EXAM 1 - Intro and Carbohydrates

● Life is complex and dynamic

○ All organisms are composed of organic (carbon based) molecules
● Life is organized and self sustaining
○ Organized systems from biomolecules to organ systems
● Life is cellular and information based
○ 2 types of cells : prokaryotic and eukaryotic cells

Characteristics of life
1. Cellular organization - living organisms are composed of uni/multicellular cells.
2. Homeostasis - ability to maintain constant internal conditions
3. Metabolism - consists of biochemical reactions that use energy
4. Reproduction - ability to reproduce (sexual or asexual)

What is Biochemistry?
- Relation of chemical processes to living organisms
- Investigates molecular basis of life

Features of living organisms

➢ Cells are the basic unit of life.
➢ Functional and highly organized.
➢ Consists of biochemical reactions; need regulation to maintain life.
➢ Consists of biomolecules; H(63%), O(25.5%), C(9.5%) and N(1.4%) make up 99+% of
atoms in the human body
○ Proteins
○ Nucleic acids
○ Carbohydrates
○ Lipids
➢ Solar energy flows from photosynthetic organisms through food chains to herbivores and
carnivores at the apex of the food pyramid.
➢ Organisms capture energy in the form of special energized molecules such as ATP and
NADPH

“What property unites H, O, C and N and renders these atoms so appropriate to the chemistry of
life?“ Their ability to form covalent bonds by electron-pair sharing.
Structural Organization of Complex Biomolecules
I. Metabolites and Macromolecules
A. building blocks have a “sense” or directionality
B. Informational
C. Three dimensional architecture
D. Weak forces maintain biological structure and determine biomolecular
interactions
II. Organelles
III. Membranes
IV. The Unit of Life is the Cell

• Weak forces profoundly influence the structures and behaviors of all biological molecules
• Weak forces create interactions that are constantly forming and breaking under physiological
conditions
• Energies of weak forces range from 0.4 to 30 kJ/mol
• Weak forces include:
• van der Waals interactions
• Hydrogen bonds
• Ionic interactions
• Hydrophobic interactions

Know these important numbers

• Van der Waals Interactions: 0.4-4.0 kJ/mol
• Hydrogen Bonds: 12-30 kJ/mol
• Ionic Interactions: 20 kJ/mol
• Hydrophobic Interactions: <40 kJ/mol
Prokaryotes
➔ Has cell wall, plasma membrane, circular DNA, no internal membrane organelles
➔ Primary source of SUPPORT/PROTECTION and maintains shape: Cell wall
➔ Selective permeability barrier: Plasma membrane
➔ Holds nucleoid and contains DNA: Cytoplasm
➔ Hair like structures used for locomotion and attachment of food: Pili or Flagella

Eukaryotes
➢ Composed of a lipid bilayer and provides shape, strength, protection and permeability
barrier; compartmentalizes the cell - Cell/Plasma membrane
○ Polar head, thread like structures are hydrophobic composed of lipid
○ Bilayer - contains 2 layers
➢ Gel-like, water based fluid; surrounds and protects organelles; site for energy production,
storage and manufacture of cellular components - cytoplasm or cytosol
➢ Contains the hereditary information; controls system of the cell in metabolic activities -
nucleus
➢ Provides rigidity to the nucleus; site of DNA and RNA synthesis - Nucleoplasm
➢ Separates components of nucleus from the cytoplasm; contains nuclear pores that
control passage of biomolecules - nuclear envelope
➢ Site of ribosomal RNA synthesis - Nucleolus
➢ Involves synthesis of membrane proteins; characterized by flattened sheets with
ribosomes - rough endoplasmic reticulum (RER)
➢ responsible for lipid synthesis and biotransformation; tubular in shape - smooth
endoplasmic reticulum (SER)
➢ RNA protein complexes responsible for protein synthesis - ribosomes
➢ Formed by fusion of vesicles that split off the ER; packaging and distribution of proteins
and lipids to internal and external compartments - Golgi apparatus
➢ Digests excess/worn out biomolecules via endocytosis - lysosomes
➢ Involves the ROS detoxification; breaks down toxic molecules such as peroxides -
Peroxisomes
➢ Powerhouse of the cell; synthesizes free ribosomes; responsible for ATP synthesis -
mitochondria

