Biochemistry And Molecular Biology (BIOC0001) Notes - Proteins and Enzymes
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Course
Biochemistry And Molecular Biology (BIOC0001)
Institution
University College London (UCL)
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...
relationship between protein structure and functio
enzymes and enzyme kinetics
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University College London (UCL)
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Biochemistry And Molecular Biology (BIOC0001)
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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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