Lecture 2

The Molecules of Life

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Overview of Foundations of Biology

Molecules of Life
Cell Structure
Cellular Communication
Cell Energetics

Genetics
Evolution

Kay

Logsdon

Learning Objectives
Types of chemical bonds and molecular
interactions in living organisms
Discriminate among the four types of
macromolecules
functional groups of the monomers or
subunits
how they are synthesized
overall chemical and physical properties
Relate structure of each class of macromolecule
to their functions in organisms

Todays Topics

Overall framework
Chemistry
Building blocks of life
Functional groups
Bonds
Polymers
Proteins
pH
Amino acids
Protein structure

Some Keywords
alpha helix
beta pleated sheet
chaperones
condensation reactions
denatured
disulfide bridge
ester linkage
functional groups
heat shock proteins
hydrolysis reaction
isomers
macromolecules

monomers
optical isomers
peptide linkage
polymers
primary structure
proteins
quaternary structure
R group
secondary structure
side chain
structural isomers
tertiary structure

How could you build a live critter?

The Periodic Table

H 375,000,000 O 132,000,000 C 85,700,000 N 6,430,000 Ca 1,500,000 P 1,020,000 S

206,000 Na 183,000 K 177,000 Cl 127,000 Mg 40,000 Si 38,600 Fe 2,680 Zn 2,110
Cu 76 I 14 Mn 13 F 13 Cr 7 Se 4 Mo 3 Co 1

What is the formula of life?

The Constituents of Life

What Kinds of Molecules

Characterize Living Things?
Most macromolecules are polymers long
chains of smaller molecules called
monomers, joined by covalent bonds
Different monomers/polymer types are defined
by the functional groups that are attached to
the carbon skeleton.
polar or nonpolar, acidic or basic, etc.
Have different chemical & physical properties

A single macromolecule may contain several

different functional groups.

The building blocks of life

protein

amino acid
nucleotide

T T T T T T

nucleic acid

sugar

polysaccharide

phospholipid

membrane

AR Kay 2013

Isomers: same atoms, different arrangements

Result in different molecular shapes
Structural
isomers
C4H10

Optical isomers
(enantiomers)

C4H10

Cis-Trans isomers

What keeps it all together?

Average thermal motion 0.6 kcal/mol

Hydrogen Bonds Can Form Between or

Within Molecules

Hydrogen Bonds

AR Kay 2013

Some Functional Groups Important to Living

Systems

How to make a polymer

Condensation

(Water out; Energy in)

Also called
DehydraIon
Synthesis

The covalent bonds between

each monomer hold energy

How to break a polymer

Hydrolysis

(Water in; Energy out)

+ Energy released

+ Energy released

Proteins

h2p://www.rcsb.org/pdb/101/motm_archive.do
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Structure and Functions of Proteins

Proteins
Polymers of 20 different
aas
Linked by peptide bond
Vary in length from
several aas to thousands
Also vary in composition
of amino acids
There are 20 different side chains (R),
distinguished by size and their
functional groups.
The R-groups are key to a proteins
shape and ultimate function in a cell.

Proteins can vary greatly in size

Titin: a huge protein (34,000 aas)
that adds flexibility to muscle
fibers

Glu His Pro

Thyrotropin releasing hormone: a

short (3 aas) polypeptide that
controls secretion of thyroid
hormone

An Aside on Acidity
When acids dissolve in water, they release
hydrogen ions: H+ (protons).
H+ ions can attach to other molecules and
change their properties.
Bases accept H+ ions.
+

HCl H + Cl

COOH COO + H +

strong acid
weak acid

Bases
strong base
NaOH Na + + OH

weak bases
HCO3 + H + H 2CO3
NH 2 + H + NH 3+

Ionization of Water

H 2O H + + OH

pH
pH = negative log of the molar
concentration of H+ ions.
+$
"
pH = log # H %

H+ concentration of pure water is 107

M, its pH = 7.
Lower pH numbers mean higher H+
concentration, or greater acidity.

Buffers
Living organisms
maintain constant
internal conditions
(homeostasis).
Buffers help maintain
constant pH.
A buffer is a weak
acid and its
corresponding base.

HCO + H H 2CO3

Amino acids are grouped according to the

properties of their side chain (R) groups.

Hydrophilic amino acids with polar but uncharged side

chains form hydrogen bonds.
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 Synthesis of
Proteins
Grow from N-terminus
C-terminus; each
additional aa joined to Cterm of previous one.
Fold into specific,
reproducible shapes as a
result of the aa
composition and order
Some proteins made from
just one polypeptide;
others made from several

Disulfide bridges
The terminalSH group of cysteine can react with
another cysteine side chain to form a disulfide
bridge, or disulfide bond (SS).
These are important in protein folding.

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Levels of Protein Structure

Primary structure (1o) - the sequence (order
and composition) of aas
Secondary structure (2o) - regular, repeate
pattern in different regions of the aa chain that
arise from hydrogen bonding between aas
Tertiary structure (3o) - three-dimensional
shape that arises from interactions (ionic, hbonds, or hydrophobic) between R groups
Quaternary structure (4o) - association of
two or more polypeptides to form the functional
protein

Primary structure

The primary structure of a protein is the

sequence of amino acids.
The sequence determines secondary and tertiary
structurehow the protein is folded.
The number of different proteins that can be made
from 20 amino acids is enormous!

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Secondary structure

helixright-handed coil resulting from

hydrogen bonding between NH groups
on one amino acid and C=O groups on
another.
pleated sheettwo or more
polypeptide chains are aligned; hydrogen
bonds from between the chains.
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TerJary structure

Tertiary structure: Bending

and folding results in a
macromolecule with specific
three-dimensional shape.

b Pleated sheet

Hydrogen bond

a Helix

The outer surfaces present

functional groups that can
interact with other
molecules.

Disulfide bridge

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Complete descriptions of tertiary structure

have been worked out for many proteins.

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 If a protein is heated, the

secondary and tertiary
structure is broken down; the
protein is said to be
denatured.
When cooled, the protein
returns to normal tertiary
structure, demonstrating that
the information to specify
protein shape is contained in
its primary structure.

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Quaternary structure

Quaternary structure
results from the
interaction of
subunits by
hydrophobic
interactions, van der
Waals forces, ionic
bonds, and hydrogen
bonds.
Each subunit has its
own unique tertiary
structure.

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Noncovalent Interactions
Between Proteins and Other
Molecules

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Conditions that affect secondary and

tertiary structure:
High temperature
pH changes
High concentrations of polar molecules
Nonpolar substances

Research Connection: Figure 3.10 of

textbook
Lab Connection: In Project 1, you will have
an opportunity to examine the effect of
changing temperature or pH on enzyme
activity.
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Chaperones
Proteins can sometimes bind to the wrong
molecules after denaturation or when they
are newly made and still unfolded.
Chaperones are proteins that help
prevent this.
Heat shock proteins (HSPs) are the
general class of stress-induced chaperone
proteins.
They are made by most eukaryotic cells,
and many also enhance protein folding.

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Chaperones Protect Proteins

from Inappropriate Binding

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SI prefixes
Giga
Mega
kilo
cenJ
milli
micro
nano
pico

G
M
k
c
m
m
n
p

109
106
103
10-2
10-3
10-6
10-9
10-12
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