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MBG301 CH3 Introduction To Proteins Primary Level

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MBG 301

General Biochemistry I

Introduction to Proteins: The Primary Level of

Protein Structure
1
23.10.2022 2

Biochemistry: Concepts and Connections

Second Edition, Global Edition

Chapter 5
Introduction to Proteins: The
Primary Level of Protein
Structure

Dean R. Appling
Spencer J. Anthony-Cahill
Christopher K. Mathews

Outline

5.1 Amino Acids

5.2 Peptides and the Peptide Bond
5.3 Proteins: Polypeptides of Defined Sequence
5.4 From Gene to Protein
5.5 From Gene Sequence to Protein Function
5.6 Protein Sequence Homology
5.7 Tools of Biochemistry

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 6
A fundamental
concept in
biochemistry is
that the structure
of a given
biomolecule is
directly related to
its function.

Myoglobin;
a relatively small
protein that functions
primarily in oxygen
binding and storage in
animal tissues.

5.1 Amino Acids

Overview of Protein Synthesis in Eukaryotic

Cells
• DNA is transcribed to
form messenger RNA
(mRNA) in the nucleus
• mRNA is exported to
the cytoplasm
• mRNA is translated into
a linear sequence of
amino acids that folds
into a 3D structure

Figure 1: The relationship

between amino acid side chains
and protein conformation
The defining feature of an amino
acid is its side chain (at top, blue
circle; below, all colored circles).
When connected together by a
series of peptide bonds, amino
acids form a polypeptide, another
word for protein. The polypeptide
will then fold into a specific
conformation depending on the
interactions (dashed lines)
between its amino acid side
chains.
© 2010 Nature Education

The Structure of α-Amino Acids

• α-Carbon is central to an amino

acid: amino group, carboxylic
acid, and amino acid-specific
side chain (R group) are
attached to it
– when R is not a hydrogen
atom, the α-carbon is an
asymmetric center
• At neutral pH (~7) the amino
acid nitrogen is protonated and
the carboxylic acid is
deprotonated to yield the
zwitterion
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 11

α-Amino Acid Stereochemisty (1 of 2)

The asymmetry of biomolecules plays a critical role in determining their structures
and functions, so we need to understand the basic stereochemistry of amino acids
to understand the biochemistry of proteins.

• The ball and stick model shows the

3D arrangement of the atoms in an
α-amino acid
• When four different groups are
attached to a carbon atom, that atom
is said to be chiral, or a
stereocenter, or an asymmetric
carbon
• The Fischer projection in the bottom
figure (right) is a 2D stereochemistry
representation
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 12

α-Amino Acid Stereochemisty (2 of 2)

• All α-amino acids (20), except glycine, contain an
asymmetric α-carbon. Then two distinguishable
stereoisomers exist.
• L-alanine is the mirror image of ᴅ-alanine
• L-alanine and ᴅ-alanine are enantiomers

• The D- and L- system is named after the Latin dexter and

laevus, which translate to left and right.
• A D-isomer is defined as a stereoisomer which rotates
light that is polarized in a clockwise direction. This differs
from an L-isomer which rotates light in an anticlockwise
direction.

Classification of Naturally Occurring Amino

Acids (1 of 2)

Classification of Naturally Occurring Amino

Acids (2 of 2)

General Properties of Amino Acids (1 of 5)

The lower the pKa value, the stronger the acid.

• Chemical analysis of naturally occurring proteins shows

that nearly all of their constituent amino acids have the L
form.
• Each of the three major classes of biological
macromolecules (polypeptides, polysaccharides, and
polynucleotides) exhibits a strong preference for one
stereoisomer class or the other.
• Most naturally occurring polysaccharides prefer D-sugars,
as do DNA and RNA.

• The preference for L-amino acids in natural proteins has

two important consequences,
1. The surface of any given protein, which is where the
interesting biochemistry occurs, is asymmetric..
2. The stereochemistry of the amino acids promotes the
formation of so-called secondary structure in proteins
(i.e., a helices and b strands), which, in turn, is a major
determinant of the overall structure of proteins.

Properties of Amino Acid Side Chains: Classes of a-Amino

Acids > aliphatic or aromatic character, polarity of the
side chain, and presence or absence of ionizable groups.
Amino Acids with nonpolar Aliphatic chains
• Glycine, alanine, valine, leucine, and isoleucine have
aliphatic side chains >> hydrophobic
• Isoleucine > R = -CH(CH3 )CH2 CH3
• Glycine > R=-H ( it is frequently found on the surfaces of
proteins due to its ability to form tight turns in protein
structures)

Amino Acids with

Nonpolar Aromatic Side
Chains
• phenylalanine, tyrosine,
and tryptophan

Amino Acids with Polar Side Chains

Serine, cysteine, threonine, asparagine, and glutamine
As a result, these five amino acids are most often found on the surfaces of
proteins, where they can contact the aqueous environment in cells or in
circulation.

