Biomolecules Flashcards
describe the structure of amino acids
consists of a central carbon atom, amino group, carboxyl group, H atom and a variable R group. the R group can vary in size and charge and this is what gives each amino acid its unique chemical properties
describe the properties of non-polar amino acids
- R group is hydrocarbon in nature and has no net charge
- amino acids are hydrophobic and unreactive, tend to be localised in the interior of the molecule (away from aqueous medium
describe the properties of polar amino acids
- R groups have no net charge
- amino acids are hydrophilic in nature
describe the properties of charged amino acids
- R groups of a.a are charged
- amino acids are either negatively-charged or positively-charged, making them hydrophilic
- acidic amino acids are negatively-charged while basic amino acids are positively-charged
describe the buffering capacity of amino acids
- in neutral solutions, most amino acids exist in a form that contains both positive and negative charges (zwitterions)
- zwitterions carry both negative and positive charges on different atoms but has a net charge of zero
- amino acids exist as zwitterions in neutral aqueous solutions by the association of protons with the amino group, making it positively-charged, and the loss of protons from carboxyl group, making it negatively-charged
- since they have both acidic and basic properties in aqueous solutions, they are amphoteric
- this allows them to act as buffers in solution, resisting small changes in pH when an acid/alkali is added, by taking up or losing protons
- in acidic environment, COO- takes up protons from surroundings, causing pH to increase back to normal
- in alkaline environment, NH3+ donates protons to the surroundings, causing pH to decrease back to normal
- this buffering property is retained even when amino acids are bonded to each other to form proteins, because of the acidic and basic R groups of individual amino acids
describe the formation of peptide bonds
a covalent bond formed between the amino group of one amino acid and the carboxyl group of another due to a condensation reaction, with the loss of a water molecule
describe the formation and breakage of ionic bonds
- a bond formed between acidic and basic R groups of amino acids
- acidic and basic R groups are ionised at certain pHs, acidic R groups are negatively-charged while basic R groups are positively-charged
- electrostatic attraction occurs between two oppositely-charged R groups, forming an ionic bond
- ionic bonds may be formed between R groups of different polypeptides or between R groups at different parts of the same polypeptide
- this bond is much weaker than a covalent bond in an aqueous medium and can be broken by changing the pH of the medium
- pH changes can therefore disrupt the 3D conformation of the protein structure
describe the formation of disulfide bonds
- covalent bond formed between sulfhydryl R groups, only the amino acid cysteine contains a -SH in its R group
- disulfide bonds may be formed between R groups of different polypeptides or between R groups of different parts of the same polypeptide
- disulfide bonds are strong and not easily broken
- proteins which have disulfide bonds in their structure will be able to withstand higher temperatures before being denatured
describe the formation of hydrogen bonds
- relatively weak non-covalent bond between an electronegative atom and a hydrogen atom attached to another electronegative atom
- hydrogen bonds can be formed between different parts of the same polypeptide or between polypeptides (formed between -CO and -NH of polypeptide backbone, between -CO/-NH and R group or between R groups)
- hydrogen bond is weak but when it occurs frequently within a molecule, total effect increases molecular stability
describe the formation of hydrogen bonds
- relatively weak non-covalent bond between an electronegative atom and a hydrogen atom attached to another electronegative atom
- hydrogen bonds can be formed between different parts of the same polypeptide or between polypeptides (formed between -CO and -NH of polypeptide backbone, between -CO/-NH and R group or between R groups)
- hydrogen bond is weak but when it occurs frequently within a molecule, total effect increases molecular stability
describe the formation of hydrophobic interactions
- occur between non-polar/hydrophobic R groups
- if a polypeptide chain contains a number of these groups and is in an aqueous environment, the chain will tend to fold such that a maximum number of hydrophobic groups will come into close contact with each other and exclude water
- if the protein is globular, hydrophobic groups tend to point inwards towards the centre of the molecule while the hydrophilic groups face outwards into the aqueous environment, making the protein soluble
- membrane proteins which are embedded within the membrane are likely to have their hydrophobic regions found within the membrane, alongside the hydrophobic hydrocarbon tails of phospholipids. their hydrophilic regions face away from the membrane, alongside the hydrophilic phosphate heads
explain primary structure and describe the types of bonds that hold the molecule in shape
- unique number and sequence of amino acids in a polypeptide chain
amino acids are linked by peptide bonds and its sequence is specified by the base sequence of DNA in the nucleus - primary structure determines the type and location of bonds present at higher levels of organisation in the protein
- it determines the overall 3D conformation and the function of a protein
- a change in one amino acid can change the amino acid sequence, leading to a change in type and location of bonds formed at higher levels of organisation in the protein, leading to a change in the specific 3D conformation and overall function of protein. e.g mutation in gene coding for haemoglobin causes sickle cell anaemia
explain secondary structure
- local folding of a polypeptide into regular structures such as the alpha-helix and beta-pleated sheets
- these regular structures are the result of hydrogen bonds formed at regular intervals between the -CO and -NH groups of the polypeptide backbone (not amino acid R groups)
explain alpha-helix structure
- an alpha-helix is formed when a hydrogen bond is formed between the O atom of the -CO group of an a.a residue and the H atom of the -NH group of the a.a that is situated four amino acid residues ahead in the linear sequence in the same chain
- one complete turn occurs for every 3.6 a.a
- it is very stable bc all -CO and -NH groups of the polypeptide backbone can participate in hydrogen bonding. regions with alpha-helices are rigid and rod-like
- R groups of some a.a in a polypeptide can interfere with the formation of an alpha-helix. a.a with bulky R groups can interfere with the formation of alpha-helix
describe and explain the beta-pleated sheet
- different sections of the polypeptide chain can be folded to form adjacent strands, which can run either in the same directtion or in opposite directions, forming parallel or anti-parallel beta-pleated sheets
- these adjacent strands are held together by hydrogen bonds, formed between -CO and -NH groups of the polypeptide backbone to form a sheet
- hydrogen bonds can occur between two or more sections of the same polypeptiode or between two or more sections of different polypeptides
- within a sheet, all -CO and -NH groups are involved in hydrogen bonding, hence the structure is very stable and rigid
- bulky amino acids interfere with the formation of beta-pleated sheets, thus most a.a that are found in these sheets have compact R groups
describe and explain tertiary structure
- formed with the bending, twisting and folding of the secondary structures of a polypeptide to form a specific 3D conformation
- specific 3D conformation is held together by hydrogen bonds, ionic bonds, hydrophobic interactions and disulfide bonds between the R grps of various a.a that lie close to each other in the 3D structure
describe and explain quaternary structure
- association of two or more polypeptides
- separate polypeptides can be held together by hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions btwn R grps of a.a of different subunits
describe denaturation
- change in specific 3D conformation of a protein molecule, molecule unfolds and no longer performs its normal biological function
- the a.a sequence (primary structure) is unaffected
explain the effect of temperature on protein structure
disrupts weak hydrogen bonds, hydrophobic interaction and ionic bonds