E2 : Introduction to protein structure

What are amino acids

protein building blocks

all contain :

• amino group (-NH₂)

• carboxyl group (-COOH)

• hydrogen atom

• R group (side chain)

• central α-carbon

What are basic properties and classes of amino acids

properties :

charge

polarity

hydrophobicity / hydrophilicity

size and shape of side chain

classes :

non-polar (hydrophobic)

polar uncharged

acidic (negatively charged)

basic (positively charged)

What are the chemical and structural aspects of the peptide bond

a peptide bond is a covalent bond between the carboxyl group of one amino acid and the amino group of another

formed via condensation reaction

creates peptide chain with an N-terminus and C-terminus

rigid and planar due to partial double-bond character

How does the formation of the peptide bond influence protein structure

links amino acids info specific sequence (primary structure)

creates rigid backbone restricting rotation

allows hydrogen bonding between peptide groups

enables folding into secondary, tertiary and quaternary structures

ultimately determines protein function

What is a primary protein structure? Give an example

unique sequence of amino acids linked by peptide bonds

changes in sequence can later protein function

What is a secondary protein structure? Give an example

local folding of th polypeptide chain stabilised by hydrogen bonds

What is a tertiary protein structure? Give an example

overall 3D shape of a single polypeptide chain

stabilised by :

• hydrogen bonds

• ionic interactions

• hydrophobic interactions

• disulfide bonds

What is a quaternary protein structure? Give an example

arrangement of multiple polypeptide chains into a functional protein

not all proteins possess quaternary structure

\What are the importance of motifs and protein domains to structural organisation and function

determine protein function

enable interactions with other molecules

allow proteins to perform multiple roles

Why is understanding protein structure relevant to drug targeting and discovery

most drugs act by binding to proteins such as receptors, enzymes and ion channels

knowledge of protein structure helps :

• identify drug targets

• design molecules that bind specifically

• improve drug efficacy

• reduce side effects

• suport rational drug design

what does the R group convey to the properties of na amino acid

the R group determines the unique chemical properties of an amino acid e.g.,

• charge

• polarity

• size and shape

• hydrophobicity / hydrophilicity

• ability to form bonds and interactions

Why is protein folding important

definition : process which a polypeptide chain adopts its correct 3D structure

importance : determines protein’s biological function

creates binding sites for substrates, drugs and other mechanisms

allows enzymes to catalyse reactions

maintains protein stability

misfiled proteins can cause diseases

What are super secondary structures and domains in proteins

super secondary structures / motifs : recurring combinations of secondary structures that perform specific functions (small structural building blocks within proteins)

domains : larger, independently folding regions of proteins that often have a specific function, contain multiple motifs