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Aimee Britton

on 1 June 2015

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Transcript of Biochemistry

Metabolism is the sum of all biochemical reactions in the cells of an organism.
Condensation and hydrolysis
Condensation reactions join monomers together to form biological molecules.

In these reactions:
A water molecule is released
A covalent bond is formed
larger molecules are formed by bonding smaller ones
Carbohydrates as simple sugars
Two monosaccharides can be joined together in a condensation reaction to form a disaccharide. A new
(covalent) bond forms.
Carbohydrates- energy storage
Functions of biological molecules:
Biology F212
Carbohydrates make up a group of molecules- ratio Cn(H2O)n.
Biochemicals and bonds
Carbohydrates- simple sugars
Carbohydrates- energy storage
Carbohydrates- structural units
Amino acids- monomers of protein
Levels of protein structure
Proteins in action
Essential oils
Water as a biological molecule
Enzymes= globular proteins
Enzymes and metabolism
Lipids=not polymers
Chemical group:
Energy storage and supply (and structure)
Structure, transport, enzymes, antibodies, most hormones.
Membranes, energy, padding, some hormones.
Vitamins and minerals
Form parts of molecules, metabolic reactions, coenzymes.
Nucleic acids
Information molecules, instructions for life
Reactions, support in plants, solvent for metabolic reactions, transport
Fibre is a type of carbohydrate that is used in waste disposal.
Hydrolysis is basically the opposite of condensation reactions.
Molecule 1
Molecule 2
Covalent bond formed in condensation
Covalent bond broken in hydrolysis
+ H20
Carbohydrates are for for energy source (glucose), storage (starch) and structure (cellulose).

Pentose (5 Carbons) and hexose (6) sugars normally occur as ring structures.
Two forms of glucose:
Chain and ring structures form.
Ring can be alpha or beta glucose
Simplest carbohydrates= monosaccharides (the monomer)
All carbohydrates made by joining these together. They contain between 2 and 6 carbon atoms and all:
Are soluble in water
Are sweet
Form crystals
Building polysaccharides (like starch, glycogen and cellulose) and breaking down larger molecules involves the making and breaking of glycosidic bonds.
To use glucose for respiration, it must be broken down (by enzymes). Alpha glucose can be broken down by plants and animals, and so is used, whereas beta glucose can/is not.
Starch- energy storage in plants:
Mix of long, straight chained amylose molecules and branched amylopectin. In plants, stored in chloroplasts and plant cells in membraned grains. Can be broken down into glucose for energy!
Glycogen- energy storage in humans:
Very similar to starch, alpha glucose, large molecule broken down to release glucose etc etc BUT Glycogen has shorter 1-4 linked glucose chains, and these are more branched. This makes it more compact and makes glycogen granules.
Both are insoluble, both hold hold the glucose in chains so they can be easily broken off for use in respiration.
Carbohydrates- structural units:
Cellulose fibres are arranged in a very specific way to form plant cell walls. Cellulose molecules join together in bundles called microfibrils. These are mega strong!
When beta glucose forms a chain, it is long and straight. These polymer chains form cellulose :)
Amino acids
All have the same basic structure.
Amino group
Acid group
The R group changes for each amino acid. There are 20.
Animals cannot store amino acids, as in excess they are toxic. So they are converted to urea and disposed of.
To join amino acids together, a condensation reaction between the amino group of one AA and the acid group of another forms a peptide (covalent) bond between the 2 acids, making a dipeptide.
Plants convert nitrates into amino acids.
Protein structure
The primary structure of a protein is given by the specific sequence of amino acids that make up the protein.
The secondary structure of a protein refers to coiling and pleating of parts of the polypeptide molecule (to form an 'alpha helix'). These coils and pleats are held in place by many hydrogen bonds.
The tertiary structure refers to the final 3D shape. This is basically the important bit, as 3D structure forms active sites etc etc.
Globular proteins roll up into a globe or ball.
They are usually soluble as hydrophilic R groups go
on the outside (and hydrophobic on the inside). They
usually have metabolic roles (e.g.enzymes).
Fibrous proteins form fibres (duh)
These are usually insoluble and have structural roles, e.g. collagen in bone and cartilage, keratin in hair and nails.
Quaternary structure- haemoglobin:
Quaternary structure refers to the fact that some proteins are made of more than one polypeptide subunit, or a polypeptide and something else.
Haemoglobin's quaternary structure consists of 4 polypeptide subunits, two alpha chains, two beta chains, making a soluble GLOBULAR protein. As with all proteins, hella loadsa bonds and interactions hold it all together.

