ABS 311

Cell Biology

Chapter 3
The Macromolecules of the Cell
 Review
 The cell is the basic structural and reproductive
unit of all biology; all living organisms consist of
one or more cells
 All cell functions have a molecular and chemical
basis, and therefore are described in terms of
molecules and chemical reactions.
 Carbon containing macromolecules are
responsible for most of the structure and function
in cells.
 synthesized by polymerization of small molecules
 self-assembly: spontaneous formation of structural
organization
 Proteins
 Proteins are the most important and ubiquitous
macromolecules in the cell
 Nine major classes
 Enzymes – catalysts in biochemical reactions
 Structural proteins – provide shape and support
 Motility – contractile or flagellating proteins
 Regulatory proteins – coordinate cellular activities
 Transport proteins – substances into or out of cells
 Hormonal proteins – signals between distant cells
 Receptor proteins – response to chemical stimuli
 Defensive proteins – protect against disease
 Storage proteins – storage of amino acids
Proteins are polymers of amino acids

 20 standard amino acids

 Structure: H O
 central carbon H | ||
amino group —N—

—C— C—OH
 carboxyl group (acid)
 R group (side chain) H |
 variable group R
 confers unique
chemical properties
of the amino acid
Proteins are linear polymers of amino acids
 Structure:
 central carbon
 amino group
 carboxyl group (acid)
 R group (side chain)
 variable group
 confers unique
chemical properties
of the amino acid
 Side chains (aka R-group)
are either:
 Non-polar (hydrophobic)
 Polar
 Charged, acidic (-) or basic (+)
Nonpolar Amino Acids
Polar and Charged Amino Acids
Let’s build some

Proteins!
 Building proteins
 Peptide bonds: dehydration synthesis
 linking NH2 of 1 amino acid to
COOH of another
 C–N bond

peptide
bond
 Building proteins
 Polypeptide chains
 N-terminal = NH2 end
 C-terminal = COOH end
 repeated sequence (N-C-C) is the
polypeptide backbone
 “grow” in one direction: N to C
 Free AA becomes AA residue

http://intro.bio.umb.edu/111-112/111F98Lect/PeptideBond.html
 Proteins
 Polymerization results
in peptide bonds

 Directionality of
polypeptide; from N-
term to C-term

 Polypeptide vs. protein

 Levels of Protein Structure
 Primary – amino acid sequence
 Secondary – Local folding patterns, alpha
helix and beta sheets
 Tertiary – 3D folding of a polypeptide
chain
 Quaternary – Association of 2 or more
polypeptides to form a multimeric protein
Levels of Protein Structure
 Protein structure & function

 function depends on structure

 all starts with the
order of amino acids
 what determines that order of
amino acids?
 amino acid sequence determined by DNA
 slight change in amino acid sequence can affect

protein’s structure & it’s function

 even just one amino acid change can make all the

difference!
Sickle cell anemia
Levels of Protein Structure
 Primary Structure is the
sequence of amino acids in the
polypeptide
Primary Structure of Cyt-c
 A Question to Ponder

How do you identify a

unknown protein and study the
function of this protein after
identification?
 Levels of Protein Structure
 Secondary Structure
is the local folding of
the polypeptide chain
 H-bond, repetitive
structure: backbone
 Two major structural
patterns are:
 Alpha helix
 Beta sheet
 Secondary (2°) structure
 “Local folding”
 Folding along short
sections of
polypeptide
 interaction between
adjacent amino acids
 H bonds between
O and H of peptide
backbone
 -helix
 -pleated sheet
Levels of Protein Structure
 Motifs are a form of
supersecondary
structure
 Levels of Protein Structure
 Tertiary Structure Long
distance “Whole molecule
folding”
 depends almost entirely on
interactions between the
various R-groups, regardless of
where they are located in the
primary sequence

 hydrophobic
interactions
 H & ionic bonds

 anchored by
disulfide bridges
 Building proteins
 Polypeptide chains
 N-terminal = NH2 end
 C-terminal = COOH end
 repeated sequence (N-C-C) is the
polypeptide backbone
 grow in one direction
Bonds and Interactions for
Protein Folding
Protein Structure
 Domains are
discrete regions of
tertiary structure
and are frequently
associated with
specific functions
Levels of Protein Structure
 Quaternary
Structure is related
to subunit
interactions and
applies only to
multimeric proteins
(those containing
multiple
polypeptides)
 Levels of Protein Structure

R groups
hydrophobic interactions,
disulfide bridges
3°
multiple
polypeptides
hydrophobic
1° interactions
aa sequence
peptide bonds
determined 2°
by DNA 4°
H bonds
 Protein folding and stability
 Principle of Self Assembly
 Non-covalent interactions and
disulfide bonds drive protein
folding into a mature
conformation
 Protein stability is also
dependent on:
 H-bonds
 Ionic bonds
 Hydrophobic interactions
 Proteins
 Proteins are the most important and ubiquitous
macromolecules in the cell-Nine major classes
 Polypeptides are linear polymers of amino acids
 Proteins are folded polypeptides with specific 2-D
structures
 20 amino acids: hydrophobic, charged, and polar
 Non-covalent interactions and disulfide bonds drive
protein folding into a mature conformation
 4 Levels of Protein Structure
 amino acid sequence
 alpha helix and beta sheets: local, repetitive, motifs
 long distance interaction: non-repetitive, R-group,
domains
 interactions between subunit of multimeric proteins
Chapter 3 - Homework
 Assigned problems – see Part B