Intro to Cell & Molecular Biology
• How do we study cell biology?
– Reductionist view
• Cells as tiny complex machines
• Sum of parts = whole
• Your goal:
– be able to explain the roles
various molecular parts play in
cell biological processes
– With the same clarity as with
macroscopic items (bicycles,
stoves, trains, etc…)
Intro to Cell & Molecular Biology
• How do we study cell biology?
– Parsimony
• the simplest explanation for all
relevant data is preferred over
more complex explanations
• The most parsimonious answer
is not necessarily perfectly
correct
• More data could make us
revise it
Chemical basis: Bonding
• Covalent Bonds: sharing of e– One pair shared = single bond
– Two pairs = double bond
– Three pairs = triple bond
C
C
C
C
C
C
• Electronegativity (EN) is the ability of an atom to
attract electrons to itself
– C = 2.5 N = 3.0 O = 3.5 H = 2.1 S = 2.6
– Sharing is unequal between different atoms in a molecule
• Polar molecules have significant EN differences
– H2O, CH3COOH
• Nonpolar molecules have little EN differences
– CH3(CH2)nCH3
• Amphipathic molecules have different EN
characteristics at different positions
– CH3(CH2)nCOOH
Chemical basis: Bonding
• Noncovalent Bonds: attractive forces between atoms of
opposite charge
– Ionic: fully chargedNa+ Cl• Strength dependent on environment (salt crystal vs aqueous)
– Hydrogen: partial charge (polar molecules)
Noncovalent bonding
• Noncovalent Bonds: continued…
– Van der Waals: transient dipole interactions
– Hydrophobic: water fearing
– Hydrophilic: water loving
Robot Lizards Exploit
Van der Waals contacts
• Based on the Gecko
• Adhesion depends on close
contact between surfaces
“StickyBot”
• Video link
H2O
• Can form 4 hydrogen bonds
– High energy barrier to liquid --> gas phase
transition
• Highly polarized
– Asymmetric structure - both H atoms on one side
– Can dissolve many compounds
H2O
• Can dissolve many compounds
– Acids: can release H+
– Bases: can accept H+
pH = - log [H+]
• Pure H2O pH = 7 , [H+] = [OH-] = 10-7 M
• Why are reactions so pH sensitive?
– Amino acid functional groups can change state based on pH
Carbon
• Central to the chemistry of life.
– Can form four covalent bonds,
with itself or other atoms.
– Carbon-containing molecules
produced by living organisms are
called biochemicals.
Chirality and Stereoisomerism
• Chirality and Stereoisomerism:
– Asymmetric carbons bond to four
different groups.
– Two mirror-image configurations:
• Enantiomers, (aka)
• Stereoisomers
– Can be either D- or Lisomers
– Natural amino acids = almost all
L-isomers
– Natural carbohydrates = almost all
D-isomers
Classes of molecules
• Miscellaneous co-factors
– Vitamins, ATP, NADPH,
etc
• Metabolic intermediates
– Glycolysis, TCA cycle, etc
• Monomers
–
–
–
–
Amino acids
rNTPs = A, G, C, U
dNTPs = A, G, C, T
Sugars
• Macromolecules
Classes of molecules
• Macromolecules
– Lipids
• Fats = glycerol esterified with 3 fatty acids
– Saturated, unsaturated, cis, trans
• Phospholipids = glycerol + 2 fatty acids + 1 phosphate
• Steroids = cholesterol and derivatives
Classes of molecules
• Macromolecules
– Lipids
• Fats = glycerol esterified with 3 fatty acids
– Saturated, unsaturated, cis, trans
• Phospholipids = glycerol + 2 fatty acids + 1 phosphate
• Steroids = cholesterol and derivatives
Classes of molecules
• Macromolecules
– Lipids
• Fats = glycerol esterified with 3 fatty acids
– Saturated, unsaturated, cis, trans
• Phospholipids = glycerol + 2 fatty acids + 1 phosphate
• Steroids = cholesterol and derivatives
Classes of molecules
• Macromolecules
– Lipids
• Fats = glycerol esterified with 3 fatty acids
– Saturated, unsaturated, cis, trans
• Phospholipids = glycerol + 2 fatty acids + 1 phosphate
• Steroids = cholesterol and derivatives
Monomers and polymers
Classes of molecules
• Macromolecules
– Carbohydrates
• ( CH2O )n
• At n ≥ 5 self-reaction to form rings
– C5 = ribose monomer
– C6 = glucose monomer
Classes of molecules
• Macromolecules
– “Nutritional” sugars:
» Glycogen = branched alpha 1-4 linkage, dense granules
in cell cytoplasm in animals
» Starch = helical and branched alpha 1-4 linkage, within
membrane bound plastids in plants
plastid
Classes of molecules
• Macromolecules
– “Structural” sugars:
» Cellulose = long and unbranched, beta 1-4 linkage,
resist tensile (pulling) forces, plants
» Chitin = unbranched, N-acetylglucosamine,
invertebrates
» Glycosaminoglycans = components of extracellular
matrix for cartilage and bone, repeating (A-B)n structure
Classes of molecules
• Macromolecules
– Nucleic Acids
• Nucleotide monomers (rNTPs, dNTPs)
• Storage and transmission of genetic information
– Phosphate + 5C ribose sugar + nitrogenous base
RNA
DNA
H
Classes of molecules
• DNA is usually double stranded
• RNA is usually single stranded
– RNA may fold back on itself to form
complex 3D structures, as in ribosomes.
