Lecture 22-23: Gene Expression Flashcards
Gene expression definition
process of using the
information in DNA to produce functional molecules
within the cell.
What are the functional molecules made during gene expression?
proteins, RNA molecules (such as mRNA, tRNA, and rRNA), and regulatory molecules.
Why is gene regulation important?
to respond appropriately to environmental cues, developmental signals, and physiological demands.
What are the steps of gene expression?
What is the biggest difference between these two processes of gene expression?
left is prokaryotes and right eukaryotes
in prokaryotes, there is no nucleus so transcription and translation occur simultaneously
What is the overall goal of transcription?
to convert the sequence of nucleotides in the DNA to a sequence of nucleotides in an RNA molecule.
What are the major players in transcription?
*Blueprints: DNA acts as the blueprints.
*Building Blocks: Nucleotides are the building blocks.
*Biological Catalyst: RNA polymerase acts as the biological catalyst.
Give an overview of transcription.
What are the phases of transcription
Components of a gene
Where is the promoter located?
upstream of the transcribed sequence
How is transcription initiated?
Transcription factors bind to the promoter and recruit RNA polymerase to the gene
In what two ways do promoters direct the transcription of a gene?
determines:
1.which DNA strand is to serve as the template strand and
2. where RNA synthesis starts.
What is a holoenzyme?
RNA and sigma form a holoenzyme
bacterial RNA polymerase
Acts as a transcription initiation
factor.
Synthesizes RNA from a DNA
template
What part of the holoenzyme recognizes and binds to the promoter?
the sigma
What allows to build a consensus sequence and provide spacing information.
Analyzing several versions of the sequence element from different genes
What is the use of mutagenesis and other similar techniques?
to confirm important sequence elements that control transcription.
How can you find the consensus sequence and spacing information in a promoter?
example: Comparing the -35 and -10 boxes in several different E. coli genes
How does eukaryote transcription differ from prokaryote transcription?
- 3 types of RNA polymerase, bacteria only 1
-
Requires several transcription factors for RNA polymerase
to bind and initiate transcription; bacterial RNA polymerase can bind to the DNA directly with the help of a single sigma factor to initiate transcription -
RNA cleavage (cutting) by an endonuclease produces the
3’ end of the transcript and releases it. (dont need to know bateria) - Newly formed RNA typically undergoes extensive RNA
processing. bacterial RNA is usually translated into protein directly after being transcribed.
What type of genes does the DNA polymerase I in eukaryotes transcribe?
What type of genes does the DNA polymerase II in eukaryotes transcribe?
What type of genes does the DNA polymerase III in eukaryotes transcribe?
How does a polymerase recognize a gene it is to transcribe?
With the help of transcription factors, it binds to the right promoters
What is the TATA box?
unique sequence in promoters for RNA pol II
Where is the TATA box located?
about 30 base pairs
upstream of the transcription
start site.
What is the pre-initiation complex and the initiation complex?
What happens during elongation? (second phase of transcription)
Are RNA proofreading mechanisms as important as DNA proofreading?
No, RNA proofreading mechanisms are less important because RNA errors are usually temporary and do not affect genetic inheritance.
What are the control elements?
What is the function of control elements?
What is the process responsible for governing the level of transcription of a gene in a particular cell type and in response to a given stimulus?
the binding of transcription initiation factors to control elements in the DNA, which directs RNA polymerase recruitment to the promoter.
What type of molecules are transcription factors?
Regulatory proteins
What are the two types of transcription factors?
- General transcription factors
- Specialized transcription factors
What’s another way to call general transcription factors?
basal transcription factors
What do general transcription factors do?
bind promoter elements and are required to form the initiation complex
What level(s) of transcription do general transcription factors result in?
moderate levels
What level(s) of transcription do specialized transcription factors result in?
high and low levels of transcription
How do you call specialized transcription factors for high levels of transcription?
activators
How do you call specialized transcription factors for low levels of transcription?
repressors
Give an example of a gene transcribed at moderate levels
Give an example of a gene transcribed at high levels
Give an example of a gene transcribed at low levels
How can primary transcripts become functional? (from immature to mature)
They undergo processes to become functional (RNA processing):
A. Nucleotides are
added/removed.