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
General Properties of Amino Acids (2 of 5) 23.10.2022 22

UV absorption spectra of tyrosine and tryptophan

• Proteins can be quantified by
examining the UV absorbance
at 280 nm, which is dominated
by tyrosine (Tyr) and tryptophan
(Trp) > aromatic amino acid
residues
• detection and/or quantification
of proteins
• In comparison, nucleic acids
absorb most strongly at 260 nm

Amino Acids with Positively Charged (Basic) Side Chains

• Histidine, lysine, and arginine

• The basic amino acids are strongly polar, so they are
usually found on the exterior surfaces of proteins, where
they can be hydrated by the surrounding aqueous
environment,

Amino Acids with Negatively Charged (Acidic) Side Chains

• Aspartic acid (aspartate) and glutamic acid (glutamate)

• Like the basic and polar amino acids, Asp and Glu are
hydrophilic and tend to be on the surface of a protein
molecule, in contact with the surrounding water or a bound
substrate.

Rare Genetically Encoded Amino Acids

• Besides the 20 common amino acids that are coded for in

DNA and are incorporated directly into proteins by
ribosomal synthesis, there are two other amino acids
encoded in gene sequences—namely,
• selenocysteine, which is widely distributed but found in few
proteins, and
• pyrrolysine, which is restricted to
a few archaea and eubacteria

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
General Properties of Amino Acids (3 of 5) 23.10.2022 26

pKa values of ionizable amino acid groups

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
General Properties of Amino Acids (4 of 5) 23.10.2022 27

Titration curve of histidine

• The charge on histidine varies
from +2 to −1, depending on
pH
• Orange dots correspond to
the pKa values for the red
hydrogen atoms
• The green dot corresponds to
the pI (net charge on the
molecule is zero)

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
General Properties of Amino Acids (5 of 5) 23.10.2022 28

Posttranslational modification of amino acids

• Posttranslational
modifications may function
in signaling pathways,
calcium binding, stabilizing
structures such as collagen,
or play roles in gene
expression or suppression

5.2 Peptides and the Peptide Bond

Peptide Bond Formation between Amino

Acids
• The condensation of two
amino acids forms a
peptide bond “amide
bond” and releases
water >> peptides
• This reaction is not
thermodynamically
favorable and is coupled
to ATP hydrolysis during
protein biosynthesis

During ribosomal protein synthesis, amino acids are added to

only one end of the growing peptide (C-terminal)

Structure of the Peptide Bond

peptide bond,
little twisting possible

Delocalization of electrons creates a planar and stable

peptide bond
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 32

• X-ray crystallography data of proteins shows that the

group of atoms about the peptide bond exist in two
possible configurations, trans and cis, which are related by
rotation around the CCO - N bond (shown above in blue):

• The peptide bond is nearly planar, and the trans form is favored.

Peptide Bond Cleavage (1 of 2)

> a peptide bond could be formed by the elimination of a water
molecule between two amino acids.
> process is thermodynamically disfavored in an aqueous environment
like the one found in cells.

• ΔGº¢ for peptide bond hydrolysis is about –10 kJ/mol.

However, peptides are stable unless strong acid at high
temperature (boiling in 6N HCL for 12–24 h) or a catalyst is
present
• Proteases are enzymes that cleave specific peptide bonds

Peptide Bond Cleavage (2 of 2)

Sequence specificities for proteases
Some of these
enzymes
are secreted into the
digestive tracts of
animals, where they
catalyze the initial
breakdown
of proteins to smaller
peptides,

• If polypeptides are thermodynamically unstable (like

polynucleotides), then how can they be synthesized in the
aqueous medium of the cell?
• The unfavorable synthetic reaction is coupled to the
favorable hydrolysis of certain organophosphate
compounds. In fact, every amino acid must be activated by
an ATP-driven reaction before it can be incorporated into
proteins.

Oligopeptides
The tetrapeptide Glu–Gly–Ala–Lys
(EGAK in one-letter code)

The direction of peptides

N >>>> C

EGAK = KAGE

Oligopeptides are peptide chains consisting of usually only

3–15 residues, while polypeptides contain more than 15
residues.
Polypeptides greater than 50 residues are generally referred
to as proteins (most globular proteins contain 250–600
amino acid residues).
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 37

Important Peptide Regions

N atoms are shown in blue, O atoms are red, C atoms are green, and H atoms are white

First, it is important to identify the N- and C- termini. What is the sequence

of this peptide?
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 38

Common Modifications of Amino- and

Carboxy-Termini in Peptides

Groups that may block N- or C-termini in proteins.

