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Ogan Gurel, MD

Biology 301
Review #1
Roosevelt University

Biology 301
Cellular and Molecular Biology
Spring 2002

Review # 1
Ogan Gurel, MD
Biology 301
Review #1

Course Syllabus
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Text chapter Text chapter


Date Lecture Topics assignments Date Lecture Topics assignments
1/23 Introduction / Molecular Bonding 2,4 3/18 – 3/22 Spring Break
1/28 Water & pH 3 3/25 Transport Channels 8
1/30 Carbohydrates & Lipids 5 3/27 Cell Signaling & Signal Transduction 11
2/4 Proteins 5 3/29 LAST DAY TO WITHDRAW
2/6 Enzymes 6 4/1 Cell Architecture 7
2/11 Nucleic Acids 5 4/3 Cytoskeleton & Cell Junctions 7
2/13 DNA Replication 16 4/8 Mitosis & Cell cycle regulation 12
2/18 Gene Expression I 17 4/10 Meiosis 13
2/20 Gene Expression II 17 4/15 EXAM II (covers lectures 2/25 through 4/3)
2/25 Prokaryotic Gene Expression I 18 4/17 Energy / ATP / Oxidation & Reduction 6, 9
2/27 Prokaryotic Gene Expression II 18 4/22 Glycolysis & Fermentation 9
3/4 EXAM I (covers lectures 1/23 through 2/20) 4/24 The Krebs (Tri-carboxylic acid) cycle 9
3/6 Eukaryotic Gene Expression I 19 4/29 Electron Transport & Chemiosmosis 9
3/11 Eurkaryotic Gene Expression II 19 5/6 Photosynthesis I 10
3/13 Plasma Membrane Structure 8 5/8 FINAL EXAM
Ogan Gurel, MD
Biology 301
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Roosevelt University

Lecture One

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Biology 301
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Covalent bonding
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Biology 301
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Polar covalent bonding


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Molecular geometry: VSEPR theory


Weak chemical bonds: Ogan Gurel, MD
Biology 301
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Hydrogen bonding
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Some simple carbon-based Biology 301


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molecules
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Three types of isomers


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Valences of H, O, N & C
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Functional groups of organic Ogan Gurel, MD
Biology 301
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compounds
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Functional groups continued


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Lecture Two

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Water is a polar molecule


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Hydrogen bonds between water Biology 301


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molecules
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Phases transitions are determined


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by intermolecular forces
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Molecular view of ice, water, Biology 301


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and steam

Ice Water Steam


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Biology 301
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Properties of Water
 Cohesion, adhesion & surface tension
 Cohesive behavior leads to capillarity
 Some thermodynamic concepts
 Water’s high heat capacity moderates temperature
changes
 The high heat of vaporization cools surfaces upon
evaporation
 Water expands when frozen: Ice floats and frozen
benzene sinks
 … this has profound implications for the global climate
 Some definitions in solution chemistry
 The mole concept
 Dissolution of salt in water
 A water-soluble protein
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Dissolution of salt in water


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Biology 301
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Dissociation of water
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 The reaction is reversible


 At equilibrium, most of the water is not ionized
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Biology 301
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Definitions of acids & bases


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 Acids donate protons


H+ and Bases accept
protons H+.
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Definition of pH: a logarithmic Biology 301


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scale of [H+] concentration

 For very small


numbers we use
logarithms for
convenience. Typical
[H+] concentrations
range from 10-14 to 10-1
molar which is simplified
by converting this to a
pH range of 14 to 1.

The pH of the blood  is ~ 7.4 which is close to neutral but slightly on the basic side.  Changes
in the blood pH of a few tenths on either side of this value can be fatal.  Does this make sense
mathematically?  On a moment­by­moment basis, how is the blood pH so tightly regulated?
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Biology 301
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Buffers attenuate changes in pH


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 Buffers minimize changes in pH  The maximum buffering capacity


because protons can be taken up occurs when the pH equals the pKa
or given up by the buffer (when [A-] = [HA]).
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Biology 301
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Lecture Three

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Polymerization Biology 301


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(dehydration synthesis)
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Biology 301
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Hydrolysis
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Introduction to carbohydrates
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The structure and classification Biology 301


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of some monosaccharides
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Linear & ring forms of glucose


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Examples of disaccharides
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Starch & cellulose compared


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Glycosidic bond & hydrolysis


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A glycosidic bond is formed 
from an alcohol on one sugar 
attacking the hemiacetal 
carbon of the other sugar.  
Hence polysaccharides can be 
described as intermolecular 
acetals. Acetals (and by 
implication — glycosidic 
bonds) are stable under basic 
conditions.
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The synthesis and structure of a Biology 301


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fat, or triacylglycerol
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Structure of a phospholipid
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Self-assembly of phospholipids
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Lecture Four

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Biology 301
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Protein Functions
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Amino acid structure


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Biology 301
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Amino acid classification


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• Twenty amino acids


• Hydrophilic vs. hydrophobic
• Charged vs. Polar
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Biology 301
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Hydrophobic amino acids


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Biology 301
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Polar amino acids


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Biology 301
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Charged amino acids


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Biology 301
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Peptide bond synthesis


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Review: Four levels of protein Biology 301


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structure
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Biology 301
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Lecture Five

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Biology 301
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Rate Laws
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The rate law is a function


of
1. the rate constant and
2. the concentrations of
the
reactants.
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Biology 301
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Reaction profile
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Biology 301
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Catalysis
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Biology 301
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Michaelis-Menten Model
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 Enzymes are used for the


catalysis and control of cell
biochemistry.
 The Michaelis-Menten model is a
general description of simple
enzyme kinetics.
 At low [S] the rate is first-order
with respect to substrate; at high
[S] the rate is zero-order
(saturated kinetics).