B. Nucleotides are
modified.
Does RNA processing occur in bacteria?
no really - very minimal (no splicing, capping etc)
What is a pre-mRNA?
an immature primary transcript, product of transcription in eukaryotes
Before RNA can be exported from the nucleus and translated, pre-mRNA must be processed into mature mRNA.
Processing pre-mRNA to mature mRNA includes:
What does this represent?
5’ Cap (modified guanine nucleotide)
What is the importance of cap and tail in RNA processing? (functions)
- Facilitate the export of mRNA to the cytoplasm.
- Help protect the mRNA from degradation by hydrolytic enzymes.
- The 5’ cap serves as a recognition signal for the translation machinery
Which genes have a polyadenylation signal sequence
protein-coding genes
What does the 5’-AAUAAA-3’ sequence in the 3’UTR (untranslated region) of the mRNA after transcription produced by the DNA template sequence 3’-TTATTT-5’ signals?
an enzyme complex that carries out cleavage and polyadenylation
What is the cleavage carried out by the enzyme complex signalled by the 5’-AAUAAA-3’ sequence?
RNA transcript is cut 10–35 nucleotides past this polyadenylation signal sequence and released.
What is polyadenylation?
post-transcriptional RNA processing step.
What is mRNA splicing?
- The coding regions (exons) of eukaryotic protein genes are interrupted by noncoding regions (introns).
- To make a functional mRNA, introns must be removed, and the exons spliced together.
Why should splicing be very precise?
Imprecision in splicing can lead to the production of malfunctioning or harmful proteins, which can result in diseases or cellular dysfunction.
What carries out mRNA splicing?
the spliceosome.
What is the spliceosome composed of?
A. Small nuclear ribonucleoproteins (snRNPs)
B. Other proteins
What are the snRNPs functions?
A. Composed of proteins and a
small nuclear RNA (snRNAs).
B. Recognize the splice sites.
C. Catalyze the removal of the
intron (hydrolysis of
phosphodiester bond).
Is the spliceosome considered an enzyme or ribozyme?
enzyme since it catalyzes the splicing of pre-mRNA molecules
Name the structures of a mature mRNA.
- 5’-UTR
- 3’-UTR
- Coding Region
- 5’-cap
- 3’ poly-A tail
Functions introns
What are alternative RNA splicing?
- A type of gene expression regulation mechanism.
- Different combinations of exons within a gene can be be
spliced together. - Several mRNAs, and consequently, several polypeptides can
be generated from one gene.
What are isoforms
Different but related polypeptides
What can happen when regulatory molecules bind control sequences?
Activate or silence a splice site
Compare the number of different proteins in an organism and its number of genes
the number of different proteins an organism can produce is much greater than its number of genes.
overall goal of translation
convert the sequence of bases in the mRNA to a sequence of amino acids in a polypeptide.
Major players in translation
Message: mRNA acts as the message.
Building Blocks: Amino acids are the building blocks.
Adaptor Molecules: tRNA molecules act as adaptor molecules.
Biological Catalyst: Ribosomes act as the biological catalyst.
What does the genetic code contain?
specific relationship between sequence of nucleotide bases in mRNA and corresponding sequence of amino acids in a polypeptide.
What is the start codon? Which amino acid does it code for?
AUG - Methionine
What are the three possible stop codons? Which amino acids do they code for?
UAA, UAG, UGA - They don’t code for any amino acid, they are simply stop signals
4 important properties of code
How does an mRNA triplet specify an amino acid?
tRNA acts as adapter molecules that hold amino acids and interact with mRNA codons
Which property of tRNA allows it to acts as an adapter molecule and “decode” the genetic code?
“speaks” both DNA and protein language
How can it specifically link codon to the right amino acids?
using its anticodon
What is this structure of?
tRNA
What is the 5’-CCA-3’ sequence at the 3’ end of each tRNA?
the attachment site for amino acids
Where is the anticodon of the tRNA found?
