BMS1021 Biochemistry

The Chemical Composition of Cells - 2

Water Proteins Carbohydrates Lipids Nucleic Acids

Dr. Jérôme Le Nours

Group Leader
Jerome.lenours@monash.edu

Comparative Immunology Laboratory

Department of Biochemistry and Molecular Biology
Biomedicine Discovery Institute
1
 Molecules within an E. coli cell

2.0 µm

You could fit 100,000,000 (100 million)

E. coli cells in a 1cm2 monolayer

We carry 100 billion E. coli cells in our gut.

Bacteria out-number human cells in our bodies by 2:1
 Learning objectives
Carbohydrates

Biological
Structure Function
importance

Proteins

• Describe the major categories of macromolecule found within a cell

• Describe the components and levels of structure within proteins and

carbohydrates

• Describe the major functions of proteins and carbohydrates

 Resources
Biology – Campbell
10/11th edition Chapter 5 pp. 66-72, 75-83
Chapter 6 pp. 102-108, 115-119

Principles of Biochemistry – Lehninger

7th edition (2017) Chapter 3 pp. 75-113
Chapter 4 pp. 115-155
Chapter 7 pp. 241-278

Lectures in BMS1011 on Carbohydrates, and Amino acids and

Proteins will cover this topic in further detail
Levels of structure within a cell
 Carbohydrates
(are polysaccharides)
• Polysaccharides made up of
HO α orientation
monosaccharides H 6 H at carbon 1

5 O
• Glucose is the most common H H
monosaccharide 4 H 1
OH H
3
• Monosaccharides are the major HO 2
OH
nutrients in cells and the source of
raw material for the synthesis of H OH
Haworth Projection
other types of molecules
α-D-Glucose
(C6H12O6)

Fructose, ribose, galactose, xylose are also

monosaccharides
 Monosaccharides join via glycosidic linkages

Enzyme
Hydrolysis Condensation /
reaction Dehydration
reaction
Enzymes

Maltose
Monosaccharides join via covalent glycosidic bonds

Sucrose
Multiple sugars joined together are called
polysaccharides
 Starch

• Starch is made from glucose alone

and is a homopolysaccharide

• The major energy storage sugar in

plants

• Two forms of starch: amylose and

amylopectin

• Stored as granules in the

chloroplasts of plant cells.

• Starch can have 500 – 20,000

glucose units

Amylose
 Glycogen

• Glycogen is a mammalian
polysaccharide. A polymer of
glucose
(homopolysaccharide).

• Glycogen is stored energy for

later use in the muscle cells,
or for release of glucose into
the blood by the liver cells.

• Similar to amylopectin but

more highly branched and
more ‘compact’.
Can be up to up to 120,000
• Stored inside cells as glucose residues in length
insoluble granules in liver
and muscle.
 Structural polysaccharides
Cellulose is made glucose monomers and is unbranched.
The bond forms between β-isomers resulting in straight
molecules. H-bonds between parallel molecules give it
1 4 strength and rigidity

Chitin is a repeating polymer of N-Acetylglucosamine

one of the main components of the fungal cell walls
and the exoskeleton of crustaceans and insects.

N-Acetylglucosamine – has an amide link between

glucosamine and acetic acid
 Structural polysaccharides
Staphylococcus aureus

Polysaccharide layer is readily

stained using crystal violet (the
‘Gram stain’)

The bacterial cell wall is made of a

complex polysaccharide covalently
cross-linked with protein collectively
called peptidoglycan
Danish bacteriologist Hans Christian Gram
 Extracellular polysaccharides
Glycosaminoglycans
• Heteropolysaccharides
• Have amino containing sugars
• N-acetylated amino sugar (eg. N-acetyl glucosamine) and a uronic acid (eg. Glucuronic acid)
• Highly polar (anionic), attract water and act as lubricants or shock absorbers
• Found the extracellular matrix of mammals and in bacteria and but not plants

Hyaluronic Acid
• High molecular weight
• Clear, highly viscous solution
• Lubricant of synovial fluid in joints, and in
vitreous humour of the eye
• Gives strength, adhesiveness and elasticity to
cartilage and tendons
~

GlcA = D-Glucuronic acid acid,

GlcNAc = N-Acetyl-D-glucosamine
 Extracellular polysaccharides
Extracellular protein molecules in eukaryotes often have polysaccharides
covalently linked (ie. are glycosylated)

( )

( )
Protein
Bacteria Yeast Insect Mammal

Galactose N-acetylneuraminic acid

Mannose N-acetylglucosamine
Fucose Polypeptide

Protects proteins from action of proteases

(degradation) and helps protein folding
 Glycoproteins
• Protein chains with covalently linked sugar chains

