subject guide notes
B1.2.1—Generalized structure of an amino acid
should be able to draw a generalized diagram of an amino acid, with the carboxyl group, R-group, hydrogen, & alpha carbon atom with amine group
B1.2.2—Condensation reactions forming dipeptides and longer chains of amino acids
amino acids are linked together through dehydration synthesis/condensation reactions
REMEMBER - water is removed as a result of this condensation reaction
a peptide bond is formed when the carboxyl group of one amino acid, binds to the amino group of another amino acid
this forms a dipeptide
this process can be repeated to form polypeptides
word equation: amino acid + amino acid dipeptide + 1 water molecule
B1.2.3—Dietary requirements for amino acids
two different classifications of amino acids - essential and non-essential
essential amino acids can’t be synthesized by the body & are obtained through the food
non-essential amino acids can be produced by the body, through the breaking down of other amino acids
B1.2.4—Infinite variety of possible peptide chains
20 amino acids are coded for in the genetic code
remember the codons and anticodons - and the amino acids connected to the anticodons, are placed in order depending on the codons on the mRNA
amino acids can be combined in any order
allows for limitless number of unique proteins with varying structures & functions
examples of polypeptides
Lysozyme - is an enzyme composed of 129 amino acids & is present in tears & saliva
has antimicrobial properties
Glucagon - hormone composed of 29 amino acid residues
is secreted by pancreas when blood sugar is low
it stimulates liver, fatty tissues & muscles to release stored glucose
B1.2.5—Effect of pH and temperature on protein structure
denaturation is caused by pH and temperature
extreme pH changes affect the protein’s charge, which affects their shape & solubility
causes irreversible changes in protein structure, causing inactivity
high temperatures can break the hydrogen bonds holding together the amino acids
this causes the protein to unfold & lose its function
B1.2.6—Chemical diversity in the R-groups of amino acids as a basis for the immense diversity in protein form and function
R-groups determine the properties of the polypeptide
they can be hydrophilic or hydrophobic
hydrophilic R-groups are polar or charged, acidic (negatively charged) or basic (positively charged)
if they’re polar, they hv partial charges which allow interaction with water
if charged, are either acidic (negatively charged) or basic (positively charged)
hydrophobic R-groups are non-polar
B1.2.7—Impact of primary structure on the conformation of proteins
remember - the sequence of amino acids & the position of each amino acid, determines the protein’s shape
so the sequence of amino acids in the primary sequence has to be correct, in order to ensure the protein’s correct function
is a linear chain (no folding or interaction)
B1.2.8—Pleating and coiling of secondary structure of proteins
refers to the local folding patterns that occur within the polypeptide chain
two common types - alpha-helix & beta-pleated sheet
the formation of each type is enabled by the hydrogen bonding between the oxygen in the carboxyl group of one amino acid & the hydrogen in the amino group of another amino acid
these hydrogen bonds occur in regular positions, which helps stabilize the protein & aid in the formation of secondary structure
alpha - helix is formed when a hydrogen bond is formed in the same polypeptide chain
repeated patterning of hydrogen bonding = forms a helical structure
beta-pleated sheet is formed when sections of polypeptide chain run parallel to each other
hydrogen bonds are formed between adjacent strands
B1.2.9—Dependence of tertiary structure on hydrogen bonds, ionic bonds, disulfide covalent bonds and hydrophobic interactions
is the further folding of polypeptide & is dependent on interaction between R-groups, which can include formation of: hydrogen bonds, ionic bonds, disulfide covalent bonds & hydrophobic interactions
disulfide covalent bonds form between pairs of cysteine amino acid residues, which contain sulfur atoms
hydrophobic interactions occur between non-polar amino acids
since they can’t interact with water, they clump together in the interior of the protein
this interaction stabilises the protein’s tertiary & quaternary structure
B1.2.10—Effect of polar and non-polar amino acids on tertiary structure of proteins
hydrophilic amino acids face the liquid & hydrophobic amino acids are clustered in the interior, which stabilises the protein
integral proteins have hydrophobic amino acids, helping them to embed in membranes
B1.2.11—Quaternary structure of non-conjugated and conjugated proteins
is when 2 or more polypeptide chains bind together to form a larger, final protein structure
Hydrogen bonding & ionic bonding are the 2 main forms holding them together
non-conjugated & conjugated proteins hv a quaternary structure
non-conjugated proteins consist of only amino acids
ex: collagen, which has 3 amino acids
ex: insulin - has 2 amino acids
conjugated proteins hv both amino acids & non-protein components, such as metal ions or carbs
can increase a protein’s function or diversity
ex: haemoglobin has polypeptide chains & a haem group, which has iron in its centre
this haem allows oxygen to bind, allowing haemoglobin to carry oxygen through the body
B1.2.12—Relationship of form and function in globular and fibrous proteins
globular proteins are usually spherical & hv irregular folds
i think this shape is caused by the hydrophilic amino acids facing the water, and the hydrophobic amino acids facing the interior
so this means that globular proteins are water-soluble, and can function as enzymes, regulators & transporters
ex: insulin - has a hydrophilic exterior. this allows insulin to interact with blood & water, allowing it to travel through blood to organs, where it can stimulate the entry of glucose and lower the blood glucose
has a hydrophobic interior which helps stabilise it
fibrous proteins are long and narrow
they are insoluble in water & provide strength and support to cells & tissues
ex: collagen - is made up of 3 polypeptide chains that’re twisted together, which provides a high amount of tensile strength