*lysosomes are only present in animal cells

*cell wall is only present in plant cells
*vacuole is bigger in plant cell
 Carbohydrates
● Polydroxy (poly-many; droxy-OH) aldehydes (H-C=O) or ketones (C=O)
● Most abundant
● Storehouse of chemical energy
● Essential component of nucleic acids
● Supportive component in plants
● Hydrate of carbon; undergoes hydrolysis

2 Major Groups of Carbohydrates:

CARBOHYDRATE GROUP FUNCTIONAL EXAMPLES

GROUP

1. Aldoses ● D-Glyceraldehyde
(3-carbons)

● D-Erythrose
(4-carbons)

● D-Ribose
(5-carbons)
Aldehyde

● D-Glucose
(6-carbons)
 2. Ketoses ● Dihydroxyacetone
(3-carbons)

● D-Erythrulose
(4-carbons)
Ketone

● D-Ribulose
(5-carbons)

● D-Fructose
(6-carbons)

Classifications:
1. Monosaccharides - one
a. Cannot be hydrolyzed to a simpler compound
b. CnH2nOn
c. Suffix ‘ose indicates that a molecule is a carbohydrate

NOMENCLATURE FOR CARBOHYDRATES:

Functional Group + Number of Carbons + Suffix
Aldo/Keto - ose

d. May have more than one chiral center

 e. Colorless, crystalline solids, water soluble and slightly soluble in ethanol and
insoluble in nonpolar solvents (diethyl ether, dichloromethane, and benzene)
2. Disaccharides - two
a. Joined by a glycosidic bond between anomeric carbon of one unit and an -OH
group of the other unit
3. Oligosaccharides - 3 to 10
a. Bonded via glycosidic linkages
b. Found in onions, cabbage, broccoli and whole wheat
c. Can distinguish blood types

4. Polysaccharides- many
a. Not sweet
b. Doesn't show positive in tollens and benedicts solutions
c. Limited solubility

Chirality: Handedness in molecules

Superimposable mirror image

- Image that coincides at all points
Ex: hand and mirror reflection of hand
Nonsuperimposable mirror image
- Image not all points coincides when laid upon each other
Ex: right hand palm and back of left hand

Terms:
Chiral - non superimposable on its mirror image
Achiral - superimposable on its mirror image
Not chiral if an object/molecule has a mirror plane or inversion center

Chiral - Asymmetric centers

➢ An atom that is bonded to four different groups

➢ Organic molecules, especially monosaccharides contain more than one chiral center

Fischer projection
❖ Two-dimensional representation for showing the configuration of the tetrahedral
stereocenters
➢ Horizontal lines represent bonds projecting forward from the stereocenter
➢ Vertical lines represent the bonds projecting to the rear
➢ Only the stereo center is in the plane
L- and D-monosaccharides
● In 1891, Emil Fischer made the arbitrary assignments of D- and L- to the enantiomers of
glyceraldehyde
○ D : the -OH on its penultimate carbon is on the right in a fischer projection
○ L : the -OH on its penultimate carbon is on the left in the fischer projection
Amino Sugars:
➔ Contain -NH2 groups in place of an OH group
➔ Only three amino sugars are common in nature

Cyclic Structures
● Aldehydes and ketones react with alcohol to for hemiacetals
● Cyclic structures are more stable than open-chain or linear form

Haworth Projection
● Five or six membered cyclic hemiacetal is represented as a planar ring
● New carbon stereocenter called anomeric carbon
● Cyclic form of sugar
Chair Conformation
➢ For pyranoses, the six membered ring is more accurately represented as a strain free
chair conformation

Essential monosaccharides:
1. Glucose
a. Most abundant
b. Grape sugar/blood sugar/ dextrose
 c. 6 membered cyclic form
d. Important in human nutrition
2. Galactose
a. Brain sugar/milk sugar
b. Used to differentiate between blood types
c. 6 membered cyclic form
d. epimer at carbon four
3. Fructose
a. Ketohexose
b. Sweetest tasting
c. High dietary sugar due to sweetness
d. 5 membered cyclic form
4. Ribose
a. Part of a variety complex molecules include RNA, DNA, ATP
b. 5 membered cyclic form

Disaccharides:
1. Maltose
a. Structurally made of 3 D-glucose units one of which must be alpha D-glucose
linked via an alpha 1-4 glycosidic link
b. Can easily be digested by humans
2. Lactose
a. Made up of beta D-galactose unit and a D-glucose unit joined by a beta
glycosidic linkage
b. lactase hydrolyzes glycosidic linkages
3. Sucrose
a. Most abundant of all disaccharides
b. Found in plants
c. Table sugar
4. Cellobiose
a. Contains two D-glucose monosaccharide units, one of which must have a beta
configuration, linked through glycosidic linkage
b. Can't be digested by humans

