leaves more room to carry oxygen.  They are biconcave and have a dent on both sides – this allows them to absorb a lot of oxygen.  They are very small so they can carry oxygen to all parts of the body and travel through capillaries one at a time. Each cell has a large surface area compared to its volume so a lot of oxygen can diffuse through the outer surface and into the centre of the cell. 
• White blood cells – defend the body against disease.  They are adapted to change shape, they can wrap around microbes and engulf them.  They can squeeze through capillary walls to reach microbes.
• Platelets – help to clot the blood if we cut ourselves,stops bacteria entering the wound.

Blood vessels

Blood is carried around the body in three different blood vessels.

• Artery – thick muscular and elastic wall to help it withstand high blood pressure as the blood leaves the heart.
• Vein – large lumen (hole) to help blood flow at low pressure; valves stop blood from flowing the wrong way.
• Capillary– thin, permeable wall to allow exchange of material with body tissue

Structure
Four chambers
Two atria – receive blood from the veins
Two ventricles – pump blood into arteries
Valves – bicuspid, tricuspid, semi-lunar valves – prevent the blood flowing backwards when the heart relaxes and so maintain blood pressure.

Four key vessels
Right hand side:
vena cava, pulmonary artery
Left hand side:
 pulmonary vein, aorta

Function
The heart pumps blood around the body. There are two sides to a heart.The right side pumps blood to the lungs. The left side pumps blood to the rest of the body
The blood leaves the heart in arteries where the pressure is high.The blood returns to the heart at low pressure in the veins.

Structure
Four chambers
Two atria – receive blood from the veins
Two ventricles – pump blood into arteries
Valves – bicuspid, tricuspid, semi-lunar valves – prevent the blood flowing backwards when the heart relaxes and so maintain blood pressure.

Four key vessels
Right hand side:
vena cava, pulmonary artery
Left hand side:
 pulmonary vein, aorta

Function
The heart pumps blood around the body. There are two sides to a heart.The right side pumps blood to the lungs. The left side pumps blood to the rest of the body
The blood leaves the heart in arteries where the pressure is high.The blood returns to the heart at low pressure in the veins.

The left and right ATRIA recieve blood from veins. The left and right VENTRICLES pump blood into arteries. The valves prevent backflow of blood.

Right Side:
Pumps blood to the lungs.
Right VENTRICLE has a thinner wall and generates less pressure so the delicate lungs arent damaged. 
Deoxygenated blood goes to lungs to gain oxgyen.

Left Side:
Pumps blood to rest of the body
Left VENTRICLE wall is thick and muscular so it can generate high pressure, allowing fast delivery of oxygen to the body tissues and taking waste away quickly.
At the same time as blood at higher pressure is pumped into the aorta to be pumped all over the body, blood at lower pressure is being pumped into the pulmonary arteries to travel shorter distance to the delicate lungs.

Double circulation- we are said to have a double circulatory system as blood goes through the heart twice. Once on its way to the lungs, and once before it travels around the body. This is an advantage to mammels.

Plant cells have the following components:
Nucleus–contains the genetic material (chromosomes)
Cytoplasm- where cells chemical reactions take place
Cell membrane- control what goes in and out of the cell
Cell wall – provides support, made of cellulose
Chloroplasts – absorb light energy for photosynthesis
Mitochondria – small rod-shaped structures that release energy during aerobic respiration 
Permanent Vacuole -  contains cell sap and provides support

Bacteria Cells:
Consist of one cell
Smaller than plant or animal, has no nucleus, no mitochondria and no chloroplasts
Contain DNA in the form of a single circular strand floating in the nucleus

Animal Cells:
Nucleus –contains the genetic material (chromosomes)
Cytoplasm- where cells chemical reactions take place
Cell membrane- control what goes in and out of the cell
Mitochondria – small rod-shaped structures that release energy during aerobic respiration 

Human babies have underdeveloped brains when born, otherwise their heads would be too big to pass through the birth canal. Just after birth the child brain is growing faster than the whole body. 

