Biological Molecules

Question 1

Molar solution

Answer 1

Contains 1 mole of solute in each litre of solution

Question 2

Covalent bonding

Answer 2

Shared pair of electrons, the attraction between the nuclei and the shared electrons

Question 3

Ionic bond

Answer 3

Ions with opposite charge have electrostatic forces of attraction between them

Question 4

Hydrogen bonds

Answer 4

Uneven distribution of electrons cause a dipole induced dipole where the less electron dense areas of a molecule are elctrostatically bonded to a less electron dense area; a polar bond

Question 5

The main organic polymers

Answer 5

Polysaccharides, polypeptides, polynucleotides

Question 6

Condensation reaction

Answer 6

Polymerisation; each new sub-unit which is attached, H2O is formed

Question 7

Hydrolysis reaction

Answer 7

Breaking polymers into its constituent parts; broken down by the addition of H2O

Question 8

Metabolism

Answer 8

All chemical processes that take place in living organisms

Question 9

Lipids

Answer 9

• Contain carbon hydrogen and oxygen
• the proportion of oxygen to carbon and hydrogen is smaller than carbohydrates
• insoluble in water
• soluble in organic solvents (alcohol/acetone)
• main group of lipids are triglycerides (fats and oils) and phospholipids

Question 10

Roles of lipids

Answer 10

• form the phospholipid bilayer that makes up the cell membrane
• source of energy - when oxidised they provide more than twice the energy provided by the same mass of carbohydrates
• Waterproofing - insoluble in water; used by plants and insects for waterproofing (waxy,lipid cuticles) to conserve water; mammals produce an oily secretion from the sebaceous glands in the skin
• insulation - fats are slow conductors of heat so when stored beneath body surface they help retain body heat. Also act as electrical insulators in the myelin sheath around nerve cells
• protection - stored around delicate organs (e.g. kidney)
• fats are solid at room temperature whereas oils are liquids

Question 11

Triglycerides

Answer 11

Have three fatty acids combined with glycerol. The fatty acid forms an ester bond with glycerol in a condensation reaction.

The glycerol molecule is the same in all triglycerides, so the different fats and oils come from variations in the fatty acids (there are over 70 different fatty acids and all have a carboxyl group attached with a hydrocarbon chain attached

Question 12

Saturated

Answer 12

No carbon-carbon double bonds

Question 13

Mono-/poly-unsaturated

Answer 13

Mono-single double bond present

Poly-more than one double bond is present

Question 14

Structure of triglycerides related to properties

Answer 14

• high carbon-hydrogen bonds : carbon atoms ratio so an excellent source of energy
• have a low mass:energy ratio so great storage molecules (much energy is stored in small vol)
• being large non-polar molecules, they are insoluble in water so do not affect osmosis in cells or the water potential of them
• high hydrogen:oxygen atoms and they release water when oxidised so provide an important soured of water, especially for organism in dry environments

Question 15

Phospholipids

Answer 15

Similar to triglycerides but one fatty acid molecule is replaced by a phosphate molecule. The fatty acid molecules repel water (hydrophobic tails), phosphate molecules attract water (hydrophilic heads)

Question 16

The structure of phospholipids related to their properties

Answer 16

• Having a hydrophobic end and a hydrophilic end, in an aqueous environment, they form a bilayer within cell-membranes and so a hydrophobic barrier is formed between the inside and outside of a cell
• the hydrophobic phosphate heads help hold at the surface of the cell-surface membrane
• the phospholipid structure allows them to form glycolipids by combining with carbohydrates within the cell surface membrane which is important in cell recognition

Question 17

Test for lipids

Answer 17

• add 5cm^3 of ethanol to 2cm^3 of sample being tested
• shake the tube thoroughly to dissolves any lipid sample
• add 5cm^3 of water and shake gently
• a cloudy-white colour indicates the presence of a lipid
• repeat the experiment with water as a control and the final solution should remain clear

Question 18

Proteins

Answer 18

complex large molecules which all have different in shape and have lots of different functions. Their monomer unit is amino acids

Question 19

Structure of amino acids

Answer 19

• amino group - a basic (alkaline) group
• carboxyl group- an acidic group
• hydrogen atom
• R group - a variety of different chemical groups; each amino acid has a different R group. The 20 naturally occurring amino acids which occur in all living organisms only differ in their R group

Question 20

The formation of a peptide bond

Answer 20

A condensation reaction occurs between amino acids; a OH from the carboxyl group of one amino acid with a H from the amino group of another amino acid form a water molecule; a peptide bond forms between the carbon atom of the carboxyl group on one amino acid and the nitrogen atom of amino group on another amino acid

Question 21

Primary structure of proteins - polypeptides

Answer 21

The sequence of amino acids in a polypeptide chain forms the primary structure of any protein. This sequence is determined by DNA.
As polypeptides have many of the 20 naturally occurring amino acids joined in different sequences it follows that there is an almost limitless number of possible combinations and, therefore, primary structures. A change in even one amino acid can result in a change in the proteins shape and may stop it carrying out its function

Question 22

Secondary structure of proteins

Answer 22

Hydrogen bonds form between Oxygen on the C-_O (which has a negative charge) and the hydrogen on the N-H (which has a positive charge) on either side of each amino acid. This causes the long polypeptide chain to be twisted into a 3D shape (e.g. an alpha helix)

Question 23

Tertiary structure of proteins

Answer 23

The alpha helices can be twisted further to form a even more complex tertiary structure. This occurs due to different types of bonds:

• disulfide bridges - which are fairly strong and not easily broken
• ionic bonds - formed between any carboxyl and amino groups that are not involved in forming peptide bonds; they are weaker than disulfide bonds and are easily broken by changes in the pH
• hydrogen bonds - numerous but easily broken

Question 24

The importance of the 3D structure of proteins

Answer 24

It makes each protein distinctive and allows it to recognise, and be recognised by, other molecules and can then interact with them in a very specific way

Question 25

Quaternary structure

Answer 25

Large proteins often form complex molecules containing a number of individual polypeptide chains that are linked in various ways. Prosthetic groups can also be attached with the molecules such as the haem group in haemoglobin

Question 26

Test for proteins

Answer 26

- Place sample of the solution to be tested in a test tube and add an equal volume of sodium hydroxide at RTP - Add a few drops of very dilute copper sulphate solution and mix gently - A purple coloration indicates the presence of peptide bonds. If no protein is present the solution will remain blue

Question 27

Enzyme action

Answer 27

Enzymes are globular proteins which act as catalysts lowering activation energy which allows reactions to occur at lower temperatures which allows metabolic processes occur at body temp; The reactant molecules must collide wit sufficient energy to alter the arrangement of their arrangement of their atoms to form the products. Many reactions require an initial amount of energy to start. The minimum amount of energy required to start a reaction is called activation energy

Question 28

Enzyme structure

Answer 28

Being globular proteins they have a specific 3D shape that is the result of their sequence of amino acids, a specific region of the enzyme is functional, this is known as the active site. The substrate fits neatly into this depression and forms an enzyme-substrate complex. The substrate is held within the active site by bonds that temporarily form between certain amino acids of the active site and groups on the substrate molecule

Question 29

Induced fit model

Answer 29

The active site forms as the enzyme and substrate interact; the enzyme is flexible and can mould itself around the substrate. As the enzyme changes shape it puts strain on the substrate molecule which distorts a particular bond/bonds in the substrate and consequently lowers the activation energy needed to break bond

Question 30

Factors affecting enzyme action

Answer 30

Temperature pH Enzymes concentration Substrate concentration

Question 31

Temperature

Answer 31

- an increase in temperature increases the kinetic energy of molecules - the substrates and enzymes move around more rapidly and collide more frequently, so there are more effective collision resulting in more SUBSTRATE-ENZYME COMPLEXES being formed and so the rate of reaction INCREASES - however if the temperature INCREASES MORE (45°C) this causes hydrogen, and other binds to break in the enzyme and so the enzyme changes shape and therefore the active site changes shape, so the substrate fits less easily SLOWING the rate of reaction - at around 60°C the enzyme becomes so disrupted that it stops working all together - DENATURATION

Question 32

pH

Answer 32

- change in pH alters the charges on amino acids that make up the active site - this means the substrate can no longer become attached so the enzyme-substrate complex can't be formed. - and significant changes in pH may cause the bonds maintaining the enzymes tertiary structure to break - changing the shape of the active site * different enzyme work best at different pH's and many enzymes are very specific in the pH (this is why the stomach is acidic, the small ingesting is more neutral etc)

Question 33

Enzyme concentration

Answer 33

- An increase in the amount of enzymes leads to a proportionate increase in the rate of reaction - if the substrate is limiting (there is not a sufficient supply to fill all the enzymes active sites at one time) then an increase in enzyme concentration will have no effect on the rate of reaction (the graph at high enzyme concentration is a straight line due to the substrate being limiting

Question 34

Substrate concentration

Answer 34

-If the concentration of enzymes is fixed and the substrate concentration is increased slowly the RoR increases in proportion to the concentration of substrate; This is because at low substrate concentrations the enzymes lave a muted amount of substrates to collide with so the active sites are not working to full capacity. As it increases, the active sites become gradually filled to the point where all of them are working as fast as they can, this means the RoR is at maximum so anymore substrate will have no effect

Question 35

Competitive inhibitors

Answer 35

- have a molecular shape similar to the substrate which allows them to occupy active site. - if substrate concentration is increased the effect of the inhibitor is reduced - the inhibitor is not permanently bonded to the active site so images it leaves another molecule can take its place - sooner or later all the substrate molecules will occupy an active site but the greater the concentration of the inhibitor the longer this will take

Question 36

Non-competitive inhibitor

Answer 36

- attach themselves to the enzyme at a binding site which isn't the active site, which alters the shape of the enzyme and thus it's active site in such a way that the substrate molecules can no longer occult it so the enzyme cannot function - as the substrate and the inhibitor are not competing for the same site, an increase in substrate concentration does not decrease the effect of the inhibitor

Question 37

Nucleotide structure

Answer 37

* Pentose sugar * phosphate group * organic base - a nitrogen containing an organic base; cytosine, thymine, uracil, adenine and guanine These are joined together as a result of condensation reactions

Question 38

Polynucleotide

Answer 38

- 2 mononucleotide can join together by a condensation reaction between the deoxyribose sugar of one and the phosphate group of another -this bond is called a phosphodiester bond - this repeated many time forms a long chain of nucleotides - polynucleotide

Question 39

RNA structure

Answer 39

-A single, (relatively) short chain of polynucleotides. The pentose sugar is ribose and the bases are guanine, cytosine, adenine, and uracil -can be in the form of: •tRNA - transfer genetic info from DNA to ribosomes •mRNA •rRNA - protein synthesis

Question 40

DNA structure

Answer 40

- 2 extremely long strands of polynucleotides, pentose sugar is deoxyribose. - The strands are joined together by hydrogen bonds between certain bases

Question 41

Base paring

Answer 41

Adenine-----thymine Guanine-----Cytosine ---- = complimentary The quantities of A and T are the same and the quantities of C and G are the same