Biological Macromolecules

Structure and Function of

Carbohydrates, Nucleic Acids,
Proteins, Lipids
Macromolecules

 These are larger organic molecules formed from

many repeating units of smaller organic
molecules. For further discussions we will focus
on the macromolecules:
 Nucleic Acids
 Proteins
 Carbohydrates
 Biologically important macromolecules are
“polymers” of smaller subunits
 The smaller sub-unites are called monomers
 Created through condensation reactions
 Broken down by hydrolysis reactions.
Macromolecule Subunit

Carbohydrates : Monosaccharides
Proteins : amino acids
Nucleic acids : nucleotides
Where do the subunits come from?
 All biological molecules are made from the following
elements.
 (C, O, H, N, P,)
 Some cells can synthesize all of the subunits given these
atomic components and an energy source
 Some cells can obtain these subunits from external sources
 Some cells can convert other compounds into these subunits
 We will discuss further in section on metabolism and cell
growth
Carbohydrates
 All have the following elements C, H, & O and have the
general formula CX (H2O)y hence the name hydrates of carbon

 A variety of functions in the cell

 Large cross-linked carbohydrates make up the rigid cell
wall of plants, bacteria, and insects
 In animal cells carbohydrates on the exterior surface of
the cell serve a recognition and identification function
 A central function is energy storage
and energy production!
 Carbohydrates
 Cell structure:
 Cellulose, LPS, chitin

Chitin in exoskeleton

Cellulose in plant cell walls Lipopolysaccharides (LPS)

in bacterial cell wall
Carbohydrate Structure
 Carbohydrates (polysaccharides) are formed from many
repeating single sugar units called monosaccharides.
 They have the following characteristics:
 All are aldehydes or ketones
 All contain several hydroxyl groups
Carbohydrate Structure
 Monosaccharides have the general formula (CH2O)n
 They are named according to the number of C atoms they
posses.
 All C atoms in a monosaccharides have an hydroxyl
group (-OH) attached except for one. This C atom will
have a aldehyde or keto group attached.
Carbohydrate Structure
Two Triose molecules will demonstrate aldose and keto
sugars:
Glyceraldehyde Dihydroxyacetone
Carbohydrate Structure
 The keto and aldehyde groups are called functional
groups.
 Groups of atoms known as functional groups can confer
special properties on carbon-based molecules.
 Example due to the aldehyde functional group aldose
sugars such as glucose are easily oxidized hence they are
powerful reducing agents.
Carbohydrate Structure
 Another example; the
addition of an –OH
group to a hydrocarbon
molecule always results
in the formation of an
alcohol.
Carbohydrate Structure
 Complex carbohydrates built from simple sugars
 Most often five (pentose) or six (hexose) carbon sugars

 Numerous –OH (hydroxyl) groups can form many types

of “cross links”
 Can result in very complex and highly cross linked
structures ( cellulose, chitin, starch, etc.)
Carbohydrate Structure
Example of two hexoses

 Glucose Galactose

 What’s the difference? Both are C6H12O6

 They are isomers of one another!
 Same chemical formula, but different structure (3D-
shape).
Carbohydrate Structure

From hence forth we will be focusing a bit on

Glucose
Carbohydrate Structure
 Glucose is six carbon monosaccharide; hence it is called
a hexoses.
 It will have either an “open chain” or “ring structure”
 The open chain can be straight, but due to the bonding
angles between carbon atoms it bend to form a stable
ring structure.
 It is only in the ring structure that glucose can be used to
form disaccharides and polysaccharides.
Carbohydrate Structure
Pentoses and hexoses are capable of forming ring (cyclic) structures.
An equilibrium exists between the ring and open form.

Linear form Ring (cyclic) form

Carbohydrate Structure
Carbohydrate Structure
 In its ring form glucose
can exist in two forms.
 α-glucose
 β-glucose
 REMEMBER
ISOMERS?

α-glucose
Carbohydrate Structure
 In α-glucose the
hydroxyl group (-OH) on
carbon atom 1 projects
below the ring.
 α-glucose is used to
make polysaccharide
starch.

α-glucose
Carbohydrate Structure
 In β-glucose the
hydroxyl group (-OH) on
carbon atom 1 extends
above the ring.
 β-glucose is used to
make polysaccharide
cellulose.

