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BIOL 202
Unit 1A
Biochemicals
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Sodium Magnesium Chloride Potassium Calcium
- Mostly as dissolved salts
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Small amounts of iron, copper, zinc, etc
Polymers
Review basic chemistry in chapter 2
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Universal solvent
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B. Krumhardt, Ph.D.
Condensation - synthesis of polymers - Òdehydration
synthesisÓ
Water
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all chemical reactions of life occur in water
Hydrolysis - breaking down macromolecules
Macromolecules of Life
Carbohydrates (CH2O)n
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Solutes are dissolved in water
H2O soluble, polar
Monosaccharides
Polar
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like likes like
H-bonds
Acids & Bases
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Acids - release H+ in water
e.g. HCl  H+ & Cl-
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Base - releases OH- in H2O
e.g.
NaOH  Na+ & OHpH Scale
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@ pH 7.0
[H+] =[OH-]
neutral pH
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@pH < 7.0
[H+] > [OH-]
acidic pH
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@pH > 7.0
[H+]< [OH-]
alkaline or basic pH
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Human blood - pH 7.4,
if  0.3 it is fatal
Buffer
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solution which stays the same pH with small additions
of small amounts of acids or bases
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e.g. glucose
ribose deoxyribose
C#
Ð Ð H-C=O
H-C=O
C=O
1
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Ð Ð H-C-OH
H-C-OH
H-C-H
2
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Ð Ð HO-C-H
H-C-OH
H-C-OH 3
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H-C-OH
H-C-OH
H-C-OH 4
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H-C-OH
H-C-OH
H-C-OH 5
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H-C-OH
H
H (6)
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H
Ð Ð ring 15
ring 14
ring 14
Disaccharides
carbonates - like baking soda
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High specific heat; much energy must be lost or gained
to lower or raise its temperature
Evaporative cooling
Ice floats, insulates water below
Life Molecules
Elements of Life
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single sugar units (monomers)
proteins - work as buffer
phosphates
Water Moderates Temperatures
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unit molecules (monomers) in chains (branching)
Mg++
Cl -
K+
2 sugar monomers covalently bonded together
e.g. sucrose (table sugar) = glucose + fructose
Polysaccharides
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many sugar monomers - polymers
starch
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Make up most of biological molecules: CHNOPS
Na+
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Ca++
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chain of glucose monomers
function - plant glucose storage
cellulose
H-
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chains of glucose monomers
¥ ¥ covalent bond is different than in starch
¥ ¥ your cells can tell - they can't break this bond
Ódietary fiberÓ
¥ ¥ Ruminants have specialized stomachs,
Òrumens,Ó that contain endosymbiotic protists that
can digest cellulose
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Glycogen
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function - structure of plant cell walls
Chains & branches of glucose
Function - animal form of glucose storage
can be - rings, long chains, branching, polar, nonpolar, acidic, basic
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Lipids
mostly not water soluble, non polar
triglycerides
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¥ ¥ saturated fatty acid has no C=C, has maximum H
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Phospholipids
¥ ¥ partly polar, partly non-polar
¥ ¥ components: 2 fatty acids, glycerol, alcohol, and
a phosphate
¥ ¥ compose phospholipid bilayers
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Sterol
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ring compound
4 rings and a "tail"
flat, polar molecules
e.g. cholesterol - part of membranes
Proteins
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polymers of amino acids
20 amino acids (AA)
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what makes them different is the side chains (-R)
(memorize, use text)
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smallest AA - side chain is H
3-D arrangement of chain
depends on the primary structure and H-bonding
between parts of chain
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¥ ¥ beta pleats
¥ ¥ alpha helix
¥ ¥ non-repeating structure
Tertiary structure
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3 fatty acids, 1 glycerol, fatty acids are usually
different
(double bond)
Ð Ð monounsaturated has 1 C=C
Ð Ð polyunsaturated has 2 or more C=C
order of AA in chain
Secondary structure
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long term energy storage
¥ ¥ unsaturated fatty acid has 1 or more C=C
Primary structure
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Monomer is amino sugar (amino-glucose)
Function - structural polysaccharides- fungi cell
walls, exoskeletons of arthropods
polypeptide = many AA in a chain
Protein = 100's of AA in a chain
Levels of Protein Structure
Chitin
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overall molecule shape
two main types: fibrous, globular
Stabilized by:
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Disulfide bridges
hydrophobic interactions
H-bonds
ionic bonds
Quaternary structure
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2 or more peptides interact to make a protein
Functions of proteins
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Enzymes - Biological Catalysts (reusable)
Structural Function e.g. Collagen
Messengers - hormones - sends message through the
blood to other parts of the body
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transporters e.g. hemoglobin
membrane receptors
Antibodies
Contraction
Storage
Signal
Sensory reception
Regulation of genes
Nucleic Acids
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polar, H2O soluble
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last P bond is a high energy bond means much
energy is released when broken
(7 Kcal/mol))
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ENERGY CURRENCY OF LIFE
Deoxyribonucleic and ribonucleic acids
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Units are bases, sugars and phosphates
DNA and RNA Bases
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DNA base
RNA base
Thymine(T) Uracil(U)
Guanine(G)
¥ Potential energy - stored capacity to do work; in
organisms it is chemical energy
Laws of Thermodynamics
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Energy can neither be created or destroyed
Ð Ð amount is constant in a system
Ð Ð E.g. plants: solar energy  chemical energy
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One usable form of energy cannot be changed into
another usable form in entirety - some energy is always
lost as heat
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Cytosine(C) Cytosine(C)
Adenosine(A)
Adenosine(A)
sugars
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RNA Characteristics
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most protein you have in your body comes from
