CHAPTER 4: REGULATION OF GENE  The protein produced by the genetic

EXPRESSION information is what is influenced by natural

selection
DNA  If a protein is modified, it cannot influence
 Carries genetic information the gene that codes for it
 Located in the nucleus  This code is expressed at the ribosome
 The monomer is a nucleotide during protein synthesis in the cytoplasm
o A phosphate  There is one way flow of information:
o A ribose sugar DNARNAProtein
o A nitrogenous base
 2 Functions: Protein Synthesis
1. Serve as self-renewing data repository  Two steps are required:
that maintains a constant source of 1. Transcription = Nuclear
genetic information for the cell The synthesis of mRNA uses the gene
2. Serve as a template for the translation on the DNA molecule as a template
of genetic information into proteins, 2. Translation = Translation
which are the functional units of the cell The synthesis of a polypeptide chain
using the genetic code on the mRNA
Definitions molecule as its guide.
 Gene: A DNA segment that contains all
genetic information required to encode RNA STEPS IN GENE EXPRESSIONS
and protein molecules. STEP 1: ALTERATION IN CHROMATIN
 Genome: A complete set of genes of a STRUCTURE
given species.  Before a gene can be transcribed, some
 Gene expression: A process of gene local alteration in chromatin structure must
transcription and translation. occur so that the enzymes that mediate
transcription can gain access to the DNA
Genetic Code  Chromatin remodeling may involve histone
 The genetic code consists of the sequence acetylation.
of bases found along the mRNA molecule  Genes within highly packed
 There are only four letters to this code (A, heterochromatin are usually not expressed
G, C and U)  Chemical modifications to histones & DNA
 The code needs to be complex enough to of chromatin influence both chromatin
represent 20 different amino acids used to structure & gene expression
build proteins.  Heterochromatin is a highly condensed form
of chromatin that is transcriptionally inactive.
Bases in DNA  In general, highly organized chromatin
 A – adenine structure is associated with repression of
 T – thymine gene transcription.
 C – cytosine  Euchromatin has a more open structure and
 G – guanine contain genes that are actively transcribed.
 Base pair rules

GENE EXPRESSION
1. Tissue – specific gene expression
2. Inducible gene expression Heterochromatin:
3. Expression of genes is regulated so that Euchromatin:
transcriptionally
some genes are active whereas others are actively
inactive
transcribed
silent.

