This image shows the primary structure of glycophorin A , a glycoprotein that spans the plasma membrane ("Lipid bilayer") of human red blood cells. Each RBC has some 500,000 copies of the molecule embedded in its plasma membrane. Fifteen carbohydrate chains are "O-linked" to serine (Ser) and threonine (Thr) residues. One carbohydrate chain is "N-linked" to the asparagine (Asn) at position 26. Two polymorphic versions of glycophorin A, which differ only at residues 1 and 5, occur in humans. These give rise to the MN blood groups The M allele encodes Ser at position 1 (Ser-1) and Gly at position 5 (Gly-5) The N allele encodes Leu-1 and Glu-5 Genotype to Phenotype Individuals who inherit two N alleles have blood group N. Individuals who are homozygous for the M allele have blood group M. Heterozygous individuals produce both proteins and have blood group MN . Glycophorin A is the most important attachment site by which the parasite Plasmodium falciparum invades human red blood cells.
Black alpha carbon. Grey carbon, red oxygen, blue nitrogen
Structure and Function of
Carbohydrates, Nucleic Acids,
Cells as chemical reactors
Living organisms obey the laws of
chemistry and physics
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!
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
RNA viruses, but not true cells
(incapable of autonomous replication)
All cells use proteins as catalysts (enzymes) for
A few examples of RNA based enzymes, which may reflect
primordial use of RNA
All cells use lipids for membrane components
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
Macromolecules are formed when
monomers are linked together to form
longer chains called polymers.
The same process of making and breaking
polymers is found in all living organisms.
Consider some generic monomers with OH groups on their ends.
These monomers can be linked together by a process called
dehydration synthesis (also called a condensation reaction) in
which a covalent bond is formed between the two monomers while
a water molecule is also formed from the OH groups.
This reaction is catalyzed by a polymerase enzyme.
This same type of condensation reaction can occur to form many
kinds of polymers, from proteins to carbohydrates, nucleic acids to
Polymers of all sorts can be broken apart
by hydrolysis reactions. In hydrolysis the
addition of a water molecule (with the help
of a hydrolase enzyme) breaks the
covalent bond holding the monomers
Biotechnology often concerned with the
manipulation of cells through the manipulation
of the macromolecules contained within those
Lipids & Carbohydrates (indirectly)
Biologically important macromolecules are
“polymers” of smaller subunits
Created through condensation reactions
Carbohydrates : simple sugars
Lipids : CH2 units
Proteins : amino acids
Nucleic acids : nucleotides
Where do the subunits come from?
All cells need a source of the atomic components of the
(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
All have general formula CnH2nOn (hydrates
(H2O) 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
A central function is energy storage
and energy production !
Carbohydrates are always composed of
carbon, hydrogen and oxygen molecules
Monosaccharides typically have five or
six carbon atoms.
Monosaccharides can, such as the ribose
and deoxyribose of RNA and DNA, can
serve very important functions in cells.
Condensation reactions form covalent
bonds between monosaccharides, called
Monosaccharides are the monomers for
the larger polysaccharides.
Polysaccharides play various roles, from
energy storage (starch, glycogen) to
Cellulose, LPS, chitin
Cellulose in plant cell walls Lipopolysaccharides (LPS)
in bacterial cell wall
Chitin in exoskeleton
Monosaccharides may also form part of
other biologically important molecules
Complex carbohydrates built from simple sugars
Most often five (pentose) or six (hexose) carbon
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.)
A Few Examples
Triose (3 carbon)
Pentose (5 carbon)
Example of two hexoses
What’s the difference? Both are C6H12O6
They are isomers of one another!
Same formula, but different structure (3D-shape).
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
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.
Ring (cyclic) form
Pentoses and hexoses are capable of forming ring (cyclic) structures.
An equilibrium exists between the ring and open form.
Monosaccharides can link
to form disaccharides
Glucose Fructose Sucrose
Most abundant carbohydrate on the planet!
