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Proteins
Dinosaur Protein
Proteins - classified by functions
Enzymes
Transport Proteins
Storage Proteins
Contractile (Motor)
Structural (Support)
Defensive (Protect)
Regulatory (Signal)
Receptors (detect stimuli)
Protein Structure
• Proteins are unbranched polymers
– Monomers are Amino Acids
• Standard Amino Acids (20/700)
Classified according to side-chain polarity
– Non-Polar
– Polar Neutral
– Polar Acidic
• W/ 2nd carboxyl group
– Polar Basic
• W/ 2nd amine group
• Essential vs.Non-essential
– PVT. TIM HALL
Amino acids central carbon = the -Carbon
Covalently bonded to
the alpha carbon is:
1) a Hydrogen atom, H
2) a carboxyl
functional group,
(COOH)
3) an amine functional
group, (NH2 )
4) a side chain (R).
Each side chain
distinguishes one
kind of amino acid
from another.
Protein Chirality
Most -amino acids
in living creatures
are Levo-oriented,
not Dextro-oriented
(opposite of chirality
in monosaccharides)
“Handedness” (L or D) in standard amino acids: Line up the C chain
vertically and look at the position of the horizontally aligned -NH2 group.
Acid-Base Properties
• Amino Acids can participate in “internal”
acid-base reactions.
There is an internal donation of a H+ ion
from the COOH group to the NH2 group.
The result is a double ion, both positive and
negative, whose charges cancel each other out.
Isolated amino acids (neutral solution) are zwitterions
Equilibrium of Amino Acids
• Depending on the pH of the solution the
equilibrium position is “pushed” in a
particular direction.
– Remember to consider the source of extra
ions!
Isoelectric Points & Electrophoresis
• Isoelectric point: the pH at which the amino
acid has no net charge (zwitterion)
• This point is measured in an electric field
• The movement of charged molecules in an
electric field is the basis for electrophoresis.
Peptide Bonds
• Peptide bonds = covalent bonds between the carboxyl group on one
amino acid and the amino group on an adjacent amino acid
– This is a Condensation Reaction
– A polypetide chain has an “N” terminal and a “C” terminal
Biochemically Important Small Peptides
• Hormones
– Ex.: Oxytocin, Vasopressin
• Both have 9 amino acids
• Neurotransmitters
– Ex.: Enkaphalins
• Morphine & Codeine bind to the same sites
• Antioxidants
– Ex.: Glutathione
Protein Structure
•
Proteins have at least 50 amino acids
– Monomeric vs. Multimeric
– Simple vs. Conjugated
4 levels of protein structure:
primary
- linear sequence of a.a.'s (held together by peptide bonds)
secondary - arrangement in space of the backbone portion (caused by
hydrogen bonds between carbonyl oxygen and amino
hydrogen at different locations on the chain)
tertiary
- complete 3-D shape of a peptide (caused by hydrogen
bonds, disulfide bonds, electrostatic attractions &
hydrophobic attractions
quaternary - spatial relationships between different polypeptides or
subunits
Primary (1o) structure:
the amino acid
sequence
Like letters forming words:
Same letters used over,
but sequence changes.
Misplaced letters
may still be readable.
Missing letters
may ruin the “word”
Human myoglobin.
Insulin
Results of changing the Primary sequence:
•
Polymorphism: proteins vary in primary sequence but have the same function.
•
•
Between species [different a.a. sequences]
Within a species [liver vs. kidney]
•
Site Specificity: unique sequences determine intra-cellular location
of transmembrane signals, binding sites, etc…
•
Families of Proteins: different but related functions evolved from a single
ancestral protein
e.g. trypsin, chymotrypsin, and elastase (protein choppers)
•
Homologous Proteins: structurally similar; may perform the same cellular
function, but in different species
•
•
e.g.: cytochrome-C
•
•
in duck & chickens = 2 variants
in yeast & horses = 48 variants
Mutation - change in primary amino acid sequence = a defective protein
•
e.g. sickle cell
Secondary structure :
Highly patterned sub-structures:
 helix or
 pleated sheet or
unstructured “random” chain
segments.
Spatial arrangement of protein backbone.
There can be many different secondary structures
present in one single protein molecule
Secondary Structure
The hydrogen
bonding between
the carbonyl
oxygen atom of
one peptide linkage
and the amide
hydrogen atom of
another peptide
linkage.
Helix
• H-bonds between every 4th amino acid
• Most are right-handed spirals
• R-groups point outward & toward Nterminal
Extensible structure – springy!
4 views of the a helix protein structure:
(a) Arrangement of protein backbone.
(b) Backbone with hydrogen-bonding shown.
(c) Backbone atomic detail shown.
R groups
point away
from the
long axis
of the helix
 pleated sheet
• Two types: parallel and anti-parallel
• R-groups point outward on sides
• NOT extensible – NOT springy
• Short segments (5-8 residues) that fold & H-bond
into ZIG-ZAG pleated sheets.
• Localized shapes.
• Resist pulling (tensile) forces = strength of
silk
 pleated sheet protein structure:
(a) emphasizing the H bonds (---) between chains.
(b) emphasizing pleats and location of R groups.