Topic Outline
I. DNA Structure and Organization
II. Transcription Process in Prokaryotic and Eukaryotic Cells
III. Translation Process in Prokaryotic and Eukaryotic Cells
I. DNA Structure and Organization
Epigenetics
Study of how factors change gene expression
Modify DNA; modify histones
Methylation of CPG Islands
Can recruit proteins that repress genes
If methylated, gene transcription will be inhibited
Needed proteins will only be expressed
Nuclear Envelop
Ex: Liver proteins in hepatocytes will not make liver proteins in
Outer membrane microglia cells
Studded with ribosomes
Where mRNA binds with the ribosome for further
translation
Inner Membrane
Structural framework
Interaction translation
Nucleolus
Where rRNA is synthesized
Ribosomal subunits are made
Heterochromatin
Highly condensed
Makes it difficult for enzymes to pass through
No transcription takes place
Euchromatin
Loose; weak attraction
Transcription occurs
Clinical Relevance
1. Drug-Induced Lupus
Antibodies target histone proteins
Test for: anti-histone antibodies
Drugs that can trigger an autoimmune reaction:
sulfonamides, hydralazine, isoniazid, procainamide, phenytoin
SLE: anti-dsDNA or anti-Smith antibodies Needs general TF to bind to promoter region for the
reading of DNA to make RNA
2. Huntington’s Disease Makes rRNA ribosomes utilized in translation
process
Nerve growth factors are responsible for the nerve’s growth 2. RNAP 2
and repair Makes mRNA and snRNA
Deacetylation: increased removal of acetyl groups from mRNA: goes through modifications, then to be
histones, leading to (-) transcription translated with the help of rRNA and tRNA
Inhibition: neuron injury or death in the basal ganglia snRNA:
abnormal hyperkinetic movement disorder 3. RNAP III
Makes tRNA, snRNA, rRNA, but mainly tRNA
Gene Regulation (Eukaryotic Cells)
Enhancers rate of transcription
Silencers rate of transcription
How does an enhancer influence a promoter region? How is it
activated and cause conformational structure in the DNA?
Specific Transcription Factors bind to the enhancers.
Specific transcription factors bind to the enhancers.
Binding of STF facilitates conformational change to DNA.
II. Transcription Process in Prokaryotic and
Eukaryotic Cells
Prokaryotic cells
Requires a specific protein for transcription to occur (RNA
Polymerase)
Enhancer + STF acts on to the promoter region; now
RNA Polymerase Holoenzyme (RNAP-H)
enhancing the transcription rate.
rate or transcription
1. Core Enzyme reads the DNA and makes RNA
Initiation (Prokaryotic Cells)
2 alpha units
2 beta units
Enzyme: RNAP-H
1 omega unit
Specific promoter regions:
-35 region
Separates from SS-PR binding, and starts to read the
-10 region: Pribnow box
DNA
+1 region: Transcription start site
Initiation (Eukaryotic Cells)
Enzyme: RNAP II
TFIID: contains TATA binding proteins; binds to the
2. Sigma Subunit binds to promoter region TATA box; helps RNA to start transcription
Locations where transcription factors will bind to:
TATA box – particular recognition sequence
Eukaryotic Cells CAAT box
GC box
Requires a RNAP and a transcription factor for transcription
to occur
1. RNAP I
G-C rich proteins: have high affinity of interaction via
hydrogen bonds, since they are attracted to each other.
3. Termination in Eukaryotes
Poly (A) Tail: polyadenylation signal A A U A A A
Activates enzymes to cleave the RNA away and terminate the
transcription process
Elongation
RNA Polymerase
Reads the template strand
Opens the DNA and stabilizes the ssDNA
Has intrinsic helicase activity; unwinds DNA
Reads the DNA from 3’ 5’
Synthesizes RNA form 5’ 3’
Amanitin: (-) inhibits RNAP in eukaryotic cells
Rifampicin: (-) inhibits RNAP in prokaryotic cells III. Translation Process in Prokaryotic and
Eukaryotic Cells
Termination
Cogon recognition in mRNA
1. Rho-dependent (prokaryotes)
Rho protein: causes RNAP to break away from the DNA
Moves up from the RNA that is being synthesized to the
RNAP
Crucial for Translation:
1. mRNA – messenger RNA
2. Rho-independent 2. rRNA – ribosomal RNA
RNAP binds to template strand and will start reading it,
making the RNA 3. tRNA – transfer RNA
Inverted Repeats: encountered by the template strand: a
single-stranded sequence of nucleotides followed downstream
by its reverse complement
Hairpin Loop
Triggers RNAP to hop off of the DNA and terminate the
transcription process
Once formed, enzymes will bind to the portion and cleave
and terminate the transcription process
Codons After reading one triplet, it does not start to read at the same
codon that is already being read
Triplets of nucleotides in RNA
Viruses: only exception
A, C, G, U 43 = 64
Picture
There is a total of 64 types of codon
61: code for amino acids
3. Redundant & Degenerate
Remaining 3 codons: STOP CODON does not encode for an
amino acid, terminating the translation process. A single amino acid may be coded for by more than one
codon
Isoleucine: three different types of codons that it codes for
Anticodons AUA, AUC, AUU
A triplet of nucleotides found in the tRNA molecule that are Methionine and Tryptophan: only code for one amino acid
complementary to the codons in mRNA.
All active tRNA molecules must contain a CCA sequence at
the 3’-end as the site for amino acid attachment and for the
interaction with the ribosome during protein synthesis.
Anticodon Loop: CCA 3’ end of tRNA
Wobble Effect (tRNA)
The phenomenon where the third base in an mRNA codon
can pair with more than one kind of base in the tRNA
anticodon.
When a tRNA molecule can bind to multiple codons for the
same amino acid.
Explains why multiple codons can code for a single amino
acid.
Due to the less-precise base pairing that can arise between
the third base of the codon and the base at the first position of
the 5’ end on the anticodon.
Picture risk of mutations
risk of giving off wrong amino acids
abnormally structured proteins
Characteristics of a Genetic Code
1. Commaless
Coding of codons in three’s does not skip any nucleotide in
the sequence
Viruses: only exception
Picture
2. Non-overlapping
Reading the codon and giving off amino acids
The tRNA Structure
D-arm: identification of tRNA by aminoacyl
tRNA synthetase
T-arm: tethers the tRNA to the ribosomes
The variable domain can change in forms of tRNA
Prokaryotes (Bacteria)