Component of plant cell walls
Indigestible by animals
β 1-4 bonds
Energy storage molecule in plants
Can be digested by animals
α 1-6 bonds
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 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
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
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
Different types of cells do different post-tranlational
More about this later
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.
are also used in animal
cells to link surface
proteins and lipid
anchors to the
Fatty acids (Polymers of CH2 units)
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 constitute a very diverse group of molecules that all share
the property of being hydrophobic.
Fats and oils are lipids generally associated with energy storage.
Fatty acids, which make up fats and oils, can be saturated or
unsaturated, depending on the absence or presence of double
bonded carbon atoms.
Other types of lipids are used for a other purposes, including
pigmentation (chlorophyll, carotenoids), repelling water (cutin,
suberin, waxes) and signaling (cholesterol and its derivatives).
Lipids are joined together by
Triglyceride is composed of 3 fatty acid
and 1 glycerol molecule
Fatty acids attach to Glycerol by covalent
Long hydrocarbon chain of each fatty acid
makes the triglyceride molecule nonpolar
Proteins serve many essential roles in the cell
Polymers of amino acids
20 naturally occurring amino acids
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
= # of possible combinations
Proteins consist of one or more polymers called
polypeptides, which are made by linking
amino acids together with peptide linkages.
Peptide linkages are formed through
All proteins are made from the same 20 amino acids.
Different amino acids have different chemical
Protein’s primary structure largely
determines its secondary, tertiary (and
Proteins subjected to extreme conditions
(large changes in pH, high temperatures,
etc.) often denature.
Proteins act as enzymes, and catalyze very
specific chemical reactions.
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
Channels, receptors, dynin, kinesin
Communication-serve as communication molecules between different
organelles, cells, tissues, organs, organisms.
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
Checkpoint proteins, cyclins, transcription factors
Polymers of 20 amino acids
All amino acids have a
Amino end (N end)
Acid end (C end, carboxy
Linked by peptide bond
20 different side chains
Properties of amino acids
Amino acids all have
The same basic structure
Chemical properties of the
amino acids yield
properties of the protein!
The 3-D shape and properties of the protein
determine its function.
Shape and properties of protein determined by
interactions between individual amino acid
Four “levels” of protein structure
), secondary (IIo
), tertiary (IIIo
Levels of Protein Structure
Linear order of amino acids in a protein:
1 A A S X D X S L V E V H X X V F I V P P X I L Q A V V S I A
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
Amino acids combine to form a chain
Each acid is linked by a peptide bond
structure by itself does not provide a lot of
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
Complete 3-D structure
of protein (single
Chymotrypsin with inhibitor
Not all proteins have
Only if they are made
of multiple polypeptide
DNA is transmitted
from generation to
high fidelity, and
a partial picture of
the history of life.
Two types of nucleic acids:
DNA stores the genetic information of organisms; RNA is used to transfer that
information into the amino acid sequences of proteins.
DNA and RNA are polymers composed of subunits called nucleotides.
Nucleotides consist of a five-carbon sugar, a phosphate group and a nitrogenous
Five nitrogenous bases found in nucleotides:
thymine (T) (DNA only)
uracil (U) (RNA only)
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.
DNA / mRNA
Information transfer / Recognition
rRNA / tRNA / snRNA
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
The DNA helix is “anti-parallel”
Each strand of the helix
has a 5’ (5 prime) end and
a 3’ (3 prime) end.
5 ‘ end
3 ‘ end
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 (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:
Almost all single stranded (exception is
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).
Several different “types” which
reflect different functions
mRNA (messenger RNA)
tRNA (transfer RNA)
rRNA (ribosomal RNA)
snRNA (small nuclear RNA)
RNAi (RNA interference)
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.
A - hairpin loop
B- internal loop
C- bulge loop
D- multibranched loop
Complex secondary structures can form in linear molecule
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