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

H
 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 Hydrogen
o Amino group
o Carboxyl (acid) group
o 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 NH
CH3 CH3 CH CH2 C
CH3 CH CH2 H C CH3 CH2 CH2
H3N+ C C O– H3N+ C C O– H3N+ C C O– H3N+ C C O– H3N+ C C O– H3N+ C C O–
H O H O H O H O H O H O
Alanine Valine Leucine Isoleucine Phenylalanine Tryptophan
(Ala) (Val) (Leu) (Ile) (Phe) (Trp)
Polar uncharged
O NH2 OH
C
O NH2
OH CH3 C CH2
H CH2 H C OH CH2 CH2 CH2
H3 N+ C C O– H3N+ C C O– H3 N+ C C O– H3 N+ C C O– H3 N+ C C O– H3 N+ C C O–
H O H O H O H O H O H O
Glycine Serine Threonine Asparagine Glutamine Tyrosine
(Gly) (Ser) (Thr) (Asn) (Gln) (Tyr)

Charged NH2
C NH2+

O O– CH2 NH3+ NH
C O– HC NH+ CH2 CH2
O
CH2 C CH CH2
C N CH2
H
CH2 CH2 CH2 CH2 CH2
H3 N+ C C O– H3 N+ C C O– H3 N+ C C O– H3 N+ C C O– H3 N+ C C O–
H O H O H O H O H O
Glutamic Aspartic Histidine Lysine Arginine
acid (Glu) acid (Asp (His) (Lys) (Arg)
 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
• Water’s 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 100–200 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 R H H O R H H O R

2 Secondary
structure

b pleated sheet a helix

3 Motifs

b a b motif 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 Unique sequence of amino acids in a protein
o Slight change in primary structure can alter function
o Determined by genes
o Condensation synthesis reactions form the peptide bonds
between amino acids
 Secondary Structure
• Repeated folding of protein’s polypeptide backbone
• stabilized by H bonds between peptide linkages in the
protein’s 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
protein’s shape; usually
rendered biologically inactive.
• Causes
• pH
• temperature
• Ionic concentration - salt-
curing 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 double stranded
o can self replicate
o makes up genes which code for proteins
o 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
• Chargaff’s 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
NH2 Adenine NH2 Cytosine
(both DNA
NCC N
P
H C C C N and RNA)
H
O P P H
NC CH C C O
U N Y N
Phosphodiester R H R H
bonds I O Guanine I O Thymine
P N M (DNA only)
O NCC N H C
E H C C
I H3C N H
S N NC C NH2 D H CN C O
H I
5-carbon N H
P E O Uracil
O sugar
S C (RNA only)
Nitrogenous base H C N H
H CN C O
P O H

OH
39
 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: