Transcript Proteins - NIU Department of Biological Sciences

Proteins
Proteins
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The most important type of
macromolecule.
Roles:
Structure: collagen in skin, keratin in hair,
crystallin in eye. Also slimy substances
like mucus and the bacterial capsule.
Enzymes: all metabolic transformations,
building up, rearranging, and breaking
down of organic compounds, are done by
enzymes, which are proteins.
– Other macromolecules such as
carbohydrates and lipids are created by
enzymes from smaller molecules.
Transport: oxygen in the blood is carried by
hemoglobin, everything that goes in or out
of a cell (except water and a few gasses) is
carried by proteins.
Also: nutrition (egg yolk), hormones,
defense, movement
Enzymes are usually roughly globular,
while structural proteins are usually fibershaped. Proteins that transport materials
across membranes have a long segment of
hydrophobic amino acids that sits in the
hydrophobic interior of the membrane.
Levels of Structure
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A polypeptide is one linear chain of amino acids. Each gene produces one polypeptide. A
protein may contain one or more polypeptides. Proteins also sometimes contain small helper
molecules (co-factors) such as heme.
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The primary structure (1o) is just the sequence of amino acids in the polypeptide.
The secondary structure (2o) is local folding patterns, mostly alpha helix and beta sheet.
The tertiary structure (3o) is the overall folding pattern of the entire polypeptide.
The quaternary structure (4o) is the joining of individual polypeptides (subunits) into an active
protein. Proteins that are just a single monomeric polypeptide have no quaternary structure.
Amino Acids
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Amino acids are the subunits of proteins.
“Amino acid” is a very general term, but we mostly refer to the 20 amino acids
coded in DNA.
– Or 22: some bacteria also code for selenocysteine and pyrolysine.
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The properties of the protein are determined by the R-groups on the amino acids.
A few types:
– hydrophobic (found in membranes and protein interiors): Leucine, isoleucine, valine,
methionine, phenylalanine, tryptophan
– positively charged (basic): lysine, arginine, histidine
– negatively charged (acidic): aspartate, glutamate
– polar but uncharged: serine, threonine, asparagine, glutamine
– chain bending (imino acid): proline
– disulfide bridge forming: cysteine
– Small: glycine, alanine, serine
Another View of Amino Acid Properties
One Letter
Amino Acid
Codes
Protein Folding
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After the polypeptides are synthesized by the cell, they
spontaneously fold up into a characteristic conformation which
allows them to be active. The proper shape is essential for
active proteins. For most proteins, the amino acids sequence
itself is all that is needed to get proper folding.
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Proteins fold up because they form hydrogen bonds between
amino acids. The need for hydrophobic amino acids to be away
from water also plays a big role. Similarly, the charged and
polar amino acids need to be near each other.
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However, chaperone proteins assist the folding of some proteins,
and they help re-fold denatured proteins after events like heat
shock.
The joining of polypeptide subunits into a single protein also
happens spontaneously, for the same reasons.
Proteins fold into a configuration that minimizes their free
energy.
Denaturation (e.g. by heating or alkaline conditions) means the
unfolding of proteins into different, non-functional
conformations.
It should be noted that some proteins have more than one stable
configuration, prions for example. It is also possible that
certain regions of proteins have no single stable configuration,
more like a glass than a crystal.
Prions
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A prion is an “infectious protein”.
Prions are the agents that cause mad cow disease (bovine spongiform
encephalopathy), chronic wasting disease in deer and elk, scrapie in sheep,
and Creutzfeld-Jakob syndrome in humans.
These diseases cause neural degeneration. In humans, the symptoms are
approximately those of Alzheimer’s syndrome accelerated to go from onset
to death in about 1 year. Fortunately, the disease is very hard to catch and
very rare, and they usually have a long incubation time. No cure is known,
and not enough is known about how it is spread to do a thorough job of
preventing it. Avoid eating brains is a good start though.
The prion protein (PrP) is normally present in the body. Like all proteins, it
is folded into a specific conformation, a state called PrPC. Prion diseases
are caused by the same protein folded abnormally, a state called PrPSc. A
PrPSc can bind to a normal PrPC protein and convert it to PrPSc. This
conversion spreads throughout the body, causing the disease to occur. It is
also a form of inheritance that does not involve nucleic acids.
Peptide Chain
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The amino acids are linked together by
peptide bonds, which are the same as
amide bonds.