– RNA may have catalytic activity; such
RNA enzymes are called ribozymes.
– Adenosine triphosphate (ATP) is a
nucleotide that plays a key role in
cellular metabolism
– Guanosine triphosphate (GTP) serves
as a switch to turn on some proteins.
DNA is a useful reference-frame for sizes
Classes of molecules
• Macromolecules
– Proteins
•
•
•
•
Amino acid monomers
Peptide bond formation
N-terminus versus C-terminus
Backbone is common, side chains (R) differ
Classes of molecules
• Macromolecules
– Proteins
• Backbone is common, side chains differ
– 4 categories of amino acid side chains
» Polar charged
D, E, K, R, H
» Polar uncharged
» Nonpolar
» Unique
Classes of molecules
• Macromolecules
– Proteins
• Backbone is common, side chains differ
– 4 categories of amino acid side chains
» Polar charged
D, E, K, R, H
» Polar uncharged S, T, Q, N, Y
» Nonpolar
» Unique
Post-translational modifications: Phosphorylation of –OH groups
Classes of molecules
• Macromolecules
– Proteins
• Backbone is common, side chains differ
– 4 categories of amino acid side chains
» Polar charged
D, E, K, R, H
» Polar uncharged S, T, Q, N, Y
» Nonpolar
A, V, L, I, M, F, W
» Unique
Classes of molecules
• Macromolecules
– Proteins
• Backbone is common, side chains differ
– 4 categories of amino acid side chains
» Polar charged
D, E, K, R, H
» Polar uncharged S, T, Q, N, Y
» Nonpolar
A, V, L, I, M, F, W
» Unique
G, C, P
Hydrophobic and hydrophilic amino acid
residues in the protein cytochrome c
Levels of protein structure
• Primary
– Sequence of the polypeptide chain
H3N-MQWERTYIHAHAPKLCVN-COOH
H3N-Met
Gln Trp Glu Arg Thr Tyr Ile…
H3N-Methionine Glutamine Tryptophan…
Levels of protein structure
• Secondary
– Alpha-helix
(collagen)
– Beta-sheet
(spider silk)
– Side-chain dependence to which form is adopted but stabilization
comes from backbone - backbone hydrogen bonding interactions
Levels of protein structure
• Tertiary
– Side-chain dependent and mediated packing of the secondary elements
– Fibrous proteins = elongated, often structural roles
– Globular = compact, often enzymes
Protein domains can be modular
• Protein Domains
– Domains occur when
proteins are composed
of two or more distinct
regions.
– Each domain is a
functional region
Protein structures can be dynamic
• Dynamic Changes
within Proteins
– May occur with
protein activity.
– Conformational
changes are nonrandom movements
triggered by various
events (e.g. binding,
chemical mods…)
Levels of protein structure
• Quaternary
– Interactions between 2 or more distinct polypeptide chains
• Protein-Protein
Interactions
– Results from largescale studies can be
presented in the
form of a network.
– A list of potential
interactions can
elucidate unknown
processes.
Disease
• Sickle-Cell Anemia (SCA)
• Painful
• Life-threatening periods of crisis
• e.g. vaso-occlusive crisis
• block blood flow in
capillaries
Disease
• Sickle-Cell Anemia (SCA)
• Hemoglobin is composed of four polypeptide chains
• Two alpha-globin subunits + two beta-globin subunits
• SCA is caused by a single amino acid substitution in beta-globin
• E6V
Protein structure and folding
• Anfinsen RNase A experiment
– Denature (unfold) protein in urea
• Observed loss of activity
– Dialyze the urea away
• Observed refolding
• Regain of activity
Demonstrated structural information
is inherent to protein sequence
• Follow a folding pathway
• Fold to the lowest energy state
Two alternate pathways for protein folding
Chaperones prevent mis-folding
• Molecular Chaperones
– HSP70 during translation of nascent peptide
• Binds exposed hydrophobic regions
• Hydrolyzes ATP in a bind-release cycle
Hartl, et al (2011)
Chaperones prevent mis-folding
• Molecular Chaperones
– HSP70 during translation of nascent peptide
• Binds exposed hydrophobic regions
• Hydrolyzes ATP in a bind-release cycle
– Chaperonins assist post-translation
Protein folding and Disease
• CJD (Mad Cow) & Alzheimers Disease
– PrPC --> PrPSc --> plaque
– APP --> Ab42 --> plaque