Polysaccharides
1. Starch
a. Storage for monosaccharides
b. Used as energy source in cells
i. Glucose is monomeric unit
ii. Storage polysaccharides in plant
c. Types:
i. Amylose - unbranched
 ii. Amylopectin - branched
2. Glycogen
a. Storage in humans and animals
b. Contains only glucose units
c. Branched chains
d. Contains up to 1 million glucose units
e. Excess glucose in blood is stored in the form of glycogen
3. Cellulose
a. Linear homopolysaccharide with glycosidic bond
b. Humans don't have enzymes that hydrolyze linkages and so they digest cellulose
4. Chitin
a. Linear polymer with all beta glycosidic linkages
i. Has an n-acetyl amino derivative of glucose
5. Hyaluronic acid
a. Highly viscous; serves as lubricant in joints and humor of the eye
b. Alternating residues of n-acetyl beta-D-glucosamine and D-glucuronate
6. Heparin
a. Blood anticoagulant
b. Acidic polysaccharide

Exam 2 - Lipids and Proteins

Lipids
● Naturally occurring organic molecules that have limited solubility in water and can be
isolated from organisms by extraction with nonpolar organic solvents

Proteins
● Most abundant biomolecule in the cell
● Amino acids are difunctional molecules containing both an amino and a carboxyl group
● Proteins or peptides (length <50aa) are polymers of amino acids.
● They adopt specific 3-dimensional conformation → native conformation
○ Native confirmation is essential for the biological function
○ Loss of structure → loss of biological function
DEFINITION OF TERMS:
Conformation: spatial arrangement of atoms in a protein
Native conformation: 3D folded conformation with active function

Functions:

Various proteins and their specific functions:

AMINO ACIDS
➢ Building blocks of proteins
➢ Basic unit of proteins
➢ Features:
○ Carboxylic acid group
○ Alpha carbon: carbon directly adjacent to the
carboxylic acid functional group
○ Amino acid
○ R group: gives each amino acid unique
properties

Amino acids according to type of side chains

1. Non-polar amino acids

2. Polar neutral amino acids

3. Acidic amino acids

 4. Basic amino acids

Chirality of Amino Acids

Acidity and Basicity

- Amino acids may act as weak acids and
bases within an AQUEOUS environment
- Side chains may also be ionized
- Different functional groups gain and lose their
electrons/H atoms at various pH and
therefore have different pKa
- Zwitterions or dipolar ions (neutral molecule
with both positive and negative electrical
charges)
- Amino grp is protonated because pKa
is close to 9
- Carboxyl grp is deprotonated/ionized
because pKa is below 3
- Net charge = 0
- Attain ZERO net charge when they reach isoelectric pH (pH which amino acid attain its
zwitterion form)
- Isoelectric point = average of pKs
 -

Protein structure
● Large molecules made of amino acids joined by amide bonds = PEPTIDE bonds
○ Peptide bond: special name given to the amide covalent bond between
alpha-carboxyl group of one amino acid and alpha-amino group of another amino
acid

○
○ Planar in nature
○ Written from left to right:
■ N-terminal end: beginning of the protein where free NH3+ group
■ C-terminal end: end of the protein where COO- group