During adolescence your reproductive organs grow a lot as you become an adult

There are four main stages:

1. Infancy (rapid growth)
2. Childhood (slow steady rate)
3. Adolescence (puberty)- rapid growth
4. Adulthood (maturity)falls to zero
   
   

Plants only grow at specific parts called meristems, at root tips, shoots, stem nodes and buds. The meristems contain stem cells which:

• are undifferentiated 
• have very small vacuoles
• have very thin walls
• are packed very closely together 
• are small and do not contain chloroplasts
• can divide, making new cells that differentiate

Differentiated plant cells cannot divide due to their thick rigid cell wall. They also have chloroplasts and a large vacuole.

Measuring increase in dry mass is best, because wet mass varies according to how much water is present in the tissues. 
Using length as a measure of growth is simple but won't account for the variable growth rate of different parts of an organism

Scientists can get stem cells from spare very early embryo's created during IVF. 
Embryonic stem cells are still able to differentiate into any type of cell. 
Medical reasearch is developing ways of using stem cell to:

• Treat Parkinson's disease
• Grow tissues or organs
• Repair spinal cord injuries 
• Treat type 1 diabetes

Use of embryonic stem cells raise ETHICAL issues as spare embryos could have developed into people. However, without stem cell research the embryos would've been discarded.

Scientists can obstain stem cells from the umbilical cord and bone marrow, which is less controvesial. However, these cannot differentiate into as many different types of cells as embryonic stem cells.

• High yield
• Resistant to diseases
• Don't bend or break stalks in wind
• Resistant to flloding/drought
• Taste good
• Long shelf life
• Contain desired amounts of particular nutrients

Selective breeding method:

• Parent plants with the desired characteristics are selected. One may have a high yield but be susceptible to disease. The other may have a low yield but be resistant to disease
• These are cross-bred - pollen from one parent plant is placed on the female parts of the other parent plant
• The seeds are collected and grown
• The offspring that have inherited both characteristics are selected and cross-bred again.
• The process is repeated until a new variety is produce with desired characteristics

Selective breed animals to get:

• More muscle and less fat for lean meat
• Higher milk yields
• Reach maturity quicker
• Have better / more wool
• Can run faster (such as racehorses and greyhound dogs)

Disadvantages:

• Reduces gene pool
  - an accumulation of harmful recessive characteristics leading to health problems
  - reduction in variation

Permanently changing the genetic makeup of an organism by inserting genes into its DNA
Enzymes are used to cute DNA, to obtain a gene for a desired characteristic, and to insert that gene into another organisms DNA. This can produce organisms with different characteristics. 
Examples:
Insulin for human - human gene for making insulin is inserted into a bacterium insted of pig pancreas. Advantages - Enough insulin to treat diabetics, no risk of transferring diseases from pigs, vegetarian diabetics will not object
Vitamin A rice – rice is the main diet for many people living in Asian countries, it does not contain vitamin A which is needed to prevent night blindness.  Scientists have added the gene to make beta-carotene from daffodils to the rice plants.  Humans eating the rice can then convert the beta-carotene into vitamin A at no extra cost.
Cotton - cotton fibres are used for textiles and the seeds provide oil and protein for animal feed or oil for maragrine. GM Cotton is resistant to caterpillar pests. GM Cotton has a gene from bacterium which codes for a toxin that kills the caterpillars. This Bt toxin has been used for decades by extracting it from bacteria. Now the plant makes it itself and kills the caterpillars.

Main principals of GE - Selection of desired characteristics, isolation of genes responsible, insertion of genes into other organisms, replication of these organisms.

GM crops are grown in Canada, USA, India, China, South America, Kenya, Mexico and Australia

77% of all soya is GM and resistant to herbicide (weedkiller), so spraying the crop wth weedkiller kills only the weeds

80% of maize grown in USA is GM for resistance to an insect pest

GM bananas, a staple crop in Kenya, are resistant to disease and also contain more nutrients

GM tomatoes have had a gene from a cold-water fish inserted into them to make them frost resistant. 

Gene therapy doesn't change an organisms genes permanently. Copies of a functioning gene or allele may be inserted into certain body cells of a person who has a recessive genetic disease, such as cystic fibrosis.

If the genes were inserted into a gamete or zygote, then all the cells of the new individual would have the healthy genes. This would be GE. There are ethical guidlines and laws to prevent it.  

