Biological Molecules

reaction that involves breaking of bonds

Hydrolysis

water is added

describe how an enzyme breaks down a substrate

• substrate shape is complementary to active site

• substrate fits into active site on enzyme

• Induced fit (enzyme’s active site changes shape slightly to bind more tightly to the substrate)

• forms enzyme substrate complex

• destabilises of bonds in substrate then forms enzyme-product complex

• product leaves the active site

repeating the investigation improve the investigation

• improve reliability

• spread of results allow calculation of mean

Pepstatin acts as a competitive inhibitor of pepsin.

what can you conclude about the structure of pepstatin? 

• similar shape to substrate

• so is complementary to the active site 

lipids: triglycerides, phospholipids, cholesterol

contains only the elements, carbon, hydrogen and oxygen - triglyceride, cholesterol

insoluble in water- triglyceride, phospholipid, cholesterol

contains glycerol- triglyceride, phospholipid

contains ester bonds- triglyceride, phospholipid

important in membrane structure- phospholipid, cholesterol

contains fatty acids- triglyceride, phospholipid

lipids produced by microorganisms differs from lipid from food that comes from animals

• less lipid content

• less saturated fat

• more unsaturated fat

levels of protein

Primary level: the sequence of amino acids, peptide bonds

Secondary level: the initial folding of the polypeptide chain into alpha helix and beta pleated sheet- hydrogen bonds

Tertiary level: the overall 3D shape, ionic bonds, hydrogen, disulfide, hydrophilic, hydrophobic

Quaternary level: alpha and beta subunits

Describe the formation of a hydrogen bond between two molecules of water and explain why water can form these bonds.

Between H and O of adjacent molecules

Between electropositive (delta + H) and electronegative (delta - O) 

as water molecule is polar

why is the ability of water to act as a solvent important for the survival of organisms?

• medium for metabolic reactions

• because it allows ionic compounds to separate (e.g. NaCl)

• To transport waste products to be expelled e.g. CO2

• absorbs oxygen, glucose, amino acids

• able to dilute toxic substances

properties of collagen that makes it a useful compoenent of blood vessel walls

• strength

• toughness

• insolubility

• not elastic

• flexible

structure of collagen

• peptide bonds between amino acids

• every 3rd amino acid is the glycine

• coiled

• left handed helix

• glycine allow twisting of polypeptide chains

• 3 polypeptide chains

• hydrogen bonds between polypeptide chains

• adjacent molecules joined by crosslinks

function of haemoglobin

transport O2

Haemoglobin vs Collagen structure

1. haemoglobin contains a prosthetic group known as haem

2. haemoglobin has globular

3. haemoglobin has 4 polypeptide chains

4. has two different subunits (2alpha globins and 2 beta globins)

5. hydrophobic R groups are facing inwards and the hydrophilic R groups are facing outwards 

description of formation of peptide bond

• between amine group and carboxyl group

• H from amine combines with OH from carboxyl 

• by condensation reaction

physical properties of water that allow organisms to survive over a range of temperatures

• High latent heat of vapourisation

• evaporation is cooling mechanism

• e.g. sweating

• High specific heat capacity 

• stable environment for aquatic organisms

• organism use less energy on temperature control

• optimal for enzyme activity for reactions

• Ice is less dense than water

• surface of ice provides habitat for organisms

• Solvent

• medium for reactions, transport, to dilute toxic substances

• Cohesion and Adhesion

• transpiration stream

• Surface tension

• habitat for insects e.g. pond skators to float 

examples of where hydrogen bonds are found in biological molecules

• between chains of cellulose

• protein secondary structure (alpha helix and beta pleated sheet)

• protein tertiary structure

two roles of cholesterol in living organisms

• regulate the fluidity of membranes

• makes bile, makes vitamine D

Why glycogen makes a good storage molecule

• insoluble- do not affect the water potential

• can be hydrolysed quickly

• lots of branches for enzymes to attach

• compact- stores a lot of energy

Alpha glucose function

respiratory substrate

structure of a haemoglobin molecule

• sequence of amino acids

• joined by peptide bonds

• Secondary structure- alpha helix and small regions of beta pleated sheet fold 

• hydrogen bonds

• Tertiary structure- secondary structure undergoes further coiling

• additional bonds form: disulfide, ionic, hydrogen, hydrophobic, hydrophilic

• Hydrophilic R group outside of molecules, hydrophobic R group on inside of molecule

• Quaternary structure- 4 polypeptides 

• 2 alpha globins and 2 beta globins

• prosthetic group is haem which contains Fe2+

How structure of collagen is similar to the structure of haemoglobin

• amino acid sequence

• peptide bonds

• helix

• 3 bonds from disulfide, hydrogen, ionic, hydrophobic or hydrophilic

• quaternary structure

• more than one polypeptide

structure of a triglyceride molecule

• glycerol and 3 fatty acids

• ester bonds

roles of lipids

• energy storage

• thermal insulation

• buoyancy

• protection

conditions associated with increased blood cholesterol levels

• type 2 diabetes

• coronary heart disease

explain properties of water

ice is less dense

• molecules spread out

• ice forms insulating layer

• water does not freeze

• organisms do not freeze, can still swim under

solubility

• ions are polar

• ion attracted to water

• organisms uptake mineral

• e.g. nitrates for amino acids

high specific heat capacity

• many stable hydrogen bonds between the molecules

• temperature affects enzyme activity

how a second amino acid would bond to cysteine in forming the primary structure of a protein

• peptide bond

• between amine group and carboxyl group

• H from amine group combines OH from carboxyl group

• by condensation reaction

How R groups interact to determine the tertiary structure of a protein

• some R groups attract or repel each other

• Disulfide bond form between S atoms

• Hydrogen bonds forms between R groups

• Ionic bonds form between oppositely charged R groups

• Hydrophilic outside the molecule

• Hydrophobic inside the molecule 

structure of glycogen vs collagen

Glycogen. Collagen

• carbohydrate. - protein

• contain C, H, O. - contain C, H, O, N

• alpha glucose. - amino acid

• no cross links - cross links

• glycosidic bond - peptide bond

• branched - linear

• one chain - 3 chains

Differences between haemoglobin and collagen

Haemoglobin (globular)

• ball shaped

• hydrophilic R group on outside, hydrophobic R group on inside

• form hydrogen bonds with water

• soluble