Amino Acids, Peptides, and Proteins

Proteins
• Occur in every living organism
• Are of many different types
• Have many different biological functions
• Keratin of skin and fingernails
• Fibroin of silk and spider webs
• Estimated 50,000 to 70,000 enzymes that
catalyze the biological functions of the human
body
• Made up of many amino acids linked together
 Amino Acids, Peptides, and Proteins
Amino acids are difunctional
• Contain both a basic amino group and an acidic carboxyl group

• Can join together into long chains by forming bonds between

the –NH2 of one amino acid and the –CO2H of another
• Peptides are chains with fewer than 50 amino acids
• Proteins are large chains of amino acids
19.1 Structures of Amino Acids
Amino acids exist in aqueous solution primarily in the
form of a dipolar ion, or zwitterion
Zwitterion
• German zwitter, meaning “hybrid”
• A neutral dipolar molecule in which the positive and
negative charges are not adjacent
 Structures of Amino Acids
Amino acid zwitterions
• Are internal salts
• Have large dipole moments
• Are soluble in water but are insoluble in hydrocarbons
• Are crystalline substances with relatively high melting points
• Are amphiprotic
• Can react as acids
• Reaction takes place
in an aqueous base
solution
• Loses a proton to
form an anion
• Can react as bases
• Reaction takes place
in an aqueous acid
solution
• Accepts a proton to
yield a cation
Structures of Amino Acids
Structures of Amino Acids
Structures of Amino Acids
Structures of Amino Acids
Structures of Amino Acids
All 20 amino acids found in proteins are α-amino acids
• The amino group in each is a substituent on the α carbon atom
– the one next to the carbonyl group
• 19 of the amino acids are primary amines, RNH2
• Differ in the side chain, the substituent attached to the α
carbon
• Proline, a secondary amine, is the only amino acid whose
nitrogen and α carbon atoms are part of the ring
Structures of Amino Acids
α Carbons of amino acids are chirality centers, except
for glycine, H2NCH2CO2H
• Nature uses only one enantiomer to build proteins
• Often referred to as L amino acids
• The nonnaturally occurring enantiomers are called
the D amino acids
Structures of Amino Acids
The 20 common amino acids can be acidic,
basic, or neutral, depending on their side
chains
• 2 (aspartic acid and glutamic acid) of the 20
have an extra carboxylic acid function in their
side chains
• 3 (lysine, arginine, and histidine) have basic
amino groups in their side chains
• 15 have neutral side chains
• Cysteine, a thiol, and tyrosine, a phenol, have
weakly acidic side chains that can be
deprotonated in a sufficiently basic solution
 Structures of Amino Acids
At physiological pH 7.3 within cells:
• The side-chain carboxyl groups of aspartic acid and
glutamic acid are deprotonated
• The basic side-chain nitrogens of lysine and arginine are
protonated
• Histidine contains a heterocyclic imidazole ring in its side
chain and is not basic enough to be protonated
• Only the pyridine-like nitrogen is basic
• The pyrrole-like nitrogen is nonbasic because its lone
pair of electrons is part of the 6π electron aromatic
imidazole ring
Isoelectric Points
Proteins have an overall pI because of the acidic or
basic amino acids they may contain
• Lysozyme has a preponderance of basic amino acids
and thus has a high isoelectric point (pI = 11.0)
• Pepsin has a preponderance of acidic amino acids
and a low isoelectric point (pI ~ 1.0)

