Macromolecules

Macromolecules are often polymers.

long molecule built by linking together small,
similar subunits
Dehydration synthesis removes OH and H during
synthesis of a new molecule.
Hydrolysis breaks a covalent bond by adding OH
and H.

Proteins
Structure:
Polypeptide chains
Consist of peptide bonds between 20 possible amino acid
monomers
Have a 3 dimensional globular shape

Proteins
Proteins are composed of 4 elements: carbon, hydrogen,
oxygen and nitrogen. The basic unit is called an amino acid
and it looks like this.

This is a 3-D image of a protein containing thousands of

amino acids connected together & folded to make this
distinct shape.

Functions of Proteins
Enzymes which accelerate specific chemical
reactions up to 10 billion times faster than they would
spontaneously occur.
Structural materials, including keratin (the protein
found in hair and nails) and collagen (the protein
found in connective tissue).

Functions of Proteins
Specific binding, such as antibodies that bind
specifically to foreign substances to identify them to
the body's immune system.
Specific carriers, including membrane transport
proteins that move substances across cell
membranes, and blood proteins, such as
hemoglobin, that carry oxygen, iron, and other
substances through the body.

Functions of Proteins
Contraction, such as actin and myosin fibers that
interact in muscle tissue.

Signaling, including hormones such as insulin that

regulate sugar levels in blood.

Proteins - C, H, O, N, S

Amino Acids
contain an amino group (-NH2), a carboxyl group (COOH) and a hydrogen atom, all bonded to a central
carbon atom

twenty common amino acids grouped into five

classes based on side groups

Non-polar amino acids

polar uncharged amino acids
charged amino acids
aromatic amino acids
special-function amino acids

Structure of Amino Acid Monomers

Consist of an asymmetric carbon covalently
bonded to:
o
o
o
o

Hydrogen
Amino group
Carboxyl (acid) group
Variable R group specific to each amino acid

Properties of Amino Acids

Grouped by polarity
Variable R groups (side chains) confer different properties
to each amino acid:
o polar, water soluble.
o non-polar, water insoluble

o positively charged
o negatively charged.

NONAROMATIC

AROMATIC

Nonpolar
CH3 CH3

CH3

CH

CH2

CH3 CH3
CH3

CH2

CH

H C

C O H3N+ C C O H3N+ C

H3N+ C

H O

Alanine
(Ala)

H3

O H3N+

CH3

Glycine
(Gly)

H
O

H3

N+

OH

C C

NH2

H3

H3

N+

CH2

CH2
H3

N+

H O

NH+

HC

CH2
H3

Threonine Asparagine Glutamine

(Thr)
(Asn)
(Gln)

CH2

N+

OH

NH2

N
H

CH

CH2
O

H3

N+

H O

Glutamic Aspartic Histidine

acid (Glu) acid (Asp
(His)

H3

N+

NH2+

CH2 NH3+

NH

CH2

CH2

CH2

CH2
CH2

CH2
O

H O

CH2
O

Charged
O

H O

CH2

CH2
N+

H O

Serine
(Ser)

O H3N+ C C O H3N+ C C O

CH2

NH2

CH2

CH2

Leucine Isoleucine Phenylalanine Tryptophan

(Leu)
(Ile)
(Phe)
(Trp)

N+

Polar uncharged
OH

CH3

C O H3N+ C

H O

Valine
(Val)

NH
C

H O

Lysine
(Lys)

H3

N+

C O

Arginine
(Arg)

H3

N+

C O

H O

Tyrosine
(Tyr)

Amino Acids
Peptide bond links two amino acids.
A protein is composed of one or more long chains of
amino acids linked by peptide bonds (polypeptides).

Protein Structure
The shape of proteins is extremely important and can
determine the function
Waters tendency to hydrophobically exclude nonpolar
molecules literally shoves the nonpolar portions of the
protein to the interior
Many shapes
Primary the specific amino acid sequences
Secondary formed by hydrogen bonding
Alpha helix coils
Beta pleated sheet - foldbacks
motifs - folds or creases
supersecondary structure

Protein Structure
Tertiary - final folded shape of globular protein
(3-dimensional shape) based on bonding of
side groups
Domains independent functional units of the
protein 100200 amino acids long - encoded by
a specific DNA sequence (exon)
Quaternary - forms when two or more
polypeptide chains associate to form a
functional protein

1 Primary structure
R
H H O
R
H H O
R
H H
C C N C C N C C N C C N C C N C
H O
H H O
H H O
R
R
R

2 Secondary
structure
b pleated sheet

b a b motif

a helix

3 Motifs

a turn a motif

Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

4 Tertiary

structure

5 Domains
Domain 1
6

Quaternary
structure
Domain 2
Domain 3

Primary Structure
o
o
o
o

Unique sequence of amino acids in a protein

Slight change in primary structure can alter function
Determined by genes
Condensation synthesis reactions form the peptide bonds
between amino acids