nuclear DNA you inherited from your parents
¥ BIOL 202
Unit 1B
Metabolism and Enzymes
B. Krumhardt, Ph.D.
Metabolism
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all the chemical reactions
of an organism
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Catabolism - breaking down of larger molecules to
smaller, releasing energy
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Anabolism - building larger molecules from smaller,
uses energy
Energy
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the capacity to do work
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Kinetic energy
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everything eventually becomes heat
Free energy
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Shifts chemical equilibrium--rules life!
release free energy (produce heat)
e.g. cellular respiration
Endergonic reactions
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After work is done the free energy has decreased
Exergonic reactions
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require input of free energy
e.g. the sun provides energy for photosynthesis
Metabolic disequilibrium
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DNA (genetic inheritance) used to make RNA (genetic
code) used to make AA sequence of all proteins
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universe headed toward randomness
portion of energy (e.g. in cell) that can do work at
a constant temperature
single strand
Often folds back and base-pairs with itself
Central Dogma of Biology
randomness, unusable energy (heat)
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exists as a double strand
¥ ¥ T base pairs with A
¥ ¥ C base pairs with G
¥ ¥ attractions between bases via hydrogen bonds
Entropy
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DNA Characteristics
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Guanine(G)
¥ ¥ deoxyribose in DNA
¥ ¥ ribose in RNA
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Ð Ð Motion - of anything (e-, atoms, people...)
Adenosine Triphosphate (ATP)
a steady input of chemical or light energy feeds the
exergonic reactions that fuel organisms
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¥ Energy coupling - mechanism to tie exergonic to
endergonic reactions - ATP used as intermediate
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Phosphate transferred to substrate, now substrate
has more chemical energy:
¥ ¥ ATP + substrate1  ADP + P-substrate1
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Intermediate participates in reaction that wouldn't
occur without phosphate and phosphate is freed:
¥ ¥ P-substrate1 + substrate2  product + phosphate
¥ ¥ (product consists of substrate1 and substrate2)
Enzymes - biological catalysts
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Catalysts - chemical agents that change the rate of a
reaction without changing themselves or being consumed
in the reaction
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Enzymes make reactions of life possible, without
enzymes, entropy
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system enzymes
Ð Ð e.g. penicillin inhibits cell wall synthesis
enzymes
enzyme characteristics
Ð Ð globular proteins
Ð Ð specific for substrate (reactant) and product
Ð Ð pH and temperature sensitive and specific (affects
Ð Ð Cooperativity - active shape of enzyme is
stabilized by substrate binding (if substrate is sufficient
to bind then product is made)
shape)
Ð Ð feedback inhibition and enzymes
Ð Ð destroyed by heat - denatured (permanent shape
¥ ¥ often the product of a series of enzymatic
reactions serves as the allosteric inhibitor of first
(few) enzymesÉwhen product is decreased more is
made
BIOL 202
Unit 1C Cells
B. Krumhardt, Ph.D.
change)
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Energy of Activation for enzymes
Ð Ð the amount of energy input required to start a
reaction
Ð Ð lowered by enzymes
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Active site of enzymes
Ð Ð spot where enzyme and substrate meet--induced
fit--binding of substrate slightly changes shape of
enzyme (H-bonding, H+ transfer from carboxyl)
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Enzymatic reactions
Ð Ð E + S  ES  E + P
Ð Ð Product is changed in shape, no longer fits active
Cells
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Metal ions like iron, copper, and zinc are often
cofactors
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Enzyme activity control
Ð Ð on/off switches
Ð Ð competitive inhibition
¥ ¥ inhibitor substance mimics substrate - blocks
active site
¥ ¥ If more substrate than inhibitor, reaction goes
forward
Ð Ð allosteric control of enzymes
¥ ¥ metabolic inhibitor or activator binds allosteric
site, stabilizing inactive or active shape of enzyme
¥ ¥ chemical binds other part of enzyme  shape
change  change in activity
Ð Ð e.g. DDT, parathion inhibits nervous
Electron microscope
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resolves 0.2 nm to 100 µm
Transmission (TEM) - thin sections
Scanning (SEM) - surface of specimen coated with
gold, scanned  3D images
required for enzyme activity
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Ð Ð resolves 0.1 µm to 10 µm
Ð Ð stain and other techniques help
beams of e- with shorter wavelengths than light
passed through object
Vital non-protein adjunct
Vitamins are coenzymes (organic cofactors) or
parts of coenzymes
Light Microscope
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Cofactors
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Resolving power
Ð Ð ability to distinguish 2 points
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enzymes
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range from <1 µm to 0.6 m in length
Microscopes
site, released
Ð Ð pH and temperature affect binding at active site of
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Cell fractionation
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Centrifuges--spin increases g (gravity)
¥ Differential centrifugation  different speeds/times
produce different cell constituents, checked by enzymes
present
Membranes
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plasma outer membrane or organelle membrane
Ð Ð Functions
¥ ¥ physical boundary
¥ ¥ transmitter of information
¥ ¥ transporter of molecules
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Structure
¥ ¥ Double layer (bilayer) of phospholipids with
embedded proteins, sterols (like cholesterol)
¥ ¥ Carbohydrate chains may be attached to proteins
or lipids - allows cellular recognition - e.g. blood
Ð Ð a large membrane-bordered vacuole contains most
grouping - surface sugar of RBC
of plant cell water
¥ ¥ Proteins may move in the phospholipid bilayer,
Ð Ð in isotonic solutions water leaving the vacuole
therefore, "fluid mosaic" model
equals that entering it; the cell becomes flaccid
ÐÐ More saturated fatty acids  less movement
Ð Ð in hypotonic solutions the vacuole fills with water
(viscous)
ÐÐ More cholesterol  less movement
(viscous)
ÐÐ Proteins are integral or peripheral
Diffusion & Transport
Ð Ð Membrane is selectively permeable
Ð Ð small molecules (H2O, CO2, O2) and lipids
 presses the cell membrane against cell wall Òturgor
pressureÓ develops; cell is ÒturgidÓ
Facilitated Diffusion
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¥ proteins provide Ócarrier" through which a molecule
can pass into/out of a cell
Ð Ð No energy required
Ð Ð Specific for certain molecules or types e.g.
(nonpolar) slip through ÒdiffuseÓ
Ð Ð Polar molecules and ions need mechanisms to get
sugars, ions, amino acids, etc.
Ð Ð Protein binds solute on one side  protein shape
through
¥ ¥ these are coated in water
changes  transported molecule released on other side
of membrane
Diffusion
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¥ movement of molecules from greater concentration to
lower concentration
Ð Ð Movement of molecule is from high to low
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concentration (of that molecule) like diffusion, but the
Ócarrier" is required - molecules too big to slip through
membrane
¥ achieves a random distribution of the molecule
Osmosis
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Diffusion of water across membrane; equals out the
concentration of water (solvent) across a membrane
Ð Ð osmotic pressure (chemical energy that causes this
flow of water)
Ð Ð Solvent: dissolver
Ð Ð Solute: that which is dissolved
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With osmosis, solvent concentration (free, unbound
water) is used & not solute concentration as used otherwise
Osmosis in animal cells
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Isotonic solutions
Ð Ð equal water concentration as inside cells "saline"
Ð Ð no net movement of water from/to cells in isotonic
saline
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Hypertonic solutions
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Hypotonic solutions
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Ð Ð More free water (less solute) than in cells 
Ð Ð water moves into cells  cell bursts (lyses,
¥ plants have cellulose cell wall - porous, but rigid, will
not collapse
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plasmolysis
Ð Ð in hypertonic solutions the cell membrane will
shrink, cell wall remains
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to open them
¥ ¥ e.g. Stimulus-gated channels in neurons
Active transport
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turgor pressure
Energy required ATP  ADP
¥ Moves solute from lower to higher concentration
(opposite of diffusion)
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Like enzymes
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e.g. Sodium-potassium pump--NKA--pumps 3 Na+ out
for every 2 K+ pumped in
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electrogenic pump of animal cells  produces more
+ charge out than in  provides "membrane potentialÓ
(voltage: -50 to -200 mV) due to electrochemical
gradient produced
Ð Ð Less free water (more solute) than in cells 
Ð Ð draws water out of cells  cell shrivels or crenates
undergoes lysis)
Osmosis in plant cells
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Ð Ð Some are gated channels
¥ ¥ voltage or chemical or other stimulus is required
Ð Ð proton pump produces similar effect, pumping H +
across a membrane
Cotransport
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cell transports 2 solutes together
Ð Ð usually one is Na+ (animals) or H+ (others), other
is energy-yielding nutrient (e.g. glucose)
Ð Ð energy price is paid by active transport of Na+ or
H+ out
Cytoplasm
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between plasma membrane and organelles/nucleus or
other internal structures
Ð Ð semifluid - cytosol - gel-like
Ð Ð ribosome and polysomes here (protein factories of
Ð Ð Proteins arrive via vesicle transport
Ð Ð Addition of sugars, phosphates & fatty acids to
cell)
¥ ¥ polysomes are ribosomes in groups on one RNA
Prokaryotic Cells - bacteria
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no nucleus, no membrane-bound organelles
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most have cell wall (complex chemical composition)
with cell membrane within, some have outer membrane too
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DNA in single circular chromosome in nucleoid
region
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most 1-10µm
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proteins
Ð Ð Routing (tagging) proteins for secretion
(exocytosis) or to other organelles
Ð Ð In plants called dictyosomes-- make cell plate
between 2 cells after cell division
Single membrane organelles
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¥ total mass of all bacteria on Earth would exceed the
total mass of all other organisms combined
Eukaryotic Cells
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most 10-100 µm
¥ nucleus and membrane-bound organelles
compartmentalize cells
Nucleus
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Function: cell reproduction & control of protein
synthesis
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Surrounded by double layer membrane with nuclear
pores that control in/out
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nuclear lamina - net-like protein structure just inside
nuclear membrane - maintains shape
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Contains nucleolus
Ð Ð concentrated area of RNA
Ð Ð Ribosome subunit synthesis - make protein,
ribosomes are protein factories of cell--subunits out
through pores
Ð Ð RNA processing
Endomembrane system
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¥ Endoplasmic reticulum--membrane stacks near
nucleus
Ð Ð Rough ER - Protein synthesis
¥ ¥ membranes studded with ribosomes
¥ ¥ (* not all protein synthesis is here; some on free
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Golgi apparatus (bodies) -membrane stacks near ER
Vacuoles
Ð Ð Plants - storage site of cell sap - membrane is
out excess water
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Peroxisomes
Ð Ð make H2O2 for lipid & alcohol metabolism
Ð Ð glyoxisomes (specialized peroxisomes)--in leaves
and germinating seeds, convert triglycerides to sugars
Ð Ð grow by incorporation of constituents from
cytosol, divide when large enough
Energy transformers of cells
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Chloroplasts--Plants
Ð Ð Site of photosynthesis
Ð Ð Triple membrane organelles
¥ ¥ Two outer membranes
¥ ¥ inner membrane stacks
Ð Ð membrane--thylakoid with chlorophyll
(green)
Ð Ð stacks--"grana"
¥ ¥ Stroma--fluid surrounding grana
Ð Ð Overview of photosynthesis:
CO2 + H2O  Carbohydrate + O2
solar energy
Ð Ð Plastids - include chloroplasts, and other nonphotosynthetic organelles - starch storage site, pigment
containing, etc.
Ð Ð Chloroplasts are the only energy transformer
may be added
¥ ¥ Carbohydrate metabolism
¥ ¥ Calcium storage - helps keep cytosolic Ca++ low
¥ ¥ Drug detoxification
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Ð Ð food vacuoles - formed by endocytosis
Ð Ð contractile vacuoles - freshwater protists - pump
¥ ¥ protein inserts to inside RER as made
¥ ¥ native conformation due to AA sequence, sugars
for vesicle transport
Ð Ð Vesicles with enzymes of hydrolysis
Ð Ð Cell may do Phagocytosis (endocytosis) & form
tonoplast, part of endomembrane system
ribosomes in cytoplasm)
Ð Ð Smooth ER
¥ ¥ Lipid synthesis, including membrane formation
Lysosomes
vesicle around a particle then vesicle fuses with
lysosome to be digested
¥ Contains chromosomes (visible, "condensed", during
cell division) or chromatin (can not see, "dispersedÒ, when
cell is not dividing)
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plastids
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Mitochondria - plants and animals
Ð Ð Site of ATP synthesis out of "food"  cells
"battery"
Ð Ð Double membrane structure
¥ ¥ inner membrane = cristae
¥ ¥ between membranes = intermembrane space
¥ ¥ inside inner membrane = matrix
¥ ¥ compartmentalization allows ATP synthesis by
cellular respiration
Ð Ð Overview of reactions:
¥ ¥ Carbohydrates + O2 + ADP  CO2 + H2O +
ATP
¥ ¥ Also site of Ca++ storage in the cell - keeps
cytosolic Ca++ low
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Endosymbiosis
Ð Ð in early evolution of eukaryotic cells mitochondria
and chloroplasts were bacteria engulfed by larger cells
Ð Ð similar to bacteria
Ð Ð double membrane (from phagocytosis)
Ð Ð they have their own circular DNA (as in
bacteria), ribosomes, protein synthesis
¥ ¥ plants
Ð Ð cellulose--secreted by cell--may be in 2 layers,
separated by pectin
¥ ¥ fungi
Ð Ð chitin
¥ ¥ bacteria
Ð Ð peptidoglycan
¥ ¥ amino-sugar polymers cross-linked by short
peptides
Extracellular matrix
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secreted by animal cells
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collagen
Ð Ð protein, tough
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proteoglycans
Ð Ð glycoproteins that collagen fibers are embedded in
fibronectins
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Note: all of your mitochondria are descended from
those in the egg made by your mother, sperm bring no
mitochondria!
Cytoskeleton
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Ð Ð glycoproteins bind cell receptor "integrins"--holds
cell in place
Intercellular junctions
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Plants
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Animals
Structural & transport/motility functions
¥ Microfilaments: muscle-like contractile protein (actin),
thin fibers
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Pseudopodia - microfilaments extend cytoplasm for
movement - "cytoplasmic streaming" - amoeboid cells
Ð Ð cell walls perforated with channels
Ð Ð cytoplasm is continuous between cells
Ð Ð tight junctions
¥ ¥ belts around cells - prevent leakage between
cells
¥ ¥ things must go through cells or not pass - control
Ð Ð desmosomes
¥ ¥ anchoring junctions - hold cells together
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Microtubules: shape maintenance & movement in cell
- motor molecule walks along microtubule to move things;
thick filaments
Ð Ð In dividing animal cells--specialized microtubules
Ð Ð gap junctions
¥ ¥ similar to channels of plants
¥ ¥ cytoplasm continuous between cells
called centrioles form at centrosome, found near
nucleus; for moving chromosomes
Cell export/import
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¥ Intermediate filaments: intermediate thickness provide structure and strength
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Projections
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Cilia (many, shorter) and Flagella (few or 1, longer)
Ð Ð Hair-like projections of cell membrane
Ð Ð in eukaryotes, special microtubules with a large
associated protein - dynein - that "walks" along them
producing a wave-like movement
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Phagocytosis
Ð Ð Cell ÒeatingÓ
Ð Ð cell engulfs particle with pseudopodia  vacuole
 lysosome for digestion
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Pinocytosis
Ð Ð Cell ÒdrinkingÓ
Ð Ð cell engulfs tiny droplets of extracellular fluid 
vesicles
Ð Ð nonspecific, may be cause of food allergies when
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¥ Microvilli - (many and shorter than cilia) - no
movement, just more surface area for absorption
Cell walls
proteins endocytosed this way in intestines
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Receptor-mediated endocytosis
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ligands bind membrane receptors  endocytosis
induced
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cell accumulates specific substances needed
receptors cluster in pits, helps with endocytosis
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Unit 1D
B. Krumhardt, Ph.D.
Bioenergetics
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Exocytosis
Signal-transduction
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First messenger--e.g., hormone--binds membrane
receptor connected to an inside protein that produces
(directly or indirectly) 
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second messenger
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intracellular substance that turns on/off enzymes in
cell
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e.g.
¥ ¥ cAMP and phosporylation (kinase activation)
¥ ¥ inositol trisphosphate and Ca++
General Signal Transduction
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¥ The first message, a signal molecule (e.g. a hormone),
binds a receptor on outside of plasma membrane
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Protein kinases put phophates on proteins
Ð Ð Phosphates are on/off switches
Ð Ð In the cascade one kinase activates the next, which
activates the nextÉ.
Ð Ð More activated molecules are made with each step
Inositol Trisphosphate and Calcium as Second Messengers
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In a resting animal cell, cytosolic Ca++ is kept low by
Ca++ pumps constantly pumping Ca++ into the smooth
endoplasmic reticulum and mitochondrial matrix, as well
as through the plasma membrane, out of the cell
Ð Ð Low cytosolic Ca++ keeps the animal cell at rest
Ð Ð  cytosolic Ca++ activates the cell
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Inositol trisphosphate is the second messenger - opens
Ca++ channels
Nuclear Response to Signal - Gene Activation
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¥ First messenger outside cell may affect transcription
(RNA synthesis) via a phosphoryation cascade
¥ Steroid hormones slip right to the nucleus and bind a
receptor to affect transcription
BIOL 202
Principles of Biology II
¥
Eaten by heterotrophs
Ð Ð herbivores eat plants
Ð Ð carnivores eat animals
Ð Ð omnivores eat both
Oxidation/Reduction Reactions- e- transfer
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Oxidation - losing an eReduction - gaining an e-
Example: Na+ + Cl-  NaCl
Ð Ð Na+ oxidized
Ð Ð Cl- reduced
Biological Reduction
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This causes the production of a second messenger
made inside the cell which turn on/off enzymes in the cell,
activating or inactivating it
Cyclic AMP as a Second Messenger
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Cyclic AMP (cAMP) made inside the cell when a
signal molecule (hormone, first messenger) binds a
receptor on outside of plasma membrane
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cAMP activates a protein kinase enzyme initiating a
phosphorylation cascade
Phosphorylation Cascade
¥ Autotrophic organisms - produce own food by
photosynthesis
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e- moves with H+
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Biological reduction: gains H+ & e-
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Biological oxidation: loses H+ & e-
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Reduction - Oxidation coenzymes
Ð Ð
NAD+ + H+ + e-  NADH + H+
Ð Ð NADP+ + H+ + e-  NADPH + H+
Ð Ð FAD+ + 2H+ + 2e-  FADH2
ATP
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energy currency of cells
Ð Ð Make ATP by cellular respiration, using energy
from food
Ð Ð Use ATP for all cellular work
Chemiosmotic phosphorylation
¥ ¥ Mitochondria and Chloroplasts:
Ð Ð H+ collect on one side of internal membrane,
pumped there by electron carriers in membrane 
Ð Ð generates an electrochemical gradient
Ð Ð ATP synthase enzyme spans membrane too
Ð Ð has channels to allow H+ to go down
electrochemical gradient
Ð Ð the H+ flow provides energy to ATP synthase:
ADP + P  ATP
Ð Ð Work: ATP  ADP + P
Aerobic Cellular Respiration
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Energy yielding reactions - catabolism
Aerobic: oxygen required
(Anaerobic: no oxygen required)
Glycolysis (cytoplasm)
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¥ Overview:
glucose (6C)+
2 NAD +
2 ADP

2 pyruvate (3C) +
2 NADH + H+ +
2 net ATP
Ð Ð -level phosphorylation
¥ ¥ Energy investment:
ÐÐ
FADH2   2 ATP
Anaerobic Catabolism
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Fermentation
or
2 ATP's are used to phosphorylate substrates,
giving them potential energy
Ð Ð Energy yield:
4 total ATP's (2 net ATP) are made as pyruvate is
produced
ÒTransitionÓ Reactions
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starts in the cytoplasm, ends in the mitochondrial
matrix
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a transport protein brings pyruvate into the
mitochondrial matrix
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each pyruvate (3C) + NAD 
acetate (2C) + NADH + H+ + CO2
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acetate binds coenzyme A, which delivers it to
KrebÕs cycle
Krebs Cycle
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a.k.a. TCA cycle, Citric Acid Cycle
¥ Occurs in the mitochondrial matrix
Krebs Cycle Overview
*
1
acetate (2C) binds oxaloacetate (4C) making citrate
(6C)
*
2
In a step-wise manner, using 8 enzymes, chemical
energy in citrate is transferred to:
¥ ¥ 3 NADH
¥ ¥ 1 FADH2
¥ ¥ 1 GTP (GTP + ADP  GDP + ATP)
3
2 C's acquired by oxaloacetate are released as CO2
4
Oxaloacetate is resynthesized in the process
(making it a cycle)
Transition Reactions & KrebÕs Cycle
*
*
¥
¥
Anaerobic Respiration
Ð Ð some other chemical other than O2 is the final eacceptor
Ð Ð used only by some anaerobic bacteria
Fermentation
¥
¥ Repletes NAD for further glycolysis when pyruvate
accumulates because no O2 is available as the final eacceptor in the respiratory chain
¥
¥
¥
¥
yeast - alcohol fermentation
Ð Ð pyruvate + NADH  ethanol + CO2 + NAD
muscle, bacteria, plants
Ð Ð pyruvate + NADH 
lactic acid + NAD
Ð Ð in animals, the liver can recycle the lactic acid
back to pyruvate ÓCori cycleÒ
Metabolism of other molecules
¥¥
Carbohydrates
ÐÐ
First must be hydrolysed to produce
monosaccharides
ÐÐ
excess glucose stored as glycogen or broken into
acetates and made into fatty acids and stored as
triglycerides
ÐÐ
other monosaccharides are converted to glucose or
molecules of glycolysis
Respiratory Chain
¥
¥
in mitochondrial cristae
¥
¥
electron transport proteins and cytochromes in cristae:
Ð Ð NADH and FADH2 from glycolysis & Krebs drop
off electrons to these
Ð Ð H+ pumped into intermembrane space as e- pass
¥¥
ÐÐ
to be utilized, proteins must first be hydorlyzed to
release amino acids
ÐÐ
ÐÐ
intermembrane space, too
¥
¥
¥
¥  H+Õs accumulate in intermembrane space 
chemiosmotic phosphorylation, a.k.a. Òoxidative
phosphorylationÓ because O2 is final electron acceptor
¥
H2O produced as e-Õs are accepted
¥
Note:
Ð Ð NADH + H+    3 ATP
the amino acids are then deaminated
the deaminated amino acids are then converted into
either glucose or acetate
from one to next, Òproton pumpÓ
Ð Ð NADH's and FADH2Õs H+Õs pumped into
proteins
¥¥
fats (triglycerides/phospholipids)
ÐÐ
lipolysis (triglyceride hydorlysis) breaks these
into:
¥ ¥ fatty acids
Ð Ð           many acetates
¥ ¥ & glycerol
Ð Ð    pyruvate
¥ ¥ fat math:
ÐÐ (3 NADH/acetate X 3 ATP/NADH) +
(1 FADH2/acetate X 2 ATP/FADH2)
= 11 ATP/acetate
DNA Replication
¥ ¥
strands of DNA base paired together uncoiled and
unzipped by enzymes (H-Bonds broken)
ÐÐ average 9 acetates/fatty acid X
Ð Ð Helicase enzyme untwists an area of the strand and
3 fatty acids/triglyceride
= 27 acetates/triglyceride
breaks the base pairs
Ð Ð Single stand binding proteins stabilize the
ÐÐ 27 acetates/ triglyceride X
11 ATP/ acetate
= 297 ATP from acetates/triglyceride
ÐÐ add 14 more ATP for the glycerol and you
have well over 300 ATP for one molecule of
fat!