← Alanyltyrosylaspartylglycine

● Workhorses of biological systems

Orders of protein structure

Primary structure
➢ Sequence of amino acids in polypeptide chain
➢ No. of peptides possible from 20 protein-derived amino acids is enormous
○ No. peptides possible for n amino acids is 20n
○ For a small protein of 60aa, 2060 possible no. of protein
○ Importance of exact amino acid sequence: peptide and its function will
completely change
Secondary Structure
➢ Ordered 3D arrangements in localized regions of a polypeptide chain
➢ Formed and stabilized by hydrogen bond between amide proton and carbonyl oxygen
➢ Most common types:
○ Alpha helix
■ Spiral structure
■ Stabilized by intramolecular H-bonds
■ Structural features: fourth amino acid way
■ R groups point outward from helix
■ Helix destabilizers
● Presence of helix breakers (proline and glycine) - small
hydrophobic residues but strong helix formers
● Electrostatic repulsion - between successive charged aa residues
● Bulkiness (steric strain) - between adjacent R-groups
○ Beta-pleated sheets
■ Formed when 2 or more polypeptides line side-by-side
■ Stabilized by hydrogen bonds
■ Structural features: beta-strands are extended into a zigzag; r-groups
extend above or below the sheet in an alternating up and down direction
■ TYPES:
● Anti-parallel
○ Run opposite directions
○ Forms linear H-bonds
(STRONGER)
● Parallel Beta-pleated sheets
○ Run in same directions
○ Forms bent H-bonds
Tertiary Structure
➢ Three dimensional conformation of entire polypeptide
➢ Stabilized by by numerous interactions between amino acid side chains
○ Covalent bonds
○ H-bonds (IMF)
○ Salt bridges (electrostatic
○ Hydrophobic interaction
 ➢ TYPES:
○ Fibrous proteins
■ Contains polypeptide chains organized approximately parallel along a
single axis
■ Structural features:
● Consist of long fibers or large sheets
● Mechanically strong
● Insoluble to water
● Play important structural role
○ Globular proteins
■ Spherical shape
■ Structural features:
● Most polar side chains are on the outside; nonpolar side chains
buried inside the structure
● Soluble in water
● Nearly all have substantial sections of alpha-helix and beta-sheet
● Functions: metabolic (catalytic, transport, etc.)
Quaternary Structure
❖ Spatial arrangement of polypeptide subunits
❖ Assembly of individual polypeptides into larger functional clusters
➢ Dimer, 2 subunits; trimer; 3 subunits; tetramer; 4 subunits
❖ Subunits are stabilized by non-covalent interactions (3 degree structure)
❖ Ex. hemogoblin

DENTURATION
➔ Change in protein native conformation → disrupts protein function
➔ Loss of secondary, tertiary and quaternary structures
➔ Usually through heating

Denturating agents
 Enzymes
● Biological catalysts
● Increasing the rate of a reaction by a factor of 109-1020
● Sudden change in deltaG or energy
● Most have suffix -ase attached to the substrate to the reaction OR to a description of the
action performed
○ Glucosidase - hydrolyzes glycosides
○ Urease - hydrolyzes urea
○ Lactate dehydrogenase - catalyze conversion of lactate to pyruvate and versa
○ Adenylyl cyclase - catalyzes formation of of cyclic AMP
● Some enzymes retain original name which give no hint to enzymatic reaction (e.g.
pepsin;trypsin)

Classification:
1. Oxidoreductases
a. Catalyze oxidation-reduction reactions
b. Requires coenzyme that is oxidized or reduced
2. Transferases
a. Catalyze the transfer of C-.N- or P containing
groups
b. Subtype are transaminase and kinase
3. Hydrolases
a. Catalyze cleavage of bonds by addition of
water (hydrolysis)
b. Includes important digestive enzymes (lipase,
protease)
4. Lyases
a. Catalyze cleavage of C-C, C-S and certain C-N
bonds to form double bonds
5. Isomerases
a. catalyze racemization of optical or geometric
isomers
6. Ligases
a. catalyze formation of bonds between carbon and
O,S,N coupled to hydrolysis of high-energy
phosphates (ATP)

Terminology
● Substrate - biomolecule acted upon by enzyme; fits into the holoenzyme
● Active site - specific region in enzyme structure that creates 3D surface complementary
to the substrate
● Holoenzyme - catalytically active enzyme-cofactor complex
● Apoenzyme - protein component of holoenzyme that is catalytically inactive
 ● Cofactor-nonprotein component required in the activity of an enzyme; NEEDED to
activate enzyme

General Properties of enzymes

★ Chemical nature: majority are proteins
a. Some are RNA - ribosomes
★ Functions at milder reaction conditions
★ Efficient in catalyzing high reaction rate than a
chemical catalyst
★ Greater reaction specificity
★ Subject to regulation
★ Enzyme Specificity:
a. Absolute specificity: catalyzes reaction
of one unique substrate to a particular product; 1 enzyme will catalyze 1 reaction
b. Group specificity: enzymes will act only on molecules that have a specific
functional group; cleaves from the peptide chain
c. Stereospecificity: catalyzes a reaction in which one stereoisomer is reacted or
formed in preference to all others that might be reacted or formed
d. Linkage specificity: enzymes will act on a particular type of chemical bond, rest of
the molecular structure is not considered.

