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LECTURE PRESENTATIONS
For CAMPBELL BIOLOGY, NINTH EDITION
Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson
Chapter 4
Carbon and the Molecular
Diversity of Life
Lectures by
Erin Barley
Kathleen Fitzpatrick
© 2011 Pearson Education, Inc.
Overview: Carbon: The Backbone of Life
• living organisms consist mostly of carbon-based
compounds
• carbon is unparalleled in its ability to form large, complex,
and diverse molecules
• proteins, DNA, carbohydrates, and other molecules that
distinguish living matter are all composed of carbon
compounds
Molecules of Life:
• the chemicals used in metabolic reactions or those
that are produced by them can be classified into 2 groups:
1. Inorganic
2. Organic
Inorganic Compounds
 water
 oxygen,carbon dioxide
 inorganic salts
Organic Compounds
 what three elements make up an organic compound?
Organic Compounds
• always contain carbon, oxygen and hydrogen
Concept 4.2: Carbon atoms can form diverse molecules
by bonding to four other atoms
• electron configuration is the key to an atom’s
characteristics
• electron configuration determines the kinds and
number of bonds an atom will form with other atoms
The Formation of Bonds with Carbon
• with four valence electron - carbon can form
four covalent bonds with a variety of atoms
• this ability makes large, complex molecules
possible
• in molecules with multiple carbons, each carbon
bonded to four other atoms has a tetrahedral
shape
• however, when two carbon atoms are joined by a
double bond, the atoms joined to the carbons are
in the same plane as the carbons
Figure 4.3
Name and
Comment
Molecular
Formula
(a) Methane
CH4
(b) Ethane
C2H6
(c) Ethene
(ethylene)
C2H4
Structural
Formula
Ball-andStick Model
Space-Filling
Model
• the valences of carbon and its most frequent partners
(hydrogen, oxygen, and nitrogen) are the “building code” that
governs the architecture of living molecules
Hydrogen
(valence  1)
Oxygen
(valence  2)
Nitrogen
(valence  3)
Urea
Carbon
(valence  4)
• Carbon chains form the skeletons of most organic molecules
• Carbon chains vary in length and shape
(c) Double bond position
(a) Length
Ethane
Propane
(b) Branching
Butane
1-Butene
2-Butene
(d) Presence of rings
2-Methylpropane
(isobutane)
Cyclohexane
Benzene
Hydrocarbons
• Hydrocarbons are organic molecules consisting of only carbon
and hydrogen
• many organic molecules, such as fats, have hydrocarbon
components
• hydrocarbons can undergo reactions that release a large amount
of energy
Nucleus
Fat droplets
10 m
(a) Part of a human adipose cell
(b) A fat molecule
Isomers
• variation in the architecture of
organic molecules can be seen as
isomers
• isomers are compounds with the
same molecular formula but different
structures and properties
– structural isomers have
different covalent
arrangements of their atoms
– cis-trans isomers have the
same covalent bonds but differ
in spatial arrangements
– enantiomers are isomers that
are mirror images of each other
(a) Structural isomers
(b) Cis-trans isomers
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
(c) Enantiomers
CO2H
CO2H
H
NH2
CH3
L isomer
NH2
H
CH3
D isomer
• enantiomers are important in the
pharmaceutical industry
• two enantiomers of a drug may have different
effects
• usually only one isomer is biologically active
• differing effects of enantiomers demonstrate
that organisms are sensitive to even subtle
variations in molecules
Drug
Condition
Ibuprofen
Pain;
inflammation
Albuterol
Effective
Enantiomer
Ineffective
Enantiomer
S-Ibuprofen
R-Ibuprofen
R-Albuterol
S-Albuterol
Asthma
Concept 4.3: A few functional groups are key to
the functioning of biological molecules
• distinctive properties of organic molecules depend on the
carbon skeleton and on the molecular components attached
to it
• a number of characteristic functional groups can replace
the hydrogens attached to skeletons of organic molecules
• the number and arrangement of functional groups give each
molecule its unique properties
Estradiol
Testosterone
Example: Modification of Hydrocarbons
• modification of a hydrocarbon with functional groups can turn a
non-polar hydrocarbon into a structure with polar characteristics
• the functional groups usually contain O, N, P or S
H H H
O
H C C C C
OH
H H H
carboxyl
group = hydrophilic
H H H
O
H C C C C
dO
H
H
H
de-protonated carboxyl
group
hydrocarbon + carboxyl group  “hydrophilic”
due to the electronegativity of the oxygen atom
• The seven functional groups that are most important in
the chemistry of life:
–
–
–
–
–
–
–
–
Hydroxyl group = negative charge
Carbonyl group
Carboxyl group = negative charge
Amino group = positive charge
Sulfhydryl
Sulfate group = negative charge
Phosphate group = negative charge
Methyl group
CHEMICAL
GROUP
Hydrophilic
Hydrophilic
Hydroxyl
Carbonyl
Carboxyl
STRUCTURE
(may be written HO—)
NAME OF
COMPOUND
Alcohols (Their specific names
usually end in -ol.)
