9/1/17

Cell and Molecular Biology

Carbon Atom
Lecture 2
nucleus

orbitals

electrons

Outer orbital should be filled to gain stability

“The properties of cells and their organelles are

derived from the activities of the molecules from
which they are composed”.

Common Atoms

How do atoms gain stability? Electronegativity

qCovalent bonds q Formed when 2 atoms sharing electrons are different
q Sharing of electrons q Electronegative atom – atom with greater attractive force
q Relatively stable (80-100 kcal/mol to break bond) q Example: H2O – O higher electronegativity (+8) than H (+1)
q number of bonds formed is determined by the number of q Factors affecting electronegativity:
electrons needed to fill outer shell
q bond formation accompanied by energy release q Number of positive charges in nucleus (more protons -> more
q reabsorption of energy when the bond breaks electronegative)
q Types: q Distance of outer electrons from nucleus (greater distance -> less
q Single bond (H-O) determines shape of electronegative)
q Double bond (O-O)
q Triple bonds (N-N)
molecule q O and N atoms are the most electronegative ones commonly
present in biological molecules
qNoncovalent bonds
q formation of attractive forces
q Types:
q Ionic bonds
q Hydrogen bonds (hydrophilic interactions)
q Hydrophobic interactions
q Van der Waals interactions

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Polarity
• O-H bonds in water are polarized (one atom [O] partially negative; the
other [H] partially positive); it is a polar molecule – such molecules have
an asymmetric charge distribution
• Biologically important polar molecules have one or more electronegative
atoms - usually O, N, S and/or P)
• Molecules without electronegative atoms & polar bonds (those consisting of
C & H) are nonpolar
• Presence of strongly polarized bonds is of utmost import in determining
molecular reactivity
– Molecules without electronegative atoms (waxes & fats) are relatively inert
– Molecules with electronegative atoms tend to be more reactive
– Many interesting biological molecules (proteins, phospholipids) have both polar
& nonpolar regions & behave very differently
Ionization
• Ability of some atoms to capture electrons from a
reacting atom during a chemical reaction
• Result of having a strong electronegativity
• Sodium (Na) & chlorine (Cl) - form table salt
– Single electron in Na outer shell migrates to electron-
deficient chlorine atom
– Each atom becomes charged (ion): Cl- (anion) and Na+
(cation); together form crystal
• Ions like Na+ and Cl- are relatively stable because of
filled outer shell
• A different electron arrangement in atom produces
highly reactive species (free radical)
– Free radicals in the body causes aging and diseases
– Atoms with outer orbitals containing 1 electron (highly
unstable)

Free Radicals Affect Human Health Non-covalent Bonds

• govern interactions between molecules or different parts of a
large biological molecule
• typically weaker bonds (linkages)
• Depend on attractive forces between positively & negatively
charged regions within same molecule or on two adjacent
molecules
– Individual ones are often weak (~1 - 5 kcal/mole); thus
readily broken & reformed
– When many of them act in concert (DNA, protein, etc.), attractive
forces add up & provide structure with considerable stability
• Noncovalent bonds mediate the dynamic interactions among
molecules within the cell

• Superoxide dismutase = destruction of superoxide radical

Ionic Bonds (Salt Bridges)

• result from transfer of electron(s) from 1 Noncovalent
bonds in
atom to another leading to atoms with
positive & negative charges that attract
each other (Ex. Salt crystal, NaCl)
• can hold molecules together (DNA-
protein)
Biological
Molecules
Important points:
1. In crystal, ions surrounded by water, prevents attraction between them
2. Bonds between free ions not important in cells because cells are
mostly water
3. Weak ionic bonds between oppositely charged groups of large
molecule much more important
4. Ionic bonds in cell generally weak (~3 kcal/mole) due to water

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Hydrogen Bonds van der Waals Forces

• Hydrophilic bonds • Attractive force between two
atoms of close distance
• Result of partial positive
charge of H when it is • Increases with shorter distance
covalently bonded to (up to around 3 Angstrom
electronegative atom units)