Models of enzyme action

● Lock-and-key model
○ Substrate binds to that portion of the
enzyme with a complementary shape
● Induced fit model
○ Binding of the substrate induces a
conformational change that results in a
complementary fit; not a perfect shape
match
Enzyme Activity
Provide an alternate, energetically favorable reaction pathway different from uncatalyzed
reaction. Enzyme activity: measure of how much a reaction rate is increased

Factors affecting enzyme activity

➔ Enzyme concentration
◆ Increased = reaction rate increased because more substrate molecules can be
accommodated in a given amount of time
➔ Substrate concentration
◆ Increased = saturation point will be attained because all active sites are fully
occupied; rate won't be increased
◆ Incoming substrate molecules must “wait their turn” for an empty active site
◆ First-order kinetics
● Reaction rate dependent on an increase
◆ Zero order kinetics
● Reaction rate is independent on increase [S];
reached saturation point
◆ Saturation point
● S are bound to all available active sites of
the E; reaction rate proceeds at max rate
(Vmax); increase S will not affect reaction
rate

MIchaelis-Menten Equation:Km and Vmax

❖ Mathematical representation of enzyme action proposed by L. Michaelis & M. Menten in
1913
 ➔ Temperature
◆ Optimal temperature: where the enzyme exhibits maximum activity
◆ Decreasing temperature = decrease in kinetic energy, less molecular collisions
decreasing reaction rate
◆ Beyond optimal temperature = disrupts tertiary structure of enzyme; Substrate
may not fit the active site and impedes catalytic activity
➔ pH
◆ Optimal pH: pH at which an enzyme exhibits maximum activity
◆ Slight change: alters charge of acidic and basic amino acid residues found in
active site
◆ Extreme (too acidic or basic): denatured enzyme irreversibly; loss of catalytic
activity

Enzyme inhibition
Molecular agents that interfere with catalysis

1. Reversible inhibition class: binds with the enzyme through noncovalent interactions
a. competitive inhibition
i. Competes with substrate for the same binding site on enzyme
 ii. High degree of structural similarity to substrate
iii. Binds only to FREE enzyme
iv. Could be reversed by increasing the substrate
concentration
v. KM is raise; Vmax same
b. Uncompetitive inhibition
i. Binds to directly enzyme substrate complex (not free
enzyme)
ii. Distorts the active site which affects catalytic function
but not its S binding
iii. Adding substrate does NOT reverse
iv. Significant only for multi substrate enzymes
v. BOTH KM and Vmax is lowered
c. Mixed inhibition (special case: noncompetitive inhibition)
i. Interacts with wither enzyme or enzyme substrate
complex
ii. Binding site is not the same as substrate
iii. Does not interfere with binding of substrate to the
active site
iv. Cannot be overcome by increase in substrate
concentration
v. KM same; Vmax lowered
2. Irreversible inhibition class: binds to E tightly, permanently blocks the enzyme; covalent
alterations in the enzyme
a. Suicide inactivators (mechanism-based inactivators)
i. Inhibitory substrate analog that generates reactive group that covalently
links to active site on enzymes

Enzyme activators (opposite of inhibitors)

Cofactor: nonprotein component required in the enzyme activity

1. Essential ions - mostly metal ions

a. Activator ions
i. Reversibly bound and often participate in the binding of the substrate
b. Tightly-bound metal ions
i. Participate in catalytic reactions; found in metalloenzymes
 2. Coenzymes - organic compounds that act as group-transfer reagents; supply reactive
groups not found on the R-groups of amino acids

Regulation
➢ Cells continually produce large amounts of an enzyme and plentiful amounts of product if
the processes are not regulated
➢ General mechanisms involved in regulation:
○ Feedback control associated with allosteric enzymes
 ○ Proteolytic enzymes and zymogens

○ Covalent modification

○ Isoenzymes (Isozymes)

LIPIDS

● Primarily hydrocarbons: low solubility in water; high solubility in non-polar solvents

● Do not have a common structural feature unlike other biomolecules

Classifications by Biochemical Functions:

1. Energy-storage Lipids
● Triacylglycerols
2. Membrane Lipids
● Phospholipids
● Sphingoglycolipids
● Cholesterol
3. Emulsification Lipids
 ● Bile acids
4. Messenger Lipids
● Steroid hormones
● Eicosanoids
5. Protective-coating Lipids
● Biological waxes

Classifications based on Structure:

1. Fatty acids and their derivatives
2. Triacylglycerols
3. Wax esters
4. Phospholipids
5. Sphingolipids
6. Steroids
7. Eicosanoids