Ketones if the carbonyl group is
within a carbon skeleton
Carboxylic acids, or organic acids
Aldehydes if the carbonyl group
is at the end of the carbon skeleton
EXAMPLE
Ethanol
Acetone
Acetic acid
Propanal
FUNCTIONAL
PROPERTIES
• Is polar as a result of the
electrons spending more time
near the electronegative oxygen
atom.
• Can form hydrogen bonds with
water molecules, helping dissolve
organic compounds such as
sugars.
• A ketone and an aldehyde may be
structural isomers with different
properties, as is the case for
acetone and propanal.
• Ketone and aldehyde groups are
also found in sugars, giving rise
to two major groups of sugars:
ketoses (containing ketone
groups) and aldoses (containing
aldehyde groups).
• Acts as an acid; can donate an
H+ because the covalent bond
between oxygen and hydrogen
is so polar:
Nonionized
Ionized
• Found in cells in the ionized form
with a charge of 1 and called a
carboxylate ion.
Hydrophilic
Hydrophilic
Amino
Sulfhydryl
Hydrophilic
Phosphate
Methyl
(may be
written HS—)
Amines
Organic phosphates
Thiols
Cysteine
Glycine
• Acts as a base; can
pick up an H+ from the
surrounding solution
(water, in living
organisms):
Nonionized
Ionized
• Found in cells in the
ionized form with a
charge of 1+.
Glycerol phosphate
• Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure.
• Contributes negative charge to
the molecule of which it is a part
(2– when at the end of a molecule,
as above; 1– when located
internally in a chain of
phosphates).
• Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds.
• Molecules containing phosphate
groups have the potential to react
with water, releasing energy.
-the H+ of a carboxyl group is often picked up by the NH2  NH3+
-creates a zwitterion
Methylated compounds
5-Methyl cytidine
• Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects the
expression of genes.
• Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
Organic macromolecules:
1. carbohydrates
2. lipids
3. proteins
4. nucleic acids
Figure 5.2
(a) Dehydration reaction: synthesizing a polymer
1
2
3
Short polymer
Unlinked monomer
Dehydration removes
a water molecule,
forming a new bond.
1
2
3
4
Longer polymer
(b) Hydrolysis: breaking down a polymer
1
2
3
Hydrolysis adds
a water molecule,
breaking a bond.
1
2
3
4
1. Carbohydrates:
• provide energy to cells
•
can be stored as reserve energy supply (humans = glycogen)
• supply “building materials” to build certain cell structures
•
e.g. cell wall of plants
• water soluble = hydrophilic
• characterized H - C - OH
•
e.g. glucose C6H12O6
sucrose C12H22O11
classified by size: simple sugars – saccharides
complex – polysaccharides
monosaccharides
disaccharides
• carbohydrates are classified many ways:
1. the location of the carbonyl group (as aldose or ketose)
-aldose = carbonyl group (C=O) is at the end of the carbon
skeleton
-ketose – carbonyl is within the carbon skeleton
2. the number of carbons in the carbon skeleton
-e.g. five carbon sugars = pentose (ribose and deoxyribose)
-e.g. six carbon = hexose (glucose, fructose and galactose)
3. also by the number of subunits – simple saccharides (sugars)
and complex polysaccharides
A. Simple carbohydrates – mono and disaccharides
• monosaccharides = single saccharide subunit
in which the # of carbon atoms is low - from 3 to 7
- formula: C:2H:O
Aldose (Aldehyde Sugar)
Ketose (Ketone Sugar)
Hexoses: 6-carbon sugars (C6H12O6)
Glucose
Galactose
Fructose
• glucose and galactose with their carbonyls at the end are aldose sugars
• glucose and galactose only differ with respect to their arrangements of H and OH groups at
one carbon!! (see purple boxes)
• fructose is a ketose sugar
Monosaccharides:
- in aqueous solutions – the monosaccharides are not linear
-they form rings
-three ways to represent the ring structure of a monosaccharide
3. Simplest form
1. Molecular
ring form
2. Abbreviated ring structure
Glucose, Fructose and Galactose
beta-glucose
(OH above the ring plane)
alpha-glucose
(OH below the ring plane)
beta-galactose
(isomer of glucose
at the 4 carbon)
A. Simple carbohydrates
• disaccharide = two monosaccharides bound together
-form by a dehydration synthesis reaction to form a
glycosidic linkage
-broken up by a hydrolysis reaction
e.g. glucose + glucose = maltose
e.g. glucose + fructose = sucrose
e.g. glucose + galactose = lactose
B. Complex carbohydrates:
• built of simple carbohydrates to form macromolecules
•multiple, repeating monomers or “building blocks”  polymer
•some serve as storage materials – hydrolyzed into individual
monosaccharides for sugars
• others serve as structural or building materials
Storage Polysaccharides
Chloroplast Starch granules
Amylopectin
•Starch & Glycogen = storage
polysaccharides
• stored by plants and animals as a future
sugar supply
•starch = storage form of glucose found in
plants
• simplest ones are joined by 1-4
linkages (e.g. amylose)
• helical and unbranched in
conformation
• stored within plastids – e.g.
