Biology F212 Biochem-->Enzymes

Water is a polar molecule.

This is because the oxygen atom pulls the shared electrons towards it, meaning that water is slightly negatively charged at the oxygen and positively charged at the hydrogen ends, so they can form hydrogen bonds with each other.

This are continuing breaking and reforming, so the molecules can move around. 

Acts as a solvent: Metabolic processes in all organisms rely on chemicals being able to react together in a solution.

Acts as a Liquid: Allows for the movement of materials, both in a cell and in multicelluar organisms.

Acts Cohesively: Water molecules stick together, forming surface tension meaning that long and thin columns of water are difficult to break.

Freezing: Water freezes and forms ice on the top of water, insulating the water below, making it less likely to freeze.

Thermal stability: Large bodies of water have constant temps. (high SHC), Take large amounts of heat away (High LHC)

Metabolic: Water takes part in many process, hydrolysis and condensation reactions.

Contains a Amine group on the left : NH2, and a carboxyl group on the right: COOH.

The bonds formed between amino acids are called peptide bonds and two amino acids together are called dipeptides.

A long chain of amino acids are called polypeptides

Poly comes from the greek language meaning 'combine many'

In the forming of bonds, a OH on the carboxyl group is removed and bonds with a H from an amine group from another amino acid. Water is formed as a result of the bonding process.

In breaking peptide bonds, water is required and splits into a H and a OH and return to their respective positions.

Primary structure:

A sequence of amino acids found in a protein molecule

Secondary structure:

The coling and folding of a protein molecule because of hydrogen bonds. Beta pleated sheets or Alpha helixs.

Teritary Structure:

The overall 3D shape of protein molecules, disulfide bridges form as well as hydrogen bonds and hydrophobic interactions occur.

Quaternary structure:

Protein structures with more than one polypeptide chain. e.g. Haemoglobin, four polypeptide chains

Haemoglobin:

-Globular Protein

-Soluble in water

-Wide range of amino acids in primary structure

-Contains protestic group, (haem)

-Mostly wound into a alpha helix structure

Collagen:

-Fibrous protein

-Insoluble in water

-No prosthetic group

-Mostly a LEFT HANDED helix structure

Three polypeptides, with around 1000 amino acid, wound around each other. Hydrogen and covalent bonds (cross-links) between chains. Has STAGGERED crosslinks for added strength.

Every third amino acid is glycine

Alpha glucose is identifyable by its C1 having a H above

Beta glucose has OH above on the C1

Forming:

Water is formed much like in peptide bond formation, a OH from a sugar is taken of the C4, and a H is removed from an OH that is on C1. Resulting in a bond between sugars with and O in the middle.

Breaking:

Water is used to break the bond resulting in water breaking down into H and OH and returning to their respective positions.

Amylose:

-Made of alpha glucose, plant storage

-Straight chain, 1,4 glycosidic bonds

-Coiled

Cellulose:

-Beta glucose

-Straight chains

-Can be broken down by enzymes in some animals (e.g. cows)

-Forms cell wall

Glycogen:

-Like amylose but has many 1,4 glycosidic bonds, but there are also many 1,6 branches

Glucose

-Simple sugar, used in respiration

Amylose

-Insoluble in water, no effect on water potential

Glycogen

-Highly branched, broken down quickly

Cellulose

-Lots of polypeptide chains, bonded together by hydrogen bonds

-Cell wall is reinforced, with other substances for support

Triglycerides have three fatty acids and are attached by a glycerol.

Phospholipid are when a phosphate group is in place of a fatty acid in a triglyceride

Triglycerides

-Compact energy stores

-Insoluble in water ( no effect on water potential)

Phospholipids

-Hydrophobic tail and hydrophilic head, used in phopsholipid bilayer membrane

Cholesterol

-Small thin molecules that CAN fit in the phopspholipid bilayer and giving strength and stability

Protein:

If present, turns from blue to lilac

Reducing sugars:

Add benedicts solution, heat to 80 degrees. Will turn from Blue to orange/red

Non-reducing sugars:

If reducing sugars test is negative, boil with HCl, cool and neutralise with sodium hydrogencarbonate. Repeat Reducing sugars test. Will turn from Blue to orange/red

Starch:

Turns from yellow to blue-black

Lipids:

Mix with ethanol, pour into water if emulsion forms, lipids are present.

-Benedicts test to show presence of reducing sugars

-Orange/brown percipiate forms

-More percipiate=More reducing sugars=More bendicts solution is 'used'

-Filter out the percipitate, so that we can measure the conc. of reducing sugars.

-This indicates an estimate for the conc. of reducing sugats

-Zero the colourimeter with water

-Take a range of known conc. of reducing sugars

-Carry out reducing sugars test on each and filter out precipitate

-Use colourimeter to give readings of the amount of light passing through the solutions, plot results on a graph

-Measure the % transmission of unknown

-Use this to find the equivalent reducing sugar conc.

DNA is a short for deoxyribonucleic acid, and it is a polynucleotide.

-made into double strands that run antiparallel (sugars point in opposite directions)

-Made of nitrogenous bases Adenine, Thymine, Guanine and Cytosine

RNA is also a polynucleotide, that in normally found in single strands

-Has Uracil instead of thymine, as a nitrogenoys base

Bonding between complinimentary pairs: Pyrimidines and purine bind together, Pyrmidines include Thymine and Cytosine, and purines include guanine and adenine. Two hydrogen bonds between A and T, and three between G and C.

Antiparallel structure causes chains to twist like a rope ladder, to form the final structure.

A gene is a sequence of DNA nucleotides that code for polypeptides

The double helix untwists

The Hydrogen bonds are broken and the DNA is unzipped, to expose the nitrogenous bases

Free complimentary DNA nucleotides bind to the exposed bases

DNA polymerase catalyses the formation of covalent bonds between the ribose and the phopsate in neigbouring nucleotides

This continues until there are two identical strands

The DNA polymerase proof reads the DNA for mistakes and removes them.

The required gene is exposed by the spliting of the hydrogen bonds between purines and pyrmidines by helicase which holds the double helix together.

RNA nucleotides form a complimentary strand, which is a copy of the DNA

The mRNA peels away from the DNA and leaves the nucleus

The mRNA goes to ribose

tRNA molecules bring amino acids to the ribose in the order depicted by the mRNA

The amino acids bond together with peptide binds, giving the protein a specific structure.

Enzymes are globular proteins (like haemoglogin) with a specific tertiary structure, which catalyses reactions in living organisms (They are biological catalysts)

Enzymes act both inter and extra cellular

Mechanisms of enzymes:

Specifity: The active site is a specific shape, only works with one type of substrate

Active site: The area on which substrates bind to on a enzyme

Lock and Key, hypothesis: The enzymes site is complimentary to the substrate

Induced fit: The enzyme molecule changes shape, to fit the substrate molecule to bind closely

Enzyme-substrate complex: The enzyme and substrate when they have binded together.

Enzyme product complex: The enzyme and product when they are binded together.

Low activation energy: Enzyme require less activation energy, so reaction occur at low temps. 

pH: Low pH= Lots of H+ ions

positively charged

H+ ions interfere with the hydrogen and ionic bonds holding the tertiary structure

pH changes the charge of amino acids at the active site and can therefore no longer bind

-At high pH COOH disscoiates to become a charged COO- group

Temperature: Up to a certain point: an increase in temp will cause an increase in rate of reaction as there are more successful collisions between enzyme and substrates.

However more energy makes the molecules vibrate straining the intermolecular bonds to strain and break. The teritary structure of enzymes has many of these bonds. As heat increases more are broken. The teritary structure decays because of this. The rate of reaction decreases. If enough bonds are broken, the tertiary structure will unravel and stop working. This is irreversible and also known as denaturing.

Enzyme concentration: As the concentration increases, so does the rate of reaction, as there are more active sites available. Until the substrate conc. becomes a limiting factorand the rate of reaction stops increasing.

Substrate concentration: As substrate concentration increases, the rate of reaction increases because there are more substrate molecules to react. At high concentrations, all the active sites become filled, so the rate of reaction remain the same.

Competetive: Have a similar shape to substrate molecule, they occupy the active site but do not react to form a product because the inhibitor is not completely complimentary to the substrate.

The level of inhibition,depends on the conc. of substrate and and inhibitor. If there is high conc of substrate and low conc of inhibitor the is a lower amount of inhibition, resulting in only a slight drop in rate of reaction. And do vica versa. They do not bind permenantly but instead bind for a short moment and then leave, the binding is reversible.

Non-competetive: These do not attach to the active site, instead the attach to a region away from the active site. The attachment of non-competetive inhibitor to enzymes changes and distorts the tertiary structure, making the enzyme ineffective, as a enzyme-substrate complex cannot form. Resulting in a decrease in rate of reaction. If there are more inhibitors than enzymes, then the rate of reaction will stop all together.

The binding of non-competetive is irrreversible and effectively become denatured.

Cofactors: Ions that increase the rate of enzyme-controlled reactions. Their presence allows enzyme-substrate complexez to form easily.

Coenzymes: Small organic molecules, non-protein molecules that bind for a short period of time. They bind just before/during, and are changed in some way. Unlike the substrate the coenzyme will be recycled and used again. Some coenzymes are part of the enzyme, they can be considered prosthetic group

Metabolic poisons may be enzyme inhibitors

Example: 

Potassium Cyanide, acts as a non-competetive inhibitor of the enzyme cytochrome oxidase, which is involved in the oxidation of ATP. When this enzyme cannot work, aerobic respiration cannot occur, and so have to respire anaerobically, which leads to a build up of lactic acid, toxic to the cells.

Medicinal drugs also work by inhibiting the activity of enzymes.