The solubilities and properties of proteins with different

pI ’s are strongly affected by the pH of the medium
• Solubility in water is usually lowest at the isoelectric
point where the protein has no net charge, and higher
above and below the pI, where the protein is charged
 Isoelectric Points
Electrophesis uses isoelectric points to separate a mixture of
proteins into its pure constituents
1. A mixture of proteins is placed near the center of a strip of paper or
gel
2. The paper or gel is moistened with an aqueous buffer of a given pH
3. Electrodes are connected to the ends of the strip and an electric
potential is applied
4. Proteins separate according to charges (determined by the pH of the
buffer strip)
• Proteins with negative charges migrate slowly toward the
positive electrode
• Proteins with positive charges migrate slowly toward the
negative electrode
Different proteins migrate at different rates
19.4 Peptides and Proteins
Peptides and proteins are amino acid polymers
Residues
• An amino in a protein chain
• Joined together by amide bonds, or peptide bonds
An amino group from one residue forms an amide bond with the
carboxyl group of a second residue
• Alanylserine is the dipeptide that results when an amide bond is
formed between the alanine carboxyl and the serine amino group
Peptides and Proteins
Two dipeptides can result from reaction between
alanine and serine, depending on which carboxyl
group reacts with which amino group
• If the alanine amino group reacts with the serine
carboxyl, serylalanine results
Peptides and Proteins
Proteins
• The protein’s backbone is continuous chain of atoms
running the length of a protein or other polymer
• The repetitive sequence of –N–CH–CO–atoms

Polypeptides
• Convention for writing peptides:
• N-terminal amino acid on the left
• Peptides with the free –NH2 group

• C-terminal amino acid on the right

• Peptides with the free –CO2H group

• The name of the peptide is indicated using

abbreviations
• Alanylserine is abbreviated Ala-Ser or A-S

• Serylalanine is abbreviated Ser-Ala or S-A

Peptides and Proteins
Amide Bonds
• Amide nitrogens are nonbasic because their unshared
electron pair is delocalized by interaction with the carbonyl
group
• The overlap of the nitrogen p orbital with the p orbital of the
carbonyl group imparts a certain amount of double-bond
character to the C-N bond and restricts rotation around it
• The amide bond is planar
• The N-H is oriented 180º to the C=O
 Peptides and Proteins
A disulfide linkage, RS-SR

• A covalent bond in peptides

• Formed between two cysteine residues
• Links chains of peptides together
• Creates loops within a single chain of peptides
• Vasopressin, an antidiuretic hormone found in the pituitary
gland
Note: the C-terminal
End of vasopressin occurs
As the primary amide, -CONH2
19.8 Protein Structure
Proteins are classified according to their three-
dimensional shape
• Fibrous proteins
• Consist of polypeptide chains arranged side by side in
long filaments
• Collagen in tendons and connective tissue
• Myosin in muscle tissue
• Tough and insoluble in water
• Are used in nature as structural materials
• Globular proteins
• Usually coiled into compact, roughly spherical shapes
• Generally soluble in water and are mobile within cells
• Most of the 3000 or so enzymes are globular proteins
Protein Structure
Four levels for the structure of proteins
• The primary structure of a protein is simply the amino acid
sequence
• The secondary structure of a protein describes how
segments of the peptide backbone orient into a regular pattern
• The tertiary structure describes how the entire protein
molecule coils into an overall three-dimensional shape
• The quaternary structure describes how different protein
molecules come together to yield large aggregate structures
Primary structure is determined by sequencing the
protein
Secondary, tertiary, and quaternary structures are
determined by X-ray crystallography
• Not possible to predict computationally how a given
protein sequence will fold
Protein Structure
α Helix and the β-pleated sheet are the most common
secondary structures

α Helix
• A right-handed coil of the protein backbone
• Each turn of the helix contains 3.6 amino acid
residues, with a distance between the coils of 540
pm, or 5.4 Å
• The structure is stabilized by hydrogen bonds
between amide N-H groups and C=O groups four
residues away, with an N-H…O distance of 2.8 Å
• Almost all globular proteins contain many helical
segments
• Myoglobin is small globular protein containing 153
amino acid residues in a single chain
Protein Structure

(a) α Helix secondary (b) Myoglobin

structure of proteins
Protein Structure
β-pleated sheet
• The peptide chain is extended
• The hydrogen bonds occur between residues in
adjacent chains
• The neighboring chains run either in the same
direction (parallel) or in opposite directions
(antiparallel)
• The antiparallel arrangement is more common and
energetically more stable
• Concanavalin A consists of two identical chains of
237 residues with extensive regions of antiparallel β
sheets
 Protein Structure
(a) The β-pleated
sheet secondary
structure of
proteins