The haem group is an essential part, but it is
a polypeptide. This kind of group is called a prosthetic group.
Enzymes are very similar in certain ways
but each is highly specific to the reaction it catalyses. All enzymes have the following traits
The active site of the enzyme is where the magic happens (like my bedroom, CHEEKY). Its highly specific to the shape of the
substrate of the reactants it catalyses
(they're complimentary). If the
shape of the active site is
altered, the reaction slows and
may not occur at all.
Enzyme action
Induced fit hypothesis
Substrate collides with active site
Active site fits closely
Enzyme-substrate complex forms
Puts a strain on the substrate
Reaction occurs even easier
Product forms and no longer fits in active site
Product is expelled
Addition of an enzyme reduces the of the reaction so it can occur. For some reactions, the activation energy requires temperatures well over 100*c and the cell wouldn't survive the boiling so the enzyme is needed so the reaction can occur. Some reactions just need to happen fast - hence the enzyme.
Immune response:
Primary defences: Skin, mucous membranes, super
antibac tears, earwax, acidic vagina

Neutrophils and macrophages engulf and destroy pathogenic cells. Macrophages initiate immune response, by engulfing the pathogen and displaying its antigens on its surface so the specific immune stuff can see it and go 'Oh crap we're under attack! Ready the lymphocytes!' Or something.
They're all globular proteins
They all act as catalysts
They're highly specific
They all have an active site
Their activity is affected by temperature and pH
The insanely dull Biodiversity and evolution stuff
(But oooh sideways arrow thingy!!)
Sampling animals
Sampling plants
Measuring biodiversity
- A group of individuals who are similar in appearance, anatomy, physiology, biochemistry and genetics, whose members are able to interbreed to produce fertile young
- The place where an organism lives
- The range of living organisms in an area
Sweep netting
Pitfall trap
Tullgren funnel
The need to sample
Must study our environment as an EIA
To limit our impact on the environment as a whole
Species Richness:
The number of species present in a habitat.
Species evenness:
A measure of the relative abundance of individuals
in each species.
In order to measure the biodiversity of a habitat, you must:
Observe the present species
Count the number of individuals
Identify individuals
Instead of counting every orgasm in an area (good luck... that'll take ages with me around), a sample can be taken.
Rules of sampling:
Must be random (ie, at coordinates randomly generated)
Must have a variety of samples.
Must sample over a long period of time (borriinngggg)
Species conservation
Why species
need to be looked after
Human activities have enhanced our survival at the cost of many species - causing them to go extinct.
Kills many organisms at a time - causing them to go extinct
Climate change
An inability to adapt (cause of reduced genetic variation) may kill off a species as they can't adapt to a changing environment.
Migration patterns my be disrupted meaning that organisms die in harsh environments.
Economic reasons
- Species many inspire new technology
Ecological reasons
- Plants regulate our atmosphere
Aesthetic reasons
- Nature is pretty damn fine
Ethical reasons
- Organisms have a right to live
To maintain and increase biodiversity so organisms can continue to adapt to survive an evolve.
(Jack's mature contribution)
Percentage Hydrogen (pH)
As the temperature increases above optimum:
Molecules vibrate more
Hydrogen and ionic bonds stain
Bonds in the tertiary structure, holding the active site's shape, break
Temperature increases and more bonds break
Active site changes shape
Active site is no longer complimentary to the substrate
Its denatured and the reaction slows to a stop
As the temperature increases to the optimum, the
molecules move around more so collide more frequently. The optimum is the point at which the molecules move fastest without the enzyme denaturing.
The bonds in the tertiary structure are due to the attraction between oppositely charged amino acid groups
The concentration of hydrogen ions effects the tertiary structure as the ions interfere with the bonds
So altering the concentration alters the tertiary structure so the active site is altered and is no longer complimentary to the substrate.
The hydrogen ions may also cluster around any negative charges in the active site, interfering with the binding of the substrate.
Inhibitor concentrations
Prosthetic groups
Ion cofactors
Inhibitors diluted
Less inhibitor collisions with enzymes
More substrate collisions with enzymes
Reaction SPEEDS UP
Increased Inhibitor concentrations
Inhibitors concentrated
More inhibitors per enzyme
Less active sites available
Reaction SLOWS
(more are occupied/altered)
Prokaryotes - No Nucleus
Protoctists - Are everything else
Walls made of chitin
Have hyphae

