Chapter 7.

From DNA to Protein: How

Cells Read the Genome

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The chemical structure of RNA differs
slightly from that of DNA

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RNA can fold into specific structures, which allows RNA
molecules to have structural and catalytic function.

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DNA is transcribed by the enzyme RNA polymerase

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Transcription of two genes as observed under the
electron microscope

Direction of transcription
RNA DNA

Non-transcribed spacer

Transcription unit Transcription unit

(Each transcribed DNA segment)

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The Transcription Cycle

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Signals in DNA tells RNA polymerase
where to start and finish

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The Transcription Cycle of Bacterial RNA Polymerase

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The nucleotide sequences that signal to a bacterial
RNA polymerase where to begin transcribing and
where to stop
Regulation of transcription in eucaryotes differs in
four important ways from that in bacteria:

1. RNA polymerases;
2. Transcription factors;
3. Eucaryotic gene regulatory proteins control
gene expression from a distance;
4. DNA package.

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Eucaryptic RNA
polymerase II
requires general
transcription
factors to initiate
transcription

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Phosphorylation of
RNA polymerase II
allows RNA
processing
proteins to
assemble on its
tail.

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Polymerase direction is determined by the orientation of the
promoter sequence, the site that RNA Pol begins transcription
Promoter sequences are asymmetric.

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Eucaryotic genes are interrupted by
noncoding sequences

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Structure of two human genes showing the
arrangement of exons and introns

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 The consensus nucleotide sequences in an RNA molecule
that signal the beginning and the end of most introns in humans

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RNA splicing is performed largely by RNA molecules instead of
proteins.

snRNAs (small nuclear RNAs) recognize intron-exon borders and

participate in the chemistry of splicing.

snRNA is complexed with protein subunits to form snRNP (small

nuclear ribonucleoprotein).

Splicesome, formed by snRNPs, performs pre-mRNA splicing in

the cell.

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Exon-intron arrangement would seem to facilitate
the emergence of new and useful proteins

RNA splicing also has a present day advantage.

The transcripts of many eukaryotic genes (estimated
at about 60% of genes inhuman) are spliced in a
variety of different ways to produce a set of different mRNAs,
Thereby allowing a corresponding set of different proteins to
be produced from the same gene.

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Schematic illustration of an export- ready mRNA molecule and
its transport through the nuclear pore

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Procaryotes and eucaryotes handle their RNA
transcripts somewhat differently

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 The genetic code
DNA A, C, G, T
RNA A, C, G, U
protein 20 amino acids
Each group of three
consecutive
nucleotides in RNA is
called a codon, and
each codon specifies
either an amino acid or
a stop codon.

RNA is a linear
polymer of 4
nucleotides given rise
through 64 different
possible combinations
of three nucleotides.
However, only 20
different amino acids
are commonly found in
proteins.

The striking feature of

BIOL 213 the code is its third-
base degeneracy.
07_21_nucl_sequence
.jpg

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 In principle, an mRNA can be translated into three
different, nonoverlapping reading frames, depending
on where the decoding process begins

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tRNA molecules are molecular adaptors, linking
amino acids with codons

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 Structure of tRNAs

tRNAs can recognize and bind both to the codon and, at another
site on their surface, to the amino acid.
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The genetic code is translated by means of two
adaptors that act one after another

aminoacyl-
the anticodon
tRNA
of tRNA
Step 1 synthetase Step 2 molecule
couples a
forms base
particular
pairs with the
amino acid
appropriate
to its
codon on the
correspond
mRNA
ing tRNA

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Question

In a clever experiment preformed in 1962, a cystine

already attached to its tRNA was chemically
converted to an alanine. These hybrid tRNA
molecules were then added to a cell free translation
system from which the normal cycteine-tRNAs had
been removed. When the reslting protein was
analyzed, it was found that alanine had been
inserted at every point in the protein chain where
cysteine was supposed to be. What this experiment
tells you about the role of aminoacyl-tRNA
synthetases during the normal translation of the
genetic code.

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Structure of the ribosome strongly
confirms the early evidence that rRNAs-
and not proteins-are responsible for the
ribosomes overall structure, its ability to
position tRNAs on the mRNA, and its
catalytic activity in forming covalent
peptide bonds.

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Overview of the translation cycle showing six
ribosomes on a single mRNA.

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 Structure of a typical bacterial mRNA molecule (Polycistronic)

(Shine-Dalgarno sequence)

Figure 7-37 Essential Cell Biology ( Garland Science 2014)

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Colinearity of genetic information

N N
N N
N
C

synthesis 5 to 3
N to C terminus
Colinearity gene 5 to 3
mRNA 5 to 3
protein N to C
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Figure 11.51a
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Chapter 7 Study Guide. From DNA to protein: How Cells Read the Genome.

Overall Goal: Understand the flow of genetic information in the cell as summarized by the central dogma. Understand the
processes of transcription and translation.

Specific Objectives:

1) Know the structure of a typical, protein-encoding, eukaryotic gene. (you will be asked to draw this on at least one exam.)

2) Know the role of the major types of RNA produced in the cell.

3) Understand the role of the promoter in transcription by prokaryotic RNA polymerase.

4) Understand the major steps in processing a primary transcript into a functional mRNA.

5) Know how ribosomes initiate translation, how they incorporate the right amino acids into a protein, and how translation is
terminated.

6) Know the basic features of the genetic code and how DNA and RNA encode protein information. Memorize the start codon
(AUG) the three stop codons (UGA, UAA, UGA).

7) Recognize that proteolysis by the proteasome is an important aspect of post-translational control.

Read How We Know: Cracking the Genetic Code. Know the experiment of Nirenberg and Matthaei, and Nirenberg and Leder.

Problems: 7-2, 7-4, 7-5, 7-7, 7-8, 7-9, 7-10, 7-11, 7-13, 7-14, 7-15, 7-16, 7-17.

Stuff we skipped in this chapter: Details of intron splicing (but you should know what an intron looks like, and what a snRNP
is). RNA and the Origins of Life.

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