3.1.4.2 Many proteins are enzymes

Enzymes are globular proteins that act as catalysts by altering the rate of a chemical reaction without undergoing permanent changes themselves. They can be reused and are therefore effective in small amounts. They catalyse a wide range of intracellular and extracellular reactions that determine structures and functions from cellular to whole-organism level.

The minimum amount of energy required to activate the reaction is known as the activation energy. For reactions to occur initially (naturally) a number of conditions must be satisfied:

• The substrates must collide with sufficient energy to alter the arrangement of their atoms to form the produce
• The free energy of the products must be less than that of the substrates

The activation energy must be initially overcome before the reaction can proceed. Enzymes lower the activation energy level. A specific region of the enzyme (the active site) is functional. It forms a small depression within the much larger enzyme molecule. Enzymes act upon substrates which fit neatly into the active site forming an enzyme-substrate complex. The substrate is temporarily held in place by temporary bonds between amino acids of the active site and groups on the substrate.

We need to know a bit about the induced fit model of an enzyme. The induced fit model proposes that the active site forms as the enzyme and substrate interact. The proximity of the substrate leads to a change in the enzyme that forms the functional active site. As it changes shape the enzyme puts strain on the substrate molecule. This strain distorts particular bonds in the substrate and consequently lowers the activation energy needed to break the bond.

We need to know about the effects of certain factors on the rate of enzyme controlled reactions. Providing there are no limiting factors the following will occur:

• enzyme concentration
• the more enzymes the more active sites so the faster the reaction
• substrate concentration
• the more substrates the faster the reaction
• concentration of competitive and non-competitive inhibitors
• competitive inhibitors block the active site. The more competitive inhibitors the lower the rate of reaction
• non-competitive inhibitors distort the active site. The more non-competitive inhibitors the lower the rate of reaction
• pH
• A pH far from the enzymes optimum will denature the enzyme and the reaction will cease
• at optimum pH the rate of reaction will be the fastest
• temperature
• A temperature far from the enzymes optimum will denature the enzyme and the reaction will cease
• at optimum temperature the rate of reaction will be the fastest

Okay so we need to be able to calculate pH from hydrogen ion concentration. To do this we use the equation:

pH = - log [H+]

3.1.5.1 Structure of DNA and RNA

Okay so we need to know alllll about DNA and RNA. To start, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are important information-carrying molecules. In all living cells, DNA holds genetic information and RNA transfers genetic information from DNA to the ribosomes. Ribosomes are formed from RNA and proteins. Both DNA and RNA are polymers of nucleotides. Each nucleotide is formed from a pentose, a nitrogen-containing organic base and a phosphate group. That was a nice little summary.


The components of a DNA nucleotide are:

•  deoxyribose
• a phosphate group
• one of the organic bases:
•  adenine
• cytosine
• guanine
• thymine

The components of an RNA nucleotide are:

• ribose
• a phosphate group
• one of the organic bases:
• adenine
• cytosine
• guanine
• uracil

A condensation reaction between two nucleotides forms a phosphodiester bond. A DNA molecule is a double helix with two polynucleotide chains held together by hydrogen bonds between specific complementary base pairs. In DNA, adenine binds to thymine and guanine binds to cytosine. It follows that a DNA molecule will have the same percentage of adenine/thymine, and the same percentage of cytosine/guanine.

An RNA molecule is a relatively short polynucleotide chain. It is also single stranded.

3.1.5.2 DNA replication

The semi-conservative replication of DNA ensures genetic continuity between generations of cells. It takes place as follows:

• The enzyme DNA helicase breaks the hydrogen bonds between the complementary base pairs of DNA
• The double helix separates into two strands and unwinds (as a result)
• Each exposed polynucleotide strand acts as a template to which complementary free nucleotides bind by specific base pairing
• Nucleotides are joined together by DNA polymerase which forms the sugar-phosphate backbone in a condensation reaction
• Each DNA molecule contains one new and one original strand, hence the name semi-conservative.

Watson and Crick devised this model of DNA replication. If i'm very honest, i'm not sure what the spec means by we need to be able to evaluate the work of scientists in validating this experiment(?). Please help if you know:)

3.1.4.1 General properties of proteins

Proteins are sort of polymers. They are made of polypeptide chains which are formed from amino acid monomer units. We need to know the structure of an amino acid:

NH2 represents the amine/amino group

COOH represents the carboxyl group

R represents the side chain/group - this is what differs in each amino acid (it is the variable part).

A functional protein often contains 3-4 polypeptide chains. 

Proteins are formed from 3, often 4, structures. These are known as the primary, secondary, tertiary and quaternary structure.