• Relatively weak interaction • Very weak interaction

(2-5 kcal/mol) (0.1-0.3 kcal/mol)

• Contributes to stability of • Important biologically as with

interactions between
double stranded DNA
antibodies and viral antigens

Water: the Biological Solvent Acid

Acids and Bases
q a molecule able to release (or donate) a hydrogen ion to medium
• Life sustaining properties: q proton dissociates & is released into medium whenever a hydrogen
– highly asymmetric atom loses an electron
– highly polarized covalent q when acid loses proton, it becomes conjugate base of the acid
bonds, q Once dissociated, proton can combine with other molecules forming:
– forms H bonds qHydronium ion (H3O+) > H + H2O
• H2O has high heat capacity qWater (H2O) > H + OH
• H2O has a high heat of vaporization qCharge amine (NH3+) > H + NH2
• High surface tension due to H bonding
and capillary action
• A good solvent
Base
– Solubilizes ions & organic molecules
q any molecule capable of accepting a hydrogen ion (proton)
– It is also the medium through which q when base picks up proton, it becomes conjugate acid of the base
materials move from compartment to
q acid always contains one more positive charge than its conjugate
compartment
base
– It also protects cell from excessive heat,
cold, damaging radiation

pH
q potential of H ions
q Measure of acidity or alkalinity
q -log[H+] where H+ is the molar concentration of
protons
q Logarithmic scale - increase of 1 pH unit means 10X
increase in OH- or 10X decrease in H+
q Biological processes sensitive to pH changes since pH
affects ionic state of biological molecules
q Amino acid R groups can acquire charge (-COOH -> -
COO-;-NH2 -> -NH3+)
q Even slight pH changes can disrupt shape & activity of
entire protein, impede biological reactions
Buffers
q Compounds that react with free hydrogen or hydroxyl ions
(resisting pH change)
q Contains weak acid (ex. carbonic acid) with its conjugate base
q Minimizes pH fluctuations; binds or releases H+ & OH- ions
depending on conditions thus protecting organisms & their cells
q Blood – H2CO3 & HCO3- ions; neutralizes H+ rise during
exercise, OH- rise during hyperventilation
q Excess H+ ions bind HCO3-; excess OH- ions neutralized by
protons
q Blood stays at pH 7.4
q pH of fluid within cell regulated by phosphate buffer system
(H2PO4- & HPO4-2)

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Biomolecules
Amphoteric Molecule q Biological molecules or
biochemicals
q a molecule that can serve as both an acid & q Often contains carbon (organic
a base molecules)
q usually both a positive & negative charge q Often contains “functional groups”
q examples: water and amino acids. linked by:
q Ester bonds – between carboxylic acids
and alcohols
H 3O H H 2O OH + H q Amide bonds - between carboxylic acids
and amines
Acid Amphoteric Base
Molecule

Types of Biomolecules Formation and Breakdown of

q Macromolecules Macromolecules
q Structural and functional units of the cell’s organelles.
q Highly organized molecules
q Polymers (composed of monomers)
q Proteins, nucleic acids, polysaccharides, lipids
q Low-molecular-weight precursors
q Building blocks of macromolecules
q Sugars, amino acids, nucleotides, fatty acids
q Metabolites
q Metabolic intermediates
q Synthesized inside the cell thru a metabolic pathway (a series
of chemical reactions starting with a specific material).
q Molecules of miscellaneous function
q Vitamins, steroids, hormones, ATP, cyclic AMP, urea

Types of Macromolecules Carbohydrates

q With sugars as building blocks
q Deposits of chemical energy
q Durable building material for cell parts.
q With a general formula of (CH2O)n
q Glycosidic bonds (covalent bonds) > energy source
q Types:
q Monosaccharides (glucose, fructose)
q Trioses – 3 carbons
q Tetroses – 4 carbons
q Pentoses – 5 carbons
q Hexoses – 6 carbons
q Heptoses – 7 carbons
q Disaccharides (sucrose, lactose)
q Oligosaccharides (forms glycolipids, glycoproteins)
q Polysaccharides (cellulose, chitin)

