MOLECULAR CELL BIOLOGY

1. PROTEINS, DNA AND
CHROMOSOMES
MODULE 1
-Haymanti Bhanot, PhD

2. SHAPE AND
STRUCTURE OF
PROTEINS
MODULE 1: LESSON 1 OF 3
BIOL6299 Fall 2022
Northeastern University
(Source: Bruce Alberts; Alexander Johnson; Julian Lewis; David Morgan; Martin Raff; Keith Roberts; Peter Walter: 6th Edition)

3. INTRODUCTION
• In this lesson we consider how the location of amino acids that form a specific
protein can determine its shape and structural characteristics in the cell.
• By the end of this lesson, you should be able to:
• Identify common protein structures and domains.
• Classify specific examples of important proteins and their cellular roles.

4. MODULE 1
– LESSON 1
OF 3
• Role of Proteins
• Major components of Proteins
• The Genetic Code
• Amino acid side chains
Protein Overview
• Primary, Secondary, Tertiary and Quaternary
Structure of Proteins
• Protein Domains
• Protein Folding
• Disulfide bonds in Protein folding
Common Protein Structure and Domains

5. PROTEIN OVERVIEW
BIOL6299 Spring 2022
Northeastern University

6. THE ROLE
OF
PROTEINS
Proteins serve as the building blocks of
cells and execute virtually all the cells
functions, like import and export of
signals or small molecules.
Proteins that carry the functions by which
they conduct many of the necessary
chemical reactions to drive cellular
processes are referred to as enzymes.

7. THE MAJOR
COMPONENTS OF
PROTEINS
• A protein molecule is made from a long
chain of amino acids, that is joined to its
neighbor molecule via covalent bond.
• Each protein differs in its sequence and
number of amino acids; therefore, it is the
sequence of the chemically different side
chains that make each protein distinct.
• The function of a protein is dependent upon
its structure, which is determined by the
sequence of amino acids that make the
protein.

8. THE MAJOR
COMPONENTS OF
PROTEINS
• The two ends of a polypeptide chain
are chemically different: one end
carries the amino group (NH3+) known
as the amino terminus, or N-terminus,
and the other end carries the carboxyl
group (COO-/COOH) known as the
carboxyl terminus or C-terminus.
• The amino acids sequence of a protein
is always presented in the N-to-C
terminus direction and is read from left
to right.

9. THE GENETIC
CODE
• There are 20 amino acids found in
proteins.
• Each amino acid has a 3 letter code
that corresponds to the nucleic acid
sequence in mRNA, summarized in the
figure.
• The genetic code can be read by
navigating from the left to right.
• For e.g., First letter, Second letter, and
the Third letter.
• E.g.; let’s decode the codon CAU.
v Genetic code is redundant.

10. POLARITY OF AMINO
ACID SIDE CHAINS
• There are equal number of polar
and nonpolar side chains of amino
acids; however, some side chains
listed in this table as polar are large
enough to have some nonpolar
properties (for e.g., Try, Thr, Arg,
Lys).
• The polarity of the amino acid side
chains that make up the polypeptide
is an essential determinant of the
final structure of protein.

11. POLARITY OF
AMINO ACID SIDE
CHAINS
BASIC AMINO ACIDS
CONTAIN SIDE
CHAINS THAT CAN
GAIN A PROTON.

12. POLARITY OF
AMINO ACID SIDE
CHAINS
ACIDIC AMINO ACIDS
CONTAIN SIDE
CHAINS THAT CAN
LOSE A PROTON.

13. UNCHARGED AMINO ACIDS CONTAIN SIDE
CHAINS THAT HAVE NO CHARGE BUT HAVE
POLAR CHARACTERISTICS AT NEUTRAL PH
(FORM HYDROGEN BONDS WITH WATER).
POLARITY OF AMINO
ACID SIDE CHAINS

14. POLARITY OF AMINO ACID
SIDE CHAINS
NON-POLAR AMINO
ACIDS CONTAIN SIDE
CHAINS THAT ARE
HYDROPHOBIC AND
CAN CONTAIN RING-
LIKE STRUCTURES.

15. COMMON PROTEIN
STRUCTURES AND
DOMAINS
BIOL6299 Spring 2022
Northeastern University

16. FOUR LEVELS OF
PROTEIN
STRUCTURE
Ø Primary
Secondary
Tertiary
Quaternary

17. ALPHA
HELICES
Formed by backbone interactions parallel to
the primary axis of helix.
It is stabilized by hydrogen bonds between
amide hydrogen of one amino acid and
carbonyl oxygen four aminos acids away.

18. COILING FEATURES OF ALPHA
HELICES – COILED-COIL
E.g.: Alpha- Keratin
Collagen
Elastin

19. BETA SHEETS
e.g: Fibronin
Anti-parallel:
folds back and forth on itself
Parallel:
neighboring polypeptide
chains, run in same orientation
Formed by hydrogen binding between adjacent parallel or anti-parallel peptide strands.
In β-sheets, the backbone N–H and C=O of one strand hydrogen bond with
the C=O and N–H of an adjacent strand, respectively.

20. ROLE OF PROTEIN DOMAINS
*** A domain typically consists of between
40 and 350 amino acids, each with
different functions.

21. SPECIFIC PROTEIN BINDING
INTERACTIONS
Head-to-Head Binding at different sites
Noncovalent bonds of protein enable it to bind to other proteins which generates larger structures in the cell.

22. IMPORTANCE OF PROTEIN FOLDING
• An important feature governing the folding of any protein is the distribution of its
polar and nonpolar amino acids.
• The nonpolar amino acid side chains
are hidden inside of the protein to form
a tightly packed hydrophobic core of
atoms that are protected from water
that surrounds the cell.
• The polar amino acid side chains tend
to gather on the outside of the protein,
where they can interact with water and
other polar molecules in the cell’s
environment.

23. PROTEINS FOLD INTO THE LOWEST ENERGY
CONFIRMATION
***MOLECULAR CHAPERONS: Conversely, many proteins use special helper proteins to aid in protein folding.
These molecular chaperons are often necessary to prevent aggregation of proteins that
have temporarily exposed hydrophobic regions, especially in newly synthesized proteins.

24. DISULFIDE BONDS STABILIZE
PROTEINS

25. ASSEMBLY
FACTORS OF
PROTEINS
Insulin:
synthesized as proinsulin, a larger
protein.
cannot spontaneously re-construct itself
if di-sulfide bonds are disrupted.

26. IN THIS LESSON
• Identified the common protein structures and domains
• Classified specific examples of important proteins and their cellular roles.