Chapter 14

Question 1

Gene Organization

Answer 1

Initial research on gene structure
was carried out by examining
mutations in bacteria and viruses

Question 2

colinear

Answer 2

1958 – Crick proposed that genes
and proteins are a
direct correspondence between
the nucleotide sequence of DNA
and the amino acid of a protein.

Question 3

Collinearity

Answer 3

is mostly true for genes found in bacterial cells
and in many viruses

• Eukaryotic genes and proteins have differences!
  * Eukaryotic cells were found to contain far more DNA than
  required to encode proteins.
• Large RNA molecules were observed in the nucleus but
  absent form the cytoplasm – suggesting some type of
  change before exported into the cytoplasm

Question 4

Exons and Introns

Answer 4

coding regions
and “intervening”, non-coding regions

The average human gene contains 8-9 introns.

All introns and exons are initially transcribed into RNA!

During or after transcription, introns are removed, and exons
are joined to yield mature RNA

Question 5

Introns

Answer 5

Introns are common in eukaryotic genes but are rare in
bacterial genes.

• Introns are present in mitochondrial and chloroplast genes as
  well as the nuclear genes of eukaryotes.
• Among eukaryotic genomes – the sizes and number of introns
  appear to be directly related to organismal complexity.
  Yeast genomes have a few short introns, Drosophila have
  longer and more numerous introns, and most vertebrate
  genes are interrupted by long introns!

Question 6

Major types of introns

Answer 6

Group I: Genes of bacteria,
bacteriophages, and
eukaryotes:Self-splicing

Group II:Genes of bacteria, archaea,
and eukaryotic organelles: self splice

Nuclear pre-mRNA:
Protein-encoding genes in the nucleus of eukaryotes: Spliceosomal

tRNA:tRNA genes of bacteria, archaea, and eukaryotes:Enzymatic

Question 7

Pre-mRNA Processing

Answer 7

Bacterial cells – simultaneous transcription and translation.

While the 3’ end of an mRNA is undergoing
transcription, ribosomes attach to the Shine-Dalgarno
sequence near the 5’ end and begin translation.

Question 8

Transcription and Translation

Answer 8

Eukaryotic cells – transcription and translation are separated
in both space and time

nucleus
cytoplasm

Question 9

RNA splicing

Answer 9

is the removal
of introns from eukaryotic
pre-mRNA.
Takes place in the nucleus,
before RNA moves to the
cytoplasm

Question 10

Consensus Sequences for Splicing

Answer 10

Consensus sequences:
* 5′ consensus sequence: GU A/G AGU: 5′ splice site

• 3′ consensus sequence: CAGG
• Branch point: the adenine “A”: ~18-40 nucleotides
  upstream of 3′-splicing site

Deletion of these important nucleotides prevents
splicing!
Pre-mRNA splicing!

Question 11

spliceosome

Answer 11

Splicing takes place within a large
structure

Question 12

trans-splicing.

Answer 12

In a few organisms, mRNAs may be produced by splicing
sequences of two or more different RNA molecules

Question 13

recursive splicing

Answer 13

Another variation when long introns are removed in multiple steps

Question 14

Splicing and disease

Answer 14

Many human genetic diseases arise from mutations that
affect pre-mRNA splicing.

Typically, Immediately after splicing, a group of proteins
called the exon-junction complex (EJC) is added upstream of each exon-exon junction to promote export of the mRNA
from the nucleus to the cytoplasm!

Incompletely spliced RNAs remain in the nucleus until
splicing is complete or until they are degraded.

Question 15

If a splice site were mutated so that splicing did not take
place, what would the effect be on the protein encoded by
the mRNA?

Answer 15

It would be longer than normal

Question 16

Minor splicing

Answer 16

a small group of introns that undergo splicing
at a different consensus sequences and a slightly different
process.
* Approximately 700-800 genes human genes have introns
that undergo minor splicing.

Question 17

Self-splicing

Answer 17

– introns with the ability to remove themselves
from an RNA molecule without any other enzymes or proteins

Question 18

Two categories of self-splicing introns:

Answer 18

• Group I introns – (found in protists,
  some bacteria and some fungi
  mitochondrial genes).
• fold into common secondary
  structure with 9 hairpins
  necessary for splicing.
• Group II introns – (present in genes
  of bacteria, archaea and eukaryotic
  organelles)
• into secondary structures.

Question 19

Alternative splicing

Answer 19

–the same pre-mRNA can be spliced more than one way

This yields different mRNAs that are translated into different amino acid
sequences and thus different proteins

Question 20

Multiple 3’ cleavage sites

Answer 20

• two
  or more potential sites for cleavage
  and polyadenylation are present in
  the pre-mRNA.
  This may or may not produce a
  different protein, depending on
  whether the site is located before
  or after the stop codon.

Question 21

Alternative 3′ cleavage sites result in _____

Answer 21

multiple mRNAs of different lengths

Question 22

RNA Editing

Answer 22

• coding sequence of an mRNA molecule is altered
  after transcription.
  The protein has an amino acid sequence that differs from that
  encoded by the gene

Question 23

gRNAs

Answer 23

If the modified sequence in an edited mRNA molecule doesn’t
come from a DNA template, then how is it specified?

contain sequences partly
complementary to segments of the unedited
mRNA.
The two molecules undergo base pairing at
these sequences.
Edits can also prematurely terminate
translation, resulting in a shortened protein

Question 24

Posttranscriptional modifications to eukaryotic
pre-mRNA

Answer 24

Addition of 5’ cap :
- Facilitates binding of ribosome to 5’ end of mRNA,
increases mRNA

3’ cleavage and
addition of poly(A) tail
-Increases stability of mRNA, facilitates binding of ribosome to mRNA

RNA splicing
- Removes noncoding introns from pre-mRNA,
facilitates export of mRNA to cytoplasm, allows for
multiple proteins to be produced through
alternative splicing

RNA editing
- Alters nucleotide sequence of mRNA

Question 25

Transfer RNA

Answer 25

Each tRNA is capable of attaching to one type of amino
acid.

• The complex of tRNA plus its amino acid is written “tRNA”
  and the attached amino acid, alanine for example: tRNAAla
• 20 different amino acids = at least 20 different tRNAs.
• In fact, most organisms possess at least 30-40 types of
  tRNA, each encoded by a different gene in DNA.

Question 26

The Structure of Transfer RNA

Answer 26

rare nucleotides
bases including:
* Ribothymine
* Pseudouridine (also occasionally
present in snRNAs and rRNA)
* Dozens of others…

• These changes are carried out by
  special tRNA-modifying enzymes

Question 27

How are rare bases incorporated into tRNAs?

Answer 27

By chemical changes in one of the standard bases

Question 28

CRISPR RNA

Answer 28

Small RNAs called CRISPR RNAs (crRNAs)
were discovered in prokaryotes.

Clustered regularly interspaced short
palindromic repeats

provide defense
against the invasion of specific foreign DNA
molecules (such as DNA originating from
bacteriophages and plasmids).

Question 29

Double-stranded RNA molecules may arise by:

Answer 29

• Transcription of inverted repeats into an RNA molecule
  that then base pairs with itself to form double-stranded
  RNA.
• Simultaneous transcription of two different RNA molecules
  that are complementary to each other and that pair,
  forming double stranded RNA.
• Infection by viruses that make double stranded RNA.

Question 30

RNA interferenc

Answer 30

powerful and precise mechanism
used by eukaryotic cells to limit the invasion of
foreign genes (from viruses and transposons) and to
censor the expression of their own genes

responsible for regulating changes in chromatin
structure, translation, cell fate, proliferation, cell death and is
used in blocking gene expression by geneticists

Speculated evolved as a defense mechanism
against RNA viruses and transposable elements that move
through RNA intermediates

Question 31

Small RNA molecules play important roles in:

Answer 31

• Transcription
• Translation
• Chromatin modification
• Gene expression
• Development
• Cancer
• Defense against foreign DNA

Question 32

The Structure of the Ribosome

Answer 32

A bacterial cell may contain as many as 20,000 ribosomes, a eukaryotic
cell – even more!

Ribosomes typically contain about 80% of the total cellular RNA.

Complex structures consisting of more than 50 different proteins and RNA
molecules!