CAPE 1: Proteins

Proteins

Proteins are organic molecules consisting of many amino acids bonded together.
Amino Acids: Monomers or building blocks of all proteins.

Parts of the Amino Acid:

a) Amino group (NH2)
b) Carboxyl group (COOH)
c) R-group: variable- 20 R-groups, so only 20 amino acids.

• Primary structure - Proteins are made up of polypeptide chains, which are amino acids joined together with peptide bonds. The unique sequence of amino acids that make up a protein or polypeptide chain is called the Primary Structure.

Primary Structure: The unique sequence of amino acids that makes up a protein or polypeptide chain.

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• Peptide bonds are created by enzyme catalysed condensation reactions and broken down by enzyme catalysed hydrolysis reactions. Breaking down proteins is important in many areas of the body, not merely in digestion. For example, in hormone regulation, cells that are targeted by hormones contain enzymes to break down those hormones. This stops their effects from being permanent and allows them to be controlled.

Peptide bonds: Bond formed when 2 amino acids bond by condensation synthesis (See diagram below.)

Dipeptide- 2 amino acids joined by peptide bond.

Polypeptide- many amino acids bonded together.

• Secondary Structure - After synthesis, polypeptide chains are folded or pleated into different shapes, called their Secondary Structure. Two common examples of secondary structures are Alpha Helices and Beta Pleated Sheets. Secondary structure is held together by many Hydrogen bonds, overall giving the shape great stability.

Secondary Structure: The way in which the primary structure of a polypeptide chain folds.

• The final 3D structure of a protein is its Tertiary Structure, which pertains to the shaping of the secondary structure. This may involve coiling or pleating, often with straight chains of amino acids in between.

Tertiary Structure: The final 3D structure of a protein, entailing the shaping of a secondary structure.

• Tertiary structure is held together by four different bonds and interactions:
  • Disulphide Bonds - Where two Cysteine amino acids are found together, a strong double bond (S=S) is formed between the Sulphur atoms within the Cysteine monomers.
  • Ionic Bonds - If two oppositely charged 'R' groups (+ve and -ve) are found close to each other, and ionic bond forms between them.
  • Hydrogen Bonds - Your typical everyday Hydrogen bonds.
  • Hydrophobic and Hydrophilic Interactions - Some amino acids may be hydrophobic while others are hydrophilic. In a water based environment, a globular protein will orientate itself such that it's hydrophobic parts are towards its centre and its hydrophilic parts are towards its edges

• Proteins with a 3D structure fall into two main types:
  • Globular - These tend to form ball-like structures where hydrophobic parts are towards the centre and hydrophilic are towards the edges, which makes them water soluble. They usually have metabolic roles,for example: enzymes in all organisms, plasma proteins and antibodies in mammals.
  • Fibrous - They proteins form long fibres and mostly consist of repeated sequences of amino acids which are insoluble in water. They usually have structural roles, such as: Collagen in bone and cartilage, Keratin in fingernails and hair.

Quaternary Structure: Some proteins are made up of multiple polypeptide chains, sometimes with an inorganic component (for example, a haem group in haemoglogin) called a Prosthetic Group. These proteins will only be able to function if all subunits are present.

Quaternary Structure: The structure formed when two or more polypeptide chains join together, sometimes with an inorganic component, to form a protein.

Haemoglobin and Collagen

• Haemoglobin is a water soluble globular protein which is composed of two α polypeptide chains, two β polypeptide chains and an inorganic prosthetic haem group. Its function is to carry oxygen around in the blood, and it is facilitated in doing so by the presence of the haem group which contains a Fe²⁺ ion, onto which the oxygen molecules can bind.

• Collagen is a fibrous protein consisting of three polypeptide chains wound around each other. Each of the three chains is a coil itself. Hydrogen bonds form between these coils, which are around 1000 amino acids in length, which gives the structure strength. This is important given collagen's role, as structural protein. This strength is increased by the fact that collagen molecules form further chains with other collagen molecules and form Covalent Cross Links with each other, which are staggered along the molecules to further increase stability. Collagen molecules wrapped around each other form Collagen Fibrils which themselves form Collagen Fibres.