Peptides and Proteins as Polyampholytes (1 of 2)

affect its stability and/or functional properties

As pH increases the overall charge on a peptide will become

more negative; as pH decreases it will become more positive.
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Peptides and Proteins as Polyampholytes (2 of 2)
23.10.2022 40

Influence of the local electrostatic environment on the side chain pKa:

• Unperturbed, the pKa of

glutamic acid is 4.2
• In proximity to a negative
charge, the pKa of the glutamic
acid is raised
• In proximity to a positive
charge, the pKa of glutamic acid
is lowered

5.3 Proteins: Polypeptides of Defined

Sequence

The Amino Acid Sequences of Human and

Whale Myoglobin (1 of 2)
although the two myoglobin
sequences are similar, they are not
identical.

The amino acid sequences of sperm whale myoglobin and human myoglobin.

The Amino Acid Sequences of Human and

Whale Myoglobin (2 of 2)
• Identical amino acids are the same in both sequences
• Conservative mutations (substitutions) conserve the
chemical property (e.g., charge; Asp for Glu) and/or the
size of the amino acid, while nonconservative
mutations involve larger differences in polarity and size
(Asp for Ala)
• Evolutionary relationships are inferred from protein amino
acid sequences
• If the amino acid side chain is in the interior of the protein,
even a “conservative” substitution could have dramatic
consequences for the stability and/or function of the
protein.
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 44

Protein Sequence Analysis Can Be

Complicated by Multiple Chains (1 of 2)
• Insulin has two chains linked by disulfide bonds

The primary structure of bovine insulin.

Protein Sequence Analysis Can Be

Complicated by Multiple Chains (2 of 2)
• Protein amino acid sequence analysis by DNA sequencing
of the gene is rapid and inexpensive, but does not identify
posttranslational modifications, so a combination of
approaches must be used
• Biosynthesis of insulin involves a variety of post-
translational modifications

5.4 From Gene to Protein

In fact, triplets of nucleotides (codons )

The Genetic Code are used to code for each amino acid,
allowing 43 , or 64, different
combinations

• The standard genetic code

shows the codons, or base
triplets, that correspond to each
amino acid residue
• The AUG start codon places a
Met at the beginning of
eukaryotic proteins,
• Three codons, UAA, UGA, and
UAG, are stop codons, which
signal termination of translation

Transcription and Translation

In many cases the N-terminal residue or even several residues will be

removed in the cell by specific proteases during, or immediately after,
translation.

When a polypeptide chain is released

Insulin Processing (1 of 2) from a ribosome following translation, its
synthesis is not necessarily finished.
- folding

Insulin Processing (2 of 2)

• Insulin is synthesized as an inactive precursor,

preproinsulin, which undergoes enzymatic cleavage to
proinsulin, followed by folding and disulfide bond
formation, followed by additional enzymatic proteolysis
• This allows insulin, like other peptide or protein hormones,
to be synthesized and stored as an inactive precursor,
available for rapid mobilization on demand.
• Because proinsulin is not an active hormone, it can be
produced and stored in the pancreas at high
concentrations, whereas similar high levels of active
insulin would be toxic. The proinsulin can then be
converted to insulin by proteolysis to rapidly secrete active
insulin when needed by the body.
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 51

5.5 From Gene Sequence to Protein

Function

Alignments of Proteins—Globins

Sequence (BLAST) alignment between human myoglobin

and human α-globin, both heme-containing proteins

• To summarize, given a newly discovered gene sequence, it

is possible to make a best guess as to the function of the
gene product based on a search of protein sequence
databases using BLAST.
• Gene seq: Some cancer treatments target a specific
receptor that is expressed on the surface of the cancer
cells. If a patient lacks the gene for that receptor, the
treatment will be ineffective.
• «personalized medicine»

5.6 Protein Sequence Homology

Alignments of Proteins – Cytochromes c

• Sequence alignment of cytochrome c, a mitochondrial

respiratory protein, from 27 organisms
• The more similar two homologous protein sequences are,
the more closely they are related evolutionarily
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 56

Phylogenetic Tree Deduced from the Multiple

Sequence Alignment of Cytochrome c

Consensus Sequences

A consensus sequence (here for cytochrome c) allows an

investigator to identify the most highly conserved amino acid
residues

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Recombinant Protein Expression (1 of 2)
Protein expression vector
• Expression vectors
are small, circular
DNA molecules and
contain an origin of
replication which
allows multiple
copies to be
produced in the cell

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Recombinant Protein Expression (2 of 2)
Protein expression vector
• The selection marker is
typically an antibiotic
resistance gene, and
allows only the
organisms harboring
the plasmid which
expresses the protein
of interest to grow in
the presence of
antibiotic

