Biology AS-F212-OCR specification and answers.

(a) describe how hydrogen bonding occurs 

between water molecules, and relate this, 

and other properties of water, to the roles of 

water in living organisms (HSW1); 

(a) describe how hydrogen bonding occurs between water molecules

• Water is described as polar because of its negatively charged Oxygen and the slightly positively charged Hydrogen ends.

• Hydrogen bonding occurs because there is attraction between the Oxygen (-) and Hydrogen (+)

• Each water molecule can form up to four of these to make a cluster that break and reform - when temperature is reduced, water molecules have reduced kinetic energy so form more Hydrogen bonds. This is why water becomes its icy solid form because Hydrogen bonds hold the semi crystaline form.

(a) relate this, and other properties of water, to the roles of water in living organisms (HSW1); 

Good solvent for charged/uncharged substances- Water molecules are attracted to ions and polar molecules like glucose. They  are used for transport in the blood, xylem and phloem.

High Specific heat capacity  - 4.2 KJ is required to increase the temperature of 1gram of water by 1 degree Celsius. The heat energy absorbed is used to break Hydrogen bonds. This prevents changes in body temperature.

High Latent heat of evaporation  - Much thermal energy is used to change water molecules to vapor - This happens in transpiration in plants, sweating/panting in mammals- Its used as a coolant. This is efficient as small amounts of water absorb much thermal energy.

High cohesion -  Hydrogen bonds stick molecules together - Helps draw up water in xylem.

Re-activity- Water reacts with many substances- Its involved in hydrolysis reactions and photosynthesis.

Incompressibility - Outside pressure cannot force water into smaller spaces - it makes hydro-static skeleton for some animals like the earthworm  and turgidity in plant cells. 

(b) describe, with the aid of diagrams, the structure of an amino acid; 

(b) describe, with the aid of diagrams, the 

structure of an amino acid; 

• The Amino group of a amino acid like glycine is the H2N and the carboxyl group is the COOH
• Only the R group differs between amino acids ( there are 20 different types of amino acid so 20 different R groups.
• R groups can be positively/negatively charged or hydrophobic/hydrophilic.

Plants and Animals

• Whilst plants are able to manufacture the amino acids they need ( if they obtain nitrate from the soil) Animals must take in proteins as part of their diet to be digested into amino acids.
• Animals cannot build some proteins from the materials they take in their bodies. These essential amino acids are fundamental to their diets.
• There's more issues for Animals - the amino acid surplus to their bodies requirements cannot be stored as they can be to toxic. So the amino group is removed in deamination in the liver to be converted to urea. This is excreted in the urine.

(c) describe, with the aid of diagrams, the formation and breakage of peptide bonds in the synthesis and hydrolysis of dipeptides and polypeptides; 

(c) describe, with the aid of diagrams, the formation and breakage of peptidebonds in the synthesis and hydrolysis of dipeptides and polypeptides; 

Cells polymerize amino acids into polypeptides  by forming peptide bonds.

(1) A peptide bond forms between an amino group and a carboxylic group by eliminating a molecule of water ( OH     H - as seen on the diagram). This is a Condensation Reaction.

(2) When you chemically add water, it breaks the peptide bond and restores the ( OH     H). This is Hydrolysis.

(d) explain, with the aid of diagrams, the term primary structure;

The Primary Structure of a polypeptide is its amino acid sequence. This is determined by the gene that codes for a polypeptide.

(The Amino acids are held together in a chain by peptide bonds. The specific assembly of amino acids is determined by the gene that is transcribed and translated into the primary structure- A2)

(e) explain, with the aid of diagrams, the term secondary structure with reference to hydrogen bonding;

The Secondary Structure is the folding of a polypeptide into (Alpha) Helix's and (Beta - Pleated sheets) Helix's that are stabilized by Hydrogen bonds.