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Monosaccharides Stereoisomers
q Backbones of carbon atoms linked by single bonds q Enantiomers (mirror image)
q Each carbon linked to hydroxyl group (except for one q Carbon acting as site of stereoisomerism is called
linked to carbonyl group, C=O) “assymetric carbon”
q Affects the structure of biological molecules

OH - up OH - below
Ketohexose Aldohexose Pyranose Planar 3D Ball and
(ketose) (aldose) Ring Ring Structure Socket
Structure
OH - right OH - left

Polysaccharides Polysaccharides
q Glycogen
q Animal starch (surplus chemical energy
q Glucose polymer joined by 1-4 glycosidic bonds (others 1-6)
q Molecular weight ranges from 1-4 million Daltons

q Starch
q Plant polysaccharide (cereals, potatoes)
q Polymer of amylose and amylopectin

q Cellulose
q Structural material (cotton, linen)
q Long unbranched polymers
q Most abundant organic material on earth

q Chitin
q Polymer of N-acetylglucosamine (acetyl amino group, HNCOCH3)
q Shells of invertebrates (crustaceans, insects)

q Glycosaminoglycans (CAGs)
q Complex structures
q Found in spaces surrounding cells

Lipids Fatty Acids

q Non-polar biomolecules q Saturated fatty acids
q Inability to dissolve in water q lack double bonds between carbon
q Ability to dissolve in organic solvents molecules (tristearate)
q Fats, steroids, phospholipids q Common in animals fats
q Fats=glycerol + 3 fatty acids (linked by q Easily packed together
ester bonds (also called triacylglycerol) q Solid above room temperature
q Fatty acids are long and unbranched
hydrocarbon chains with 1 carboxyl end q Unsaturated fatty acids
q Fatty acids are amphiphatic (COOH end q with double bonds (linseed oil) producing
kinks in structure
is hydrophilic while hydrocarbon end is
hydrophobic) q Difficult to package (space-filling)
q Lower melting temperature
q Stored in animal body in adipocytes
q Better sources of energy compared to
carbohydrates (2X)

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Soap Micelles Liposomes for Drug Delivery

q Complexes
formed when
hydrophobic end
of fatty acids bind
with grease (inner
side)

q Hydrophilic ends
interacts with
water molecules
(outside

Steroids Cholesterol
q 4-ring hydrocarbon
skeletons
q Cholesterol
q Important component
of cell membranes
q Precursor for the
synthesis of steroid
hormones
(testosterone,
progesterone,
estrogen)
q Absent in animal cells

Cholesterol Levels Phospholipids

q 2 fatty acid chains + glycerol backbone + polar group (choline)
connected by a phosphate group
q Diacylglycerol
q Polar molecule
q Polar head group + phosphate group > hydrophilic
q Fatty acid chains > hydrophobic
q Parts of cell membranes

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Proteins 20 Essential Amino Acids

q Main actors in the cell’s activities
(catalysts, defense, growth,
differentiation, metabolism,
regulatory functions, etc.)
q More than 10,000 kinds in
mammalian cell
q Capable of unlimited shape and
structure
q High degree of specificity
q Polymers of amino acids
q Amino acids are connected by
peptide bonds forming polypeptide
chain (units are called residues)

20 Essential Amino Acids Disulfide Bridge

Keratin
Antibody

Protein Structure Protein Structure

q Primary Structure
q Sequence of amino acids (20n)
q Order is dictated by the genome q Secondary Structure (3-
q Determines the 3D structure of the protein and its function dimentional structure)
q Mutation in a single amino acid changes the structure and q Alpha Helix
function of proteins. q backbone assumes
q Example: sickle cell anemia (change of a glutamic acid, aa6, cylindrical, twisting spiral
(charged polar) residue to valine (nonpolar) q Backbone inside helix and
side chains project
outwards
q 3.6 aa / turn
q 1.5 A between adjacent
residues
q Hydrogen bonds
q Examples: keratin,
hemoglobin