BIOL 202 Unit 1E
Molecular Genetics
B. Krumhardt, Ph.D.
Eukaryotic Chromosomes
¥
¥ composed of protein & DNA
Hershey & Chase:
¥
¥
¥
¥
experiment to determine which was genetic material
Ð Ð viruses made of protein and DNA
¥
separated strands
¥
¥ ¥
New complementary nucleotides base pair
Ð Ð NTPÕs
Ð Ð uses ATP to add P-P to each nucleotide, pays
energy price
¥ ¥
Enzyme, DNA polymerase, binds new nucleotides
together, releases P-P
¥
2 batches of T2 bacteriophage (virus of bacteria)
¥
¥
Bases
¥
¥
Chargaff's Rule
¥
¥
Watson & Crick
¥
¥
¥
¥ Note: DNA polymerase contains an ÒeditingÓ feature;
it checks that the correct bases are paired
Ð Ð  mutations
picture
¥
¥
¥
¥ Leading strand 5Õ Phosphate to 3Õ OH: DNA
polymerase works on through
Ð Ð Lagging strand: DNA polymerase works in pieces
ÒOkazaki fragmentsÓ
¥ ¥ Priming: primase adds 10 RNA units
¥ ¥ New nucleotides base pair and DNA
polymerase binds  Okazaki fragments
¥ ¥ RNA primer replaced by DNA polymerase
elongating fragments
¥ ¥ Ligase enzyme binds fragments
Ð Ð Saw Rosalind FranklinÕs X-ray crystallography
Double Helix Model
Ð Ð Origins of replication
¥ ¥ Enzymes of DNA synthesis recognize a certain
along the chromosome
Ð Ð [pyrimidine] = [purine]
Ð Ð [G] = [C]
Ð Ð [A] = [T]
knowing ChargaffÕs rule, proposed a structure for
DNA - the double helix model
works on both strands at the same time
¥ ¥ Results in the production of Òreplication forksÓ
Ð Ð 2 with 2 rings: purines (adenine and guanine)
Ð Ð 2 with 1 ring: pyrimidines (thymine cytosine)
¥ ¥ One look at x-ray diffraction photos and
¥
DNA sequence and begin replication there
Ð Ð labeled DNA with *P  one batch
Ð Ð labeled protein with *S  other
¥ added to bacteria & found only the *P entered the cell
*S stayed out, therefore, DNA is the genetic material
DNA structure
¥ Priming: primase enzyme adds 10 RNA units to
allow DNA polymerase add nucleotides (DNA polymerase
only adds to existing stands)
¥ ¥
results in 2 double strands with each having one
ÒoldÓ and one ÒnewÓ strand - (ÒnewÓ strand of one pair
identical to other ÒoldÓ strand - therefore the process is
called "semiconservativeÒ
¥
thymine (T) base pairs with adenine (A) (H-bonds)
Telomere problem
¥
guanine (G) base pairs with cytosine (C) (H-bonds)
¥
¥
3D = helix
¥
DNA is antiparallel
Ð Ð one strand is 5Õ to 3Õ
Ð Ð one strand is 3Õ to 5Õ
¥
¥ As the RNA primer of leading DNA strand is
removed, there is no way to fill it in with DNA, so the
chromosomes get shorter and shorter with age
¥ In germ cell lines, the enzyme telomerase has a short
RNA primer in the enzyme to produce longer telomeres in
the gamete
One gene - one enzyme hypothesis
¥ ¥
ÒCentral Dogma of BiologyÓ
¥ ¥
enzyme
enzyme
enzyme
1
2
3
A  B  C  D
¥ ¥
1,2, and 3 are different enzymes, requiring different
genes, BUT some proteins are made of more than one
polypeptide, therefore, one gene - one polypeptide
hypothesis is more correct
How is protein made
¥ ¥
DNA  RNA  protein
transcription translation
RNA synthesis
¥
¥
¥
transcription
¥ RNA made essentially in the same manner as DNA,
but only certain parts of the DNA unzip for RNA synthesis
¥
¥
¥
¥
¥
¥
¥
¥
enzyme is RNA polymerase
Starts at the promoter downstream of a TATA box
Other transcription factors also must assemble
Stops at unknown (as yet) termination signal
¥
¥
RNA processing
Ð Ð Occurs in the nucleolus of eukaryotes
Ð Ð Addition of
¥ ¥ 5Õ cap of modified GTP
¥ ¥ Poly-A tail
¥ ¥ Splicing out introns
ÐÐ Interruptions in expressed portions of the
gene (ÒexonsÓ)
ÐÐ snRNPÕs Ð small nuclear ribonucleotide
¥
¥
¥
Ð Ð 3 bases complimentary to codon
¥ base pair with mRNA codons & participate in the
transfer of the amino acid to growing peptide chain
¥ ¥
1 amino acid might have 4 different tRNA with 4
different anticodons, but more likely, the anticodon will
contain an unusual base to base pair with any third base of
the codon ( the first 2 bases make the codon specific)
¥ ¥
called the "Wobble HypothesisÓ because the unusual
third anticodon base allows wobble in base pairing
¥ ¥ ÒChargingÓ a tRNA
Ð Ð aminoacyl transferase specifically attaches amino
acid to proper tRNA
Ð Ð AA + ATP 
AA-P + ADP
Ð Ð AA-P + tRNA 
AA-tRNA + P
Ð Ð Pays energy price
Ribosomal RNA (rRNA)
¥ ¥
ribosomes do protein synthesis (translation) - rRNA is
an important part of this machinery along with proteins
Ð Ð rRNA = ÒribozymesÓ
Ð Ð enzymes are proteins
¥ ¥
one ribosome covers 3 codons during translation (9
bases)
Polypeptide synthesis
¥¥
consists of initiation, elongation, and termination
Initiation
¥
phosphates Ð help align the RNA for splicing
¥ ribosome (rRNA + protein) binds mRNA in the
cytoplasm in 2 steps
Ð Ð small subunit then large subunit
Ð Ð binds first AUG codon after the 5Õ end of the
Types of RNA
Messenger RNA (mRNA)
¥ ¥ contains the genetic coding for the protein
¥ ¥ genetic code - a triplet code
Ð Ð 3 bases code for 1 amino acid
Ð Ð the 3 bases coding for one amino acid are called a
mRNA
Ð Ð the methionine-activated tRNA (activated = AA
atop) base pairs with codon
(codon - anticodon base pairing)
codon
Ð Ð different combinations of bases code for certain
amino acids
¥
¥
¥
ÐÐ
Exceptions are for a few amino acids in
mitochondria, chloroplasts, Paramecium, etc.
