PROTEINS

WHAT ARE PROTEINS
WHAT ARE PROTEINS

• Proteins are a class of biomolecules
• They are polymers made of building blocks known as amino acids
Why are proteins important?
Why are proteins important?
• Structure, support, movement, and external protection
• Storage and transport
• Energy Source
• Nitrogen Source
• Regulation/Balance
• Internal protection
• Catalysis
Hemoglobin
Levels of Structure in Proteins
Primary level
• Identity of polypeptide chains in terms of its building block sequence
Primary level
• Identity of polypeptide chains in terms of its building block sequence
• Amino acids are the building blocks
• Sequence is usually read from N-terminal to C-terminal
General structure of an amino acid
General structure of an amino acid
Lines, dashes and wedges
Nonpolar side chains
Aromatic side chains
Polar side chains, uncharged
Polar side chains, charged
• All protein-derived amino acids have at least 1 chiral carbon.
• Except for G
• This is usually the α-carbon
• These α-amino acids are usually present in the L-configuration
• Except for P, which is usually D
REVIEW: Stereochemistry
• Organic compounds can have the same molecular formula but
entirely different identities.
• Isomers
REVIEW: Stereochemistry
Constitutional isomers
• Compounds that differ in the connection of atoms
• C2H6O
Stereoisomers
• Also called configurational isomers
• cis-trans isomers
• Isomers with chiral centers
Cis-trans isomers
Chiral centers
• Chirality
Chiral centers
• Chirality
Chiral centers
• Chirality
Chiral centers
• Chirality
enantiomers
Unfortunately…
Amino Acids usually have chiral centers, too.
• Alanine
• Alanine
• Alanine
• Alanine
Isoelectric point
• Amino acids have ionizable groups that can serve as weak acids or
weak bases.
Isoelectric point
weak bases.
Isoelectric point
weak bases.
Isoelectric point estimation
• Low pH
• Amino acid net charge is positive
• Carboxylic acid is neutral (R-COOH)
• Amino group is positive (R-NH3+)
• Low pH
• High pH
• Amino acid net charge is negative
• Carboxylic acid is negative (R-COO-)
• Amino group is neutral (R-NH2)
• Low pH
• High pH
• Amino acid net charge is negative
• Amino group is neutral (R-NH2)
• Isoelectric point
• Amino acid net charge is zero
• Amino group is still positive (R-NH3+)
• Isoelectric point, pI, is estimated as the average of the pKa values
leading to the ionization of the target polypeptide/amino acid from the
positively charged form (pKa+1) to the negatively charged form (pKa-1).
• pI = (pKa+1 + pKa−1)/2
• pI = (pKa+1 + pKa−1)/2
For alanine
• pI = (pKa+1 + pKa−1)/2
For alanine
pI = (2.34 + 9.69)/2 = 6.015 ≈ 6.02

EXAMPLE 2
• Histidine
• Basic side chains add to the positive charge “limit” for the amino
acid/polypeptide (e.g. lysine, arginine)
• Acidic amino side chains add to the negative charge “limit” for the
amino acid/polypeptide (e.g. aspartic acid)
PRACTICE
• Estimate the pI for
• Glycine
• asp
•R
PEPTIDE BONDS
• Covalent bond between amino
acids in forming polypeptides
PEPTIDE BONDS
NAMING OF PEPTIDES
• Peptide names vary depending on the sequence of the AA residues.
• Each amino acid is read starting from the amino terminal to the carboxyl
terminal
• Amino terminal (N-terminal) is the end containing a free α-amino group.
• Carboxyl terminal (C-terminal) is the end with a free carboxyl group
NAMING OF PEPTIDES
• Peptide names vary depending on the sequence of the AA residues.
• Each amino acid is read starting from the amino terminal to the carboxyl
terminal
• Amino terminal (N-terminal) is the end containing a free α-amino group.
• Carboxyl terminal (C-terminal) is the end with a free carboxyl group
• If amino acid sequence is written and structure is not shown, the N-terminal is
generally considered to be the one on the left end and the C-terminal is the one
at the right end
NAMING OF PEPTIDES
• For peptide names, you simply consider the N-side AA residues to be
an alkyl substituent to the next AA.
e.g.
NAMING OF PEPTIDES
e.g.
• phe-trp
NAMING OF PEPTIDES
e.g.
• phe-trp
• Phenylalanyltryptophan
• FW
EXAMPLE
• Pentapeptide
EXAMPLE
• Pentapeptide
• Peptide name is serylglycyltyrosylalanylleucine

EXAMPLE
• Pentapeptide
• Peptide name is serylglycyltyrosylalanylleucine

• ser-gly-tyr-ala-leu
EXAMPLE
L-aspartyl-L-phenylalanine methyl ester (aspartame)