Walls made of cellulose
Autotropic (make their own food)
Heterophic (rely on others for food)
Capable of movement
(the fun ones)
Scientists classify organisms mainly for convenience but it also helps us to see the evolutionary links between organisms and to make it easier
to identify organisms.
Modern classification
Is in all organisms as it proves the genetic code.
Sequence of bases is unique
Sequence can be analysed and compared with another
Similar sequence - closely related
Different sequence - distantly related
- Cytochrome C
Is in all organisms as its a protein used in respiration
Amino acid sequence is unique
Sequence can be analysed and compared with another
Similar sequence - closely related
Different sequence - distantly related
Increased substrate concentration
More collisions between enzyme and substrate
More enzyme-substrates form
Initial reaction rate increases
Until the rate reaches its maximum and it levels off
All the active sites are occupied
Substrate concentration isn't the limiting factor
Increased enzyme concentration
More active sites become available
More enzyme-substrate complexes form
Initial reaction rate increases
Until the rate reaches its maximum and it levels off
All the active sites are occupied
Enzyme concentration isn't the limiting factor
Enzyme concentration
Somebody call Blue Sky studios... OCR have just come up with an amazing storyline
Ex situ - Out of the normal environment
Eg Zoos or seed banks
In situ - In the normal environment
Eg nature reserves
Protects biodiversity
Illegal hunting
Crop raids
Protects culture
Limited space
Lack of variation
Collection disturbance
Can be reintroduced
EIA - Environmental Impact Assessment
Minimise the impact of construction on the biodiversity of an area
Ensure potential environment impacts are considered pre-build
Arrange for a rapid response to endangerment of the environment
CITES - Convention on International Trade of Endangered Species
Monitor international trade of endangered species
Ensure trade doesn't compromise species survival
Prohibits wild plant trade
Selection pressure
Natural selection
Discontinuous - Variation with discrete groups with no intermediates
Continuous - Variation in which there are a range of values between extremes
Genetic - Combination of alleles
- Mutation
If an individual has a beneficial characteristic - they'll survive
If an individual lacks a beneficial characteristic - they'll die
A factor in the environment that threatens an individual's survival, eg:
Disease - Those who can develop resistance survive
Food availability - Those who can get food will survive
Antibiotics/insecticides - Those who can develop resistance survive
Predators - Those who can run faster survive
Desirable characteristic is passed on the offspring of surviving individuals
A feature that enables long-term survival
Behavioral - behavior that allows survival
(eg hibernation)
Anatomical - a structure that enhances survival (eg hands)
Biochemical - ensures correct cell functioning (eg unique enzymes)
Can build up a trend
Can be dated
Cytochrome C
Used in respiration so is in every organism
Amino acid sequences can be compared
Similar sequence - closely related
Different sequence - distantly related
Contains genetic info so is in every organism
Base pairing sequences can be compared
Similar sequence - closely related
Different sequence - distantly related
Bind at the same time as the substrate
Are altered but recycled
Often carry substrates between enzymes
Inorganic non-proteins
Permanent co-enzymes
Contribute to final 3D shape
Alters active site and charge distributions
Combine with enzyme or substrate
Allows enzyme-substrate complex to form easier
As it affects the charges
(wait what!?)
Secondary defence: Non- specific phagocytes.
Pathogen engulfed by macrophage
Antigens removed from pathogen and presented
Correct T lymphocytes selected as only the correct type have the receptors complimentary to the antigens on their surface
Reproduction of T helper cells (clonal expansion)
Reproduction of T killer cells (clonal expansion)
Release of specific interleukins / cytokines
Correct B lymphocytes activate as only the correct B lymphocytes have complimentary receptors to the specific interleukins/ cytokines
T killer cells search for infected cells and attach to the complimentary antigens on the infected cell surface
H O secreted to kill the cell and the pathogen inside
2 2
Reproduction of B lymphocytes
Some differentiate into plasma cells
Plasma cells manufacture antibodies
Some differentiate into memory cells
Memory cells provide immunological memory
Specific immune response
Variable region allows binding to specific antigens
Hinge region allows flexibility to bind to multiple antigens in agglutination
Constant region allows binding to any macrophage
Agglutination - A large antibody can bind many pathogens
together, making the collection too large to enter a host cell
Neutralisation - Antibodies cover all the antigens on a
pathogen so it cant bind and enter a host cell
Pathogen attaches to phagocyte
Pathogen engulfed by membrane infolding
Lysosomes release lysins into phagosome
End products of digestion are absorbed (or antigens removed and presented)