(f) explain, with the aid of diagrams, the term tertiary structure, with reference to hydrophobic and hydrophilic interactions, disulfide bonds and ionic interactions; 

(f) explain, with the aid of diagrams, the term tertiary structure, with reference to hydrophobic and hydrophilic interactions, disulfide bonds and ionic interactions; 

• The tertiary structure is its 3-D shape that's held in place by a number of bonds and interactions.
• This 3-D structure is vital for its function; for instance hormones must be a specific shape in order to fit the receptors of a target cell.

(1) Disulfide bonds - amino acids, like cysteine, contain sulphur and where two are found close to each other a covalent bond can form ( Diagram )

(2) Ionic bonds - R groups can sometimes carry a charge and ionic bonds can form between them. (Diagram )

(3) Hydrogen bonds - When slightly charged groups are found close to slightly negative groups, Hydrogen bonds form. (Diagram)

(4) Hydrophobic/ Hydrophilic interactions( in a water based environment)  - Hydrophilic amino acids tend to be found on the outside of globular proteins and Hydrophobic amino acids are found in the center. (Diagram)

3-d shapes of proteins fall into tow categories that determine their shape; 

• Globular - roll up to form balls - are usually soluble - Enzymes, plasma proteins and antibodies are examples of globular proteins.

• Fibrous  - Form fibres - are usually insoluble - usually have structural roles - examples include collagen, cartilage and keratin.

(g) explain, with the aid of diagrams, the term quaternary structure, with reference to the structure of haemoglobin; 

• A protein has a quaternary structure if it's made of two or more polypeptide sub-units joined together ,or a polypeptide and an inorganic component.
• Haemoglobin is used as an example of proteins with quaternary structures because it consists of four polypeptides joined together and held in place by interactions between R groups. (Hydrogen and ionic bonding)

(h) describe, with the aid of diagrams, the structure of a collagen molecule;

• Collagen is a fibrous protein consisting of three polypeptide chains (one chain=1000 amino acids)
• Strength of the molecule is determined by Hydrogen bonding and is strengthened further by covalent bonds between collagen molecules.
• A collagen fibril is formed and many fibrils form collagen fibres.

(i) compare the structure and function of haemoglobin (as an example of a globular protein) and collagen (as an example of a fibrous protein); 

 Globular Haemoglobin vs Fibrous Collagen:

• Soluble in water : Insoluble in water

• Wide range of amino acid constituents in primary structure:35% of primary structure is glycine

• Contains a prosthetic group (Haem): Doesn't have a prosthetic group

• Much of the molecule is wound into alpha helix structures : Much of the molecule consists of left handed helix structures

(j) describe, with the aid of diagrams, the molecular structure of alpha glucose as an example of a monosaccharide carbohydrate; 

• All larger carbohydrates are made by joining monosaccharides together.
• In Alpha Glucose the OH is below the plane of the ring whereas Beta Glucose's OH is above the plane.

(k) state the structural difference between alpha- and beta-glucose; 

• Alpha glucose: The OH group is below the plane of the ring.

• Beta Glucose : The OH group is above the plane of the ring.

• They are both glucose molecules but, this slight difference leads to some very different properties

(l) describe, with the aid of diagrams, the formation and breakage of glycosidic bonds in the synthesis and hydrolysis of a disaccharide (maltose) and a polysaccharide (amylose); 

• Two monosaccharides (Alpha glucose) are joined together in a condensation reaction to form the disaccharide maltose.

• This is repeated many times to form amylose, a polysaccharide. 

• A covalent glycosidic bond is formed and water is eliminated.

• Hydrolysis uses a water molecule to break the glycosidic bond.

(m) compare and contrast the structure and 

functions of starch (amylose) and cellulose; 

• Starch (Structure) - Large molecules of many alpha glucose molecules joined by condensation reactions - it's an unbranched polymer that forms a helix

• Starch (Function) - Energy storage carbohydrates - starch in plants ;glycogen in animals and fungi

• Cellulose (Structure) - A polymer of Beta glucose - cellulose forms straight chains with many projecting -OH groups that form hydrogen bonds with adjacent cellulose molecules - cellulose molecules are in bundles called microfibrils and these are laid down in different directions to give added strength to cell walls.