• Collagen has many functions:
  • Form the structure of bones
  • Makes up cartilage and connective tissue
  • Prevents blood that is being pumped at high pressure from bursting the walls of arteries
  • Is the main component of tendons, which connect skeletal muscles to bones

• Haemoglobin may be compared with Collagen as such:
  • Basic Shape - Haemoglobin is globular with four chains while Collagen is fibrous with three chains
  • Solubility - Haemoglobin is soluble in water while Collagen is insoluble
  • Amino Acid Constituents - Haemoglobin contains a wide range of amino acids while Collagen has 35% of it primary structure made up of Glycine
  • Prosthetic Group - Haemoglobin contains a haem prosthetic group while Collagen doesn't possess a prosthetic group
  • Tertiary Structure - Much of the Haemoglobin molecule is wound into α helices while much of the Collagen molecule is made up of left handed helix structures

Functions of Proteins & Named Examples

1) Enzyme catalysis: Enzymes help reactions occur more easily. Example- Amylase(Converts starch to simple sugar.)
2) Defense: Antibodies - Globular proteins that "recognize" foreign microbes.
3) Transport- Hemoglobin (red blood cell protein).
4) Structure / Support- Collagen, which forms the matrix of skin, ligaments, tendons and bones.
5) Motion- Actin, a muscle protein responsible for muscle contraction.
6) Regulation- Hormones which serve as intercellular messengers. Example -Insulin (blood sugar regulation).

Denaturation: protein shape altered with changes in pH, temperature. Change in shape alters activity of enzyme. Enzymes function within a narrow range of these factors. The organised strucutre of protein is affecting by denaturation in varied ways:

1. In Primary Structure: the sequence of amino acids held together by covalent peptide bonds, is not disrupted by denaturation.
2. In Secondary Structure: denaturation, proteins lose all regular repeating patterns such as alpha-helices and beta-pleated sheets, and adopt a random coil configuration
3. In  Tertiary structure: denaturation involves the disruption of:
• Covalent interactions between amino acid side-chains (such as disulfide bridges between cysteine groups)
• Noncovalent dipole-dipole interactions between polar amino acid side-chains (and the surrounding solvent)
• Van der Waals (induced dipole) interactions between nonpolar amino acid side-chains.
4. In quaternary structure: Denaturation, protein sub-units are dissociated and/or the spatial arrangement of protein subunits is disrupted.

Denaturing Agents

Denaturing Agents	Explanation of denaturation
Temperature	Heat can be used to disrupt hydrogen bonds and non-polar hydrophobic interactions. This occurs because heat increases the kinetic energy and causes the molecules to vibrate so rapidly and violently that the bonds are disrupted. Eg. When eggs coagulate when fried or boiled
pH	When the pH is adjusted to the normal isoelectric point for protein, its net charge will be zero (zwitterion). If the pH is lowered far below the isoelectric point, the protein will lose its negative charge and contain only positive charges. The like charges will repel each other and prevent the protein from aggregating as readily, preventing formation of amine bonds
Acids and bases	acids and bases disrupt salt bridges held together by ionic charges
Alcohols	Hydrogen bonding occurs between amide groups in the secondary protein structure. Hydrogen bonding between "side chains" occurs in tertiary protein structure in a variety of amino acid combinations. All of these are disrupted by the addition of another alcohol.
Heavy metal salts	Heavy metal salts act to denature proteins in much the same manner as acids and bases. Heavy metal salts usually contain Hg+2, Pb+2, Ag+1 Tl+1, Cd+2 and other metals with high atomic weights. Since salts are ionic they disrupt salt bridges in proteins. The reaction of a heavy metal salt with a protein usually leads to an insoluble metal protein salt. Eg. Disulphide bridges are easily disrupted this way
Reducing agents	If oxidizing agents cause the formation of a disulphide bond, then reducing agents, of course, act on any disulphide bonds to split it apart.
Detergents	·         hydrophobic parts of the detergent associate with the hydrophobic parts of the protein (coating with detergent molecules) ·         hydrophilic ends of the detergent molecules interact favourably with water (nonpolar parts of the protein become coated with polar groups that allow their association with water) ·         hydrophobic parts of the protein no longer need to associate with each other ·         Dissociation of the non-polar R groups can lead to unfolding of the protein chain (same effect as in nonpolar solvents).
Agitation	Whipping action stretches the polypeptide chain until the bonds break.

CSEC - How the eye works

CSEC - The eye and how it works

How the eyes adapt to different light intensities

Too much light would damage the receptor cells in the retina. Too little light wouldn't allow them to work properly.

The iris contains a pigment that gives our eyes their nice colour, this protects the retina from getting too much light. A darker iris colour gives more protection. But that isn't flexible enough to cope with constant changes in light intensity.

Instead, there is yet another reflex!

The iris contains two sets of muscles

One muscle is radial, arranged round the pupil like spokes in a wheel.

The other is circular, arranged concentric rings around the pupil.

When there is too much light, the pupil is closed down by contracting the circular muscle.

When there isn't enough light, the radial muscles in the iris contract, pulling the pupil wider. This lets more light through to the retina.

Each iris has both circular and radial muscles in it at the same time. Have a look in a mirror, or at your friend's eye - much more fun!