Positive:
More people can be fed, as GM crops produce higher yields
Many people have no problem with the idea of eating GM produce.
GM farms may have increased productivity while using fewer inputs, so food cost may fall
Most GM crops have been safe so far
Disadvantages:
Poor farmers that would be benefit from high yields may not be able to afford the seeds
If some have a problems with GM products, they won't eat it ad farmers lose money
GM crops may change the ecosystem in ways that cannot be reversed.
GM crops could cross-pollinate with wild plants which could lead to unexpected side effects
Potential benefits of GM:
During 1960's and 1970's there was a green revolution. selective breeding to increase yield alongside use of pesticides and fertilisers helped boost wold food production.However, many farmers applying pesticides have become ill or died as a result of exposure to them, also using a lot of fertiliser has damaged the soil.Global warming and shortage of water limit growth in crops. Crops that are resistant to pests could be developed, allowing us to use fewer pesticides, less harmful to useful insects in environment. High yield reduce fertilisers. Drought resistant reduce need for water. GM crops play important role in future of agriculture.

Nuclear Transfer Clone (Dolly) 

• Egg cell taken from sheep A and the nucleus is removed.
• An udder cell is taken from sheep B and the nucleus is removed.
• The nucleus from sheep B is put into the egg cell of sheep A.
• An electric shock was given to the resulting egg to make it divide
• It developed into an embryo that was put into a surrogate mother sheep.
• The egg cell is put into a sheep to grow.
• The cell grows into a clone of sheep B (where the nucleus containing the genetic information came from)

Human cloning:
Spare eight-cell embryos can be split and allowed to develop into cloned embryos. Cells from these can be used for stem cell research. In the future organs for transplants may be grown from stem cells. Soon, human trials using tissue from specially bred modified pigs could be used to treat someone with diabetes, Huntingtons disease, Parkinsons disease and blindness. Replacement organs from the pigs may be transplanted into humans. Genetically modifying the pigs may overcome rejection problems. There are fears that viruses may pass from pigs to humas so experts say trials should be closely monitered.

Tissue culture:
Plants can be cloned using tissue culture.  This must be carried out using aseptic technique so no bacteria or moulds contaminate the cultures

1. Plants with desired characteristics are chosen
2. A large number of small pieces of tissue are taken from the parent plant
3. They are put into sterile liquid or jelly that contain the growth medium
4. The tissue pieces are left in suitable conditions to grow into plants

Asexual Reproduction:
Mitosis
One parent needed
No Gamete
No mixing of genetic information
Offspring are genetically identical to parent (clone)
Growers take cutting of the plants. They cut off a bit of stem or root and grow it into a new plant which is a clone

Advantages of cloning plants
All the plants are genetically identical
Cloning is quite a quick process in comparison to growing plants from seeds
Cloning enables growers to produce plants that are difficult to grow from seed such as bananas 

Disadvantages
The plants are all genetically identical. If the environment changes or a disease breaks out it is unlikely any of the plants will survive.
Cloning plants over the years has resulted in very little genetic variation

Potential benefits:

• Creation of replacement organs and tissues
• Could allow infertile parents to have children
• Extending life by replacing ageing tissues and organs

Potential issues:

• Humans created as tools or products for medicine
• Clones would be identical twins of the cell donor
• Research to perdect cloning could lead to damaged clones
• Decreasing genetic diversity caused by asexual cloning

DNA Replication:
DNA is a double-stranded molecule which unzips to create 2 strands. This exposes the DNA on each strand. Spare DNA bases in the nucleus line up against each separated strand of DNA. They only align next to their complementary DNA base, forming base pairs. 2 molecules of DNA are now formed.
When each chromosome has made a copy of iteslf these duplicated chromosomes line up across the centre of the cell. Then each double chromosome splits into its two identical copies. Each copy moves to opposite ends of the cell. Two new nuclei form, each with a full set of chromosomes. The cell divides into two genetically identical cells. 

Advantages of being muti-cellular
Organisms can be larger, and have lots of different cells and funtions but not all organisms are in contact with the outside environment, this means they can't rely on diffusion alone to recieve oxygen and nutrients they need to remove their waste. So, they need organ systems such as specialised organ systems (such as the nervous system and endocrine systems, allowing communication between cells, the circulatory system supplying cells with nutrients, the respiratory and digestive systems, controlling exchanges with the environment)

Mitosis in mature organisms for repair and replacement