Download Macromolecules

Biological Macromolecules
Structure and Function of
Carbohydrates, Nucleic Acids,
Proteins, Lipids
Cells as chemical reactors

Living organisms obey the laws of
chemistry and physics

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Can think of cells as complex chemical reactors in
which many different chemical reactions are
proceeding at the same time
All cells more similar then different if
looked at on the inside!
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Strip away the exterior and we see that all cells need
to accomplish similar tasks and in a broad sense they
use the same mechanisms (chemical reactions)
Reflects a singular origin of all extant living things!
Similarities among all types of cells

All cells use nucleic acids (DNA) to store information

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All cells use proteins as catalysts (enzymes) for
chemical reactions
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A few examples of RNA based enzymes, which may reflect
primordial use of RNA
All cells use lipids for membrane components
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RNA viruses, but not true cells
(incapable of autonomous replication)
Different types of lipids in different types of cells
All cells use carbohydrates for cell walls (if present),
recognition, and energy generation
All cells use nucleic acids (RNA) to access
stored information
LUCA (Last Universal Common Ancestor)
Macromolecules

Biotechnology often concerned with the
manipulation of cells through the manipulation
of the macromolecules contained within those
cells

DNA
Proteins
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Lipids & Carbohydrates (indirectly)


Biologically important macromolecules are
“polymers” of smaller subunits

Created through condensation reactions
Macromolecule
Carbohydrates
Lipids
Proteins
Nucleic acids
Subunit
:
:
:
:
simple sugars
CH2 units
amino acids
nucleotides
Where do the subunits come from?
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All cells need a source of the atomic components of the
subunits
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(C, O, H, N, P, and a few other trace elements )
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 general formula CnH2nOn (hydrates
(H2O) of carbon)

A variety of functions in the cell

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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
Monosaccharides may also form part of
other biologically important molecules
Carbohydrate Structure

Complex carbohydrates built from simple sugars
 Most often five (pentose) or six (hexose) carbon
sugars
 Numerous –OH (hydroxy) groups can form many
types of “cross links”
 Can result in very complex and highl;y cross
linked structures ( cellulose, chitin, starch, etc.)
Carbohydrate Structure
A Few Examples

Triose (3 carbon)


Glyceraldehyde
Pentose (5 carbon)

Ribose
Carbohydrate Structure
Example of two hexoses

Glucose

What’s the difference? Both are C6H12O6

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Galactose
They are isomers of one another!
Same formula, but different structure (3D-shape).
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.
 An oligosaccharide gives a "few" carbohydrate units on
hydrolysis, usually 3 to 10.
 A polysaccharide gives many carbohydrates on
hydrolysis, examples are starch and cellulose.
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

Monosaccharides can link
to form disaccharides
Glucose
+
Fructose
Sucrose
Carbohydrate Structure
Glycosidic Bond
β-D Glucose
Sucrose (Glucose + Fructose)
What does the β mean?
Carbohydrate Structure
They are isomers of one another
α-isomer
β-isomer
Common small carbohydrates
Glyceraldehyde
Fructose
Ribose
Lactose
Complex Carbohydrates

Cellulose
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Most abundant carbohydrate on the planet!
Component of plant cell walls
Indigestible by animals
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β 1-4 bonds
Starch
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Energy storage molecule in plants
Can be digested by animals
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α 1-6 bonds
Cellulose
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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 in their
digestive systems. Only animals
capable of breaking down
cellulose are tunicates.
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
Complex Carbohydrates

Glycogen
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Branched chain polymer of glucose
Animal energy reserve
Found primarily in liver and muscle

α 1-4 & α 1-6 bonds

Glycogen
polysaccharides can be linked to other
molecules to form glyco-proteins and glyco-lipids
Glycoproteins
Some examples

Polysaccharide component of antibodies has major effect
on antibody function

Polysaccharides attached to proteins on surface of red
blood cells (RBC) determine blood type (A,B,O)

Polysaccharides are attached to proteins in the Golgi
apparatus through a process of post-translational
modification

Different types of cells do different post-tranlational
modifications

More about this later
Glycosylation of mAb
MW ~150 K
Fab express antigen binding
regions
Fc region interacts with ligands
and determines effect.
N-linked glycosylation (Asn 297)
required for effector function
Glycoform structure (N-linked)

Consits of a core structure

Branched hepatosaccharide
GlcNac
GlcNac
α (1-6)
Man
GlcNac
Man
α (1-3)
Man
GlcNac
Glycoform Structure
Core required for effector function
GlcNAc
Fuc
GlcNac
α (1-6)
Man
Man
α (1-3)
Man
GlcNAc
“outer arm” sugar residues
Influence effector functions
(ADCC, α-inflammatory, etc)
GlcNAc
GlcNAc
Gal
Gal
Neu5Ac
Neu5Ac
Glycolipids

Polysaccharides can also be attached to lipid molecules
•An outer-membrane constituent of gram negative bacteria, LPS, which includes O-antigen, a
core polysaccharide and a Lipid A, coats the cell surface and works to exclude large
hydrophobic compounds such as bile salts and antibiotics from invading the cell. O-antigen are
long hydrophilic carbohydrate chains (up to 50 sugars long) that extend out from the outer
membrane while Lipid A (and fatty acids) anchors the LPS to the outer membrane.
Glycolipids

Polysaccharides (blue)
are also used in animal
cells to link surface
proteins and lipid
anchors to the
membrane.
Lipids

Lipids
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Fatty acids (Polymers of CH2 units)
Glycerol
Triglycerides
Other subunits (phosphate, choline, etc) may be attached
to yield “phospholipids”