• Cellulose (Function) - Structural - found in plants where it forms cell walls to prevent plants from bursting when fully turgid.

(o) explain how the structures of glucose, starch (amylose), glycogen and cellulose molecules relate to their functions in living organisms;

• Glucose, starch and glycogen consist of alpha glucose molecules that provides energy via respiration and an energy storage.

• Cellulose consists of many Beta glucose molecules joined together by condensation reactions that ensure they are insoluble in water and very strong - this relates to their structural function in plants as it forms cell walls.

(p) compare, with the aid of diagrams, the structure of a triglyceride and a phospholipid; 

• Triglyceride molecules consist of one glycerol molecule bonded to 3 fatty acids by a condensation reaction between an acid group of a fatty molecule and the OH of the glycerol - a water molecule is produced.
• A phospholipid is identical to a triglyceride but the 3rd fatty acid is a phosphate group. 

(q) explain how the structures of triglyceride, phospholipid and cholesterol molecules relate to their functions in living organisms; 

• Triglyceride (Structure): Glycerol plus 3 fatty acids

• (Function): A compact energy store that insoluble in water so doesn't affect cell water potential - its also stored as fat for thermal insulation/protection.

• Phospholipid (Structure): Glycerol plus two fatty acids and a phosphate head

• (Function) - Forms a molecule part hydrophobic and hydrophilic so the ideal basis of a cell surface membrane - it may have carbohydrates attached to the phosphate group and this type of glycolipid  would be involved in cell signalling.

• Cholesterol (Structure) Four carbon bases ring structures

• Function : forms a small,thin molecule that fits into a lipid bilayer giving strength and stability - its also used to form steroid hormones

(r) describe how to carry out chemical tests to identify the presence of the following molecules: protein (biuret test), reducing and non-reducing sugars (Benedict’s test), starch (iodine solution) and lipids (emulsion test); 

• Protein and the biuret test : the colour change is blue to lilac

• Reducing sugar and the Benedict test (heated to 80 degrees Celsius: the colour change is blue to orange-red

• Non-reducing sugar and the Benedict's test ( if reducing sugar test is negative ,boil with hydrochloric acid, cool and neutralise with sodium hydrogencarbonate solution/sodium carbonate solution and repeat the Benedict's test: the colour change is Blue to orange -red on the second test.

• Starch and iodine : the colour change should be brown to blue-black

• Lipids and the emulsion test(add ethanol to extract (dissolve) lipid and pour alcohol into water in another test tube: a white emulsion should form near the top of the water.

(s)Describe how the concentration of glucose in a solution may be estimated by using a colorimeter; 

• A colorimeter shines a beam of light through a sample containing cuvette

• A photoelectric cell picks up the light that has passed through the sample 

• The more copper sulfate that is used up in the Benedict's test in a sample, the less light will be blocked out and the more light transmitted.

• A calibration curve must be made to quantify the amount of glucose present 

• Firstly, you would need to take a range of known concentrations of reducing sugar and carry out the Benedict's test on each one (filtering the precipitate out of each one)

• Use the colorimeter to give readings of the amount of light passing through the solutions 

• Plot a graph to show light getting through (transmission) against reducing sugar concentration and take a reading from the unknown sample - then extrapolate off the equivalent reducing sugar concentration 

(t) state that DNA is a polynucleotide, usually double stranded, made up of nucleotides containing the bases adenine, thymine, cytosine and guanine

(u) State that RNA is a polynucleotide, usually single stranded, made up of nucleotides containing the bases adenine, uracil and guanine ( Thymine is replaced by Uracil)

(v) State that DNA is a double stranded polynucleotide.

(w) Describe how a DNA molecule is formed by Hydrogen bonding;

Two DNA strands run parallel to eachother and the chains are the same distance apart because the bases pair up in a certain way.