Proteins
Transcription Translation
we
DNA
no
RNA
in
Polypeptide
Functions Of Proteins Peptide- short chain of amino acids, 50 amino acids
• Catalysis: Enzymes e.g. Proteases- hydrolyse
proteins, ATPases- hydrolyse ATP, ATP Kinases- adds Examples
phosphate, Nucleases- hydrolyse nucleotide acids • Oxytocin: 9 amino acids
• Movement: Muscle Proteins e.g. Myosin, Actin, -> Contracts uterus & helps lactation, synthetic
Flagella version to induce labour
• Cellular Control: • Somatostatin: 14 amino acids
-> Hormones e.g. Insulin, Growth Hormone, Sex -> Inhibits release of growth hormone, used for
Hormones ulcer treatments
-> Receptors e.g. give specific ligand recognition to • Melittin: 26 amino acids
induce response -> Bee Venom, used to treat rheumatoid
arthritis El
• Transport:
-> Respiratory Proteins e.g. Haemoglobin- oxygen • Calcitonin: 32 amino acids
carrying, Cytochromes- electron transport -> Regulates calcium, used to treat osteoporosis
-> Storage e.g. Ferritin- stores iron in its soluble & non- • Beta Amyloid: 42 amino acids
toxic form -> BAD one, causes Alzheimer’s, present in
• Structural: amyloid plaques in brain
-> Skin, Bones e.g. Collagen • Insulin: 51 amino acids
-> Hair, Nails e.g. Keratin -> Control glucose levels, used in treatment of
diabetes
• Immune System: Defense against toxins/pathogens
e.g. Antibodies, T-cell Receptors, Complement System
Function Of Proteins Depends On
• Amino acid composition + sequence (unique to protein)
• Structure (size + shape)
• Chemical properties of amino acids- can vary depending on 3D structure
• Post translational modifications- e.g. phosphorylation, glycosylation
• Other molecules that bind to proteins e.g. cofactors, metal ions, ligands
or protein-protein interactions
α-carbon is
Amino Acids Are L Isomers α-Amino
H
α-Carbon
(tetrahedral)
asymmetrical
(chiral) for 19
amino acids,
group
• Proteins- linear polymers of amino acids as
4ha
only 1 (where
• 20 different kinds of amino acids, each with
different R group
O
H2N C COOH
9.6
R=hydrogen) is
non-chiral- same
pka α-Carboxylic mirror image
• Order in which amino acids are bonded forms the R
sequence or primary structure group
20 types
, AA AA AA AA
Primary Sequence The sequence of amino acids in a polypeptide
• Formed by bonding COOH group of one amino acid, to the NH2 group of
another
i
• Water is removed via condensation reaction = amino
• Peptide/Amide bond is formed acid
• Takes place in ribosomes as mRNA is translated into polypeptide sequence residue
H H H O H
H2N C COOH
0 H2N C COOH H2N C C N C COOH
y f
H2O
R R R H R
N-terminus C-terminus
Peptide Bond mmmmm
Geometry
if
• -N-C-C- repeats through polypeptide
t
sequence
• Is called peptide backbone
c C
• C-N bond should have length of 1.49
• C=N bond should have length 1.27 f's
• However, actual C-N bond length for o
peptide bond is 1.32 as there is
resonance stabilisation • C-N bond is shown as single bond in figures, but it is not
• Peptide bond is planar, which implies able to rotate freely like a single bond
rotation is restricted • It behaves partially like a double bond due to resonance
iii side
• Free rotations possible on either stabilisation
of C
• Planes can rotate by certain torsional
angles C-N (by angle phi) C-CO (by
angle Psi) EXCEPTIONS: Proline Prefers CIS
• Favoured rotations point R groups • Cyclic structure double bond character lost
opposite each other in Trans • Rotation is possible and steric constraints are not so
configuration high
hummmann
• Nearly all amino acids prefer to be in • Proline can go into cis or trans conformations
trans configuration to avoid steric
constraint pKa- pH at which an ionisable group is
50% ionised and 50% non-ionised
Ionisation (acid-base properties)
R Varies According To: • Amino and acid groups attached to alpha carbon
• Polarity- 7 polar, 8 non-polar can be titrated
• Charges- 2 ACIDIC, 3 BASIC Ionisation of weak acid:
• Size & Shape: large bulky aromatic ->
small e.g. H
AH
winoA- + H+
Equation below defines ratio of protonated to non-
• H-Bonding: 12 of them have this ability protonated (conjugate base) form
• Proteins are diverse in structure &
function cunning
pH = pKa + log([A-]/[H+])
-> called Henderson-Hasselbatch