Exam 3: Nucleic Acid

● Nucleosides are composed of an aldopentose sugar linked through its anomeric carbon
to the nitrogen atom of a heterocyclic purine or pyrimidine base
● Composed of nucleotides bonded together to a phosphate group
● Polymers of nucleotides
● Key biomolecules for continuity of life
● Direct process of protein synthesis
 ● Determine inherited characteristics of every living thing

Deoxyribonucleic acid (DNA)

➢ Genetic material in all free-living organisms and most viruses
➢ Eukaryotes
○ Found in nucleus, mitochondria and chloroplasts
○ Typically broken up into chromosomes
➢ Prokaryotes
○ DNA is found in a specialized cell region called nucleoid
○ Chromosomes are much smaller and circular
➢ Chromosomes contain tens of thousands of genes

Ribonucleic acid (RNA)

➔ Genetic RNA of certain viruses
➔ Found in all living cells
➔ Plays an important role in certain processes such as protein synthesis

Nucleotides
★ Building blocks of DNA and RNA
★ Monomer of nucleic acids which is similar to amino acids which is building blocks of
proteins
★ Consists of a sugar (ribose or deoxyribose) covalently bonded to a phosphate group and
to a heterocyclic amino containing aromatic ring system
★ Nucleotide is nucleoside without phosphate group

★ Bases
 ○ Substituted pyrimidines or purines

★ Strong acids
○ Phosphate has a pKa of 1.0

★ Capable of conversion between tautomeric forms (spontaneous isomerization of nitrogen

base to an alternative hydrogen bonding form possibly resulting in mutation)
★ Considered reversible shifts of proton position of molecule
 ★ Conjugated double-bond systems in the nucleobases allow them to absorb light in the
UV region
○ Large molar coextinction in UV region

Primary level of organization

● Nucleotides are joined together by forming phosphodiester linkages forming a nucleic
acid polymer
○ Between 3’-carbon of one nucleotide and 5’-carbon of the other nucleotide
● Backbone - linked chain of sugar and phosphate
● Phosphates are negatively charged

Stability and Formation of phosphodiester linkages

● Water molecules can be eliminated as a phosphodiester linkage is formed
● Free energy change is about +25 kJ/mol, thus, nucleic acids are metastable
○ Breakdown of nucleic acids is spontaneous but kinetically low
● In dehydrated conditions, DNA is very stable
○ Allows complete genome sequencing of ancient organisms
● Acid treatment catalyzes hydrolysis of phosphodiester bonds in nucleic acids
○ Both RNA and DNA
● Alkaline treatment catalyzes hydrolysis in RNA but not in DNA

● Nucleases are enzymes that breakdown both DNA and RNA

● Unfavorable thermodynamics of formation of phosphodiester bonds require energy-rich
(deoxy)ribonucleoside triphosphates
● Phosphoanhydride bonds between alpha, beta and gamma linkages are energy-rich
● Further cleavage of pyrophosphate has a G of -19 kJ/mol
Primary level of organization
❖ 5’ end and 3’ end
❖ G and C phases reacts with a nucleotide with adenine base
❖ Condensation reaction between ^ molecules, happens with a concomitant release of
pyrophosphate compound which makes reactants thermodynamically favorable with a
low with low gibbs energy change

❖ Unique feature of DNA and RNA synthesis - template directed

➢ Basis for transmission of genetic information
❖ DNA polymerase and RNA polymerase
➢ Enzymes that synthesize nucleic acids
➢ Follows the template strand - an existing strand to which the growing chain is
based on
❖ 3’ → 5’ phosphodiester linkage implies 5’ → 3’ DNA synthesis
❖ Different notations

❖ For the following, the convention is written from 5’ to 3’ ACGTT (Nitrogenous base)

Secondary level of organization

➢ Structure of DNA molecule was solved by Rosalind Franklin, Maurice Wilkins, Francis
Crick and James Watson
➢ Erwin Chargaff
○ G=C and A=T
➢ Two DNA chains oriented in opposite directions
➢ Held together by hydrogen bonds between bases
➢ Right-handed double helix
➢ Sugar-phosphate groups are directed outside
 ➢ Watson-Crick complementary base pairing
○ Predominantly keto forms of G and T confirmed watson-crick complementary
base pairing
○ Distances between 1’ carbon of deoxyribose of A-T and G-C are the same
-1.08nm
○ G-C pairing is stronger than the A-T pair since the former is composed 3
hydrogen bonds

