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Lecture notes Biomedical Sciences (BSc) BB1701 Biochemistry
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Lecture Notes on BB1701 Biochemistry at Brunel University
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TEST BANK FOR BIOCHEMISTRY, 9TH EDITION, LUBERT STRYER, JEREMY BERG, JOHN TYMOCZKO, GREGORY GATTO
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TEST BANK FOR BIOCHEMISTRY, 7TH EDITION: BY JEREMY M. BERG
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Biochemistry Exam 2 Notes / Study Guide / Summarized
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Biochemistry – Chapter 2: Protein composition and structure- Proteins are the most versatile macromolecules in living systems and serve crucial functions
in essentially all biological processes
- Functions:
o Catalysts
o Transport and store other molecules such as oxygen
o Provide mechanical support and immune protection
o Generate movement
o Transmit nerve impulses
o Control growth and differentiation
- Key properties
o Proteins are linear polymers built of monomer units called amino acids.
Primary structure: a sequence of linked amino acids
Secondary structure: a three-dimensional structure formed by hydrogen
bonds between amino acids near one another
Tertiary structure: a three-dimensional structure formed by long-range
interactions between amino acids.
Quaternary structure: a three dimensional structure in which the functional
protein is composed of several distinct polypeptide chains
Protein function depends directly on this three-dimensional structure
o Proteins contain a wide range of functional groups
Alcohols
Thiols
Thioesters
Carboxylic acids
Carboxamides
Basic group
Most of these groups are chemically reactive. Their reactive properties are essential
to the function of enzymes.
o Proteins can interact with one another and with other biological macromolecules to
form complex assemblies. Examples are macromolecular machines that
Replicate DNA
Transmit signals
Carry out many other essential processes
o Some proteins are quite rigid, whereas others display a considerable flexibility
Rigid proteins function as structural elements in the cytoskeleton or in
connective tissue
Flexible proteins act as hinges, springs or levers that are crucial to protein
function, to the assembly of proteins with one another and with other
molecules into complex units, and to the transmission of information within
and between cells.
2.1 Proteins are built from a repertoire of 20 amino acids
- An α-amino acid consists of a central carbon atom, called the α-carbon, linked to an amino
group, a carboxylic group, a hydrogen atom, and a distinctive R group (side chain).
- With four different groups connected to the tetrahedral α-carbon atoms, α-amino acids are
chiral; they may exist in one or the other of two mirror-image forms, called the L isomer and
the D isomer.
,- L isomers have an S absolute configuration. The counter clockwise direction of the arrow
from highest to lowest priority substances indicates that the chiral centre is of the S
configuration
- Only L amino acids are constituents of proteins. Evidence shows that L amino acids are
slightly more soluble than a racemic mixture of D and L amino acids which tend to form
crystals
- Amino acids in solution at neutral pH exist predominantly as dipolar ions (zwitterions). In the
dipolar form, the amino group is protonated (-NH 3+) and the carboxyl group is deprotonated
(-COO-).
o In acid solution both groups are protonated and in basic solution both groups are
deprotonated
- The twenty side chains vary in size, shape, charge, hydrogen-bonding capacity, hydrophobic
character and chemical reactivity
- Classification of side groups:
o Aliphatic side chains – only contain C and H arranged in straight and branched
chains. These are saturated side chains so there are no double bonds.
Hydrophobicity increases with chain length.
Examples are glycine, alanine, valine, leucine and isoleucine.
Proline also has an aliphatic side chain, but it differs from other members
because its side chain is bonded to both the nitrogen and the α-carbon
atoms. This forms a cyclic structure and it restricts polypeptide geometry
o Aromatic side chains – contain benzene ring
Examples are phenylalanine, tyrosine and tryptophan
o Hydroxyl side chains – contain hydroxyl (OH) group
Hydrophilic, very reactive
Examples are serine and threonine
o Sulphur-containing chains – contain sulphur atoms
Examples are methionine and cysteine
o Basic side chains – positively charged amino acids
Examples are histidine, lysine and arginine
They are highly hydrophilic
Histidine contains an imidazole group, an aromatic ring that also can be
positively charged
o Acidic side chains – negatively charged amino acids
Examples are aspartate, glutamate, asparagine and glutamine
Asparagine and glutamine are uncharged derivatives of the acidic amino
acids aspartate and glutamate. Each of these two amino acids contains a
terminal carboxamide in place of a carboxylic acid.
- Abbreviations for amino acids
, Amino acids Three-letter One-letter
abbreviation abbreviation
Alanine Ala A
Arginine Arg R
Asparagine Asn N
Aspartic acid Asp D
Cysteine Cys C
Glutamine Gln Q
Glutamic acid Glu E
Glycine Gly G
Histidine His H
Isoleucine Ile I
Leucine Leu L
- How did this
Lysine Lys K
particular set
Methionine Met M
of amino acids
Phenylalanine Phe F
become the
Proline Pro P
building blocks
Serine Ser S
of proteins?