(b) The structure of

concanavalin A
 Protein Structure
The forces that determine the tertiary structures of a protein are
the same forces that act on all molecules, regardless of size,
to provide maximum stability
• Hydrophilic (water loving) interactions of the polar side chains of
acidic or basic amino acids
• Acidic or basic amino acids with charged side chains
congregate on the exterior of the protein, where they can be
solvated by water
• Amino acids with neutral, nonpolar side chains congregate on
the hydrocarbon-like interior of a protein molecule away from
the aqueous medium

Other factors for stabilization of a protein’s tertiary structure

• Formation of disulfide bridges between cysteine residues
• The formation of hydrogen bonds between nearby amino acid
residues
• The presence of ionic attractions, called salt bridges, between
positively and negatively charged sites on various amino acid side
chains within the protein
Protein Structure
Tertiary structure of a globular protein
• Held together by weak intramolecular attractions
• A change in temperature or pH is often enough to
disrupt the structures and causes denaturation of the
protein
• Denaturation occurs under mild conditions so that the

primary structure remains intact but the tertiary

structure unfolds from a specific globular shape to a
randomly looped chain
Protein Structure

Denaturation
• It is accompanied by changes in both
physical and biological properties
• Solubility is drastically decreased
• Most enzymes lose all catalytic activity
• Most denaturation is irreversible
• In some cases spontaneous renaturation of an
unfolded protein to its stable tertiary structure
occurs and is accompanied by a full recovery
of biological functions
Nucleic Acids
Nucleic Acids are the chemical carries of a cell’s genetic
information
• Deoxyribonucleic acid (DNA)
• Holds the information that determines the nature of a
cell
• Controls cell growth and division
• Directs biosynthesis of the enzymes and other proteins
required for cellular functions
• Ribonucleic acid (RNA)
• Nucleic acid derivatives such as ATP are involved as
phosphorylating agents in many biochemical
pathways
• Several important coenzymes, including NAD+, FAD,
and coenzyme A, have nucleic components
24.1 Nucleotides and Nucleic Acids
Nucleic acids are biopolymers
• Composed of nucleotides which are joined together to form a
long chain
• Nucleotide
• Composed of nucleosides bound to a phosphate group
• Nucleoside
• Composed of an aldopentose sugar linked through its
anomeric carbon to the nitrogen atom of a heterocyclic
purine or pyrimidine
Nucleotides and Nucleic Acids

DNA
• Sugar component is 2′ -deoxyribose (the prefix
2′ -deoxy indicates that oxygen is missing from the 2′
position of ribose)
• Contains four different amino bases
• Two substituted purines (adenine and guanine)
• Two substituted pyrimidines (cytosine and thymine)
RNA
• Sugar component is ribose
• Contains adenine, guanine, and cytosine
• Thymine is replaced by a closely related pyrimidine