Adapting to different objects - Accommodation

The eye also has to adapt to be able to focus a clear image of an object no matter how far away it is from the eye. Again, this is under the control of the nervous system.

When the eye looks at an object that is far away the ciliary muscle pulls on the suspensory ligaments. These pull on the lens and make it flatter (less convex). This brings the rays of light from the object into crisp focus on the retina.

But with an object closer to the eye, the lens needs to be more convex (fatter). To do this, the ciliary muscles relax to allow the rubbery lens to return to its naturally rounder shape.

The brain's careful control of the ciliary muscles allow it to adjust the convexity of the lens to give a perfectly focussed image on the retina.

This retinal image is not the same as the object that is being looked at. The image is inverted.

CSEC: Parts of the eye and their function

CSEC - The Eye - functions of the various parts

THE EYE

Learn the part of the eye and the function of each part.

Parts of the eye	Function
Cornea	This dome-shaped layer protects your eye from elements that could cause damage to the inner parts of the eye.
Sclera	This is a smooth, white layer on the outside. The sclera provides structure and safety for the inner workings of the eye, but is also flexible so that the eye can move to seek out objects as necessary.
Pupil	The pupil appears as a black dot in the middle of the eye. This black area is actually a hole that takes in light so the eye can focus on the objects in front of it.
Iris	The iris is the area of the eye that contains the pigment which gives the eye its colour. This area surrounds the pupil, and uses muscles to widen or close the pupil. This allows the eye to take in more or less light
Lens	The lens sits directly behind the pupil. This is a clear layer that focuses the light the pupil takes in. It is held in place by the ciliary muscles, which allow the lens to change shape depending on the amount of light that hits it so it can be properly focused.
Retina	The light focuses by the lens will be transmitted onto the retina. This is made of rods and cones, and is connected to the optic nerves that will transmit the images the eye sees to the brain so they can be interpreted.
Ciliary Body	Ciliary body is a ring-shaped tissue which holds and controls the movement of the eye lens, and thus, it helps to control the shape of the lens.
Choroid	The choroid lies between the retina and the sclera, which provides blood supply to the eye, to gives nutrition
Vitreous Humour	The vitreous humour is the gel located in the back of the eye which helps it hold its shape.
Aqueous Humour	The aqueous humour is a watery substance that fills the eye which allows the eye to maintain its shape. If a patient's aqueous humour is not draining properly, they can develop glaucoma.
Fovea	an indentation in the centre of the retina. This small part of our retina is responsible for our highest visual acuity
suspensory ligament	the ring of tissue which holds the lens in place

Lets see how you do when you try to label the L.S. of the eye. (DO NOT CHEAT NOW ;) )

CSEC & CAPE: DRAWING RULES FOR BIOLOGICAL DRAWINGS

Drawing Rules:

• Drawings should be done on plain paper (without lines) only.

• Paper should be bordered 1 cm form the margin at all for sides.

• Only sharp pencils should be used on your drawing paper (NO PEN).

• Each drawing should have a title which is to be written in CAPITAL letters and can be place at the bottom of the paper. 
It should begin as follows eg. DRAWING OF A _______________.

• Each drawing must have a magnification; this will give you the comparative size of your drawing to that of the original specimen. It can be calculated as follows
Magnification = length of drawing / length of specimen
The figure is always to 2 decimal places. Eg. Mg X 0.53 (no units required)

• Both the title and magnification should be singly underlined with the exception of Scientific names which will double underlined and written using the rules for written scientific names.

• Drawings should be large, clean and clear and to one side of the paper this is to accommodate labels.

• Smooth continuous lines should be use, no sketching or double lines allowed.

• Label lines should be drawn with a straight edge and should be parallel to each other (they should never cross), they should all end at the same place on the page.

• Labels should be to one side of the drawing (no arrow heads at the end if label lines)

• Labels should be written with pencil in lower case script

• No shading allowed instead you are allowed to stipple (use dots) or dashes (-) or lines to show contrast

Thanks to drawitneat for the diagrams

CAPE 1: carbohydrates

Carbohydrates  

Carbohydrates contain only the elements carbon, hydrogen and oxygen. The group includes monomers, dimers and polymers, as shown in this diagram:

Review Table

Monosaccharides (simple sugars) 

These all have the formula (CH₂O)_n, where n can be 3-7. The most common and important monosaccharide is glucose, which is a six-carbon or hexose sugar, so has the formula C₆H₁₂O₆. Its structure is:

a-glucose (used to make starch and glycogen)	or more simply
b-glucose (used to make cellulose)

 Glucose forms a six-sided ring, although in three-dimensions it forms a structure that looks a bit like a chair. The six carbon atoms are numbered as shown, so we can refer to individual carbon atoms in the structure. In animals glucose is the main transport sugar in the blood, and its concentration in the blood is carefully controlled. There are many isomers of glucose, with the same chemical formula (C₆H₁₂O₆), but different structural formulae. These isomers include fructose and galactose.