¥
¥
¥¥
genetic code is ÒredundantÓ
Ð Ð from 1 to 6 codons code for a single amino acid
Transfer RNA (tRNA)
methionine always first amino acid
Elongation
¥
most are specific for 1st two bases, nonspecific for 3rd
¥ nearly universal; same 3 bases  same amino acid in
most all organisms
carry anticodons
¥ a second tRNA (tRNAAA2) binds the 2nd codon
associated with the ribosome
ÐÐ
¥
¥
codon-anticodon base pairing
¥ the bond between met & tRNAmet is broken & met
transferred to atop AA2 on the 2nd tRNA
Ð Ð enzymatic reaction (peptidyl transferase)
¥
the tRNAmet leaves
¥ ¥
the ribosome slides down the mRNA one codon
Ð Ð 5Õ to 3Õ
¥ ¥
the tRNAAA3 binds the codon
¥ ¥
the bond between metAA2 & the tRNA for AA2 is
broken and Met-AA2 is transferred to atop AA3 atop
tRNAAA3 (peptidyl transferase)
¥ ¥
....and so on until
Termination
¥ ¥
a stop codon - UGA, UAA, or UAG - is reached
¥ ¥
polypeptide complete - released from ribosome
¥ ¥
ribosome disassociates into 2 subunits
¥ ¥
mRNA disassociates from ribosome and degraded by
RNAase
 •
Variations of This Mechanism
¥ ¥
polysomes - as space on the mRNA becomes
available after the ribosome moves along the strand
another ribosome can bind & start peptide synthesis & as
these move along another may bind .....
¥ ¥
polysome = many ribosomes on one mRNA
¥ ¥ NOTE: if gene isn't right  no protein
Ð Ð enzyme absent - can't do reaction
Ð Ð biochemical reactions used to identify bacteria
¥
¥
RER protein synthesis:
Ð Ð ribosomes make peptides and insert them through
ER membrane
Ð Ð how does the ribosome "know" to go to ER?
¥ ¥ signal sequence - a certain sequence of AA
signals this (made first)
Ð Ð the signal sequence inserts through a protein on ER
membrane and is enyzmatically clipped off as more
AA added
Ð Ð protein synthesis continues & peptide enters the
ER or folds in & out of the membrane
Ð Ð protein may be enclosed in ER or embedded in ER
membrane
Ð Ð vesicles bud off ER  Golgi
¥ ¥ addition of sugars in both ER & Golgi
¥ ¥ required for routing
Summary of variations in protein synthesis & routing
¥¥
Cytoplasmic protein synthesis on free ribosomes or
polysomes  cytoplasmic proteins
ÐÐ
(* some of these may enter the appropriate
organelle/nucleus by various mechanisms)
OR
¥¥
RER protein synthesis
ÐÐ
protein to inside ER  inside vesicles  inside
organelles
ÐÐ
protein to inside ER  secreted by fusion with
plasma membrane
ÐÐ
protein in ER membrane  protein in plasma or
organelle membrane
Overview of protein synthesis
 Œ DNA in nucleus contains sequence of bases (A,G,T, &
C) that provide triplet code
transcription off DNA  mRNA containing triplet
codons
 • 3 bases per amino acid
 • bases A,G,U,C




Ž mRNA moved to cytoplasm - ribosomes attach
• tRNA containing anticodons & specific amino acid
base pairs with mRNA codon
• amino acid is moved to 2nd amino acid on 2nd tRNA
when it base pairs   "translationÒ
‘ **** sequence of DNA  sequence of mRNA 
sequence of AA (primary structure) of protein
¥ ¥ presence or absence of certain enzymes reflects
the genetic differences between species