Infectious diseases
Parasites - eg. Plasmodium (malaria)
Live in or on a host
Harming it in some way
Bacteria - eg Mycobacterium Tuberculosis (TB)
Small and divide rapidly
Release toxins when dividing
Fungi - eg Tinea (ringworm)
Reproductive hyphae release spores
Irritates the skin
Virus - eg HIV/AIDS
Invade cells and take over DNA
Use it to reproduce
Until the cell bursts (causing damage and releasing new bacteria)
A person with Malaria has gametes in the blood
Female anopheles mosquito sucks up blood
Plasmodium develops in the mosquitoes stomach
Plasmodium moves to the mosquito's salivary gland
An uninfected person is bitten (using saliva as anticoagulant)
Plasmodium migrates to the liver
Plasmodium gametes move to the blood
Malaria is a parasite
Female anopheles mosquito is the vector
Plasmodium cause malaria
Limited to tropical areas
Caused by human immunodeficiency virus
Virus attacks T helper cells reducing ability to resist infection
Transmitted by:
Unprotected sex
Needle sharing
Across the placenta
Blood exchange
Caused by Mycobacterium Tuberculosis bacteria
Usually found in the lungs
How cytokines/ interleukins stimulate specific groups of B lymphocytes to divide (Jan 2011)
Spreading is more likely in the following conditions:
Poor ventilation
Poor health
The cytokine receptor has a specific shape.
This cytokine binds to the receptor on the cell surface membrane of a specific B lymphocyte.
This stimulates clonal expansion (by mitosis) of said B lymphocyte.
May also be contracted from milk or beef
Keywords/points for an answer on how smoking causes lung cancer:
Tar contains carcinogens
Benzopyrene (is a carcinogen)
Gets into lung cells
Causes mutation
Uncontrollable mitosis
Lung cancer.
Carbon monoxide:
The World
Health Organisation
Binds with haemoglobin and reduces oxygen carrying capaciy.
This an increase heart rate.
It also damages the endothelium of the arteries.
White blood cells come to fix the damage, and promote the deposition of fatty substances (because what could possibly go wrong?)
WHO's aim is to get all people to the highest level possible of health
(hehe is a pun)
Mimics neurotransmitters at synapsed and makes you alert!
Stimulates adrenaline release (increased heart rate)
Constricts arterioles which could actually lead to amputation!
Makes platelets sticks and could cause a thrombosis (blood clot)

Settles in airways and on alveoli because it paralyses the cilia so they can't waft it out.
Bacteria still gets trapped in the mucus but it can divide there and form a mucus-bacteria bad blockage in the bronchioles leading to not breathing which can cause death.
This causes a 'smokers cough'
This damages the lining of the airways and the smooth muscle in the bronchioles thickens, constricting the lumen and reducing air flow.
Can cause alveoli to burst!
They can use this information to:
Raise awareness
Identify individuals at risk
Research vaccines
They use epidemiology to:
Identify the cause of the disease
Identify risk factors and groups
Determine the
The implications of a low simpsons index..
Full transcript