1. Amino acid sequence (polypeptide chain)
2. This sequence is folded into a pleated sheet/alpha helix which is held together by the -NH and -C=O from amino acids (these really form hydrogen bonds twisting the chain)
3. The pleated sheet/alpha helix is further folded into a specific tertiary structure which is bonded by disulphide bridges/ionic bonds/hydrogen bonds
4. Potentially a number of individual polypeptide chains are linked in various ways. They may also be associated with prosthetic (non-protein) groups.

We can test for proteins using the biuret test:

Place a sample of the solution to be tested in a test tube

Add an equal volume of sodium hydrogen solution at room temperature

Add a few drops of dilute copper (2) sulphate solution

Mix gently

Purple = protein

Blue = no protein

3.1.3 Lipids

Two lipids we need to know about are triglycerides and phospholipids. They are organic as they contain carbon (they also contain hydrogen and oxygen). Lipids are insoluble in water but soluble in organic substances (e.g acetone/alcohols). The proportion of oxygen to carbon and hydrogen is smaller than in carbohydrates.

Triglycerides are composed of three fatty acids and a glycerol. They are formed from the condensation of these molecules (three fatty acids and a glycerol) forming an ester bond between the glycerol and each triglyceride. If the R-group of the fatty acid (RCOOH) is said to be unsaturated it just means it has carbon-carbon double bonds (monounsaturated means one carbon-carbon double bond). Fatty acids are hydrophobic.

Phospholipids are composed of two fatty acids, a glycerol, and a phosphate group. The phosphate ‘head’ is hydrophilic and the fatty acid ‘tail’ is hydrophobic. In this way, phospholipids are polar.

Triglyceride structure and function:

High ratio of energy-storing carbon-hydrogen bonds to carbon atoms so are an excellent store of energy

Low mass-energy ratio (much energy can be stored in a small volume)

Large and non-polar = insoluble so does not affect the water potential of cells

Release water when oxidised = provide an important source of water

Phospholipid structure and function:

Polar so form a bilayer in aqueous solutions/environments

hydrophilic heads hold at the surface of the cell-surface membrane

They form glycolipids by combining with the cell-surface membrane which are important in cell recognition

The emulsion test:

Take a dry/grease-free test tube

Add 2cm^3 of the sample and 5cm^3 of ethanol

Shake thoroughly - this dissolves any liquid present

Add 5cm^3 of water and shake gently

Cloudy-white emulsion/colour indicates a lipid is present (clear = no lipid). As a control, repeat with water as the sample.

3.1.2 Carbohydrates

As mentioned in 3.1.1, monosaccharides come together in a condensation to form either a disaccharide/polysaccharide - the bond that forms is a glycosidic bond. There are three disaccharides we need to be aware of:

Maltose is formed from the condensation of two glucose molecules

Sucrose is formed from the condensation of a glucose molecule and a fructose molecule (think like, sucrose is a lot in fruit so FRUctose for FRUit)

Lactose is formed from the condensation of a glucose molecule and a galactose molecule (think gaLACTOSE makes LACTOSE).

There are two isomers of glucose we need to be able to draw,  α-glucose and β-glucose. Here’s what they look like (pretty similar):

There are also three types of polysaccharide we need to know (these are formed by the condensation of many glucose units). Glycogen and starch are formed by the condensation of many α-glucose molecules, whilst cellulose is formed from the condensation of many β-glucose molecules. The structure and function of each polysaccharide is as follows…

Starch

Does not affect the water potential of cells (is insoluble)

Very compact

Branched

1-4 and 1-6 glycosidic bonds

α-glucose

does not diffuse out of cells (large and insoluble)

Glycogen

Does not affect water potential (insoluble)

does not diffuse out of cells (insoluble)

1-4 and 1-6 glucosidic bonds

α-glucose

branched (more than starch)

Cellulose

1-4 glycosidic bonds

inverted β-glucose molecules

straight unbranched chains that run parallel

chains cross-linked by hydrogen bonds forming microfibrils and fibrils add collective strength

Testing for reducing sugars:

Add 2cm^3 of the sample to a test tube (crush in water if not liquid)

Add an equal volume of benedicts reagent

Heat the mixture gently in a water bath for 5 minutes (gently boiling)

clear/blue = trace/none

green = very low

yellow = low

orange = medium

red = high

Testing for non-reducing sugars:

Following a negative benedicts test…

Add 2cm^3 of the sample to a test tube (crush in water if not already liquid)

Add 2cm^3 dilute HCl

place the test tube in a gently boiling water bath for 5 minutes

Slowly add sodium hydrogen carbonate

Test with pH paper to ensure the solution is alkaline

re-test with benedicts reagent.