β-glucose
Carbohydrate Structure
 Monosacharides can be joined to one another to form
disaccharides, trisaccharides, ……..polysaccharides
 Saccharide is a term derived from the Latin for sugar (origin = "sweet sand")

 Carbohydrates classified according to the number of

saccharide units they contain.
 A monosaccharide contains a single carbohydrate, over
200 different monosaccharides are known.
 A disaccharide gives two carbohydrate units on
hydrolysis.
 A polysaccharide gives many carbohydrates on
hydrolysis, examples are starch and cellulose.
Carbohydrate Structure
 Disaccharides are formed by the Condensation reaction
between two monosaccharides; usually hexose (glucose,
galactose & fructose).
 Condensation means the removal of water.
 The bond formed as a result of this condensation reaction
is called a Glycosidic bond.
 The Glycosidic bond is usually formed between carbon
atom 1 & 4 of neighbouring units.
 Called a 1,4 bond or 1,4 linkage.
Carbohydrate Structure
 Monosaccharides can link
to form disaccharides

Sucrose
Glucose + Fructose
Carbohydrate Structure
Disaccharides formed by α-glucose

2 α-glucose starch molecules

Carbohydrate Structure
Disaccharides formed by α-glucose
 Starches
 Starches are carbohydrates in which
300 to 1000 glucose units join
together. It is a polysaccharide used
to store energy for later use. Starch
forms in grains with an insoluble
outer layer which remain in the cell
where it is formed until the energy is
needed. Then it can be broken down
into soluble glucose units. Starches
are smaller than cellulose units, and
can be more readily used for energy.
In animals, the equivalent of starch
is glycogen, which can be stored in
the muscles or in the liver for later
use.

 α-1,6 bonds
Starches
 Starch is formed by thousands of α-glucose residues.
 Starch has two components; Amylose & Amylopectin
 Amylose has a straight chain structure consisting of
several thousand glucose residues joined by 1,4
glycosidic bonds.
 These α 1,4 bonds (linkages) cause the chain to coil
helically into a more compact shape.
Starches
 Amylopectin is also compact as it has many branches
and it possess up to twice as many glucose residues as
Amylose.
 This branching occurs as a result of the 1,6 glycosidic
bonds
 Glycogen is very similar in structure to amylopectin but
shows more branching.
 Glycogen
Starches
 Starch and glycogen function primarily as energy and
food stores.
 They can easily be converted back to simple sugars by
hydrolysis reactions.
 Starch is a convenient storage material for several
reasons:
 They are large; hence not very soluble in water (insoluble).
 Due to there insolubility, they exert no osmotic or chemical
influences in the cell.
Carbohydrate Structure
Disaccharides formed by β-glucose

When two β-glucose molecules line up, the only way the -OH group on carbon atom
1 can line up with the –OH group on carbon atom 4 to form the glycosidic bond is if
one of the molecules is rotated through 180 0
Carbohydrate Structure
Disaccharides formed by β-glucose
Cellulose
 Cellulose is the most abundant organic molecule found
on earth due to it being a structural constituent of all
plant cell walls.
 It is due to the rotation of successive β-glucose residues
through 180°that forms the basis for the structural
difference between starch and cellulose.
 Cellulose consists of long chains of glucose residues, and
each chain consists of about 10,000 glucose residues.
 The β 1,4 linkages causes the chains to remain straight.
Cellulose
 The hydroxyl groups (-OH) project outwards from each
chain in all directions and form hydrogen bonds with
neighbouring chains.
 These cross linkages bind neighbouring chains rigidly
together.
 Chains associated in groups of 60-70 form microfibrils,
while microfibrils bundled together are called
macrofibrils.
 These Macrofibrils have high tensile strength and in cell
walls they are arranged in several layers in a glue like
matrix.
 Cellulose
 Cellulose is a linear
polysaccharide in which some
1500 glucose rings link together.
It is the chief constituent of cell
walls in plants.
 Human digestion cannot break
down cellulose for use as a food,
animals such as cattle and
termites rely on the energy
content of cellulose. They have
protozoa and bacteria with the
necessary enzymes (cellulase) in
their digestive systems. Only
animals capable of breaking
down cellulose are tunicates.
Complex Carbohydrates
 Cellulose
Most abundant carbohydrate on the planet!
 Component of plant cell walls
 Indigestible by animals
 β 1-4 bonds

 Starch
 Energy storage molecule in plants
 Can be digested by animals
 α 1-6 bonds
Complex Carbohydrates
 Glycogen
 Branched chain polymer of glucose
 Animal energy reserve
 Found primarily in liver and muscle
 α 1-4 & α 1-6 bonds
polysaccharides can be linked to other
molecules to form glyco-proteins and glyco-
lipids
Lipids
 Lipids are those water
insoluble organic
compounds, that are
formed by the
condensation reaction
between a fatty acid and
a alcohol.
Lipids
Fatty Acids
 They all have the functional carboxyl group (-COOH)

 All fatty acids have the general formula R.COOH where “R”
can be hydrogen or a group such as CH3 or C2H4 increasing
by CH2 for each subsequent member of the series.