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Protein Structure Protein Structure

q Tertiary Structure
q Conformation of the entire protein
q Secondary Structure (3-
q Stabilized by non-covalent bonds between
dimentional structure)
R groups of the protein
qBeta-pleated Sheet
q Determined by X-ray crystallography, NMR
q Several segments of
polypeptide lying side by q Types:
side q Fibrous proteins – highly elongated shape
q Hydrogen bonds q Ex. Collagen, elastin, keratin
perpendicular to axis of the q Globular proteins – compact shape
polypeptide chain q Ex. myoglobin
qHinges
qTurns
qLoops
qFinger-like extensions

Protein Domains Protein Motifs

q Defined arrangement of alpha helices and/or beta
strands
q Distinct modules
independent of each
other
q Represents different
function
q Result of gene
evolution (fusion of
genes) – highly Coiled coil motif Alpha/beta barrel
conserved (myosin) (triose phosphae isomerase)
q Example: mammalian
phospholipase C “Proteins undergo conformational changes as they
perform their activities”

Protein Structure Multiprotein Complexes

q association of different proteins with different but related
q Quaternary Structure functions
q undergo protein-protein interactions
qAggregates of more than 1 subunits or polypeptide chains
q Example: Pyruvate dehydrogenase complex
qLinked by disulfide bonds or hydrophobic interactions
q with 60 polypeptides
qHomodimer (same subunits) or Heterodimers (different subunits)
q 3 different enzymes (glycolysis and TCA cycle)

Tranforming growth factor -b2 (TGF- b2 )

Hemoglobin

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Protein Folding Steps in Protein Folding

q Natural ability of proteins to form
a structure rendering its
functionality.
q Function of “molecular
chaperones”- guides unfolded or
misfolded proteins to fold
correctly.
q First identified in “ribonuclease A”
by breaking the disulfide bonds q Formation of alpha helices and beta sheets (secondary structure)
using mercaptoethanol (reducing
q Hydrophobic interactions forming a molten state (hydrophobic
agent). residues are driven at the central core)
q Denaturation – unfolding of q Formation of noncovalent bonds resulting to tighter packing
proteins using detergents, urea,
organic solvents etc. q Formation of covalent and disulfide bonds

Consequences of Protein
Misfolding
q Non-functional proteins
q Can cause disease
q Example: Creutzfeld-Jacob Disease
(CJD)
qloss of motor coordination and
dementia
qCaused by an infectious proteins called
“PRIONS” (causes mad cow disease)
qResult of misfolded proteins
qAbnormal prions forms amyloid plaques Normal prion
in the brain similar to AD (Alzheimer’s
Disease)
Protein Engineering
q Alteration of genes in order to form a protein with desired structure
(and hopefully function).
q Produced by “site-directed mutagenesis”
q Uses:
qIdentifying the function of specific protein residues
qIncrease the efficacy of protein drugs
qReduction of side effects of certain protein drugs
qProduction of custom-made drugs (structure-based drug design)
q Example:COX 2 specific inhibitor (similar function as aspirin but no side
effects). Aspirin is anti-inflammatory, anti pain and fever by inhibiting the action
of cyclooxygenese 2 enzyme but has side effect on COX 1).
Abnormal Prion

Nucleic Acids
q Made up of nucleotides
q Storage and transmission of genetic
RNA Complexes
information
q Partly structural or catalytic functions
q Types:
qDeoxyribonucleic acid (DNA)
qRibonucleic acid (RNA)
q Nucleoside = sugar and nitrogenous base
connected by ester bond)
q Phosphodiester bond nucleoside to PO4.

Ribosomal RNA Ribozyme

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Proteomics – 2D Electrophoresis Proteomics – Mass Spectrometry

Proteomics – Protein Chips

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