• Carbohydrate chains of varying complexity Examples

Extracellular - hormones (FSH), immunoglobulins, and
milk proteins
Membrane associated - ABO blood group markers
• Can be intracellular,
membrane bound or free in
the extra cellular fluid

• Important in cell-cell
communication and as
markers on cell membranes
 Proteoglycans
Glycosaminoglycan (polysaccharides with amino containing sugars)
molecules attached covalently to a membrane protein molecule or secreted
protein

• Predominantly carbohydrate

• Act as tissue organisers, mediate

growth factors, regulate
extracellular assembly of
molecules e.g. collagen
 Proteoglycans
• Can form very large complexes or aggregates

• Found in connective tissue, e.g. Basal lamina, cartilage, and extracellular fluid

• In cartilage aggrecan core proteins have multiple chains of glycosaminoglycan attached;

many core proteins then bind to one long hyaluronate molecule, which in turn IS attached to
molecules such as collagen
 Proteins
a polymer made up of amino acids or polypeptide)

• function as enzymes in cellular metabolism

• provide structural support

• many hormones are proteins

• receptor molecules on cell surfaces are often proteins

• antibodies help protect against disease

• act as transporters inside and outside cells

• contractile and motor proteins move muscles and cilia/flagella

Proteins (and polypeptides)

Composed of amino acids

R
General formula
R
CH
H3N CO
Amino
group O
Alanine Carboxylic
acid group
 Amino acids

There are 20
common amino
acids which differ in
their R- group
(shading)
Amino acids join via peptide bonds to form
dipeptides

Hydrolysis Condensation /
reaction Dehydration
reaction
Proteases (digestion) Enzymes in ribosome (translation)

N-terminus C-terminus
Peptides and proteins
A pentapeptide
Ser-Gly-Tyr-Ala-Leu

Val-Thr-Ala
 The four levels of protein structure

Polypeptide Protein (folded, 3D-structure and functional)

 Secondary structure 1. - the α-helix

• Backbone atoms wind in a

helical manner

• One turn every 3.6 residues

• Intrachain hydrogen bonding is

an important stabilising feature

• H from amino group in a

peptide bond is hydrogen
bonded to an oxygen four
residues away (in the primary
sequence) on carbonyl of
another peptide bond

• Side chains (R groups) project

H bond
outwards
α- helix
Secondary structure 1. - the α-helix
 Secondary structure 2 - β-Sheet
• Relatively flat sheet with side-chains projecting above and below the plane

• Held together by H-bonds between backbone of polypeptide

• Chains forming sheet not necessarily close in the primary sequence. Only if a β-turn is
present do consecutive strands form part of anti-parallel sheet

Other
N structures /
domains
also exist –
you will
learn more
later in the
BMS course

β- sheet
 Secondary structure – Fibroin as an example

Fibroin fibres found in spider silk and silk cloth

are made up of layers of anti-parallel β-sheets.

Close packing makes for a very strong fibre

 Tertiary Structure

Tertiary structure is held

together by bonds between
amino acid side-chains

• H-bonds
• Ionic interactions
• Covalent bonds
• Hydrophobic interactions
• van der Waals interactions

Tertiary

Sequence specifies conformation and hence function.

 Tertiary Structure - myoglobin
Myoglobin

• Protein holds an oxygen binding haem group in a

special pocket

• Found in muscle cells

• Stores O2

• Single protein chain

• Contains 8 α-helices but no β-sheets

• Interior consists almost entirely of hydrophobic residues

Myoglobin
 Quaternary structure
Haemoglobin

• Found in red blood cells

• Made up of four proteins

(subunits) that each bind
oxygen

• Releases oxygen more readily

than myoglobin because of
allosteric cooperativity
between subunits of
the quaternary structure

Haemoglobin
 Protein structure is dynamic

• Proteins require a specific structure,

known as a conformation to function

• These structures may need to be

dynamic
Competitive inhibitor
(at active site)
• Inhibitors bind and change protein
preventing activity
Allosteric inhibitor

• This is exploited in some drugs Hepatitis C virus

NS3 Protein
(serine protease)

Hep Protease
 Summary

Carbohydrates Proteins

Polysaccharides made up of
Polypeptides made up of amino acids
monosaccharides

Monosaccharides join up via glycosidic Amino acids join together via peptide
linkages bonds

Branched or unbranched,
Four levels of structure - primary,
homopolysaccharides or
secondary, tertiary and quaternary
heteropolysaccharides

Enzymes, receptors, hormones, defensive

Storage, structural components or
molecules, transporters, structural and
biologically active agents
motor molecules etc.