Proteins - Deans Community High School

Higher Human Biology : Unit 1 Summary Notes

Proteins

Proteins are an extremely important class of molecule in living organisms.

They have many important functions;



Components of cell membranes



Used in transportation (haemoglobin)



Enzymes for cell metabolism



Structural- to add strength to tissues etc



Cell defence uses such as antibodies.

Structure

Proteins are made from the building blocks called amino acids and contain the elements;



Carbon



Hydrogen



Oxygen



Nitrogen



Sulphur

Kirkland HS &CC Biology Department

The amino acids are linked together with peptide bonds to form a polypeptide chain. This is known as the PRIMARY

STRUCTURE of the protein.

The polypeptide chains can interact with one another and additions of hydrogen bonds between amino acids of ten results in a helix structure know as the SECONDARY

STRUCTURE of a protein.

Further coiling of the protein to form 3D shapes is called

TERTIARY STRUCTURE.

1


Types of protein

Proteins can be divided into 3 groups;



Fibrous



Globular



Conjugated

Fibrous Proteins

Are formed from long chains of protein molecules and mostly have a structural role.

1. keratin in hair and nails to provide protection

2. collagen in bones, tendons and skin to provide strength.

3. elastin to provide strength and elasticity to artery walls.

4. actin and myosin to allow muscles to contract (below)

Globular Proteins

The proteins coil up into a ball.

1. enzymes in cell reactions like protein synthesis.

2. hormones such as insulin

3. antibodies to defend the body against antigens

4. transport proteins.

5. membrane proteins

Conjugated Proteins

Consist of a globular protein and a non-protein part.

1. haemolglobin (globin + iron) for oxygen transportation

2. Cytochrome, glycoprotein and lipoprotein

Kirkland HS &CC Biology Department 2


Enzymes

Enzymes are biological catalysts and are made of proteins. They have the following properties;



They can act inside the cell and outside the cell



They can control the build up (synthesis) of molecules or the breakdown (degradation) of molecules



They have active sites where the reaction is carried out.



They are specific to one reaction



They act on a substrate to produce a product.



Their speed of reaction is affected by temperature, pH, substrate concentration, enzyme concentration and inhibitors.



Each enzyme has a working range (OPTIMUM).



Inhibitors can be competitive and non-competitive.



Competitive inhibitors work by blocking active sites, non-competitive work by changing the shape of active sites.



Co-enzymes act as enzyme activators.

Intracellular and extra-cellular proteins

Processes which occur inside cells are controlled by intracellular enzymes and those which occur outside the cells are controlled by extra-cellular proteins.

Intracellular example; cytochrome oxidase (aerobic respiration)

Extra-cellualr example; pepsin (digestion)

How an enzyme works (degredation reaction)


How an enzyme works (synthesis reaction)


Factors affecting enzyme action a) Temperature

At low temperatures the reaction takes place very slowly, but as the temperature increases the rate of reaction also begins to increase until the optimum temperature (40 o C) is reached. At temperatures above this point the enzymes atoms will vibrate so much that some of the hydrogen bonds will break. These hydrogen bonds give the enzyme is specific shape.

The active sites shape changes (DENATURES) and the enzyme-substrate complex can no longer form. The rate of reaction now decreases.


Higher Human Biology : Unit 1 Summary Notes b) pH

Each enzyme works best at a particular pH and although most work between pH 5-9 (optimum pH7), there are some enzymes that will require either acid or alkali conditions to work efficiently. c) Enzyme concentration

As the concentration of the enzyme is increased the rate of reaction will increase unless the substrate concentration then becomes the limiting factor. If this is the case then the reaction rate will show a levelling off on the graph as there will be limited enzyme-substrate complexes forming. d) Substrate concentration

As the substrate concentration increases, the initial rate of reaction will also increase. However, if the substrate concentration continues to increase then a levelling off on the graph can again be seen. This is due to all the enzyme active sites being occupied and the enzymes working continuously.


Higher Human Biology : Unit 1 Summary Notes e) Inhibitors

An inhibitor is a substance which decreases the rate of reaction and may even stop enzyme activity.

Competitive Inhibitors are molecules which compete for the enzymes active site and block any substrates from binding. This is due to their similar shape.

Non-competitive inhibitors attach themselves to a region on the enzyme, but not the active site. The shape of the active site is therefore altered before the substrate can bind to it and the rate of reaction is once again reduced.

Enzyme Activation

Some enzymes do not function properly unless activators or co-enzymes are present. Many vitamin and minerals act as activators, which is why they are essential in our diets.

Activators



Zinc



Iron



magnesium

Co-enzymes



vitamin B and other vitamins.



Inborn errors of metabolism

The word metabolism refers to all of the chemical processes in the human body. A metabolic pathway is the sequence that occurs during this process and often occurs in stages.

Each stage of the pathway is controlled by an enzyme so it therefore essential that the enzyme is made and is fully functional to play its role in the process.

Sometimes errors do occur which block a pathway and can have serious consequences. The pathway can not continue and a build up of a metabolite will result.

*Phenylketonuria (PKU)*

Phenylalanine

Enzyme A

Without enzyme A, phenylalanine accumulates in the blood and may be converted phenylpyruvic acid which is secreted in urine. These products disrupt the normal development of organs (including the brain.) A diet alteration to obtain tyrosine from food may be required after post-natal screening and a low phenylalanine diet.



DNA, RNA and Protein synthesis

DNA

DNA is the chemical which carries the genetic code and is found in the nucleus of living cells. DNA determines which proteins are made in our cells by the sequence of amino acids which are in turn coded for by the sequence of DNA.

DNA amino acids protein

Chromosomes are thread-like structures found in the nucleus which contains DNA.

DNA is made up of repeating units of nucleotides.

A molecule of DNA consists of

2 strands which are twisted to form the coiled double helix structure of DNA which is instantly recognisable.

This diagram shows one strand of DNA and a section of the nucleotides.

Each nucleotide has;



Deoxyribose sugar



Phosphate group



One of 4 bases a) Adenine b) Thymine c) Guanine d) Cytosine



The chain is known to a have a sugar-phosphate backbone which is due to the strong chemical bonds between the sugar and phosphate groups on adjacent nucleotides.

Weak hydrogen bonds will form between the bases on one strand and their complimentary base partner on the opposite strand.

The two strands will then twist to form the double helix structure.

RNA

The other type of nucleic acid is called RNA. This exists as a single strand.

Each nucleotide consists of;



a molecule of ribose sugar



a phosphate group



one of four bases

1. adenine

2. uracil

3. guanine

4. cytosine

Comparisons of DNA & RNA

DNA

Double stranded

Thymine base

Deoxyribose sugar

RNA

Single stranded

Uracil base

Ribose sugar

There are two main types of RNA that you will have to know.

1. mRNA (messenger RNA) . This is formed in the nucleus of the cell using a DNA strand as a template.

2. tRNA (transfer RNA).

This is found in the cytoplasm and picks up specific amino acids and brings them to ribosomes.



The sequence of the bases in a DNA molecule make up the genetic code which determines the sequence of amino acids. The code is read in a series of 3 bases known as triplets.

1. A DNA triplet of bases = CODON

2. A mRNA triplet of bases = CODON

3. A tRNA triplet of bases = ANTICODON

Protein synthesis occurs in two stages, Transcription and Translation.

Transcription



Takes place in the nucleus



An enzyme binds to the DNA helix to cause part of it to unwind



Weak hydrogen bonds break allowing the strands to separate



Free mRNA nucleotides attach to the exposed section of DNA and an mRNA strand is formed



The DNA strand rewinds due to enzyme action



The mRNA strand leaves through a pore in the nucleus



Translation



Takes place on the ribosomes in the cytoplasm



These are either free ribosomes or are attached to RER.



The end of the mRNA strand binds to the ribosome



In the cytoplasm tRNA molecules specifically attach to amino acids



A tRNA molecule with a complimentary anti-codon binds to the mRNA codon



This occurs over and over again and peptide bonds form between adjacent amino acids



tRNA molecules can then be re-used as can the mRNA strand

The base pairing rule is as follows;

Base DNA nucleotide

A T

T

G

C

A

C

G

RNA nucleotide

U

A

C

G



Release of proteins

Proteins pass along into channels of the rough endoplasmic reticulum for transportation.

The RER membranes pinch off to form vesicles carrying the protein. The vesicles fuse to the golgi apparatus releasing the proteins for packaging. A vesicle will now pinch off carrying the packaged and processed protein and will fuse with the membrane to be secreted.



Energy Transfer

All living things respire. Respiration is the chemical process that releases energy from food. This is used to;



grow



repair tissues



movement etc

Oxidation

Is the removal of electrons from a substance. This can involve the removal of hydrogen from a substrate which is then said to be oxidised.

Reduction

Is the addition of electrons from a substance. This can involve the addition of hydrogen from a substrate which is then said to be reduced.

Remember:

*O xidation I s L oss and R eduction I s G ain ( OIL RIG )*

ATP

Adenosine Triphosphate is constantly manufactured in cells from;

ADP ( Adenosine Diphosphate) + Pi (inorganic phosphate)

Energy is released for cell processes by ATP being broken down to form ADP

+ Pi. This is known as a reversible reaction due to ADP +Pi also being used to build up ATP by phosphorylation.

Respiration occurs in 3 stages of reactions;

1. Glycolysis (in the cytoplasm)

2. Krebs cycle (in the matrix of the mitochondria)

3. Cytochrome System (in the cristae of the mitochondria)



Glycolysis



Requires no oxygen to occur



Involves the breakdown of 6C glucose to form 2 x 3C of pyruvic acid units



A net gain of 2ATP results



Hydrogen is released through oxidation



NAD (hydrogen carrier) picks up the hydrogen and becomes NADH

2



The carrier molecule transfers the hydrogen to the cytochrome system



The pyruvic acid diffuses into the matrix of the mitochondria and is converted to a 2C called Acetyl CoA.

Krebs Cycle



Oxygen is required



The 2C Acetyle CoA molecule joins with a 4C compound to make 6C

Citric Acid



Citric acid is gradually converted back to 4C



All of the carbons are lost as CO

2



The hydrogen removed are bound to NAD and transferred to the cytochrome system.



Cytochrome System



Requires oxygen



The NADH

2 produced during

Kreb’s are now transferred to the system of hydrogen carriers.



The transfer of hydrogen releases enough energy to produce 3ATP



The oxidation of 1 glucose molecule can generate 38 ATP.



Oxygen is the final hydrogen acceptor and results in water being produced.

Anaerobic respiration

If oxygen is not available then their will be no final oxygen acceptor. 2ATP only will be produced and the pyruvic acid will be converted to lactic acid for storage until oxygen becomes available again.



Sources of Energy

Glucose is the most common respiratory substrate, but carbohydrates, fats and proteins can all be used as sources of energy within the cell.

Carbohydrates

These include starch, sugar and glycogen. All carbohydrates have the chemical elements carbon, hydrogen and oxygen. Carbohydrates include monosaccharides, disaccharides and polysaccharides.

Monosaccharides .



These are simple sugars such as glucose and fructose.



Their structure is often presented as a 6 sided unit.

Glucose 

Are soluble in water.



Many have reducing properties and are know as

Reducing Sugars.

Fructose



Are sugars made of two monosaccharide units joined together.



Examples include maltose and sucrose







Are soluble in water.

Disaccharides.

Sucrose can be hydrolysed to break it down into glucose and fructose which are reducing sugars.

Maltose has reducing properties, but sucrose is not a reducing sugar.



Polysaccharides.



Are composed of many monosaccharide molecules joined together.



Examples include starch and glycogen.

Glycogen





Are insoluble in water.

Tested for using iodine solution

All of the carbohydrates are a rich source of energy. Monosaccharides enter glycolysis straight away, but disaccharides and polysaccharides must be broken down first.