base called uracil

Nucleotides and Nucleic Acids

The pyrimidines and purines found in DNA and RNA

 Nucleotides and Nucleic Acids

Structures of the four deoxyribonucleotides

 Nucleotides and Nucleic Acids

Structures of the four ribonucleotides

Nucleotides and Nucleic Acids

• In naming and numbering nucleotides,

positions on the sugars are given a prime
superscript to distinguish them from positions
on the amine base
• DNA and RNA differ dramatically in size
• Molecules of DNA have molecular weights up
to several billion
• Molecules of RNA are much smaller,
containing as few as 60 nucleotides, and have
a molecular weight as low as 22,000
Nucleotides and Nucleic Acids
• Nucleotides are linked together in DNA and RNA by
phosphodiester bonds between the phosphate group at C5′ on
one nucleotide and the 3′ -hydroxyl group of the sugar of
another nucleotide
• C3′ is one free hydroxyl group at the end of the nucleic
polymer (the 3′ end)
• C5′ is another free hydroxyl group at the end of the nucleic
polymer (the 5′ end)
• Sequence of nucleotides in a chain is described by starting at
the 5′ end and identifying the bases in order of occurrence
(using G, C, A, T or U)
24.2 Base Pairing in DNA:
The Watson-Crick Model
Samples of DNA isolated from different tissues
of the same species have the same
proportions of heterocyclic bases
Samples of DNA from different species often
have greatly different proportions of bases
• Composition of human DNA
• 30% each of adenine and thymine
• 20% each of guanine and cytosine
• Composition of the bacterium Clostridium
perfringens
• 37% each of adenine and thymine
• 13% each of guanine and cytosine
 Base Pairing in DNA:
The Watson-Crick Model
In 1953, James Watson and Francis Crick proposed the
secondary structure of DNA
• DNA under physiological conditions consists of two
polynucleotide strands
• Strands run in opposite directions and coil around each
other in a double helix
• The helix is 20 Å wide
• The two strands are
complementary and
are held together by
hydrogen bonds
between specific pairs
of bases
• A with T

• C with G
 Base Pairing in DNA:
The Watson-Crick Model
• There are 10 base pairs per turn
• Each turn is 34 Å in length
• The two strands of the double helix coil in such a way that two
kinds of “grooves” result
• A major groove 12 Å wide
• A minor groove 6 Å wide
• The grooves are lined with
hydrogen bond donors and
acceptors
• A variety of flat, polycyclic
aromatic molecules are able
to slip sideways, or intercalate,
between the stacked bases
• An organism’s genetic
information is stored as a
sequence of deoxyribonucleotides strung together in the DNA
chain
Base Pairing in DNA:
The Watson-Crick Model
“Central dogma of molecular genetics”
• The function of DNA is to store information and pass it to RNA
• The function of RNA is to read, decode, and use the information
received from DNA to make proteins
• Three fundamental processes take place:
• Replication – process by which identical copies of DNA are
made so the information can be preserved and handed down
to offspring
• Transcription – the process by which the genetic messages
are read and carried out of the cell nucleus to ribosomes,
where protein synthesis occurs
• Translation – the process by which the genetic messages
are decoded and used to synthesize proteins
DNA Sequencing

Two methods of DNA sequencing are available

• The Maxam-Gilbert method
• Uses chemical techniques
• Sanger dideoxy method
• Uses enzymatic reactions
• The more commonly used of the two
• Method responsible for sequencing the entire
human genome of 2.9 billion base pairs
• In commercial sequencing instruments, the
dideoxy method begins with a mixture of the
following:
• The restriction fragment to be sequenced
24.7 DNA Synthesis
Synthesis of short DNA segments, called
oligonucleotides or oligos
• A nucleotide has multiple reactive sites that must be
selectively protected and deprotected at the proper times
• Coupling of the four nucleotides must be carried out in the
proper sequence
• Automated DNA synthesizers allow the fast and reliable
synthesis of DNA segments up to 200 nucleotides in
length
• A protected nucleotide is covalently bonded to a solid
support
• One nucleotide at a time is added to the growing chain by
the use of a coupling reagent
• After the final nucleotide has been added, all the
protecting groups are removed and the synthetic DNA is
cleaved from the solid support
24.8 The Polymerase Chain
Reaction
Polymerase chain reaction (PCR)
• A method for amplifying small amounts of DNA to
produce larger amounts
• Invented by Kary Mullis in 1986
• PCR produces multiple copies of a given DNA
sequence
• Makes it possible to obtain several micrograms
(1 ug = 10-6 g; about 1011 nucleotides) in a few
hours when starting from less than 1 picogram of
DNA with a chain length of 10,000 nucleotides
(1 pg = 10-12 g; about 100,000 molecules)
 Carbohydrates
Carbohydrate
• Broad class of polyhydroxylated aldehydes and ketones
commonly called sugars
• Synthesized by green plants during photosynthesis
• Name derived from glucose
• Glucose was the first simple carbohydrate obtained in pure
form
• Molecular formula of glucose, C6H12O6, was thought to be a
“hydrate of carbon, C6(H2O)6”
• ~ 50% of the dry weight of earth’s biomass consists of
glucose polymers
Carbohydrates