Transcription Translation
we
DNA
no
RNA
in
Polypeptide
Functions Of Proteins Peptide- short chain of amino acids, 50 amino acids
• Catalysis: Enzymes e.g. Proteases- hydrolyse
proteins, ATPases- hydrolyse ATP, ATP Kinases- adds Examples
phosphate, Nucleases- hydrolyse nucleotide acids • Oxytocin: 9 amino acids
• Movement: Muscle Proteins e.g. Myosin, Actin, -> Contracts uterus & helps lactation, synthetic
Flagella version to induce labour
• Cellular Control: • Somatostatin: 14 amino acids
-> Hormones e.g. Insulin, Growth Hormone, Sex -> Inhibits release of growth hormone, used for
Hormones ulcer treatments
-> Receptors e.g. give specific ligand recognition to • Melittin: 26 amino acids
induce response -> Bee Venom, used to treat rheumatoid
arthritis El
• Transport:
-> Respiratory Proteins e.g. Haemoglobin- oxygen • Calcitonin: 32 amino acids
carrying, Cytochromes- electron transport -> Regulates calcium, used to treat osteoporosis
-> Storage e.g. Ferritin- stores iron in its soluble & non- • Beta Amyloid: 42 amino acids
toxic form -> BAD one, causes Alzheimer’s, present in
• Structural: amyloid plaques in brain
-> Skin, Bones e.g. Collagen • Insulin: 51 amino acids
-> Hair, Nails e.g. Keratin -> Control glucose levels, used in treatment of
diabetes
• Immune System: Defense against toxins/pathogens
e.g. Antibodies, T-cell Receptors, Complement System
Function Of Proteins Depends On
• Amino acid composition + sequence (unique to protein)
• Structure (size + shape)
• Chemical properties of amino acids- can vary depending on 3D structure
• Post translational modifications- e.g. phosphorylation, glycosylation
• Other molecules that bind to proteins e.g. cofactors, metal ions, ligands
or protein-protein interactions
α-carbon is
Amino Acids Are L Isomers α-Amino
H
α-Carbon
(tetrahedral)
asymmetrical
(chiral) for 19
amino acids,
group
• Proteins- linear polymers of amino acids as
4ha
only 1 (where
• 20 different kinds of amino acids, each with
different R group
O
H2N C COOH
9.6
R=hydrogen) is
non-chiral- same
pka α-Carboxylic mirror image
• Order in which amino acids are bonded forms the R
sequence or primary structure group
20 types
, AA AA AA AA
Primary Sequence The sequence of amino acids in a polypeptide
• Formed by bonding COOH group of one amino acid, to the NH2 group of
another
i
• Water is removed via condensation reaction = amino
• Peptide/Amide bond is formed acid
• Takes place in ribosomes as mRNA is translated into polypeptide sequence residue
H H H O H
H2N C COOH
0 H2N C COOH H2N C C N C COOH
y f
H2O
R R R H R
N-terminus C-terminus
Peptide Bond mmmmm
Geometry
if
• -N-C-C- repeats through polypeptide
t
sequence
• Is called peptide backbone
c C
• C-N bond should have length of 1.49
• C=N bond should have length 1.27 f's
• However, actual C-N bond length for o
peptide bond is 1.32 as there is
resonance stabilisation • C-N bond is shown as single bond in figures, but it is not
• Peptide bond is planar, which implies able to rotate freely like a single bond
rotation is restricted • It behaves partially like a double bond due to resonance
iii side
• Free rotations possible on either stabilisation
of C
• Planes can rotate by certain torsional
angles C-N (by angle phi) C-CO (by
angle Psi) EXCEPTIONS: Proline Prefers CIS
• Favoured rotations point R groups • Cyclic structure double bond character lost
opposite each other in Trans • Rotation is possible and steric constraints are not so
configuration high
hummmann
• Nearly all amino acids prefer to be in • Proline can go into cis or trans conformations
trans configuration to avoid steric
constraint pKa- pH at which an ionisable group is
50% ionised and 50% non-ionised
Ionisation (acid-base properties)
R Varies According To: • Amino and acid groups attached to alpha carbon
• Polarity- 7 polar, 8 non-polar can be titrated
• Charges- 2 ACIDIC, 3 BASIC Ionisation of weak acid:
• Size & Shape: large bulky aromatic ->
small e.g. H
AH
winoA- + H+
Equation below defines ratio of protonated to non-
• H-Bonding: 12 of them have this ability protonated (conjugate base) form
• Proteins are diverse in structure &
function cunning
pH = pKa + log([A-]/[H+])
-> called Henderson-Hasselbatch