Lipids .

Lipids release twice as much energy as carbohydrates, but they take longer to break down.



Lipids include fats and oils, phospholipids and steroids.



They all have the chemical elements carbon, hydrogen and oxygen.



Are good stores of energy as they are insoluble in water.



When glycogen stores are depleted in a marathon, fat is then used as the respiratory substrate.



Functions of lipids

Energy stores ~ twice as much energy released and insoluble.



Heat insulation ~ fat stores under skin



Protection ~ fat around vital organs protect them from damage.



Nerve insulation ~ myelin around nerves increases the rate at which impulses are transported.



Vitamin transport ~ fat soluble vitamins such as A,D,E and K



Hormones ~ manufatures certain hormones such a steroids like oestrogen/testosterone.



Membrane structure ~ bilayer



Cell Transport

All living cells are surrounded by a plasma membrane. This consists of protein and phospholipids molecules and is said to be fluid-mosaic in structure. This is due to the phospholipid bilayer showing continual movement and the patchy arrangement of proteins.


Phospholipids.

Each molecule has one end which is soluble in water known as the hydrophilic (water loving) head and one end which is composed of fatty acids which are hydrophobic (water repelling).

18



Proteins.

Membrane proteins have many functions;



Some are enzymes in the membrane for chemical reactions

(respiration)



Receptor sites for hormones



Carriers to actively pump molecules across membranes



Provide structural support giving support



Some for channel or pores to allow small molecules to pass



Some are markers for self-recognition to identify the cell type

The plasma membrane

Serves as a boundary between the cell and its environment and is involved in the absorption and secretion of materials. It is also selectively permeable which allows only small molecules to pass through while other substances can be transported across the membrane by active transport.

The membrane can be damaged by high temperature (denatures protein components) and alcohol dissolves phospholipids).

Transport

The uptake of materials by a cell is known as absorption while the discharge of materials from a cell is known as secretion. This is normally carried out by diffusion, osmosis and active transport in cells.

Diffusion

Is the movement of molecules from a high concentration to a low concentration until they are evenly spread. This allows substances like carbon dioxide and oxygen to enter and leave the cell.

19


Osmosis

This is the movement of water molecules from a high water concentration gradient to a low water concentration gradient through a selectively permeable membrane.

Both diffusion and osmosis are passive processes.

ISOTONIC solutions shows an equal concentration to the solute.

When an animal cell is placed in a HYPERTONIC solution it is due to the solution being at a higher concentration than the contents of the cell.

When an animal cell is placed in a HYPOTONIC solution it is due to the solution being at a lower concentration than the contents of the cell.



Active transport

This is an active process which moved ions/molecules from a low concentration to a high concentration across a semi-permeable membrane.

As it occurs against a concentration gradient, it requires oxygen, a respiratory substrate (glucose) and energy from ATP/

Endocytosis/Exocytosis

Large insoluble molecules can not pass through the membrane as such, but they can be transported from one side to the other in packages of membrane.

The membrane forms around them to form a tiny vesicle and this can be moved in (endocytosis) or out (exocytosis) of the cell.

If the large insoluble molecule is engulfed then this is known as phagocytosis, but if it is fluid that is engulfed it is known as pinocytosis.





Immunity

Immunity is the ability to resist infection by a disease causing organism called a pathogen. To protect ourselves a wide variety of defence mechanisms are used.

Innate Immunity

These are inborn defence mechanisms such as;



Skin (acts as a barrier)



Sebum (waterproof wax to protect skin)



Stomach acid



Lysozyme (enzyme in tears)



Phagocytosis



Interferon to target viruses.

Acquired Immunity

This type of immunity is acquired during a persons life and could be from breast milk/placenta (naturally acquired) or from a vaccine (artificially acquired).

This depends on the action of antibodies and antigens.

Antigens

Are proteins/polysaccharides on the surface of a cell membrane. Each organism has its own unique set of antigens so invaders or non-self antigens are recognised as being foreign to the body. Specialised white blood cells called lymphocytes recognise foreign antigens and produce antibodies as a response.