Stabilization from Base Stacking

● Aromatic ring systems have distributed electrons around the ring
● Allows interaction between bases via stacking
● Two adjacent base pairs that are stacked on each other are rotated
with respect to each other
● Favored by van der Waals attractive forces

Beta-form DNA
➔ Standard conformation of the double-helical DNA
➔ Base pairs are perpendicular to the helical axis
➔ Helix forms two grooves of unequal sizes
◆ Major groove - wider and more accessible
◆ Minor groove - narrower and less accessible

Different Helical Forms of DNA

Syn- and Anti- conformation
● Syn conformation - bulk nitrogenous phase in close proximity to the sugar
● Anti conformation - pointing away from the sugar base

Hairpins and Cruciforms

● Self-complementarity in single-stranded molecules allows chain to fold back on itself
(hairpin structures)
○ Forms an antiparallel helix
● Cruciform are cross-like double hairpin structures
○ Sequence must be palindromic, called inverted repeats

G-Quadruplexes
● Cyclic tetramers between guanines due to strong hoogsteen-types base pairs
● G-rich polynucleotides are difficult to work with due to association

Tertiary level of organization

❖ Circular DNA
➢ No free 5’ or 3’ ends
➢ May be small or large
➢ May be single or double stranded
❖ Supercoiling of circular DNA
➢ Consequence of elastic deformation of DNA when ends of double helix cannot
rotate relative to one another
➢ Large-scale conformational effect in DNA
➢ Double helix winds into superhelix
➢ More compact than the relaxed circular DNA
❖ Consider a DNA that has 105 base pairs in length
➢ 10 complete helical turns - 10 twists (T)
➢ Each strand also crosses each other 10 times - linking number (L) of 10
❖ Before sealing, rotate one end by one turn
➢ Creates a strained structure upon closure because you now have 11.67 base
pairs per turn
❖ To stabilize, it writhes to recreate a helix with 10.5 base pairs per turn
 ➢ Underwound by one turn, W of -1
➢ Negative supercoiling
❖ DNA can be overwound (positive supercoiling) by creating an extra twist
❖ Most naturally occurring circular DNA are underwound
❖ Degree of supercoiling can be defined in terms of superhelix density

❖ Topoisomerases are enzymes that regulate supercoiling in circular DNA

❖ Eukaryotes
➢ DNA is associated with a protein called histones through non-covalent
interactions
❖ Chromatin
➢ DNA makes double turn forming a superhelix
■ Regular intervals on a core of eight histone units

RNA structure
● Single stranded
● Loops back onto itself containing several structural elements: hairpin loops, bulges,
internal loops, junctions and helices
● GNRA tetraloop motifs

● Short, one gene long at most

● Four major types:
○ Messenger RNA (mRNA)
■ Transmits genetic info from nucleus to the cytoplasm
■ Intermediate between DNA and protein product
■ Turning on of gene leads to protein encoding
■ RNA polymerizing enzyme catalyzes synthesis of RNA
■ Carries the same information as its gene
■ Base T is replaced with Uracil
 ○ Ribosomal RNA (rRNA)
■ Major component of ribosomes
■ Involved in amino acid assembly during protein synthesis
■ Helps mRNA bind in the right spot
■ 60S (large) and 40S (small) subunits in human cells
■ Can also act as enzymes to form peptide bonds
○ Transfer RNA (tRNA)
■ Carries of amino acids in protein synthesis
■ Consist of single strand of RNA that has complementary segments,
making it double stranded
■ Complex 3D structure resembling clover leaf
○ Regulatory RNA
■ Noncoding RNA to regulate expression of other genes
■ MicroRNA (miRNA) and small expression interfering RNA (siRNA)
● Binds to specific mRNA molecules to reduce their stability
● Interferes with translation

Stability
★ DNA is more stable than RNA which is why genetic information is stored in DNA
★ RNA self-cleaves through nucleophilic attack of 2’-OH to the phosphorus

Nucleic Acid Denaturation

● Loss of secondary structure

● Breaking the base pairs and base stacking interactions require input of enthalpy (positive
change in H)
● Random coil is more entropic than helix (positive change in S)

● Hyperchromism occurs upon denaturation

○ Cooperative transition
 STRUCTURE OF CHROMOSOME AND GENE

Gene - basic physical and functional unit of heredity

● Smallest DNA viruses have a dozen genes or fewer, RNA viruses have only four
● More complex organism = larger genome size & more genes