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Protein Expression Vector (1 of 2)
Producing His-tagged proteins
• 6–10 histidine codons (the
“His-tag”) are cloned
upstream or downstream of
the target gene
• The His-tag cause the
protein to adhere to a
column containing
immobilized dicationic
metals such as Zn2+ or Ni2+
(i.e., immobilized metal
affinity chromatography or
IMAC)

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Protein Expression Vector (2 of 2)
Producing His-tagged proteins
• The His-tagged target
protein can be
selectively eluted with an
imidazole buffer
– imidazole has a
higher affinity to the
“His-tag” than the
immobilized
dicationic metals

A mixture of (cellular) proteins is separated as a result

of differential interactions with the column matrix. The more
a protein interacts with the matrix, the later it will elute
from the column
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Affinity Chromatography

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Ion Exchange Chromatography (2 of 2)
Ion exchange resins
• DEAE (diethylaminoethyl) cellulose and CM
(carboxymethyl) cellulose are widely used resins
• At a pH above the isoelectric point a protein carries a
negative charge and will bind to DEAE-cellulose
• Protein can be selectively eluted by applying a gradient of
pH or increasing ionic strength

• A biochemist wants to separate two peptides by ion

exchange chromatography. At the pH of the mobile phase
to be used on the column, one peptide (A) has a net
charge of -3, due to the presence of more Glu and Asp
residues than Arg, Lys, and His residues. Peptide B has a
net charge of +1. Which peptide would elute first from a
cation-exchange resin? Which would elute first from an
anion-exchange resin?

• A cation-exchange resin has negative charges and binds

positively charged molecules, retarding their progress
through the column. Peptide B, with its net positive charge,
will interact more strongly with the cation-exchange resin
than peptide A, and thus peptide A will elute first. On the
anion-exchange resin, peptide B will elute first. Peptide A,
being negatively charged, will be retarded by its interaction
with the positively charged resin.

• Separation of proteins is based on the apparent sizes of

the molecules
• Larger proteins elute earlier because they are excluded
from the interior volume of the chromatography matrix
• Smaller proteins elute later because they are retained
within the pores of the chromatography matrix, resulting in
a longer residence time on the column

Edman method
Sequencing larger proteins

Enzyme Aminoacid Cutting site

Trypsin Arg/Lys C-ter
Chymotrypsin Phe/Trp/Tyr C-ter
Protease V8 Asp/Glu C-ter
Pepsin Phe/trp/Tyr N-ter
Thermolysin Leu/Ile/Trp/Tyr/Val/Ala/Phe N-ter
Carboxypeptidase A All C-ter aminoacid except Pro/Arg/Lys -Free aminoacid from the C-ter
Carboxypeptidase B Only Arg/Lys when C-ter - Does not cut if Pro is the
penultimate aminoacid

http://www.proteinsandproteomics.org/content/free/tables_1/table11.pdf
https://web.expasy.org/peptide_cutter/

BENG545 Protein Expression and Purification

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Identification of a Protein of Interest Using
Proteomics Methods (1 of 3)
• A totalion current (TIC) chromatogram for a complex
mixture of peptides separated by HPLC (High-performance
liquid chromatography)

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Identification of a Protein of Interest Using
Proteomics Methods (2 of 3)
• Fragmentation of the ions selected by a TIC chromatogram
gives a set of ions that can be further separated by mass-
to-charge ratio in the mass spectrometer

Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
Identification of a Protein of Interest Using
Proteomics Methods (3 of 3)
• MS-MS spectrum for one of the parent ions (and
subsequent analysis) after mass spectrometric separation
of an HPLC ion peak

Internet Addresses for the Major Protein and DNA

Sequence Data Banks

Data Banks Containing Protein Sequences
• ExPASy Proteomics Server: http://expasy.org/
• Protein Information Resource (PIR):
http://pir.georgetown.edu/
• UniProt: http://www.uniprot.org/
Data Banks Containing Gene Sequences
• GenBank: http://www.ncbi.nlm.nih.gov/genbank/
• European Bioinformatics Institute (EBI):
http://www.ebi.ac.uk
• GenomeNet: http://www.genome.jp/
Copyright © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved.
23.10.2022 83

• Proteins are polymers of α-amino acids

– twenty common amino acids (and two rare),
distinguished by their side chains (R groups), are
incorporated into proteins
• Proteins are produced by condensation of amino acids via
peptide bond formation
• The unique defined sequence of amino acids constitutes
the primary structure of proteins
• In cells, genes are transcribed into messenger RNA
(mRNA), which is then translated into a polypeptide strand
at the ribosomes

• Using recombinant expression techniques, proteins can be

produced in non-native organisms at very high yields
– Genes of interest are incorporated into these non-
native organisms, and then transcribed and translated
by these organisms
• Depending on the certain properties of the produced
proteins, they can be purified at high purity by various
chromatographic techniques, and the proteins’ masses
and sequences can be determined

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