 Fatty acids have hydrophobic tails consisting of hydrogen and

carbon; which are called hydrocarbon tails. This is the “R”
section of the formula.

 Many of the properties of lipids are as a result of these

hydrocarbon tails; including their insolubility in water.
Lipids
Diagram below Showing the Structure of a Typical Fatty
Acid Molecule.
Lipids
 Fatty acids can be classified as
either being saturated or
unsaturated.
 Saturated fatty acids contain
only carbon to carbon single
bonds.
 Unsaturated fatty acids
contain one or more double
bonds.
Lipids
 As stated earlier lipids are formed by the condensation
reaction between a fatty acid and a alcohol.

 The lipid that we will focus on is Triglyceride

 A triglyceride is formed by the condensation reaction

between glycerol (alcohol) and three fatty acid
molecules.
Lipids
 Glycerol possess three
hydroxyl groups which each
undergo a condensation
reaction with a fatty acid.
 Note the three hydroxyl
groups.
Lipids
Lipids
 Unlike the example above this
example actually shows the
“R” section of the formula
R.COOH.
 In this case “R” is C5H11 and
the formula for the fatty acid
is C5H11COOH
 Lipids
 Phospholipids are lipids
containing a phosphate group.
 They are most commonly
formed when one of the
hydroxyl groups of glycerol
undergoes a condensation
reaction with a phosphoric
acid rather than a fatty acid.
 The resulting molecule posses
a phosphate head that is
hydrophilic and the two tails
that are hydrophobic.
Lipids
Function
 Energy Storage
 Triglycerides
 Cell membranes and cell compartments
 Bi-layer structure
 Outer or plasma membrane
 Nuclear membrane
 Internal structures
 Er, Golgi, Vesicles, etc.
Lipids
 Lipids have the following functions:
 Phospholipids contributes to the function of the structure of the cell
surface membrane (called a phospholipid bilayer).

 They are a highly concentrated source of energy stores. They are the
body's second choice however, because they are more difficult than
carbohydrates to convert into energy. Animals store extra fat when
hibernating.

 They provide insulation when stored below the dermis of vertebrates,

especially those in cold climates.

 In aquatic animals this storage of fat below the dermis takes the form
of blubber where it aids in buoyancy.
Phospholipid bilayer
Proteins
 Proteins serve many essential roles in the cell

 Polymers of amino acids

 20 naturally occurring amino acids that form proteins.

 Plant make all the amino acids they need, but animals need to rely on
their diet to get some of their amino acids. These are called essential
amino acids.
Amino Acids
 Amino acids have a central carbon atom called the α
carbon atom.
 Attached to this α carbon atom is an acidic carboxyl
group (-COOH)
 Also attached is a basic amino group (-NH2) and an
hydrogen atom.
 The fourth position is the only variable region of the
amino acid called the “R” Group
 This R group gives each molecule its uniqueness.
 Amino Acids

 Structure of Amino
Acid
Amino Acids

Glycine Alanine
Amino Acids
 Molecules such as amino acids that have both an acidic
and a basic group are described as Amphoteric.

 These molecules exist mainly as ions and can carry both

a positive charge on the basic part and a negative charge
on the acid part.

 Such ions are described as dipolar and are called

zwitterions
Amino Acids
 Amino acids are combined to form proteins.
 The amino acids are joined together by a type of bond
called a peptide bond.
 Once the bond has been formed the protein (polypeptide
chain) typically folds into a specific shape due to four
other bonds:
 Ionic bonds
 Hydrogen bonds
 Disulphide bonds
 Hydrophobic interactions
Amino Acids
 Peptide bonds are covalent in nature and formed by
condensation reactions; thus water is removed in the
process.
 The reaction takes place between the amino group of one
amino acid and the carboxyl group of a neighbouring
amino acid.
 At the end of the day a dipeptide is formed.
 If many amino acids join together the molecule is called
a polypeptide (protein).
Amino Acids
Amino Acids
Protein
 As stated earlier once an polypeptide bond is formed it
folds into a specific shape as a result of four other bonds:

 Hydrogen bonds – when hydrogen is apart of a OH group or NH

group it becomes slightly positively charged (electropositive). In
this state it can be attracted to a neighbouring electronegative
oxygen such as the O of a C=O group or the N of a NH group.
C=O groups and NH groups exist along the length of the
polypeptide chain.
Protein
Protein
 Ionic bonds – acidic and basic R groups exist in an ionised
(charged) state at certain pHs. Acidic R groups are negatively
charged while basic R groups are positively charged. Hence they
can be attracted to each other forming ionic bonds. In aqueous
environments these bonds are weaker than covalent bonds and
can be easily broken by changes in the pH of the medium.

 Disulphide bonds – if a sulphydryl group (-SH) is apart of an R

group neighbouring sulphydryl groups can be oxidised to form
disulphide bonds. These bonds may be formed between different
polypeptide chains or different parts along the same polypeptide
chain.
Protein
 Hydrophobic Interactions – Some R groups are non-polar and
therefore hydrophobic. If a polypeptide chains contains such R
groups and is in aqueous environment, the chain will tend to
fold so that the maximum number of hydrophobic groups tend to
point inwards the center of the roughly molecule while the
hydrophilic groups face outwards into the aqueous environment.
Protein Function
Some examples
 Structure- form structural components of the cell including:
 Cytoskeleton / nuclear matrix / tissue matrix
 Lamins, collagen, keratin…….

 Movement - Coordinate internal and external movement of cells,

organells, tissues, and molecules.
 Muscle contraction, chromosome separation, flagella………
 Micro-tubueles, actin, myosin

 Transport-regulate transport of molecules into and out of the cell / nucleus

/ organelles.
 Channels, receptors, dynin, kinesin

 Communication-serve as communication molecules between different

organelles, cells, tissues, organs, organisms.
 Hormones
Protein Function
Some examples
 Chemical Catalyst – serves to make possible all of the
chemical reactions that occur within the cell.
 Enzymes (thousands of different enzymes)

 Defense-recognize self and non-self, able to destroy

foreign entities (bacteria, viruses, tissues).
 Antibodies, cellular immune factors

 Regulatory-regulates cell proliferation, cell growth, gene

expression, and many other aspects of cell and organism
life cycle.
 Checkpoint proteins, cyclins, transcription factors
Properties of amino acids
 amino acids:
acidic
basic
hydrophobic

 Amino acids all have

The same basic structure

 Chemical properties of the

amino acids yield
properties of the protein!
Properties of amino acids
Protein Structure
 The 3-D shape and properties of the protein
determine its function.

 Shape and properties of protein determined by

interactions between individual amino acid
components.

 Four “levels” of protein structure

 Primary (Io), secondary (IIo), tertiary (IIIo), and
quaternary (IVo) (sometimes).
Levels of Protein Structure
Primary Structure
 Amino acids combine to form a chain

 Each acid is linked by a peptide bond

 Io structure by itself does not provide a lot of

information.
Protein Structure
 II0 (secondary) structure
 Based on local interactions between amino acids
 Common repeating structures found in proteins. Two
types: alpha-helix and beta-pleated sheet.
 In an alpha-helix the polypeptide main chain makes up
the central structure, and the side chains extend out and
away from the helix.
 The CO group of one amino acid (n) is hydrogen
bonded to the NH group of the amino acid four
residues away (n +4).
 Can predict regions of secondary structure
Ribbon Diagram

α-helical regions
Beta sheet
 Two types parallel
and anti-parallel
Beta Sheet ribbon diagram

parallel
antiparallel
Protein Structure
 III0 (tertiary structure)
 Complete 3-D structure
of protein (single
polypeptide)

hexokinase

Chymotrypsin with inhibitor

Protein Structure
 IV0 (quaternary)
structure
 Not all proteins have
IV0 structure
 Only if they are made
of multiple polypeptide
chains
Protein Explorer
 Web site that will show a model of a protein
who’s structure has been solved.

http://molvis.sdsc.edu/protexpl/frntdoor.htm

 3-D structures must be experimentally determined

through the technique of X-ray crystalography.
 Scientists are working on computer predictions of 3-
D structure but so far not much progress.
Nucleic Acids
 DNA –deoxyribonucleic acid
 Polymer of deoxyribonucleotide triphosphate (dNTP)
 4 types of dNTP (ATP, CTP, TTP, GTP)
 All made of a base + sugar + triphosphate

 RNA –ribonucleic acid

 Polymer of ribonucleotide triphosphates (NTP)
 4 types of NTP (ATP, CTP, UTP, GTP)
 All made of a base + sugar + triphosphate

 So what’s the difference?

