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Molecular Biology
Informational8
Macromolecules
DNA/RNA/PROTEINS
Cells
Chemical Machines
Coding devices
Informational Flow
REPLICATION:
DNA/DNA
TRANSCRIPTION:
DNA/RNA (mRNA)
TRANSLATION:
mRNA (RIBOSOMES)/PROTEINS
GENETIC CODE:
TRIPLET NUCLEOTIDE BASE=AMINO ACID
RIBOSOMES- SYNTHESIS MACHINERY
Polysystronic
Transcription
DNA-------------------- RNA
Types of RNA
mRNA- Messenger
tRNA- Transfer
rRNA- ribosomal
DNA Versus RNA
1. Ribose sugar 2C-OH
2. Pyrimidine Uracil/Thymine
3. Single Stranded (May have secondary Structures)
RNA Functions
1. Genetic- carry Genetic Information Transcribed
From DNA Template
2. Functional:
Macromolecule: Ribosomes or tRNA
Catalytic Activity
Overview Transcription (DNAmRNA)
RNA Polymerases
Varies with Bacteria, Archaea, Eucaryae
Steps Involved
Initiation
Elongation
Termination
RNA Polymerase
One Type in cytoplasma
DNA Dependant
N.T Sequence codes for single polypeptide Chain “GENE”
Transcribed to mRNA
“Polycistronic” More than one gene coded at a time
“Operons” Gene Cluster into 1 transcriptional Unit
“REGULATION”
PROMOTER SITE: START SITE
NO PRIMER NECESSARY
Antisense Strand
Initiation Site
3’
5’
ORF
P
-35
1st nt
Genes
-10
Pribnow Box
-35 TTGAGA
-10 TATAAT
5’
3’
RNA POLYMERASE BINDING
Sigma 
Regulation Operons
RNA Polymerase
“HALOENZYMES” 5 SUBUNITS
SIGMA 1ST TO BIND TO PROMOTER
Formation of Phosphodiester bonds (R.N.T)
Must used AntiSense DNA Strand as Template
rNTPS- ATP, CTP, UTP, GTP
TRANSCRIPTION
INITIATION- PRIBNOW BOX- SIGMA- POLYMERASE
TRANSCRIPTIONAL BUBBLE, PDE, PURINE 1ST NT
ELONGATION: ANTISENSE DNA SEQUENCE
TERMINATION:
1. rho PROTEIN DEPENDANT (NT SEQUENCE RNA)
2. rho INDEPENDENT (HAIR PEN LOOP)
INITIATION
1st N.T Purine
TERMINATION
Specific Sequences on DNA Strand Stops Transcription
Two Ways:
1. Rho Dependant Protein- Sequence RNA Molecule
2. Rho Independent
inverted repetes on DNA Molecule
Hair pen Loop on RNA
rRNA Operon
Spacer
Methylated (Ribonuclease)
TRANSLATION
RNA--------- PROTEINS
THREE TYPES RNA
1. mRNA
2. tRNA
3. rRNA
mRNA
Linear
Carries genetic info transcribed from DNA
CODONS- 3 sequence n.t. coding for Amino Acids
Short Lived, used Once dis-assimbled
tRNA
1. Transferring Agent to bring selected rNTP to rRNA
2. 4 Loops “folded Clover leaf”
3. Amino Acid Binding site 3’ End
4. Anticodon- Determine AA Requested on mRNA
5. Energy Required- Amino Acyl-tRNA Synthetases
The structure of E. coli
N-formyl-methionyl-tRNAfMet
Activation
AA + ATP------------ AA-AMP
AA-AMP
P.P
+ RNA---------- AA-tRNA
+ AMP
r RNA
1. Acts as “Decoding Box”
2. Recognizes and holds mRNA in place
3. Forms peptide bond- AA.AA
4. Proof Reads for Accuracy
16S rRNA
Small Sub Unit
Recognizes and Hold mRNA
23S rRNA
Large Sub Unit Catalyzes Synthesis of AA.AA
Translation & Genetic Code
Watson & Crick 1953
Unstable mRNA 1961
Genetic Code 1962
Gobind Khorana
Nirenburg
CODON
3 Letter N.T. Sequence = Amino Acid
Conventional 5’------------ 3’
N Terminus--------------C Terminus
“GUG”
“UGU”
Val
Cys
Degenerate
4 letter in alphabet
Codes for 64 Amino Acids
Multiple Codes for Some Amino Acids
“Alanine”
GCA
GCC
GCG
GCU
“Wobble Effect” Relax Code for 3rd Letter
Start Codon ‘1”
Universal for Bacteria “AUG”
N-formylmethiomine
STOP Codon (3)
UAG
UGA
UGG
SYNTHESIS
INITIATION
ELONGATION
TERMINATION
INITIATION
SHINE-DALGARNO:
AGG AGG START Sequence on 16S RNA
mRNA Binds to AGG AGG to attach mRNA to 16SRNA
at Start site- m RNA 5’-------3’
Attachment Signs LSU rRNA to bind to SSU
ELONGATION
30s rRNA initiates binding on mRNA and 16S rRNA Complex
Creates three Positions APE
A= Aminoacyl_tRNA Synthetase
P = Peptidyl Transferase
E = Exit Site
Figure 13.15 (Part 2) Protein synthesis
Termination
STOP CODONs
UAA
UAG or UGA
Release Factors: RF 1, 2, or 3