Threonine Thr T
o They are
Tryptophan Trp W
diverse: their
Tyrosine Tyr Y
structural and
Valine Val V
chemical
Asparagine or Asx B
properties
aspartic acid
span a wide
Glutamine or Glx Z
range of
glutamic acid
proteins with
the versatility to assume many functional roles.
o Many of these amino acids were probably available from reactions that took place
before the origin of life.
o Other possible amino acids may have been too reactive
2.2 Primary Structure: amino acids linked by peptide bonds to form polypeptide chains
- Proteins are linear polymers formed by linking the α-carboxyl group of one amino acid to the
α-amino group of another amino acid (peptide bond). The formation of a dipeptide from two
amino acids is accompanied by the loss of a water molecule.
- The biosynthesis of peptide bonds requires an input of free energy.
- Peptide bonds are quite stable kinetically because the rate of hydrolysis is extremely slow
- A series of amino acid joined by peptide bonds form a polypeptide chain, and each amino
acid unit in polypeptide is a called a residue. A polypeptide chain has polarity because its
ends are different. The amino end is taken to be the beginning of a polypeptide chain
- Examination of the geometry of the protein backbone reveals several important features:
o The peptide bond is essentially planar → all amino acids in the peptide bond lie in
the same plane
o The peptide bond resonates between a single bond and a double bond → rotation
about this bond is prevented and thus the conformation of the peptide backbone is
constrained
o The peptide bond is uncharged allowing polymers of amino acids linked by peptide
bonds to form tightly packed globular structures
- Two configurations are possible for a planar peptide bond. In the trans configuration the two
α-carbon atoms are on opposite sides of the peptide bond. In the cis configuration these
, groups are on the same side of the peptide bond. Almost all peptide bonds in proteins are
trans. This is because there are steric clashes between groups attached to the α-carbon
atoms that hinder the formation of the is form but do not arise in the trans configuration.
- The bonds between the amino group and the α-carbon atom and between the α-carbon
atom and the carbonyl group are single bonds → rotation permitted → proteins can be
folded in different ways. The angle of rotation about the bond between the nitrogen and the
α-carbon atom is called phi (φ). The angle of rotation about the bond between the α-carbon
atom and the carbonyl atoms is called psi (ψ). A clockwise rotation corresponds to a positive
value (between -180° and +180°). The ψ and φ angles determine the path of the polypeptide
chain.
- Not all ψ and φ angles are possible due to steric collisions. The allowed values can be
visualised on a plot called a Ramachandran diagram.
0.3 Secondary structure: Polypeptide chains can fold into regular structures
- Secondary structure is the spatial arrangement of amino acid residues that are nearby in the
sequence.
- Alpha helices, beta strands, and turns are formed by a regular pattern of hydrogen bonds
between the peptide NH and CO groups of amino acids that are near one another in the
linear sequence.
- Periodic structures
o The first proposed structure by Pauling and Corey was the α-helix. This is a rodlike
structure. A tightly coiled backbone forms the inner part of the rod and the side
chains extend outward in a helical array.
It is stabilised by hydrogen bonds between the NH and CO groups of the
main chain. The CO group of each amino acid forms a hydrogen bond with
the NH group of the amino acid that is four residues ahead in the sequence.
Each residue is related to the next one by a rise (translation) of 1.5Å
(0.15nm) along the helix and a rotation of 100°, which give 3.6 amino acid
residues per turn of helix.
The pitch of the α helix is the length of one complete turn along the helix
axis and is equal to the product of the rise and the number of residues per
turn → 1.5 x 3.6 = 5.4Å (0.54nm)
The screw sense describes the direction in which a helical structure rotates
with respect to its axis. This can be right-handed or left-handed.
The Ramachandran diagram shows that both helices lie in regions of allowed
conformations. However, right-handed helices are energetically more
favourable because there is less steric clash between the side chains and the
backbone. All α helices found in proteins are right-handed
Not all amino acids can be readily accommodated in an α helix. Some of
them branch at the β-carbon atom, which tends to destabilise α helices
because of steric clashes. Others tend to disrupt α helices because their side
chains contain hydrogen-bond donors or acceptors in close proximity to the
main chain, where they compete for main-chain NH and CO groups. Proline
also is a helix breaker because it lacks NH groups and because its ring
structure prevents it from assuming the φ value to fit into an α helix
The α helical content of proteins ranges widely, from none to almost 100%.
About 25% of all soluble proteins are composed by α helices connected by
loops and turns of the polypeptide chain. Single α helices are usually less
than 45Å long.
o Another structure is the β pleated sheet. It is composed of two or more polypeptide
chains called β strands. A β strand is almost fully extended and these are sterically
allowed
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