Common five-carbon, or pentose sugars (where n = 5, C₅H₁₀O₅) include ribose and deoxyribose (found in nucleic acids and ATP) and ribulose (which occurs in photosynthesis).

Disaccharides (double sugars) 

Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond. The reaction involves the formation of a molecule of water (H₂O) and is known as dehydration or condensation: 

see animation: dehydration or condensation of monosaccharides

This shows two glucose molecules joining together to form the disaccharide maltose. Because this bond is between carbon 1 of one molecule and carbon 4 of the other molecule it is called a 1-4 glycosidic bond. Bonds between other carbon atoms are possible, leading to different shapes, and branched chains.

This kind of reaction, where H₂O is formed, is called a condensation reaction. 

The reverse process, when bonds are broken by the addition of water (e.g. in digestion), is called a hydrolysis reaction. 

see animation:hydrolysis of carbohydrates (di- and polysaccharides 

In general:

polymerisation reactions are condensations breakdown reactions are hydrolyses

 There are three common disaccharides:

• Maltose (or malt sugar) is glucose 1-4 glucose. It is formed on digestion of starch by amylase, because this enzyme breaks starch down into two-glucose units. Brewing beer starts with malt, which is a maltose solution made from germinated barley. Maltose is the structure shown above.
• Sucrose (or cane sugar) is glucose 1-2 fructose. It is common in plants because it is less reactive than glucose, and it is their main transport sugar. It is the common table sugar that you put in your tea.
• Lactose (or milk sugar) is galactose 1-4 glucose. It is found only in mammalian milk, and is the main source of energy for infant mammals.

Polysaccharides 

Polysaccharides are long chains of many monosaccharides joined together by glycosidic bonds. There are three important polysaccharides:

• Starch is the plant storage polysaccharide. It is insoluble and forms starch granules inside many plant cells. Being insoluble means starch does not change the water potential of cells, so does not cause the cells to take up water by osmosis (more on osmosis later). It is not a pure substance, but is a mixture of amylose and amylopectin.

Amylose is simply poly-(1-4) glucose, so is a straight chain. In fact the chain is floppy, and it tends to coil up into a helix.
Amylopectin is poly(1-4) glucose with about 4% (1-6) branches. This gives it a more open molecular structure than amylose. Because it has more ends, it can be broken more quickly than amylose by amylase enzymes.
Both amylose and amylopectin are broken down by the enzyme amylase into maltose, though at different rates.

Glycogen is similar in structure to amylopectin. It is poly (1-4) glucose with 9% (1-6) branches. It is made by animals as their storage polysaccharide, and is found mainly in muscle and liver. Because it is so highly branched, it can be mobilised (broken down to glucose for energy) very quickly.

•  Cellulose is only found in plants, where it is the main component of cell walls. It is poly (1-4) glucose, but with a different isomer of glucose. Starch and glycogen contain a-glucose, in which the hydroxyl group on carbon 1 sticks down from the ring, while cellulose contains b-glucose, in which the hydroxyl group on carbon 1 sticks up. This means that in a chain alternate glucose molecules are inverted.

This apparently tiny difference makes a huge difference in structure and properties. While the a1-4 glucose polymer in starch coils up to form granules, the b14 glucose polymer in cellulose forms straight chains. Hundreds of these chains are linked together by hydrogen bonds to form cellulose microfibrils. These microfibrils are very strong and rigid, and give strength to plant cells, and therefore to young plants and also to materials such as paper, cotton and sellotape.

The b-glycosidic bond cannot be broken by amylase, but requires a specific cellulase enzyme. The only organisms that possess a cellulase enzyme are bacteria, so herbivorous animals, like cows and termites whose diet is mainly cellulose, have mutualistic bacteria in their guts so that they can digest cellulose. Humans cannot digest cellulose, and it is referred to as fibre.

Chitin - (poly glucose amine), found in fungal cell walls and the exoskeletons of insects. The structure resembles that of cellulose, except that the hydroxyl groups on C# 2 have been replaced by acetylamino groups. 

• Other polysaccharides that you may come across include:
• .Pectin (poly galactose uronate), found in plant cell walls.
• Agar (poly galactose sulphate), found in algae and used to make agar plates.
• Murein (a sugar-peptide polymer), found in bacterial cell walls.
• Lignin (a complex polymer), found in the walls of xylem cells, is the main component of wood.
  
  

Structure of Polysaccharides