Some other commonly known peptides
PEPTIDE BONDS
• Formation of peptide bonds
remove the ionizable
components of the chain.
• The -COOH group of the AA in
the left
• The –NH2 group of the AA in
the right.
PEPTIDE BONDS
• This affects the pI of the
polypeptide compared with
the initial AAs
pI of Peptides
• For EK
• E has 3 ionizable groups (amino, carboxyl, side chain)
• K has 3 ionizable groups (amino, carboxyl, side chain)
• Dipeptide EK only has 4 ionizable groups

• Amino end (from E)
• Side chain of E
• Carboxyl end (from K)
• Side chain of K
pI of peptides
• N-terminal of the peptide: pK2 (E) = 9.67 (+1)
• C-terminal of the peptide: pK1 (K) = 2.18 (-1)
• All of the side chains of the AAs: pKR (E) = 4.25 (-1), pKR(K) = 10.53
(+1)
Dipeptide EK
• What is the maximum positive charge for the dipeptide?
• What is the maximum negative charge?
• What is the pI?
Polypeptides vs. Proteins
• What is the difference?
2°structure
• The 3-dimensional arrangement of a small region of amino acids in a
single polypeptide chain
• Key factor is H-bonding
2°structure
• The 3-dimensional arrangement of a small region of amino acids in a
single polypeptide chain
• Key factor is H-bonding
• Can be one of either

• α-helix
• β-pleated sheet
α-helix
Some α-helix features
• Coil of the helix is clockwise or right-handed
• There are 3.6 amino acids per turn
• C=O of each peptide bond is hydrogen bonded to the N-H of the
fourth amino acid away
• C=O----H-N hydrogen bonds are parallel to helical axis
• All R groups point outward from helix
How to check for helix handedness?
Factors affecting the helical structure
• Proline
Factors affecting the helical structure
• Electrostatic repulsion
• Steric strain
• I, V, T
ORGANIC CHEMISTRY REVIEW
• Steric Strain
• Substituents of molecules are big enough to cause electron cloud interference
with one another
Some -Pleated Sheet features
• Polypeptide chains lie adjacent to one another; may be parallel or
antiparallel
• R groups alternate, first above and then below plane
• C=O and N-H groups of each peptide bond are perpendicular to axis
of the sheet
• C=O---H-N hydrogen bonds are between adjacent sheets and
perpendicular to the direction of the sheet
Antiparallel
Image Source: ScienceDirect

Reverse Turns
• A small substructure found in β-sheets, facilitating the change in
direction of the polypeptide
• Can include gly and pro
Tertairy (3°) structure
• Overall 3D structure of a polypeptide chain
• Includes longer-range interactions between residues
• Many are classified as either fibrous or globular

Supersecondary structures
• Combinations of α and β structures
•  unit
•  unit
• -meander
• Greek key
• -barrel
Supersecondary structures
• Source: https://phys.org/news/2018-01-scientists-elucidate-
mechanism-inserting-protein.html
Fibrous proteins
• Polypeptide chains are usually arranged in parallel along a single axis
• Keratin
• Collagen
Globular Proteins
• Structure folds into a somewhat spherical shape
• Usually influenced by its environment
Globular Proteins
• Structure folds into a somewhat spherical shape
• Usually influenced by its environment
• Hydrophobic residues go inside the globular structure
• Hydrophilic residues are exposed, interacting with the aqueous environment
• Can introduce pockets in the globular structure.
Summary of Interactions Influencing Protein
Structure
• Covalent interactions
• Disulfide bridges
• Noncovalent interactions
• H-bonding
• Hydrophobic interactions
• Electrostatic attraction and repulsion
• Residue to residue
• Ligand to residue
Summary of Interactions Influencing Protein
Structure
Quaternary structures
• The association of multiple polypeptide chains into aggregations that
have a particular function
• Leads to the formation of multisubunit proteins
• Dimers
• Trimers
• Tetramers
Hemoglobin
Heme
Heme
Protein Denaturation
• The loss of the native structure of a protein leading to the loss of
biological activity
• Factors that disrupt protein structure:
• Heat
• pH change
• Detergents
• Mercaptoethanol
• Urea
Factors that affect protein function
• Presence of prosthetic groups/cofactors
• Apoenzyme/apoprotein
• holoenzyme
• Denaturation
• Inhibitors

PROTEINS

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WHAT ARE PROTEINS

WHAT ARE PROTEINS

pI = (2.34 + 9.69)/2 = 6.015 ≈ 6.02

• Peptide name is serylglycyltyrosylalanylleucine

• Peptide name is serylglycyltyrosylalanylleucine

L-aspartyl-L-phenylalanine methyl ester (aspartame)

• Dipeptide EK only has 4 ionizable groups

• Can be one of either

Image Source: ScienceDirect

• Many are classified as either fibrous or globular

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