  Using some simple algebra and approximations show how Michaelis­Menten kinetics reduces 
to first­order at low substrate concentrations and zero­order at high substrate concentrations. 
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Biology 301
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Enzyme reaction cycle


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Ogan Gurel, MD
Biology 301
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Feedback (negative) inhibition


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 Feedback inhibition is a very


common regulatory mechanism in
biology.
 Negative feedback systems are
stable systems.

  Negative feedback systems are not just confined to enzyme pathways.  Show how some of the 
pituitary­endocrine  feedback  loops  follow  the  same  paradigm.    Another  example  is  the 
relationship  between  acid  secretion  and  gastrin  secretion  by  parietal  cells  and  antral  cells  in 
the stomach. 
Ogan Gurel, MD
Biology 301
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Types of inhibition
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Biology 301
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Lecture Six

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Biology 301
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Phosphoanhydrides & Phosphoesters


Phosphoanhydrides are
common in ATP and other
“high-energy compounds.”
Phosphodiesters compose the
backbone of DNA and RNA.
Ogan Gurel, MD

The structures of nucleotides and


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polynucleotides
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Biology 301
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The Double Helix


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Ogan Gurel, MD
Biology 301
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Chromatin Structure

 CHROMATIN = DNA + PROTEIN


(histones)
 Chromatin is involved in the
packaging and regulation of
DNA and is organized in a
hierarchical fashion of
successive DNA packing
arrangements.
Ogan Gurel, MD
Biology 301
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DNA > RNA > Protein


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Biology 301
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Lecture Seven

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Biology 301
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Hershey - Chase experiment


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Biology 301
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Purines & Pyrimidines


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Biology 301
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The Double Helix


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Biology 301
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Base pairing in DNA


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A model for DNA replication: the Biology 301


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basic concept
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Biology 301
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Three models of DNA replication


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The Meselson-Stahl experiment tested


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three hypotheses of DNA replication


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Biology 301
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Replication begins at the “origin”


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Incorporation of a nucleotide into a


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DNA strand
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The two strands of DNA are anti- Biology 301


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parallel
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Synthesis of leading & lagging Biology 301


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strands
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Biology 301
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Priming DNA synthesis


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Biology 301
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A summary of DNA replication


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Biology 301
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Excision repair of DNA damage


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Biology 301
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Lecture Eight

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The Central Dogma


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Biology 301
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Genotype & Phenotype


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• Archibald Garrod (1909) and “inborn errors of metabolism”


(e.g. alkaptonuria)

• Beadle & Tatum (1930s) studied eye color in Drosophila

•Inherited instructions in DNA direct protein synthesis. Thus,


the proteins are the links between genotype and phenotype,
since proteins are directly involved in the expression of
specific phenotypic traits
Ogan Gurel, MD

Beadle & Tatum: Biology 301


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one gene – one enzyme hypothesis

• One gene – one polypeptide hypothesis


• One gene – one RNA transcript hypothesis
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Flow of information in prokaryotes &


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eukaryotes
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Biology 301
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DNA to protein: triplet code


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Ogan Gurel, MD
Biology 301
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The dictionary of the genetic code

• Nirenberg (NIH) &


Khorana (MIT) – early
1960s

• UUU -> phenylalanine

• Redundancy
• no ambiguity
• Early evolution
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Biology 301
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Stages of transcription
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Biology 301
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Transcription initiation
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Biology 301
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Transcription elongation
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Biology 301
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Transcription termination
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• Poly-A tail (AAUAAA in eukaryotes)

• Relatively easy to unhybridize

• Prokaryotes: ready for translation immediately


• Eukaryotes: pre-mRNA must first be processed
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Biology 301
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RNA processing
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• Involves modifications at the 5’ and 3’ ends

• Followed in eukaryotes by RNA splicing which


involves modification of the internal mRNA
sequence
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Biology 301
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RNA splicing
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Ogan Gurel, MD
Biology 301
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Lecture Nine

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Biology 301
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Types of RNA in the eukaryotic cell


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Translation: the basic concept


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Biology 301
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Structure of tRNA
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An aminoacyl-tRNA synthetase joins


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a specific amino acid to a tRNA


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Biology 301
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Anatomy of a ribosome
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Biology 301
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Initiation of translation
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Shine Dalgarno
Sequence in mRNA
is complementary
to a sequence in
the rRNA in the small
ribosomal subunit
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Biology 301
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Translation elongation
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Biology 301
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Termination of translation
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Summary of transcription & Biology 301


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translation in a eukaryotic cell