 The sugar (ribose vs. deoxyribose) and one base (UTP vs.
TTP)
Function

 Nucleic Acids
 Information Storage
 DNA / mRNA
 Information transfer / Recognition
 rRNA / tRNA / snRNA
 Regulatory
 microRNA ?
 DNA
Information for all proteins stored in DNA
in the form of chromosomes or plasmids.
Chromosomes (both circular and linear)
consist of two strands of DNA wrapped
together in a left handed helix.

The strands of the helix are held together

by hydrogen bonds between the individual
bases. The “outside” of the helix consists of
sugar and phosphate groups, giving the DNA
molecule a negative charge.
Complimentary Base Pairs

A-T Base pairing G-C Base Pairing

DNA Structure
 The DNA helix is “anti-parallel”
 Each strand of the helix
has a 5’ (5 prime) end and
a 3’ (3 prime) end.
 DNA Structure
3’ end
5 ‘ end

Strand 2 Strand 1
(Crick strand) (Watson strand)

5’end
3 ‘ end
DNA Structure
 1 atgatgagtg gcacaggaaa cgtttcctcg atgctccaca gctatagcgc caacatacag
 61 cacaacgatg gctctccgga cttggattta ctagaatcag aattactgga tattgctctg
 121 ctcaactctg ggtcctctct gcaagaccct ggtttattga gtctgaacca agagaaaatg
 181 ataacagcag gtactactac accaggtaag gaagatgaag gggagctcag ggatgacatc
 241 gcatctttgc aaggattgct tgatcgacac gttcaatttg gcagaaagct acctctgagg
 301 acgccatacg cgaatccact ggattttatc aacattaacc cgcagtccct tccattgtct
 361 ctagaaatta ttgggttgcc gaaggtttct agggtggaaa ctcagatgaa gctgagtttt
 421 cggattagaa acgcacatgc aagaaaaaac ttctttattc atctgccctc tgattgtata

Because of the base pairing rules, if we know one

strand we also know what the other strand is.
Convention is to right from 5’ to 3’ with 5’ on the left.
Chromosomes and Plasmids
 Chromosomes are composed of DNA and
proteins.
 Proteins (histone & histone like proteins) serve a
structural role to compact the chromosome.
 Chromosomes can be circular, or linear.
 Both types contain an antiparallel double helix!
 Genes are regions within a chromosome.
 Like words within a sentence.
For an animation of the organization of a human chromosome see:
http://www.dnalc.org/ddnalc/resources/chr11a.html
Region (red box) of
chromosome XI from the
bakers yeast S. cerevisiae.
Red and Blue colored
boxes are genes
(ORF). Note that either
strand may encode a gene,
but that all genes start at
the 5’ end and finish at the
3’ end.

http://www.yeastgenome.org/
RNA
 Almost all single stranded (exception is
RNAi).
 In some RNA molecules (tRNA) many of the
bases are modified (i.e. psudouridine).
 Has capacity for enzymatic function.
 One school of thought holds that early
organisms were based on RNA instead of
DNA (RNA world).
RNA
 Several different “types” which
reflect different functions
 mRNA (messenger RNA)
 tRNA (transfer RNA)
 rRNA (ribosomal RNA)
 snRNA (small nuclear RNA)
 RNAi (RNA interference)
 RNA function
 mRNA – transfers information from DNA to
ribosome (site where proteins are made)
 tRNA – “decodes” genetic code in mRNA, inserts
correct A.A. in response to genetic code.
 rRNA-structural component of ribosome
 snRNA-involved in processing of mRNA
 RNAi-double stranded RNA, may be component of
antiviral defense mechanism.
RNA

A - hairpin loop
B- internal loop
C- bulge loop
D- multibranched loop
E- stem
F- pseudoknot

Complex secondary structures can form in linear molecule

mRNA

 Produced by RNA polymerase as product of transcription

 Provides a copy of gene sequence (ORF) for use in

translation (protein synthesis).
 Transcriptional regulation is major regulatory point
 Processing of RNA transcripts occurs in eukaryotes
 Splicing, capping, poly A addition
 In prokaryotes coupled transcription and translation can
occur