If reducing sugars are present it is because they were produced from the hydrolysis of non-reducing sugars.

3.1.1 Monomers and polymers

Carbon atoms readily form bonds with other carbon atoms forming a backbone to which other atoms can attach. This means that a large number of different types/sizes of molecules can form (based on carbon). Carbon containing molecules are known as organic molecules.

Chains of individual molecules are known as polymers - the individual molecule being known as a monomer. Examples include saccharides (monosaccharides are the individual unit, polysaccharides are the chain of monomers), amino acids (the amino acid is the monomer, a polypeptide is the polymer), and nucleotides (nucleotides are the monomers, polynucleotides are the polymer). If two monomers are bonded together it is known as a ‘di-‘ (e.g a disaccharide, and a dipeptide)

To join monomers together we use condensation reactions. These bind molecules with the elimination of water when the chemical bond forms.

To break apart polymers into their constituent monomers we add water (known as a hydrolysis reaction) to break the chemical bond formed upon condensation.

3.1.6 ATP

ATP is the main energy source used to carry out processes within cells. It is a phosphorylated macromolecule with three parts:

• adenine (a nitrogen-containing organic base)
• ribose (a sugar molecule with a 5-carbon ring structure (pentose sugar) that acts as the backbone to which other parts are attached
• phosphates - a chain of three phosphate groups

The bonds between these phosphate groups are unstable so they have a low activation energy (this basically means they are easily broken down). When they break they release a considerable amount of energy - often only the last Pi (inorganic phosphate) is broken off. They are broken down by hydrolysis - the addition of water and the reaction is catalyzed by ATP hydrolase:

ATP + water --> ADP + Pi + energy

This is a reversible reaction meaning that energy can be used to add a Pi to ADP to reform ATP (this is the reverse to the reaction above). This reaction is catalyzed by ATP synthase. This is a condensation reaction and can occur in three ways:

• in chlorophyll-containing plants during photosynthesis (photophosphorylation)
• in plant and animal cells during respiration (oxidative phosphorylation)
• in plant and animal cells when phosphate groups are transferred from donor molecules to ADP (substrate-level phosphorylation)

ATP roles:

Okay so this isn't in the spec but we did a lot about it in class so, let me know if you think it is useful for me to write about the roles of ATP/why it is good?

3.1.7 Water

Water is a major component of cells and has several properties that are important in biology. In particular water:

• is a metabolite in many metabolic reactions
• has a relatively high specific heat capacity  meaning it buffers temperature changes. Because the water molecules stick together it takes a lot of inputted energy to break them turning liquid water into a gas. This means it takes a lot of energy to heat a given mass of water meaning water can act as a buffer and resist temperature changes which is good for aquatic animals.
• has a relatively large latent heat of vapourisation. This means that a lot of energy is required to evaporate one kilogram of water. This means that evaporation is effective in cooling because a lot of the body's thermal energy goes into heating a small mass of perspiration (sweat) and the body doesn't lose much water.
• has strong cohesion between water molecules - it is a dipolar molecule made up of two atoms of hydrogen and one of oxygen. The O2 atom has a slightly negative charge whilst the H atoms have a slightly positive charge meaning a water molecule has both negative and positive poles. The negative pole of one water molecule is attracted to the positive pole of another forming a hydrogen bond. this causes water to stick together and have a cohesive nature. This supports columns of water in the tube-like transport cells of plants and produces surface tension where water meets air which provides habitats for organisms such as pond skaters.

Not on the spec but also useful to know, water:

• is a solvent, readily dissolving substances such as gases (O2 and CO2), wastes (ammonia and urea), inorganic ions and small hydrophilic molecules (amino acids, monosaccharides, ATP), and enzymes (whose reactions take place in solution)
• is not easily compressed so provides support e.g turgor pressure and the hydrostatic skeleton of animals
• is transparent meaning aquatic plants can photosynthesise and light rays can penetrate our lenses and the jelly-like fluid that fills eyes so light can reach the retina

3.1.8 Inorganic ions

Inorganic ions occur in body fluids, in solution in the cytoplasm of cells, and also as part of larger molecules (some in high concentrations and some in very low concentrations).

Every inorganic ion has a specific role which depends on its properties. There are a few that we study in detail that we need to be aware of:

• hydrogen ions in pH (here)
• iron ions as a component of haemoglobin (they play a role in transporting oxygen, here)
• sodium ions play a role in the co-transport of glucose and amino acids (here)
• phosphate ions are components of both DNA and ATP (here)