VIETNAMATIONAL UNIVERSITY HCMC
INTERNATIONAL UNIVERSITY
BTBC209IU
Biochemistry 1
Nguyen Kim Truc (PhD)
Office: A1.705
Email:
[email protected]AY 2019-2020, semester 2
Class outline
• Take attendance by typing full name and ID
• Lecture 9
• Group 2 and group 5 presentations
Amino acids _ Protein (cont.)
Proteins are made up of smaller building blocks called amino acids
Protein structure
• Proteins are unbranched polymers of amino acids
• Amino acids join head-to-tail through formation of covalent
peptide bonds
• Peptide bond formation results in release of water
• The peptide backbone of a protein consists of the repeated
sequence –N-Cα-Co-
• “N” is the amide nitrogen of the amino acid
• “Cα” is the alpha-C of the amino acid
• “Co” is the carbonyl carbon of the amino acid
Peptide bond formation
Peptide formation is the creation of an amide bond
between the carboxyl group of one amino acid and the
amino group of another amino acid.
Peptide bond characteristic
• is usually found in the trans conformation
• has partial (40%) double bond character
• has a length of about 0.133 nm - shorter than a typical single
bond but longer than a double bond
• Peptide bond does not rotate
• Due to the double-bond character of the peptide bond, the six
atoms of the peptide bond group define a plane – the amide
plane
Peptide bond characteristic
The trans conformation of the peptide bond
Peptide bond characteristic
Peptide bond characteristic
Peptide bond characteristic
Peptides
• Short polymers of amino acids
• Each amino acid unit is called a residue
• 2 residues - dipeptide
• 3 residues - tripeptide
• 12-20 residues - oligopeptide
• many residues - polypeptide
Protein
One or more polypeptide chains
• One polypeptide chain - a monomeric protein
• More than one - multimeric protein
• Homomultimer - one kind of chain
• Heteromultimer - two or more different chains
• Hemoglobin, for example, is a heterotetramer
• It has two alpha chains and two beta chains
Proteins - Large and Small
• Insulin – consists of an A chain of 21 residues, and a B chain of
30 residues -total mol. wt. of 5,733
• Glutamine synthetase - 12 subunits of 468 residues each - total
mol. wt. of 600,000
• α-Connectin (a muscle protein) - MW 2.8 million
• β-Connectin - MW of 2.1 million, with a length of 1000 nm - it
can stretch to 3000 nm
Proteins - Large and Small
Proteins - Large and Small
Size of protein molecules
Molecular weights:
Insulin, 5,733
Cytochrome c, 12,500
Ribonuclease, 12,640 Lysozyme, 13,930
Myoglobin, 16,980
Proteins - Large and Small
Molecular weights:
Hemoglobin, 64,500;
Immunoglobulin, 149,900;
Glutamine synthetase, 600,000.
Size of Protein Molecules
Sequence of Amino Acids in a Protein
• Is a unique characteristic of every protein
• Is encoded by the nucleotide sequence of DNA
• Is thus a form of genetic information
• Is read from the amino terminus to the carboxyl terminus
Protein Structure is Described in Terms
of Four Levels of Organization
The four levels of protein structure are:
- Primary (1o) – the amino acid sequence
- Secondary (2o) - local structures stabilized by H bonds
- Tertiary (3o) - overall 3-dimensional shape of the folded protein
- Quaternary (4o) - subunit organization
Architectural Arrangements Characterize
Protein Structure
(a) Proteins having structural roles in cells are typically
fibrous and often water insoluble. (b) Myoglobin is a
globular protein. (c) Membrane proteins fold so that
hydrophobic amino acid side chains are exposed in
their membrane-associated regions.
Protein Structure and Function Are
Tightly Linked
The three-dimensional structures of proteins and their biological
functions are linked by several overarching principles:
• Function depends on structure
• Structure depends on sequence and on weak, noncovalent forces
• The number of protein folding patterns is large but finite
able to soluble in water
• Structures of globular proteins are marginally stable
• Marginal stability facilitates motion
• Motion enables function move -> communicate
Noncovalent Interactions Stabilize the
Higher Levels of Protein Structures
What are these “weak forces”?
What are the relevant numbers?
• van der Waals: 0.4 - 4 kJ/mol
• hydrogen bonds: 12-30 kJ/mol
• ionic bonds: 20 kJ/mol
• hydrophobic interactions: <40 kJ/mol
Noncovalent Interactions Stabilize the
Higher Levels of Protein Structures
• Secondary, tertiary, and quaternary structure of proteins is formed
and stabilized by weak forces
• Hydrogen bonds are formed wherever possible
• Hydrophobic interactions drive protein folding
• Ionic interactions usually occur on the protein surface
• van der Waals interactions are ubiquitous
Electrostatic Interactions in Proteins
An electrostatic interaction between a positively charged
lysine amino group and a negatively charged glutamate
carboxyl group.
Electrostatic Interactions in Proteins
An electrostatic interaction between lysine and glutamate side
chains in IRAK-4, an enzyme that phosphorylates other proteins. The
positively charged amino group (left) forms an ionic interaction with
the negatively charged glutamate (right).
What Role Does the Amino Acid
Sequence Play in Protein Structure?
All of the information necessary for folding the peptide chain into
its "native” conformation is contained in the primary amino acid
structure of the peptide.
Secondary Structure
Secondary structures are local structures that are stabilized by
hydrogen bonds
• Alpha helices
• Other helices
• Beta sheet (composed of "beta strands")
• Tight turns (aka beta turns or beta bends)
• Beta bulge
The α-Helix
Four different representations of the α-helix
The α-Helix
• Residues per turn: 3.6
• Rise per residue: 1.5 Å (0.15 nm)
• Rise per turn (pitch): 3.6 x 1.5 Å = 5.4 Å
• The backbone loop that is closed by any H bond in an alpha
helix contains 13 atoms
• The non-integral number of residues per turn was a surprise
to crystallographers
The α-Helix
Two proteins that contain substantial amounts of α-helix
The α-Helix Has a Substantial Net Dipole Moment
The arrangement of N-H and C=O
groups (each with an individual dipole
moment) along the helix axis creates a
large net dipole moment for the helix.
The numbers indicate fractional
charges on respective atoms.
Exposed N-H and C=O groups at the ends of an α-
helix can be “capped”
Four N-H groups at the N-terminal end
of an α-helix and four C=O groups at
the C-terminal end lack partners for H-
bond formation. The formation of H
bonds with other nearby donor and
acceptor groups is referred to as helix
capping.
Amino acids can be classified according to their
alpha-helix tendencies.
The β-Pleated Sheet
The β-pleated sheet is composed of β-strands
Strands in a β-sheet may be parallel or antiparallel
Rise per residue:
• 3.47 Å for antiparallel strands
• 3.25 Å for parallel strands
• Each strand of a β-sheet may be pictured as a helix with
two residues per turn
The β-Pleated Sheet
A “pleated sheet” of paper with an antiparallel β-sheet drawn on it.
The β-Pleated Sheet
H bonds in parallel and antiparallel β-sheets.
Helix-Sheet Composites in Spider Silk
Spider web silks are composites of α-helices and β-sheets. The
radial strands of webs must be strong and rigid: they have a higher
percentage of β-sheets. The circumferential strands (termed capture
silk) must be flexible; they contain a higher percentage of α-helices.
Group presentation
• Group 2: Bacteria membrane structure and functions
• Group 5: Gram-positive and Gram-negative bacteria
Q&A