Charged phosphate groups will create a polar molecule with a
hydrophobic (nonpolar) end and a hydrophillic (polar) end
Lipids
Phospholipids
Lipids
Function
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Energy Storage
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Triglycerides
Cell membranes and cell compartments
Bi-layer structure
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Outer or plasma membrane
Nuclear membrane
Internal structures
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Er, Golgi, Vesicles, etc.
Phospholipid bilayer
Hydrophillic heads
Hydrophobic tails
Steroids
Proteins
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Proteins serve many essential roles in the cell
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Polymers of amino acids
20 naturally occurring amino acids
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A few modified amino acids are used
The large number of amino acids allows huge diversity
in amino acid sequence
N = # of amino acids in a protein
N20 = # of possible combinations
Protein Function
Some examples

Structure- form structural components of the cell including:

Cytoskeleton / nuclear matrix / tissue matrix
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Movement - Coordinate internal and external movement of cells,
organells, tissues, and molecules.
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Muscle contraction, chromosome separation, flagella………
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Micro-tubueles, actin, myosin
Transport-regulate transport of molecules into and out of the cell / nucleus
/ organelles.
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Lamins, collagen, keratin…….
Channels, receptors, dynin, kinesin
Communication-serve as communication molecules between different
organelles, cells, tissues, organs, organisms.

Hormones
Protein Function
Some examples
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Chemical Catalyst – serves to make possible all of the
chemical reactions that occur within the cell.
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Defense-recognize self and non-self, able to destroy
foreign entities (bacteria, viruses, tissues).
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Enzymes (thousands of different enzymes)
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
Protein Structure
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Polymers of 20 amino acids
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All amino acids have a
Common “core”
Amino end (N end)
Acid end (C end, carboxy
end)
Linked by peptide bond
20 different side chains
Properties of amino acids
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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
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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.
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Four “levels” of protein structure
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Primary (Io), secondary (IIo), tertiary (IIIo), and
quaternary (IVo) (sometimes).
Levels of Protein Structure
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I0 (primary) structure
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Linear order of amino acids in a protein:
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1AASXDXSLVEVHXXVFIVPPXILQAVVSIA
31 T T R X D D X D S A A A S I P M V P G W V L K Q V X G S Q A
61 G S F L A I V M G G G D L E V I L I X L A G Y Q E S S I X A
91 S R S L A A S M X T T A I P S D L W G N X A X S N A A F S S
121 X E F S S X A G S V P L G F T F X E A G A K E X V I K G Q I
151 T X Q A X A F S L A X L X K L I S A M X N A X F P A G D X X
181 X X V A D I X D S H G I L X X V N Y T D A X I K M G I I F G
211 S G V N A A Y W C D S T X I A D A A D A G X X G G A G X M X
241 V C C X Q D S F R K A F P S L P Q I X Y X X T L N X X S P X
271 A X K T F E K N S X A K N X G Q S L R D V L M X Y K X X G Q
301 X H X X X A X D F X A A N V E N S S Y P A K I Q K L P H F D
331 L R X X X D L F X G D Q G I A X K T X M K X V V R R X L F L
361 I A A Y A F R L V V C X I X A I C Q K K G Y S S G H I A A X
391 G S X R D Y S G F S X N S A T X N X N I Y G W P Q S A X X S
421 K P I X I T P A I D G E G A A X X V I X S I A S S Q X X X A
451 X X S A X X A
Single letter code for amino acids, also a three letter code.
Refer to your genetic code handout.
Levels of Protein Structure
Primary Structure
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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
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II0 (secondary) structure
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Based on local interactions between amino acids
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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
antiparallel
parallel
Protein Structure

III0 (tertiary structure)

Complete 3-D structure
of protein (single
polypeptide)
hexokinase
Chymotrypsin with inhibitor
Protein Structure

IV0 (quaternary)
structure
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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
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3-D structures must be experimentally determined
through the technique of X-ray crystalography.
Scientists are working on computer predictions of 3D structure but so far not much progress.
Nucleic Acids
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DNA –deoxyribonucleic acid
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RNA –ribonucleic acid
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Polymer of deoxyribonucleotide triphosphate (dNTP)
4 types of dNTP (ATP, CTP, TTP, GTP)
All made of a base + sugar + triphosphate
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
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Nucleic Acids

Information Storage

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Information transfer / Recognition

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DNA / mRNA
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
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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
5 ‘ end
Strand 2
(Crick strand)
3’ end
Strand 1
(Watson strand)
5’end
3 ‘ end
DNA Structure
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1
61
121
181
241
301
361
421
atgatgagtg gcacaggaaa cgtttcctcg atgctccaca gctatagcgc caacatacag
cacaacgatg gctctccgga cttggattta ctagaatcag aattactgga tattgctctg
ctcaactctg ggtcctctct gcaagaccct ggtttattga gtctgaacca agagaaaatg
ataacagcag gtactactac accaggtaag gaagatgaag gggagctcag ggatgacatc
gcatctttgc aaggattgct tgatcgacac gttcaatttg gcagaaagct acctctgagg
acgccatacg cgaatccact ggattttatc aacattaacc cgcagtccct tccattgtct
ctagaaatta ttgggttgcc gaaggtttct agggtggaaa ctcagatgaa gctgagtttt
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.
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Proteins (histone & histone like proteins) serve a
structural role to compact the chromosome.
Chromosomes can be circular, or linear.
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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
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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
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mRNA (messenger RNA)
tRNA (transfer RNA)
rRNA (ribosomal RNA)
snRNA (small nuclear RNA)
RNAi (RNA interference)
RNA function
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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
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Produced by RNA polymerase as product of transcription
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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