The Central Dogma

 Proposed by Francis Crick 1958
 DNA holds the coded hereditary information
in the nucleus
 Chromatin Structure Influences the Initiation
of Transcription
o DNA is commonly depicted as linear
o Chromosomal DNA in nucleus is
organized into a higher order structure
called chromatin, which contains DNA,
histones, & other nuclear proteins
o Packaging is required to fit DNA
 Histone Modifications
o Chromatin consists of DNA associated
with histones and other nuclear proteins
o Basic building block of chromatin is the
nucleosome
o Transcription from DNA in chromatin
requires partial disruption of regular  Histone Acetylation
nucleosome structure & some o In histone acetylation, acetyl groups
unwinding of DNA are attached to positively charged
o Alteration in interaction between DNA & lysines in histone tails
histones is called chromatin remodeling o This loosens chromatin structure,
o One mechanism of chromatin thereby promoting the initiation of
remodeling involves histone acetylation transcription
o Histone acetyltransferases (HATs)
- acetylate histones & thus
produce local alterations in
Histone chromatin structure that are
tails
more favorable for
transcription
Amino acids o Histone deacetylases (HDACs)
available
for chemical - remove the acetyl groups,
modification leading to tighter binding
between DNA and histones
and inhibition of transcription.
 Methylation
o The addition of methyl groups
(methylation) can condense chromatin;
the addition of phosphate groups
(phosphorylation) next to a methylated
amino acid can loosen chromatin
o An important, related alteration in
Unacetylated histones Acetylated histones
chromatin structure is the state of
methylation of the DNA
o DNA methylation, the addition of methyl
groups to certain bases in DNA, is
associated with reduced transcription in
some species
o DNA methylation can cause long-term
inactivation of genes in cellular
differentiation
o Clusters of methylated cytosine
nucleotides bind to a protein that
prevents activators from binding to DNA.
o Methylated histone proteins are
associated with inactive regions of
chromatin.
 o Control elements, segments of
STEP 2: INITIATION OF TRANSCRIPTION noncoding DNA: serve as binding sites
 Transcription for transcription factors that help
o Occurs in nucleus regulate transcription
o Genetic info in DNA base triplets is o Control elements & transcription factors
copied into a complementary sequence they bind are critical to the precise
of codons in a strand of RNA regulation of gene expression in
o Transcription of DNA is catalyzed by different cell types
enzyme RNA Polymerase – must be  Eukaryotic Regulation
instructed where to start the 1. General transcription factors are
transcription process and where to end required for transcription initiation
it. required for proper binding of RNA
 Gene Action: Protein Synthesis polymerase to the DNA
o Sequence of 3 successive DNA 2. Specific transcription factors increase
nucleotides is called BASE TRIPLET transcription in certain cells or in response
o 3 successive RNA nucleotides are to signals
called CODON  Eukaryotic Transcription
o When translated, a given codon o General transcription factors bind to the
specifies a particular amino acid promoter region of the gene.
 3 RNA Polymerases - enzyme that o RNA polymerase II then binds to the
catalyzes the DNA-dependent synthesis of promoter to begin transcription at the
RNA start site.
1. RNA polymerase I (pol I): transcribes o Enhancers are DNA sequences to
genes encoding ribosomal RNA which specific transcription factors
2. RNA polymerase II (pol II or RNAPII): (activators) bind to increase the rate of
transcribes genes into mRNA, which is transcription.
later translated into protein o Coactivators and mediators are also
3. RNA polymerase III (pol III): transcribes required for the function of transcription
genes that encode tRNA & small- factors.
nuclear RNA  coactivators and mediators bind to
 RNA Polymerase II (pol II) transcription factors and bind to
o Catalyzes mRNA synthesis, when other parts of the transcription
acting alone it is incapable of apparatus
initiating transcription at specific  Transcription Factors
sites o Transcription factors may be divided
o Initiation of transcription requires an into:
assembly of proteins-general 1. Discrete domains that bind DNA
transcription factors – Basal (DNA-binding domains)
transcriptional machinery 2. Domains that activate transcription
 Segment of DNA where RNA polymerase (transactivation domains)
attaches to it is a special sequence of
• The first
nucleotides called PROMOTER, located protein that
near the beginning of a gene binds to DNA
 Transcription is
o RNA polymerase (enzyme) transcribes transcription
factor IID
DNA into RNA; complementary base (TFIID)
pairs • Followed, in
 Cytosine (DNA) – Guanine (RNA) order, by
 Guanine (DNA) – Cytosine (RNA) other general
 Thymine (DNA) – Adenine (RNA) transcription
factors
 Adenine (DNA) – Uracil (RNA) • Each of
these
proteins is
 Organization of Eukaryotic Gene essential for
transcription.
STEP 3: TRANSCRIPT ELONGATION STEP 5: RNA PROCESSING
 RNA polymerase proceeds down the DNA  TATA BOX – most important element in
strand and sequentially adds promoters (Goldberg-Hogness)
ribonucleotides to the elongating strand of 5’
RNA. o Sequence: TATAAAA
 Initiation of transcription can be regulated by o Function: It is the binding site for TFIID,
transcriptional activators and transcriptional which is required for RNA polymerase
repressors. binding.
o It controls the frequency of
transcriptional initiation
o Transcription factor known as TFIID
binds specifically to TATA box & first
component of basal transcriptional
machinery to assemble.
o TATA box is believed to determine the
site of transcription initiation.
 Primary Transcript

