Delve into the complexities of Biochemistry and Molecular Biology with this meticulous set of notes tailored for Year 1 students at University College London, specifically focusing on the proteins and enzymes chapter. Explore the nuances of amino acids, dissecting their properties and biological si...
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
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