The ribosome synthesizes these bonds
through a condensation/dehydration
reaction
The peptide backbone is made up of
the C and N involved in the peptide
bond, plus the Cα that links them.
The beginning of every protein is the
N-terminus and the end is the Cterminus.
– This means that there is a free amino
group at the N terminus and a free acid
group at the C terminus.
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Although all proteins are synthesized
with a methionine (or N-formyl
methionine in bacteria) at the N
terminus, this amino acid is often
removed by an enzyme shortly after
protein synthesis.
Peptide Bond Conformation
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The peptide bond, the C=O bonded to
N-H, is a rigid planar structure, with the
O and N atoms in trans.
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Due to delocalized electrons over the
whole 4 atom group, similar to the
aromatic ring
An exception: proline creates a bond in
the cis configuration, because the N is
bonded to the alpha carbon through the
side chain.
Thus there are 2 bonds in the backbone
that can rotate, the bonds leading to the
Cα .
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The bond to the N is called phi (φ) and
the bond to the C is called psi (ψ).
Phi and psi have preferred angles,
caused by hydrogen bonding and steric
hindrance.
Ramachandran Diagrams
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When the phi and psi angles from a large number of proteins are plotted, it is found that
most amino acids fall into a small part of the possible bond angles.
These diagrams give rise to the notion of two main secondary structures, the alpha helix and
the beta sheet.
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There are also left-handed alpha helices and epsilon structures, but they are rarer.
These structures are held together by hydrogen bonds between the atoms of the peptide
bond.
Secondary Structures in Proteins
• Alpha helices are generally rather
short, just one or a few turns of the
helix.
• Beta sheets come in a variety of
forms, some containing just a single
strand and others having several
strands, sometimes parallel and
sometimes antiparallel.
– Beta sheets are rarely planar—they
usually roll up in various ways
– Connecting the strands of a beta
sheet are tight turns called beta
turns, which usually contain amino
acids with very small side chains,
such as glycine.
Protein Structure
• Proteins can be described
as having various regions
of alpha helix and beta
sheet, with loops in
between that aren’t part of
the regular secondary
structures.
Between Secondary and Tertiary
Structures
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Secondary structures are local elements, primarily
alpha helices and beta sheets. Tertiary structure is
the folding pattern of the entire protein.
Alpha helices and beta sheets are often combined
into specific elements called folds or supersecondary
structures, which can be found in many different
proteins.
– The two shown here are the Greek key motif,
composed of 4 beta sheet strands and the TIM barrel,
composed of 8 alpha helices and 8 beta sheet strands.
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Proteins are often thought of as being composed on
one or more domains. Each domain is a relatively
independent unit, separated from others on the linear
polypeptide. Introns generally fall between domains
in the DNA.
Bioinformatics of Proteins
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The goal of bioinformatics is to determine the organism’s phenotype from the
DNA sequence. From an evolutionary standpoint, phenotype is what natural
selection acts on, and thus phenotype is the most conserved element between
closely related species.
The phenotype is primarily determined by the organism’s proteins. In turn,
protein function is determined by the three-dimensional structure of the
protein. Structure is highly conserved in evolution.
It is very easy to go from a DNA sequence to a protein primary structure. The
only real complications are determining the exact start site and location of
introns. Protein sequence is more conserved than DNA sequence, due to the
degeneracy of the genetic code and the fact that many amino acid substitutions
have little effect on the protein.
However, going from primary sequence to three dimensional structure has
proven to be quite difficult. Large amounts of resources are devoted to this
problem, and we will look at some of this later.
But the point is, we try to infer function primarily by comparing protein
sequences between genes of known function and new genes. Looking at
protein structure would work much better, but it is currently too difficult.
Structure Conservation
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A good example of 3-dimensional
structure being conserved in the
absence of sequence conservation
is the fructose bis-phosphate
aldolase, the glycolytic enzyme that
splits fructose 1, 6-bis-phosphate
into glyceraldehyde 3-phosphate
and dihydroxyacetone phosphate
(reversibly).
Eukaryotes, Bacteria, and Archaea
all have this enzyme, but the lack
of sequence homology caused them
to be divided into class 1, class 1A,
and class 2 enzymes.
X-ray crystallography shows that
all three have a common structure,
the TIM barrel, composed on
alternating alpha helices and beta
sheets.