Biochemistry And Molecular Biology (BIOC0001) Notes - Proteins and Enzymes

Introduction to the Structure-Function Relationship in Proteins
What is a Protein?
 Proteins
o Examples
 Haemoglobin
 Enzymes
 Collagen
 Insulin
 Antibody
 Calcium pump
o Monomers
 21 different amino acids
 Made of carbon + oxygen + nitrogen + hydrogen + sulfur
 Structure
 Alpha carbon attached to:
o Amino group
o Carboxyl group
o Side chain – determines property of amino acids
 Only varying structure in amino acids
o Properties
 Hydrophobic amino acids
 Have carbon rich side-chains
 Hydrophilic / polar amino acids
 Form hydrogen bonds with water
 Charged amino acids
 Interact with oppositely charged amino acids
o Structure
 Primary structure
 Linear sequence of amino acids encoded by DNA
o Joined by peptide bonds – links amino group on one amino acid + carboxyl
group on another amino acid = condensation reaction (releases water
molecules)
o Protein backbone = formed by links between NH and OH group between
amino acids
 Secondary structure
 Alpha helix
o Right handed coil
o Stablilised by hydrogen bonds between amine and carboxyl group of nearby
amino acids
 Beta sheet
o Sheet
o Hydrogen bonds stabilise two or more adjacent strands of amino acids
 Tertiary structure
 3D shape of the protein
o Determined by the characteristics of amino acids in the chain
 Globular
o Hydrophobic side chains face inwards away from water molecules
 Charged amino acids – allow proteins to interact with molecules that have
complementary charges
 Quaternary structure

,Introduction to the Structure-Function Relationship in Proteins
 2 or more polypeptides interact to form one functional molecule with several
subunits
o Protein representation
 Diagrams
 Space-filling diagram – shows all of the atoms that make up the protein
 Ribbon diagram – shows the organisation of the protein backbone
 Surface diagram – shows the areas of the protein accessible to water molecules
 CPK colour scheme
 Oxygen – red
 Hydrogen – white
 Nitrogen – blue
 Sulfur – yellow
 Phosphorus - orange
 Functions examples
o Defense
 Antibodies
 Flexible arms of antibodies recognise and bind to pathogens
o Trnasport
 Calcium pump
 Aided by magnesium and powered by ATP to move calcium ions out of the cell
during muscle contraction
o Communication
 Insulin
 Maintains its shape while travelling through the blood to maintain the blood glucose
level
o Storage
 Ferritin
 Spherical protein
 Has channels which allow iron atoms to enter and exit
o Structure
 Collagen
 Strong triple helix – used for structural support throughout the body
 Forms fibrils which join to make fibres
o Enzymes
 Alpha-amylase
 Begins digestion of starches in our saliva

,Amino Acids
Amino Acids
 Common features
o Common amino acids = alpha amino acids
 Due to alpha carbon in centre bound to:
 Alpha amino group
 Alpha carboxyl group
 R-group = sidechain
o Has various functional groups
o Influences protein structure and function
 Hydrogen atom
 Stereoisomerism
o Amino acids – have a chiral centre
 Alpha carbon is bound to four different groups (NH 2 + CO + R-group + H)
o Determining enantiomers
 Draw the “fissure projection” of the amino acid – carboxyl group on top + side chain on the
bottom
 L-amino acids
o Amino group is on the left side
 D-amino acids
o Amino group is on the right side
o Amino acids in proteins are L-enantiomers
o Carbon-containing side chains
 Central carbon = alpha carbon
 Carbons on side chains
 Β-carbon
 γ-carbon
 Branched carbon
o δ1 carbon
o δ2 carbon
 Amino acid alphabet – 22 amino acids




o
 Amino acids
o Non-polar amino acids – found within proteins – stabilising the structure with hydrophibic
interactions
 G – gly – glycine
 Small side chain – hydrogen
 Found in spaces that are not
accessible to other larger amino acids
 Has no enantiomers – due to no
chiral carbon
 A – ala – alanine
 Has a methyl group
 V – val – valine

, Amino Acids
 Has an isopropyl group
 I – ile – isoleucine
 Has a hydrocarbon group
 L – leu – leucine
 Has an isobutyl group
 M – met – methionine
 Has an s-methyl group
 Contains sulfur
o Polar uncharged amino acids – on the surface of proteins – soluble in water = forms hydrogen bonds
 S – ser – serine
 Has a hydroxyl group
 T – thr – threonine
 Has a hydroxyl group
 N – asn – asparagine
 Has a carboxamide group
 Q – gln – glutamine
 Has a carboxamide group
o Polar charged amino acids – on the surface of proteins
 D – asp – aspartic acid
 E – glu – glutamic acid
 H – his – histidine
 Positively charged
 Has an imidazole group
 K – lys – lysine
 Positively charged
 Has a lysyl group
 R – arg – arginine
 Positively charged
o Non-polar aromatic amino acids – participates in hydrophobic interactions
 F – phe – phenylalanine
 Y – tyr – tyrosine
 More polar than phenylalanine due to OH group
on side chain
 W – trp – tryptophan
 More polar than phenylalanine due to NH group
on side chain
o Special amino acids
 P – pro – proline
 Imino acid – contains an NH2+ group rather than an NH3+
group
 Has a ring structure – more rigid = reducing flexibility
 C – cys – cysteine
 Contains sulfhydryl group SH group – can form disulfide
bridges
 Disulfide bridges
o 2 cysteine amino acids can be oxidised to form a
disulfide bridge
 Protein folding and the hydrophobic effect
o In soluble proteins
 Hydrophobic (non-polar) amino acids – found in the interior of the protein
 Hydrophilic (polar) amino acids – found on the surface of proteins