 Repression
o Repression of transcription is important
for tissue specificity in that it allows cells
to silence certain genes where they o RNA that is initially transcribed from a
should not be expressed gene
o Transcriptional repressors act by 3 o Also called heterogeneous nuclear RNA
ways: (hnRNA)
1. Repression by competition – Repressors o Before it is translated into protein,
inhibit binding of transcriptional activators primary transcript must be processed
because they compete for DNA binding into a mature mRNA in the nucleus
sites that are identical to, or overlap with, o Primary transcript is colinear with coding
those for activators strand of gene & contains sequences of
2. Repression by Quenching – Inhibit the both exons and the introns.
activity of transcriptional activators not by  Pre-mRNA splicing
interfering with DNA binding, but by a o Eukaryotic genes contain introns that
direct protein-protein interaction with must be removed from the primary
activators transcript to create mature mRNA; this
3. Active Repression – Repressors bind to process is calles pre-mRNA splicing
NRE (or silencer) and then interacts o Splicing involves the joining of two sites
directly with basal transcriptional on the RNA transcript, the 5' splice-
machinery donor site and the 3' splice-acceptor
site, and removal of the intervening
STEP 4: TERMINATION OF TRANSCRIPTION intron
 After producing a full-length RNA, the
enzyme halts elongation.
 Transcript elongation may be regulated by
premature termination in which the
polymerase falls off (or is displaced from)
the template DNA strand; such termination
results in the synthesis of truncated
transcripts.
  To produce a mature mRNA that can be o Types
translated into protein, the cell must process  Messenger RNA (mRNA) <5%
the primary transcript in four steps.  Ribosomal RNA (rRNA) Up to 80%
1. Pre-mRNA Splicing  Transfer RNA (tRNA) about 15%
2. Cell adds guanosine base, methylated at 7  mRNA – provides the plan for the
position, by a 5'-5' phosphodiester bond to polypeptide chain
5' end of transcript o Translation of mRNA on ribosomes
o result is 5' methyl cap - required for always begins at the codon AUG
export of mRNA from nucleus to o Encodes methionine, & proceeds until
cytoplasm as well as for translation of ribosome encounters one of the three
mRNA. stop codons (UAG, UAA, or UGA)
3. Cleavage of RNA transcript about 20  rRNA
nucleotides downstream from o Coiled
polyadenylation signal, near 3' end of o Found in ribosomes
transcript o Made as subunits in the nucleolus
4. Addition of a string of 100 to 200 adenine o rRNA provides the platform for protein
bases at site of the cleavage to form a synthesis
poly(A) tail  tRNA – translates the message on the
o Poly(A) tail adds stability mRNA into a polypeptide chain
Steps in translation
STEP 6: NUCLEOCYTOPLASMIC TRANSPORT 1. mRNA molecule binds to small ribosomal
 The next step in gene expression is the subunit and a special tRNA called
regulated export of the mature mRNA from INITIATOR tRNA – binds to the start
the nucleus into the cytoplasm.
codon (AUG) on mRNA, where translation
 Expression of certain genes, especially
those with premature stop codons, is begins
prevented at the step of nucleocytoplasmic 2. Large ribosomal subunit attaches to small
transport. subunit, creating a functional ribosome
3. One end of tRNA carries a specific amino
STEP 7: TRANSLATION acid and the opposite end consists of a
 At the initiation stage – regulatory proteins triplet of nucleotides called ANTICODON
bind the 5’ end of mRNA with the cap. – by pairing, tRNA anticodon attaches to
Activation or inactivation of protein factors to mRNA codon
initiate translation
4. Anticodon of another tRNA with its amino
 Location: Ribosomes in cytoplasm acid attaches to complementary mRNA
 Translation codon next to the initiator tRNA – peptide
o Process in which mRNA associates with bond is formed between amino acids
ribosomes and directs synthesis of a carried by initiator tRNA and tRNA next to
protein by converting the sequence of it
nucleotides in mRNA into a specific 5. After peptide forms, empty tRNA detaches
from ribosome & ribosome shifts mRNA
sequence of amino acids. strand by one codon. - tRNA bearing the
 RIBONUCLEIC ACID (RNA) newly forming protein shifts, another tRNA
o Found all over the cell with its amino acid binds to a newly
o (nucleus, mitochondria, chloroplasts, exposed codon
ribosomes and the soluble part of the 6. Protein synthesis ends when the
cytoplasm) ribosomes reaches a stop codon, at which
time the completed protein detaches from
 Structural characteristics of RNA molecules the final tRNA
o Single polynucleotide strand which
may be looped or coiled (not a double STEP 8 – mRNA Degradation
helix)
 Finally, the mRNA is degraded in the
o Sugar Ribose (not deoxyribose)
cytoplasm by a combination of
o Bases used: Adenine, Guanine,
endonucleases and exonucleases
Cytosine and Uracil (not Thymine)