chloroplast
• some are more complex – with branch
points (1-6 linkages) – e.g.
amylopectin
• hydrolyzed into glucose by enzymes –
found in both plants and animals
Amylose
(a) Starch:
1 m
a plant polysaccharide
Mitochondria Glycogen granules
Glycogen
(b) Glycogen:
0.5 m
an animal polysaccharide
• glycogen = storage
form of glucose found
in animals
• very highly branched
• hydrolyzed into
glucose (in liver)
Structural Polysaccharides
•
•
•
cellulose -major component of the tough wall of plant cells
polymer of glucose, but the glycosidic linkages differ
the difference is because there are two ring forms for glucose: alpha () and beta
()
– when glucose forms a ring – the OH group at carbon 1 can either be positioned above
or below the plane of the ring
– above – beta form
– below – alpha form
– starch – all glucoses are in the alpha form
– cellulose – all glucoses are in the beta form – which makes every other glucose
upside down
(a)  and  glucose
ring structures
 Glucose
(b) Starch: 1–4 linkage of  glucose monomers
 Glucose
(c) Cellulose: 1–4 linkage of  glucose monomers
•
cellulose differs from starch in many ways:
– unlike starch – cellulose is not helical or branched
– some OH groups on its glucose monomers are free to hydrogen bond with OHs from
neighbouring cellulose molecules
– results in cellulose molecules grouped parallel to one another = called microfibrils
– strong cable-like building material – found in the cell wall of plants
– enzymes that digest starch are unable to break the beta linkages of cellulose because of
their different shapes
– prokaryotes possess cellulase
• large numbers of these bacteria in the gut of herbivores
– humans unable to hydrolyze cellulose – “insoluble fiber”
•
cellulose “scrapes” the lining of the GI tract and causes the production of mucus (aids in smooth passage of other
food through the GI tract)
Cellulose
microfibrils in a
plant cell wall
Cell wall
Microfibril
10 m
0.5 m
Cellulose
molecules
 Glucose
monomer
Lipids
• many types
– 1. triglycerides = fats and oils
– 2. phospholipids
– 3. steroids
• cholesterol – animal cell membranes, basis for steroid
hormones
• bile salts - digestion
• vitamin D – calcium regulation
• Adrenocorticosteroid hormones
• Sex hormones
– 4. Eicanosoids
• prostaglandins
• leukotrienes
– 5. Others
•
•
•
•
•
fatty acids
carotenes – synthesis of vitamin A
vitamin E – wound healing
vitamin K – blood clotting
lipoproteins – HDL and LDL
2. Lipids
A. Fats
• energy supply
• most plentiful lipids in your body
• composed of C, H and O
• “building blocks” = 3 fatty acid chains (hydrocarbons
usually from 16 to 18 carbons)
PLUS 1 glycerol molecule
fatty acid
fatty acid
fatty acid
glycerol portion
fatty acid portion
• formed through dehydration synthesis reactions to
form an ester linkage
• the three fatty acids joined to glycerol creates a
triacylglycerol, or triglyceride
• fats separate from water because water
molecules form hydrogen bonds with each other
and exclude the fats
Ester linkage
Fatty acid
(in this case, palmitic acid)
Glycerol
(a) One of three dehydration reactions in the synthesis of a fat
(b) Fat molecule (triacylglycerol)
© 2011 Pearson Education, Inc.