Bacterial Genomes
➢ All cells must be able to pack large nucleic acid molecules into a limited space
○ E.coli genomes is 1mm in length and must be packed in cell no longer than 5
micrometer
➢ Packing must be organized such that it is accessible on demand
➢ Each loop is about 50kbp in length
➢ Compacted structure, called a nucleoid, is in the cytosol of bacteria with small number of
attachment to membrane

Eukaryotic Genome size

● No simple relationship between genome size and organismal complexity

● Bacteria and archaea have one

chromosome per cell
● Eukaryotic cell has 2 copies of each
chromosome (except for sex chromosomes)
○ Human 1st-22nd pair of
chromosome: autosome (by pair); 23rd is not
by pair
● Evidence of eukaryotic genome
complexity/size:
○ Considerable amount of
noncoding DNA sequences
○ Number of protein-coding genes
is far lower than the total potential coding capacity
 ○ Most protein are encoded by genes (exons) but are interrupted by noncoding
segments (introns)
○ Multiple repeating sequences

Repetitive Sequences: Satellite DNA

➢ Multiple tandem repeats of very short, simple sequences
○ Ex: (ATAAACT)n
➢ Usually makes up 10% to 20% of the total genome
➢ Do not code for proteins
➢ Found to be highly concentrated near the centromeres of
chromosomes (structural role)

Repetitive Sequences: Introns

❖ Coding regions - exons - are interrupted by noncoding regions -
introns
❖ Present in most eukaryotic structural genes
❖ Frequently exceed exons in total length
❖ Serves as loci for genetic recombination
➢ Allows functional parts of proteins to be interchanged in evolution (exon shuffling)
❖ Positive regulation of gene expression

Multiple Gene Variants

● Variant of genes for the SAME type of protein are expressed in different tissues or at
different stages of development
○ Ex. Different globins in embryo, fetus, and adult stages of mammals
● Each of these proteins exists in a complete gene in every cell of the animal
○ Introns in each gene of these proteins must contain control signals
○ Only expressed in erythropoietic cells
● Pseudogenes are expressed genes that are nonfunctional
○ These bear strong sequence similarity to functional genes

Nucleus
★ Contains the chromatin (fibers) that turn into chromosomes
★ Chromosomes held in place by the nuclear envelope
○ Studded with nuclear pores (9 micrometer in diameter)
○ Nuclear pore selectively transports RNA and protein molecules
★ Nuclear pore complex is an assembly of 500-1000 nucleoporins
○ Involves helper proteins: exportins and importins
★ Nuclear envelope disintegrates during mitosis, and protected by telomere
★ Diploid chromosomes condense into compact structures
○ Newly replicated chromosomes are joined at the centromere
★ At each end of eukaryotic chromosomes are telomeres that protect DNA from
degradation
○ Ensures that each chromosome is completely copied during replication
 ★ Telomere - end cap; protects from degradation
★ Centromere - center of chromosome
★ Origin of replication - region where DNA replication begins

Chromatin
● Eukaryotes also use extensive negative supercoiling as means of achieving compaction
● Chromatin is a compact protein-DNA complex, including histones
● Histones are sets of five highly conserved, low molecular weight, strongly basic proteins

Histones
❖ Small highly basic proteins rich in LYSINE and ARGININE amino acids
❖ Fundamental building blocks of chromatin structure
❖ Present in about 1 gram per gram of DNA
❖ H2A to H4 are in equimolar quantities

Other Chromosomal proteins

● Includes polymerases, nuclear receptors and transcription factors
● Among the most abundant are topoisomerases and SMC proteins (structural
maintenance of chromosomes)
○ Cohesins help hold sister chromatids together immediately after replication until
condensation of chromosomes at metaphase
○ Condensins play a role in chromosome condensation as cells enter mitosis

Nucleosome
➢ Regular beaded pattern in the chromatin structure
➢ 146 base pairs DNA wrapped about an octamer of histone molecules
➢ DNA makes about 1.7 left-handed solenoidal superhelical turns about the
octamer-histone fold
➢ Length of DNA between nucleosome vary between 2–100 base pairs
➢ Internucleosomal or linker, DNA is occupies by H1 type histones and nonhistone proteins
➢ Fold into a thicker condensed fiber about 30 nanometer in diameter
➢ Chromatin exists in 2 major forms:
○ Euchromatin - transcriptionally active
○ Heterochromatin - transcriptionally inactive