Antibodies

These are proteins which attack and destroy substances entering the body which carry foreign antigens. Each antibody will only respond to one type of antigen and are said to be specific.

Active sites



Naturally Acquired Immunity

There are 2 types of lymphocytes; B- lymphocytes and T-lymphocytes.

T- lymphocytes



Known as T-cells which mature in the thymus



Attack and destroy body cells infected with bacteria or viruses



The infected cells are recognised by the antigens on the surface of the cells (markers)

 Known as a ‘ cell-mediated response

.’

B-lymphocytes



Known as B-cells mature in the bone marrow



Produce specific antibodies



Antibodies bind to specific antigens making them inactive.



The antibody-antigen complex can now be destroyed by T-cells or can be engulfed by phagocytosis

 Known as a ‘ humoral response

.’

Memory Cells

After being exposed to an antigen, some B-cells and T-cells specific to the antigen remain in the body as memory cells. If the same antigen is experienced again then these memory cells quickly enable the immune system to produce more antibodies.

When a disease causing organism infects a person their body responds by producing antibodies. This is known as a primary response. A primary response can take a few days to happen and prevent it then often too late to the person becoming ill.

If a person survives and is then exposed to the same antigen again the disease is nearly always prevented due to the secondary response being much quicker and the concentration of antibodies produced much higher.



Rejection of transplanted tissue

Lymphocytes treat antigens on the surface of a transplanted organ as foreign.

The antibodies then destroy these antigens causing the tissue rejection. The only ways to minimise the rejection is to choose donors who are genetically similar to the recipient and use Immuno-supressor drugs (reduce the bodies immune response).

Acquired Immunity

This may be either active or passive. Active immunity is the production of antibodies and T-cells during a primary immune response to an antigen that has been acquired naturally or by infection or artificially by vaccination. This gives permanent immunity.

Passive Immunity is the introduction of antibodies from another source. They can be acquired across the placenta or in breast milk.

Summary

Immunity Active immunity Passive immunity

Natural immunity

Artificial immunity

Antibodies made by the body after an infection

Antibodies made after a vaccination

Antibodies pass across placenta or given in breast milk

Antibodies given by injection/inoculation

Advantages and disadvantages

Autoimmunity

Slow acting, but long term response

Quick acting, but short term response

Sometimes the immune system can malfunction and fail to recognise the body as ‘self.’ In these cases the immune system attacks its own body cells as if they were foreign (multiple sclerosis/ rheumatoid arthritis)

Allergies



Hay fever, food allergies, asthma etc

 Caused by an immune response to an antigen called ‘allergen.’



These are found on pollen grains, fungal spores, house dust etc



An antibody reaction takes place and histamine is produced



This causes the symptoms of allergic reactions.



Viruses



Micro-organisms which show living and non-living characteristics



They can only reproduce within the living cell of another organism

(host)



Always associated with disease



Are highly specific in their choice of host cell



They contain DNA/RNA



They have a protective protein coat



Some have an outer covering over the protein coat and are enveloped.

Viruses can only reproduce by using the hosts cells nucleotides, ATP and amino acids.

APPROACH Virus approaches the host cell

ATTACHMENT Virus becomes attached to the host cell by binding with certain molecules on the surface of the cell. It will thrusts it’s tail into the cell

PENETRATION

Virus will inject it’s DNA/RNA into the cell. This allows the virus to assume control over the host cells machinery

REPLICATION The DNA/RNA replicates using bacterial nucleotides.

PROTEIN

SYNTHESIS

DNA/RNA from the virus is transcribed into viral mRNA. This codes for more protein coats to be formed.

ASSEMBLY

RELEASE

Each viral DNA/RNA become enclosed in a protein coat

Host cell bursts releasing many copies of the virus either by lysis or buds

Viruses can be spread by;



Droplets – cold virus (coughing)



Faeces -- polio virus



Animals

– rabies (bites)



Contact

– HIV (blood/sexual contact)


Proteins - Deans Community High School

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