• fatty acids -differ in chain length with each fat
-differ in the location and number of double bonds
within the hydrocarbon chains
1. single C bonds - saturated
2. double C bonds - unsaturated
monounsaturated:
1 double bond
polyunsaturated:
2 or more double bonds
• Saturated fatty acids
have the maximum
number of hydrogen
atoms possible and no
double bonds
• Unsaturated fatty
acids have one or
more double bonds
(a) Saturated fat
Structural
formula of a
saturated fat
molecule
Space-filling
model of stearic
acid, a saturated
fatty acid
•
the fatty acid tails are more flexible
forms a solid
the molecules of an unsaturated fat cannot pack closely together enough to
solidify
•
•
•
Structural
formula of an
unsaturated fat
molecule
Space-filling model
of oleic acid, an
unsaturated fatty
Cis double bond
acid
causes bending.
at room temperature – the molecules of a saturated fat are packed closely
together
•
•
•
(b) Unsaturated fat
the C=C bonds produce a “kink” in the fatty acid chain making it difficult to pack
them together
if the fat contains one fatty acid that is unsaturated – then the fat is considered
unsaturated
in hydrogenated oils – the unsaturated fats have been chemically converted to
saturated by adding hydrogens
•
prevents their separation into an oil form – keeps them solid
-a gram of fat stores twice as much energy vs. a gram of a polysaccharide like starch
-adipose tissue evolved due to animal movement
-much less bulky than polysaccharides like starch
-although plants did evolve oils in their seeds to decrease the amount of
space needed for the energy required
-some fatty acids cannot be made by the body and must be taken in through food =
essential fatty acids
e.g omega-3 fatty acids
-polyunsaturated fatty acids -important in regulating cholesterol levels (lower LDL levels in
the blood)
-increase calcium utilization by body
- reduce inflammation (arthritis?)
- promote wound healing
B. Phospholipids
• similar to fat molecules - glycerol + 2 fatty acids
•modified through the replacement of one FA with a phosphate group (negative electrical
charge)
• phosphate gp  hydrophilic “head”
• fatty acid gps  hydrophobic “tails”
• when added to water – self-assemble and form a form a phospholipid
bilayer – major component of the plasma membrane
C. Steroids
• backbone is called cholesterol = 4 fused carbon rings
• synthesized in the liver
• diversity through attached functional groups
e.g. testosterone, estrogen
aldosterone
3. Proteins
• nearly every dynamic function of a living organism depends on
proteins
•Greek – proteios = “first place”
•more than 50% of the dry mass of most cells
•numerous roles:
• structural – support of cells and tissues
• storage - energy source
• transport across cell membranes
• hormones and their receptors – signaling
• chemical messengers - signaling
• antibodies - defense
• metabolic role - enzymes
Enzymatic proteins
Defensive proteins
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
Antibodies
Enzyme
Virus
Bacterium
Storage proteins
Transport proteins
Function: Storage of amino acids
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.
Transport
protein
Ovalbumin
Figure 5.15-a
Amino acids
for embryo
Cell membrane
Figure 5.15-b
Hormonal proteins
Receptor proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.
High
blood sugar
Insulin
secreted
Normal
blood sugar
Receptor
protein
Signaling
molecules
Contractile and motor proteins
Structural proteins
Function: Movement
Examples: Motor proteins are responsible for the
undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of
muscles.
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.