Secondary Structure
Repeated folding of proteins polypeptide backbone
stabilized by H bonds between peptide linkages in the
proteins backbone
2 types:

alpha helix,

beta pleated sheets

Tertiary Structure
Irregular contortions of a protein due to bonding
between R groups
Weak bonds:
o H bonding between polar side chains
o ionic bonding between charged side chains
o hydrophobic and van der Waals interactions
Strong bonds:
o disulfide bridges form strong covalent linkages

Quaternary Structure
Results from interactions among 2 or more
polypeptides

Factors That Determine Protein

Conformation
Occurs during protein synthesis within cell
Depends on physical conditions of environment
pH, temperature, salinity, etc.
Change in environment may lead to denaturation of protein
Denatured protein is biologically inactive
Can renature if primary structure is not lost

Chaperone Proteins
Chaperone proteins are special proteins which help
new proteins fold correctly.
o Chaperone deficiencies may play a role in facilitating certain
diseases.

Unfolding Proteins
Denaturation refers to the
process of changing a
proteins shape; usually
rendered biologically inactive.
Causes
pH
temperature
Ionic concentration - saltcuring and pickling used to
preserve food

Nucleic Acids
Nucleic acids make up DNA and RNA which
are gigantic molecules that carry your
hereditary information from generation to
generation and are used to make proteins
Nucleic acids are made up of lots of nucleotides
(the smallest units) strung together. DNA takes the
shape of a double helix.

Nucleic Acid Structure

Nucleic acids are composed
of long polymers of repeating
subunits, nucleotides.
o five-carbon sugar
o Phosphate group
o nitrogenous base
Purines double ringed
o adenine and guanine
Pyrimidines single ringed
o cytosine, thymine, and
uracil

Nucleic Acids
Polymer of ribofuranoside
rings linked by phosphate
ester groups.
Each ribose is bonded to
a base.
o Ribonucleic acid (RNA)
o Deoxyribonucleic acid
(DNA)

Nucleic Acids - C, H, O, N, P
Two kinds:
DNA:
o
o
o
o

double stranded
can self replicate
makes up genes which code for proteins
is passed from one generation to another

RNA:
o single stranded

o functions in actual synthesis of proteins coded for by

DNA
o is made from the DNA template molecule

Nucleotide Monomer Structure

Both DNA and RNA are composed of nucleotide
monomers.
Nucleotide = 5 carbon sugar, phosphate, and
nitrogenous base

Deoxyribose in DNA

Ribose in RNA

Nucleic Acid Structure

DNA exists as double-stranded molecules.
double helix
complementary base pairing
Chargaffs rule
Chargaff's rules state that DNA from any cell of
all organisms should have a 1:1 ratio
of pyrimidine and purine bases and, more
specifically, that the amount of guanine is equal
to cytosine and the amount of adenine is equal
to thymine

hydrogen bonding
RNA exists as a single stand.
contains ribose instead of deoxyribose
contains uracil in place of thymine

Base Pairings

Building the Polymer

Phosphate group of one nucleotide forms strong
covalent bond with the #3 carbon of the sugar of the
other nucleotide.

Functions of Nucleotides
Monomers for Nucleic Acids
Transfer chemical energy from one molecule to
another (e.g. ATP)

Structure of DNA
b-D-2-deoxyribofuranose is the sugar.
Heterocyclic bases are cytosine, thymine
(instead of uracil), adenine, and guanine.
Linked by phosphate ester groups to form the
primary structure.

Structure of DNA

DNA:
Double helix
2 polynucleotide chains
wound into the double helix
Base pairing between
chains with H bonds
oA-T
oC-G

Double Helix of DNA

Two complementary
polynucleotide chains
are coiled into a helix.
Described by Watson
and Crick, 1953.

59

Phosphate group
P

P
OH
39

Cytosine
(both DNA
C C N and RNA)
C
C O
N
H
Thymine
O
(DNA only)
C
N
H
C
CN C O
NH2

H
P
P H
NC CH
N
U
Y
H
Phosphodiester R
R
O Guanine I
bonds
I
N
M
NCC N H
E H C
I H3C
C
C
NH2 D H
S
N N
I
H
H
N
5-carbon
O
E
sugar
S
C
Nitrogenous base
H C N
H CN C
O
H

H C

NH2 Adenine
NCC N

Uracil
(RNA only)
H
O

Ribonucleosides
A b-D-ribofuranoside bonded to a
heterocyclic base at the anomeric
carbon.

Ribonucleotides
Add phosphate at 5 carbon.

Additional Nucleotides
Adenosine monophosphate (AMP), a regulatory
hormone.
Nicotinamide adenine dinucleotide (NAD), a
coenzyme.

Adenosine triphosphate (ATP), an energy source.

Summary of the Organic

Molecules: