proteins Flashcards
what are some differences between fibrous proteins and globular proteins?
- fibrous proteins have an elongated, rope-like structure while globular proteins have a compact and spheroidal structure
- fibrous proteins have a repetitive a.a. sequence while globular proteins have specific, non-repetitive a.a. sequence
- fibrous proteins generally perform structural functions while globular proteins generally perform metabolic functions
describe the structure of an amino acid
1 basic amine group (-NH2)
1 acidic carboxyl group (-COOH)
1 hydrogen atom
1 R group
how are zwitterions formed?
the carboxyl group loses on H+ ion which associates with the amine group to form —COO- and —NH3+ respectively. the resulting amino acid contains one positive charge and one negative charge, forming an electrically neutral, dipolar ion
why can amino acids act as buffer?
amino acids are amphoteric as they possess both acidic and basic properties
are amino acids with non-polar R groups hydrophobic?
yes
such amino acids tend to be located in the interior to be shielded from the aqueous medium
are amino acids with polar R groups hydrophobic?
no, they are hydrophilic
are amino acids with charged R groups hydrophobic?
no, they are hydrophilic
acidic a.a. have a net negative charge while basic a.a. have a net positive charge
how are peptide bonds formed?
through a condensation reaction, a peptide bond is formed between the amine group of one a.a. and the carboxyl group of another
how does the ability of polypeptides to buffer solutions compare to that of amino acids?
amino acids have a better ability to buffer solutions compared to polypeptides
what are the 4 levels of protein structure?
primary structure
secondary structure
tertiary structure
quaternary structure
what is defined as the primary structure of a protein?
the unique number and linear sequence of amino acids that constitute the polypeptide chain
what are the two types of secondary structure of a protein?
alpha helix and beta pleated sheet
where do hydrogen bonds form?
hydrogen bonds are formed between the NH group of one amino acid and the C=O group of another
hydrogen bonds are individually weak but collectively stabilise the struture
what is the shape of an alpha helix?
the alpha helix takes the form of an extended spiral spring
where are the R groups in an alpha helix located?
the R groups project outside the helix, perpendicular to the main axis
this is to prevent steric interference with the polypeptide chain and with each other
what is the shape of a beta pleated sheet?
the beta pleated sheet takes on an extended zigzag, sheet-like conformation
what is the difference between hydrogen bonds occurring in alpha helix and those occurring in beta-pleated sheet?
in the beta pleated sheet, hydrogen bonding can occur between C=O and N-H groups within the same polypeptide chains OR between C=O and N-H groups of neighbouring chains
while in alpha helix, hydrogen bonding occurs between the O atom of the C=O group of an a.a. residue and the H atom of an a.a. residue situated 4 a.a. residues ahead
what is defined as the secondary structure of protein?
the regular coiling and folding of regions of the polypeptide chain giving rise to repeated patterns
what is defined as the tertiary structure of protein?
the further bending, twisting and folding of the polypeptide chain with the secondary structures to give an overall specific 3D conformation of a protein
what bonds are involved in the tertiary structure of protein?
- ionic bonds
- hydrogen bonds
- hydrophobic interactions
- disulfide bonds
what is defined is the quaternary structure of protein?
the overall protein structure that results from the association of two or more polypeptide chains to form a functional protein
what is a multimeric protein?
proteins with more than one or more polypeptide/subunits
what is the structure of haemoglobin?
haemoglobin is a multimeric protein consisting of 4 polypeptide chains, namely 2 alpha and 2 beta chains. it is a tetramer made up of 2 identical dimers.
why is haemoglobin soluble in aqueous mediums?
each polypeptide chain is folded such that hydrophobic a.a. residues are generally buried in the interior of the molecule and those at the surface are generally hydrophilic.
describe subunit cooperativity in haemoglobin
when an iron (ii) ion in the first haemoglobin subunit binds 1 molecule of oxygen, the F helix is pulled closer to the haem group
this creates a strain on the other haemoglobin subunits
so the remaining subunits change their 3D conformation slightly, allowing their respective haem groups to bind oxygen more readily, increasing the remaining subunits’ affinity for oxygen
what is the amino acid sequence of a collagen polypeptide?
a collagen polypeptide is made up of a repeating tripeptide sequence of glycine-x-y
x is often proline
y is often hydroxyproline or hydroxylysine
proline residues prevent collagen from forming an alpha helix
what kind of protein is collagen?
fibrous protein
name the levels of protein structure involved in collagen
primary structure
secondary structure
quaternary structure
NO tertiary structure
how is the quaternary structure of collagen formed?
three parallel alpha chains wind around each other with a gentle, right-handed rope-like twist to form tropocollagen
what bonds are responsible for holding together tropocollagen?
hydrogen bonds between the N-H group of gly residue in one alpha chain and the C=O group of another residue in a neighbouring chain
hydroxyl groups of hydroxyproline and hydroxylysine participate in inter chain hydrogen bonding
covalent cross links are present, giving the collagen fibre high tensile strength
describe how a collagen fibre is formed
tropocollagen molecules are linked to each other by covalent cross linked between the C terminus of one molecule and the N terminus of another, giving rise to collagen fibril
the aggregation of collagen fibrils form collagen fibre
what is defined as denaturation?
the loss of the specific 3D conformation of a protein molecule
what are the 5 denaturants of proteins?
heat
changes in pH
organic solvents
urea
detergents
how does the iron ion (held in a porphyrin ring) relate to the structure of haemoglobin?
the iron ion binds one of the oxygen atoms in a molecule of oxygen. the iron ion can combine reversibly with oxygen and enhances the release of oxygen in metabolically active tissues
where do hydrophobic interactions, ionic bonds and disulfide bonds occur in proteins?
hydrophobic interactions occur between hydrophobic R groups of amino acid residues
ionic bonds occur between oppositely charged R groups of amino acid residues
disulfide bonds occur between sulfhydryl groups of any 2 cysteine residues