Actin
Myosin
Collagen
Muscle tissue
100 m
Connective
tissue
60 m
• life would not be possible without enzymes
• enzymes are a type of protein that acts as a catalyst to speed up
chemical reactions
• function relies upon their 3D conformation and the physical environment
they are working in
3. Proteins
•building blocks = amino acids
Side chain (R group)
 carbon
Amino
group
Carboxyl
group
a.a. = amino group at 1 end, carboxyl at the
other
- between is a single C called the alpha
carbon
-the alpha carbon is assymetrical and is
bound to: 1. H atom
2. R group
• 22 amino acids available for human protein synthesis
– 20 of them are coded for by our DNA
• the R group give the amino acid a unique physical and chemical
character
• divided into three groups
– polar amino acids
– non-polar amino acids
– electrically charged amino acids –basic or acidic
the 20 amino acids coded by
DNA:
1. non-polar:
1. Methionine – Met or M
2. Phenylalanine – Phe or F
3. Tryptophan – Trp or W
4. Proline – Pro or P
5. Glycine – Gly or G
6. Alanine – Ala or A
7. Valine – Val or V
8. Leucine – Leu or L
9. Isoleucine – Iso or I
2. polar:
1. Serine – Ser or S
2. Threonine – Thr or T
3. Cysteine – Cys or C
4. Tyrosine – Tyr or Y
5. Asparagine – Asp or N
6. Glutamine – Glu or Q
3. acidic
1. Aspartic acid – Asp or D
2. Glutamic acid – Glut or E
4. basic
1. Lysine – Lys or K
2. Arginine – Arg or R
3. Histidine – His or H
• amino acids joined together by a dehydration synthesis reaction
forming a peptide bond = between the NH2 of 1 a.a. and the COOH
of the next amino acid
Figure 5.17
2 a.a.  dipeptide
Peptide bond
3 a.a.  tripeptide
New peptide
bond forming
4 or more a.a.  polypeptide
Side
chains
Backbone
Amino end
(N-terminus)
Peptide Carboxyl end
bond (C-terminus)
• the 3D architecture is critical to protein function
• 3D shape is determined by the sequence of amino
acids
-i.e. the chemical properties of the amino acid
can determine whether the protein will twist or
kink or be linear
-when a cell forms a polypeptide – it
spontaneously begins to fold (takes no energy)
-folding is driven by the bonds between
different regions of the pp chain
-the types of bonds depend on the amino
acid sequence
(a) A ribbon model
•BUT – the physical environment can also affect 3D shape
• e.g. pH, salt, temperature
•IMPORTANT: polypeptide does not mean protein!!!!
•polypeptides have 4 types of structures or conformations
(b) A
which affect their ultimate function
space-filling model
Protein conformation:
1. primary - a.a. sequence of polypeptides
e.g. transthyretin – 127 amino acids
-sequence is determined by the genetic code found
in the DNA
-if randomly created – then a 127 AA polypeptide could be
made 20127 different ways!!
Tertiary
structure
Secondary
structure
Quaternary
structure
 helix
Hydrogen bond
 pleated sheet
 strand
Hydrogen
bond
Transthyretin
polypeptide
Transthyretin
protein
2. secondary – sections of the AA chain fold into -helical coils or -pleated sheets
-found in most proteins
-the result of H bonding
- O and N atoms have partial negative charges
-the weakly positive H atom attached to the N is attracted
to the positive O of a nearby AA
-alpha helix – produced by H bonding every 4th AA
-beta pleated sheet – H bonding between two or more regions of the PP
lying side by side
3. tertiary – secondary structure folds into a unique 3D shape
-tertiary conformation is superimposed on the secondary structure
-gives rise to the overall 3D shape and function of the protein
-results from interactions between the R groups
Tertiary
structure
Secondary
structure
 helix
Hydrogen bond
 pleated sheet
 strand
Hydrogen
bond
-one interaction = hydrophobic interactions
-non-polar AAs face in when the protein folds
-due to hydrophobic interaction with water
-van der Waals keep these AAs close together
-other interactions:
-hydrogen bonding
-between polar AAs
-between the +ve and –ve charges of the acidic
and basic AAs (ionic bond)
Hydrogen
bond
Hydrophobic
interactions and
van der Waals
interactions
Disulfide
bridge
Ionic bond
Polypeptide
backbone
-3D shape is reinforced through the
formation of disulfide bridges
4. quaternary = joining of 2 or more polypeptides chains
-aggregate into one function macromolecule
-individual polypeptide chains are called subunits
Heme
Iron
 subunit
 subunit
Collagen
 subunit
 subunit
Hemoglobin
MEDICAL APPLICATION: Sickle-Cell Disease: A
Change in Primary Structure
• A slight change in primary structure can affect a protein’s
structure and ability to function
• Sickle-cell disease, an inherited blood disorder, results from a
single amino acid substitution in the protein hemoglobin
Sickle-cell hemoglobin
Normal hemoglobin
Primary
Structure
1
2
3
4
5
6
7
Secondary
and Tertiary
Structures
Quaternary
Structure
 subunit


Exposed
hydrophobic
region
 subunit

10 m

Sickle-cell
hemoglobin

Red Blood
Cell Shape
Molecules do not
associate with one
another; each carries
oxygen.
Normal
hemoglobin

1
2
3
4
5
6
7
Function
Molecules crystallize
into a fiber; capacity
to carry oxygen is
reduced.


