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Unit II: Basic Genetic Mechanisms and

Working with Cells

Chapter 6:
How Cells Read the Genome (DNA Protein)
Quality Control Mechanisms in Translation

Chapter 7:
Control of Gene Expression

Chapter 8:
The Cell Biologists Tool Kit

Online module on Monday 2/20: Translation (mRNA protein)


EXAM I SCORES POSTED Monday 2/20 and returned in lab
Questions/Objectives
Textbook Readings:
5th Edition: p.329-349; 357-360; 383-
399
6th Edition: p. 299-319; 325-328; 351-
I. What are the essential molecular components of
362
transcription (DNA RNA) ?
a) RNA (structure, types of)
b) RNA polymerase
c) DNA template and coding regions

II. What are the basic mechanisms of transcription?


a) Prokaryotes
b) Eukaryotes

III. How must mRNA molecules be processed prior to being


translated into protein?
8 Common Features of All Cells

1. Cells are highly complex and


2. organized.
Cells possess a genetic
program.
3. Cells are capable of producing more of
themselves.
4. Cells are biochemical factories that constantly
acquire and utilize energy.
5. Cells engage in mechanical activities.
6. Cells are able to respond to stimuli.
7. Cells are capable of self regulation.
8. Evolution first happens at the level of molecules and
cells.
DNA nucleotide sequences specify biological messages
organized into genes
Central Dogma

Flow of information
I Transcription
Fixed set of DNA Working RNA copies
molecules

Transcription Components:
- RNA nucleotides
- RNA Polymerase
-DNA template
- RNA polymerase recruiting factors
Ia Transcription: RNA the differences
Ribose instead of deoxyribose Mostly single-stranded

Uracil instead of thymidine

Figure 6-4 Molecular Biology of the Cell ( Garland Science 2008)


Ia RNA polynucleotide chains, though single-stranded,
can exist in some rather unique configurations held
together via.

Conventional base pairing and/or nonventional base pairing

Figure 6-6 Molecular Biology of the Cell ( Garland Science 2008)


Ia Types of RNA molecules
mRNA represents only ~5% of total cellular RNA
Up to 80% of cellular RNA is ribosomal RNA (rRNA) makes
up the structural and catalytic core of ribosomes
Other non-coding RNAs make up the remaining 15%.
Examples:
siRNA small interfering RNA Regulate gene expression
by targeting specific mRNA
Sequences for degradation/inhibition
miRNA microRNA

Involved in mRNA splicing


snRNA small nuclear RNA
(a process well discuss later)
Ia
Our focus: rRNA, mRNA, and tRNA

Translates
mRNA
nucleotide
Structural template for translation sequence into
component of amino acid
ribosome sequence
Ib Transcription: RNA polymerase

RNA polymerase
Multi-subunit enzyme
carries out transcription

Catalyzes nucleotide
polymerization within its
ATP active site
UTP
CTP
GTP
Energy stored in the
phosphoanhydride bonds of
incoming ribonucleoside
triphosphates powers
polymerization
Figure 6-8a Molecular Biology of the Cell ( Garland Science 2008)
Ib Transcription: The DNA Template
Transcription generates a single-stranded RNA molecule that is
complementary to the DNA template strand.
Sense DNA strand = strand NOT
used for transcription
has same nucleotide sequence as
resulting RNA (except has Ts
instead of Us)
Antisense DNA strand = template
used for transcription
RNA is ALWAYS synthesized 53
(and so DNA is read 35) by RNA
polymerase
Ib Transcription: The DNA Template
A given gene within a DNA molecule is composed of three
basic parts:
a) Promoter (initiating site of transcription)
b) Coding region (portion that will be transcribed)
c) Terminating region (termination site of transcription)

Terminating region
Transcription: The DNA Template
A given gene within a DNA molecule is composed of three basic parts:
a) Promoter (initiating site of transcription)
b) Coding region (portion that will be transcribed)
c) Terminating region (termination site of transcription)
Transcription: Molecular Mechanisms

Prokaryotes

Eukaryotes
Pro
IIa Transcription: Molecular Mechanisms Ba kary
c o
exa teria tes:
mp
le
Three Basic Steps:
1. Initiation
2. Elongation
3. Termination

Initiation

Holoenzyme = RNA Polymerase

+ Sigma factor
Figure 6-11 (part 1 of 7) Molecular Biology of the Cell ( Garland Science 2008)
IIa Transcription: Molecular Mechanisms Pro
Ba kary
c o
exa teria tes:
Elongation mp
le

Figure 6-11 Molecular Biology of the Cell ( Garland Science 2008)


Pro
II a Transcription: Molecular Mechanisms Ba kary
c o
exa teria tes:
mp
Termination le

weaker base pairing

Strong base pairing


3

Figure 6-11 (part 7 of 7) Molecular Biology of the Cell (


Garland Science 2008)
IIb Eu
kar
Transcription: Molecular Mechanisms yot
e s

Three Basic Steps:


1. Initiation
2. Elongation
3. Termination
IIb
Transcription: RNA polymerase 3 types in Eukaryotes

Our focus
IIb
Transcription initiation: two minimal components

TATA box:
short stretch of DNA sequence (Ts and As) within
the promoter of a gene
~25 nucleotides upstream of the start of the coding
sequence

General transcription factors:


group of accessory proteins that bind within the
TATA box and help:
a) orient the RNA polymerase
b) modify chromatin structure and fully
activate transcription
IIb Transcription: Initiation Eu
kar
yot
es
The General Transcription Factors

1. Binds first

2. Binds next

Figure 6-16 (part 1 of 3) Molecular Biology of the Cell ( Garland Science 2008)
Eu
IIb Transcription Initiation kar
yot
es
The General Transcription Factors
3. Remaining factors assemble next,
along with RNA polymerase

TFIIHs dual role:


a) helicase activity unwinds DNA
template

b) Kinase activity phosphorylates the


C-terminal Domain (CTD) of RNA
polymerase enabling its release from
the transcription initiation complex
and its movement along the DNA

Figure 6-16 (part 2 of 3) Molecular Biology of the Cell ( Garland Science 2008)
Transcription initiation: Other additional components
Eu
IIb Transcription Elongation kar
yot
es

Figure 6-16 (part 3 of 3) Molecular Biology of the Cell ( Garland Science 2008)
IIb Transcription: Termination Eu
kar
yot
e s

In eukaryotes,
termination is coupled
to processes that
modify the 5 and 3
ends of the mRNA
transcript.
Information in the
CTD of RNA Pol II
recruits mRNA
processing factors.

Figure 6-23 Molecular Biology of the Cell ( Garland Science 2008)

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