It is the triplet on the loop at the opposite of the attachment site
What is the purpose of the anticodon
base pairs with the mRNA codon.
What does the tertiary structure of tRNA look like?
upside-down L-shape
How do you call a charged tRNA?
aminoacyl tRNA
How do you call the enzymes that charge the tRNA?
aminoacyl tRNA synthetases.
Is energy required to attach an amino acid to RNA? IN which form?
Yes, ATP
It is possible that the same aminoacyl tRNA synthase adds one or more tRNAs with the correct anticodon
no, for each of the 20 amino acids, there is a different
aminoacyl tRNA synthetase that can add that amino acid to
one or more tRNAs with the correct anticodon.
What i this green structure?
aminoacyl tRNA synthetase
Steps of tRNA charging
What type of works is being
carried out during tRNA charging?
During tRNA charging, an amino acid is attached to its corresponding tRNA molecule by an enzyme called aminoacyl-tRNA synthetase, forming an aminoacyl-tRNA complex.
How does energy coupling apply in tRNA charging?
Energy coupling in tRNA charging involves the use of ATP to power the attachment of an amino acid to its corresponding tRNA by aminoacyl-tRNA synthetase
Ribosome functions
What is the ribosome composed of?
it is a complex of proteins and ribosomal RNA (rRNA).
can be separated into
two major subunits:
A.Small subunit
B. Large subunit
Compare bacterial and eukaryotic ribosomes
- Bacterial and eukaryotic
ribosomes are
structurally and
functionally similar but
have significant
differences. - Some antibiotic drugs
specifically target
bacterial ribosomes
without harming
eukaryotic ribosomes.
What are the three tRNA binding sites of a ribosome
A. The A (aminoacyl) site.
B. The P (peptidyl) site.
C. The E (exit) site
What is the function of the different binding sites of the ribosome?
In which subunit of the ribosome are the binding sites?
large subunit
What happens during termination of translation?
Is the translation of polypeptides alone sufficient to make functional proteins?
no, several steps are (may be) required to process a
polypeptide into a functional protein
What are the possible steps to make polypeptides functional proteins?
- Folding via molecular chaperones
- Binding with other subunits to form a protein
- Posttranslational modifications
- Association with cofactors
What do post-transcriptional and post-translational modifications do to the proteome?
increases it
Place the genome, transcriptome and proteome in order of the abundance in a cell?
What is necessary for proteins to carry out its function after going through modifications?
protein targeting: a protein must be transported to the appropriate cellular location or
outside of the cell
requires a chemical modification to the folded protein
The signal is recognized by a specific targeting
system and the protein is transported to a specific
location.
Where are proteins targeted to?
- Cytosol
- Organelles
A. Nucleus
B. Endomembranesystem
C. Semiautonomous
organelles - Plasma membrane
- Outside of the cell
On what three points are cells selective?
- which genes they express,
- how strongly they are
expressed (i.e., level)
3.when they are expressed.
Why is gene expression regulation important in unicellular organisms?
allows a cell to:
A. Change cell activities in
response to its
environment.
B. Use limited resources and
energy efficiently.
Why is gene expression regulation important in multicellular organisms?
allows a cell to:
A. Change cell activities in response to signals from other cells and the cell’s environment.
B. Develop into a specific cell type during development.
C. To participate in a coordinated response in the adult body.
Is control in regulation of gene expression always positive
Regulation can be positively or negatively
What are the types of controls and levels of control?
Why do insertions and deletions of nucleotide-pairs have disastrous effect on protein structure and function?
- Produce a frameshift and is referred to as a frameshift mutation.
- The addition or deletion shifts the codon reading frame.
- A frameshift changes all of the codons after the mutation and results in extensive missense.
- If the polypeptide does not contain any of the right amino acids, it is a non-functional protein.
- Extent of missense and effect on polypeptide depends on the position of the mutation in the gene.
Give a summary of the types of point mutations