Carbohydrates act as chemical intermediates by which

solar energy is stored and used to support life on
earth
 21.1 Classification of Carbohydrates
Carbohydrates are classed as
simple or complex
• Simple sugars , or
monosaccharides
• Carbohydrates like glucose
and fructose that cannot be
converted into more simple
sugars by hydrolysis
• Complex carbohydrates
• Made up of two or more
sugars
• Sucrose is a disaccharide
comprised of one glucose
and one fructose
• Cellulose is a
polysaccharide comprised
of several thousand linked
glucose units
 21.7 The Eight Essential
Monosaccharides
Humans need to
obtain eight
monosaccharides
for proper
functioning
• All are used for
synthesis of
glycoconjugate
components of
cell walls
The Eight Essential
Monosaccharides
• Fucose is a deoxy sugar
• The –OH group at C6 is replaced by –H
• N-Acetylglycosamine and N-acetylgalactosamine are amide
derivatives of amino sugars
• The –OH group at C2 is replaced by an –NH2 group
• N-Acetylneuraminic acid is the parent compound of sialic acids
• Eight essential monosaccharides all synthesized from D-glucose
Disaccharides

Lactose
• Lactose is a disaccharide that occurs naturally in
human and cow’s milk
• Lactose is a reducing sugar and exhibits mutarotation
• Lactose contains a 1 4-β-link between C1 of
galactose and C4 of glucose
Disaccharides
Sucrose
• Sucrose is ordinary table sugar and is among the
most abundant pure organic chemicals in the world
• Sucrose is obtained from sugar cane (20% sucrose by
weight) or from sugar beets (15% sucrose by weight)
• Sucrose is a disaccharide that consists of 1 equivalent
of glucose and 1 equivalent of fructose
• 1:1 mixture often referred to as invert sugar because
the sign of optical rotation inverts (changes) during
hydrolysis from sucrose ([α]D = +66.5) to a
glucose/fructose mixture ([α]D = -22.0)
• Honeybees have enzymes called invertases that
catalyze the hydrolysis of sucrose
• Honey is primarily a mixture of sucrose, glucose, and
fructose
Disaccharides

• Sucrose is not a reducing sugar and does not

undergo mutarotation
• Glucose and fructose are joined by a glycoside link at
the anomeric carbons of both sugars, C1 of glucose
and C2 of fructose
21.9 Polysaccharides and Their
Synthesis
Polysaccharides are complex carbohydrates in
which tens or even thousands of simple
sugars are linked together through glycoside
bonds
• Only one free anomeric –OH on end of long
polymeric chain
• Not reducing sugars
• Do not exhibit noticeable mutarotation
• Cellulose and starch are the two most widely
occurring polysaccharides
Polysaccharides and Their Synthesis

Cellulose
• Cellulose consists of several thousand D-glucose units linked by
1 4-β-glycoside bonds like those in cellobiose
• Used by nature to impart strength and rigidity to plants
• Used commercially as raw material for cellulose acetate
(acetate rayon) and cellulose nitrate (guncotton) the major
ingredient of smokeless gun powder
Polysaccharides and Their Synthesis

Starch and Glycogen

• Starch is a polymer of glucose found in
potatoes, corn, and cereal grains
• Monosaccharide units are linked by 1 4-α-
glycoside bonds like those in maltose
• Starch is separated into two fractions:
• Amylose accounts for about 20% by weight of
starch
• Amylopectin accounts for about 80% by weight of
starch
• Amylose is nonlinear and contains 1 6-α-glycoside
branches approximately every 25 glucose units
Polysaccharides and Their Synthesis
Polysaccharides and Their Synthesis
Polysaccharides and Their Synthesis

• Starch is digested in the mouth and stomach by α-glycosidase

enzymes which catalyze the hydrolysis of α-glycoside links but
leave the β-glycoside links in cellulose untouched
• Humans can digest potatoes and grains but cannot digest
grasses and leaves
• Glycogen is a polysaccharide that serves as long-term storage
of energy for the human body
• Glycogen contains both 1 4 and 1 6 links