10 m
Protein Folding in the Cell
• the AA sequence of more than 10 million proteins is now known
• the 3D structure of more than 20,000 proteins are also known
– used to predict a protein’s structure from its primary structure
• BUT – the folding process is not straightforward
– most proteins probably go through several stages on their way to a stable structure
• one thing is known – that initial protein folding is spontaneous
© 2011 Pearson Education, Inc.
Protein Folding in the Cell
•
Chaperonins –proteins that assist the proper folding of other proteins
– don’t fold the protein
– detects when a protein is mis-folded and targets it for destruction
– found in the cytoplasm and in the endoplasmic reticulum
– made of a ‘cap’ on top a ‘hollow cylinder’
– the cylinder keeps the protein protected while it folds spontaneously
– other monitoring systems also exist to verify folding
– destruction of the mis-folded protein – by a proteosome
•diseases such as Alzheimer’s, Parkinson’s, and mad
cow disease are associated with mis-folded proteins
Polypeptide
Correctly
folded
protein
Cap
Chaperonin
(fully assembled)
© 2011 Pearson Education, Inc.
Steps of Chaperonin
Action:
1 An unfolded polypeptide enters the
cylinder from
one end.
2
The cap attaches, causing
the cylinder to change
shape in such a way that
it creates a hydrophilic
environment for the
3
The cap comes
off, and the
properly folded
protein is
released.
Protein Folding in the Cell
EXPERIMENT
• determining 3D protein structure uses a
branch of science called X-ray
crystallography
–
–
–
•
the molecule is crystallized
the atoms of the molecule diffract the X-rays
diffraction pattern is analyzed by computer
software and a 3D ribbon structure is
generated – known as bioinformatices
Diffracted
X-rays
X-ray
source X-ray
beam
Crystal
Digital detector X-ray diffraction
pattern
RESULTS
RNA
DNA
another method is nuclear magnetic
resonance (NMR) spectroscopy - does not
require protein crystallization
RNA
polymerase II
4. Nucleic acids
• known as DNA, RNA
• C,H,O,N,P
• building blocks = nucleotides or nucleic acids
Sugar-phosphate backbone
5 end
• nucleotide:
5C
•5 carbon sugar (pentose)
3C
phosphate group (negative
charge) located at the 5’ carbon
organic base located at the 1’
carbon
sugar and the base is known as a
nucleoside
bases: 5 types: adenine (A)
cytosine (C)
5C
guanine (G)
3C
thymine (T)
uracil (U)
3 end
Nucleoside
Nitrogenous
base
5C
1C
Phosphate 3C
group
Sugar
(pentose)
(b) Nucleotide
(a) Polynucleotide, or nucleic acid
 There are two families of
nitrogenous bases
Nitrogenous bases
Pyrimidines
Cytosine
(C)
Thymine
(T, in DNA)
1. Pyrimidines (cytosine,
thymine, and uracil) have a
single six-membered ring
Uracil
(U, in RNA)
2. Purines (adenine and
guanine) have a sixmembered ring fused to a
five-membered ring
Sugars
Purines
Adenine (A)
Guanine (G)
(c) Nucleoside components
Deoxyribose
(in DNA)
Ribose
(in RNA)
• polynucleotide chain - formed by a phosphodiester bond between
the phosphate (5’) of 1 n.t. and the sugar of the
next (3’)
-phosphodiester bond is comprised of a phosphate group linking two sugars
Sugar-phosphate backbone
5 end
5C
3C
• two major types of nucleic acids:
1. RNA sugar = ribose
phosphodiester
2. DNA sugar = deoxyribose
bond
HOCH2
O
OH
H
H
OH
OH
ribose
HOCH2 O
OH
H
H
OH
H
deoxyribose
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
• so a DNA/RNA chain “grows” in
one direction only
-5’ to 3’
A. RNA
single polynucleotide chain
bases: A, C, G and uracil
(U) in place of T
3 major types: mRNA
tRNA
rRNA
B. DNA
double polynucleotide chain = double helix
sense strand (5’ to 3’) anti-sense strand
2 chains held by hydrogen bonds
between the bases
bases pair up in a complementary fashion
A=T
C G
c. ATP
individual n.t’s can have metabolic functions
e.g. adenosine = adenine + ribose
-adenine modified by adding three phosphates
major source of ATP = breakdown of glucose
1 glucose molecule
glycolysis
Kreb’s cycle
oxidative phosphorylation
36 ATP