Chapter 14 Flashcards
Gene Organization
Initial research on gene structure
was carried out by examining
mutations in bacteria and viruses
colinear
1958 – Crick proposed that genes
and proteins are a
direct correspondence between
the nucleotide sequence of DNA
and the amino acid of a protein.
Collinearity
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
Exons and Introns
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
Introns
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!
Major types of introns
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
Pre-mRNA Processing
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.
Transcription and Translation
Eukaryotic cells – transcription and translation are separated
in both space and time
nucleus
cytoplasm
RNA splicing
is the removal
of introns from eukaryotic
pre-mRNA.
Takes place in the nucleus,
before RNA moves to the
cytoplasm
Consensus Sequences for Splicing
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!
spliceosome
Splicing takes place within a large
structure
trans-splicing.
In a few organisms, mRNAs may be produced by splicing
sequences of two or more different RNA molecules
recursive splicing
Another variation when long introns are removed in multiple steps
Splicing and disease
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.
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?
It would be longer than normal
Minor splicing
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.
Self-splicing
– introns with the ability to remove themselves
from an RNA molecule without any other enzymes or proteins
Two categories of self-splicing introns:
- 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.
Alternative splicing
–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
Multiple 3’ cleavage sites
- 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.
Alternative 3′ cleavage sites result in _____
multiple mRNAs of different lengths
RNA Editing
- 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
gRNAs
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
Posttranscriptional modifications to eukaryotic
pre-mRNA
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
Transfer RNA
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.
The Structure of Transfer RNA
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
How are rare bases incorporated into tRNAs?
By chemical changes in one of the standard bases
CRISPR RNA
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).
Double-stranded RNA molecules may arise by:
- 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.
RNA interferenc
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
Small RNA molecules play important roles in:
- Transcription
- Translation
- Chromatin modification
- Gene expression
- Development
- Cancer
- Defense against foreign DNA
The Structure of the Ribosome
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!
