Download Biochemistry Course #: - College of Pharmacy at Howard University

BIOCHEMISTRY COURSE –
PHARMACY BIOMEDICAL PREVIEW
PROGRAM, SUMMER 2016
Ginika Ezeude, B.A. Biochemistry
Barnard College of Columbia University
2nd Year Pharmacy Student
Contact: [email protected]
1. LEVELS OF PROTEIN
STRUCTURE
- Primary, Secondary, Tertiary, Quaternary
BUILDING BLOCKS OF BIOLOGICAL
MACROMOLECULES
PROTEINS: NATURE’S LEGOS
● Structure
o
Muscle, collagen, hair
● Movement
o
Muscles (Actin, Myosin)
● Enzymes
o
Molecular Machines
o
Promote chemical reactions in Anabolism and
Catabolism
o
Life
WHAT ARE PROTEINS MADE OF?
Proteins are chains of Amino Acids
● About Amino Acids:
o 20 Amino Acids exist (normally)
o We produce 11 of them in our
bodies
 anabolism and catabolism
o 9 are considered “essential”
and must be obtained via our
diet
o All AA have the same basic
structure
PEPTIDES AND PROTEINS
Proteins play a significant role in biological pathways and thus the preservation of life.
 Proteins and peptides are polymers of amino acids
C-terminal of one aa interact
with the N-terminal of another
amino acid, looses water
molecule to form an amide
bond (peptide bond).
PEPTIDES AND PROTEINS
Oligopeptide
Polypeptide
PEPTIDE BOND
C-terminus slight –ve charge
Rigid peptide bonds
are unable to rotate
freely thereby
limiting the range of
conformations
Ф – phi (N-Cα )
Ѱ – psi angle (Cα–
C)
N-terminus slight +ve charge
3-D STRUCTURE OF PROTEINS
Secondary structures of a protein
α – HELIX
Ramachandran
Plot
3.6 residues
5.4Å
H-bond
the helix has 3.6 residues per turn
α – helix
•ѱ = -45° to -50°
•Ф = -60°
wenxiang diagram
α – HELIX
Factors affecting the Stability of the α - helices
1. The electrostatic repulsion or attraction between successive amino acid
residues with charged R groups.
2. The bulkiness of the adjacent R groups
3. The interactions between R groups spaced 3 or 4 residues apart.
4. The occurrence of Pro and Gly residues
5. The interaction between amino acid residues at the ends of helical
segment and the electric dipole inherent in the α – helix
What do you think would happen if there
was stretch of Glu residues present ?
Repulsion
α – HELIX
What do you think would happen if Pro residues present ?
Non-polar bulky group does not participate
in H-bond interaction and will introduce a
kink in the α – helix structure
Pro
What do you think would happen if Gly residues present ?
To much conformational flexibility
Gly
α – HELIX
Recall: A net dipole extends along the helix
structure
What do you think would happen if a positively
charged residue was present at the amino end or
vise versa ?
Positively charged amino acid at the
amino terminus is destabilizing
β – SHEETS
H-bond formed between adjacent
segments of the polypeptide chain.
The adjacent polypeptide chains can orient
themselves to have the same amino-to-carboxyl
orientation (Parallel) or opposite orientation
(Antiparallel).
β – sheets
•ѱ = 140°
•Ф = -130°
β – SHEETS
•180° turn involving four
amino acid residues.
•Carbonyl oxygen of the
first residue forming a
hydrogen bond with the
amino-group hydrogen of
the fourth.
Gly and Pro residues often occur in turns,
why?
Gly
Pro
PROTEIN TERTIARY AND QUATERNARY STRUCTURES
Classify proteins into two major groups:
1. Fibrous proteins, having polypeptide chains arranged in long strands or sheets
2. Globular proteins, having polypeptide chains folded into a spherical or globular shape.
FIBROUS PROTEIN
Cross section of a strand of hair
containing the α keratin protein
intermediate filament
GLOBULAR PROTEIN
Quaternary Protein Structure of
Human Hemoglobin
Red Molecules represent α-globin
Blue molecules represent β-globin
Green molecules symbolize heme
Globular proteins include enzymes, transport
proteins, motor proteins, regulatory proteins,
immunoglobulins, and proteins with many other
functions.
Differences between fibrous and globular proteins;
1. Typically fibrous proteins consist largely of a single type of secondary structure.
Globular proteins often contain several types of secondary structure.
2. The two groups differ functionally in that the structures that provide support, shape, and external
protection to vertebrates are made of fibrous proteins, whereas most enzymes and regulatory
proteins are globular proteins.
HEMOGLOBIN
Hemoglobin
●Four polypeptide units
○ “tetramer”
●2 identical alpha chains
●2 identical beta chains
○ “hetero”
●Often referred to as a
“dimer of dimers” because
it has 2 alpha chains and 2
beta chains
If Hemoglobin had four
identical units…
●homo-tetramer
HEMOGLOBIN VS. MYOGLOBIN
● Myoglobin is like 1 of
hemoglobin’s 4
subunits
● Similar functions
o O2 binding
o Hg: binds 4 O2
 O2 transport
o Mg: binds 1 O2
 O2 “storage”
PROTEIN STRUCTURE: KEY POINTS
● Primary Structure is
determined by DNA
sequence
o Easy to predict (read the
DNA)
● Tertiary Structure is determined
by hydrophillic/hydrophobic
interactions
o Nearly impossible to predict
● Secondary Structure is
determined by hydrogen
bonds
o Alpha-helixes and Betasheets have predictable
motifs
● Quaternary Structure is
determined by DNA sequence
(again)
o alpha, beta, delta, gamma
chains/units link together...
2. MECHANISM OF
PROTEIN FOLDING
- Why do they fold?
- What stabilizes them in their conformation?
WHY DO PROTEINS FOLD?
• To facilitate specific reactions that are necessary for
specific physiological function.
• Failure of protein to fold or mis-fold results in the
disruption of pathophysiological pathways.
Parkinson’s disease
Allergies
STABILIZATION OF PROTEIN CONFORMERS
Protein Conformation- spatial arrangement of atoms in a protein
Native Conformation –proteins in their functional, folded conformation. It is the typically the
most thermodynamically most stable conformer, having the lowest Gibbs free energy (G).
Stability – the tendency of a protein to maintain a native
conformation
∆G = ∆H - T∆S
Betz, S. F. Disulfide bonds and the stability of globular proteins. Protein Sci. 1993, 2, 15511558.
Forces Contributing to the Stability of Proteins
• Intramolecular interactions
• Stabilization of dipoles of α helices.
• Solvent environment
MECHANISMS OF PROTEIN FOLDING
Radford, S. E. Protein folding: progress made and promises ahead. Trends Biochem. Sci. 2000, 25, 611-618.
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