Biological Sciences - Gene Expression

Most functions of cells are preformed by what?

Proteins

What is a gene?

A segment of DNA that contains the instructions for making a particular set of proteins. Codes for an RNA molecule that is not mRNA.

What are the two processes for making proteins within a cell?

Transcription and Translation

What happens in Transcription?

DNA is used as a template to make an RNA molecule.

What happens in Translation?

An mRNA molecule is used as a template to make a protein.

What comes first, transcription or translation?

Transcription

What does it mean when we say a gene is being expressed?

It means the information being encoded in the gene is being utilized to produce a functional product, typically a protein.

A continuous strand of coding DNA that does not have introns is found in what organisms?

Bacteria and Prokaryotic

Coding regions in a gene that are interrupted by non-coding segments of DNA are found in what types of organism?

Eukaryote’s

Where does transcription and translation occur in a bacterial cell?

Both occur in the cytoplasm

Where does transcription occur in eukaryotic cells?

Nucleus

During gene transcription in eukaryotes, both _______ and ______ are transcribed.

Exons and introns

Transcription produces…

An pre-mRNA molecule that contains both the exons and introns.

When are the introns removed?

During RNA processing/modification

What is RNA Processing?

An event that includes the modifications of RNA after transcription, which typically involves the removal of introns and the splicing together of exons.

When does RNA processing take place?

RNA processing takes place after transcription before translation in a eukaryotic cell.

Where does translation occur in eukaryotic cells?

Cytoplasm

In eukaryotic cells, can an mRNA molecule be translated before it’s done being made? Why?

No, in eukaryotic cells, an mRNA molecule cannot be translated before it is fully made because transcription occurs in the nucleus, and the mRNA must be fully processed and exported to the cytoplasm before translation can begin.

Do transcription and translation occur in the same place in eukaryotic cells?

NO

What is produced as a result of transcription?

An pre-mRNA molecule that contains both exons and introns.

After modifications/processing have/has been made to the pre-mRNA what is the RNA termed?

Mature RNA, which is without introns.

What happens once the pre-mRNA is made into RNA?

It can be exported from the nucleus into the cytopplasm where it can begin translation.

In transcription, what is used as a template to make an RNA molecule?

DNA

RNA uses Uracil in place of?

Thymine

Adenine in DNA pairs with what in RNA?

Uracil

What are the monomers called that make RNA?

Ribonucleotide triphosphates, ATP, UTP, GTP, CTP

What is the enzyme that synthesizes RNA together by connecting nucleotides?

RNA Polymerase

What is a gene?

A very tiny segment of a much larger chromosome.

How does a cell know where a gene begins and ends?

The promoter - Begins
The Terminator - Ends

What is the promoter of a gene?

The segment of DNA that specifies the beginning of a gene. RNA Polymerase recognizes and binds to the promoter to begin RNA synthesis.

What is the terminator of a gene sequence?

The segment of DNA that specifies the end of a gene. After RNA polymerase reads this segment it releases the finished RNA and lets go of the DNA.

What are the three steps to transcription?

Initiation, elongation, and termination

What happens in the initiation portion of transcription in bacteria and eukaryotes?

The initiation of transcription involves the binding of RNA polymerase to the promoter region of the DNA, followed by the unwinding of the DNA strands and the synthesis of the RNA transcript.

What happens in the elongation portion of transcription?

The RNA strand is elongated as nucleotides are sequentially added in the 5’ to 3’ direction, antiparallel to DNA.

What happens in the termination phase of RNA synthesis?

During the termination phase of RNA synthesis, the RNA polymerase enzyme reaches a termination signal in the DNA sequence, causing it to detach from the RNA strand and release the newly synthesized RNA molecule. This process marks the end of transcription.

What is an intron?

Introns are segments of RNA that do not code for proteins and are excised from the pre-mRNA during the splicing process.

What is an exon?

A coding sequence of DNA that is transcribed into RNA and retained in the final mRNA molecule. Exons are the segments that are expressed and ultimately translated into proteins.

Where does RNA processing/modification occur in eukaryotes?

RNA processing occurs in the nucleus of eukaryotic cells, where pre-mRNA undergoes capping, polyadenylation, and splicing before being exported to the cytoplasm.

What three modifications does processing include?

1.) Addition of a 5’ cap to the 5’ end

2.) Splicing

3.) Addition of a poly A tail to the 3’ end

What does the 5’ cap consist of?

A modified guanine nucleotide that is added to the 5' end of pre-mRNA. It protects the RNA from degradation and assists in ribosome binding during translation once the mRNA reaches the cytoplasm.

What does the poly A tail consist of?

A sequence of adenine nucleotides added to the 3' end of pre-mRNA. It stabilizes the RNA and aids in its export from the nucleus. assists in ribosome binding during translation once the mRNA reaches the cytoplasm.

What is Splicing?

The process of removing introns and joining exons in pre-mRNA to create a mature mRNA molecule that can be translated into a protein.

How are exons attached to eachother?

Exons are joined together by spliceosomes, which are complexes of RNA and protein that facilitate the splicing process.

What is the advantage to alternative splicing?

It allows a single gene to produce multiple protein isoforms, increasing protein diversity and enabling regulation of gene expression in different cell types or conditions.

Pre-mRNA can participate in…

Alternative splicing to generate different mRNA variants.

What happens to mRNA in translation?

It is decoded by ribosomes to synthesize proteins.

Ribosomes play an important part in translation because?

They facilitate the decoding of mRNA and the formation of peptide bonds between amino acids.

What is the job of a tRNA?

The job of a tRNA is to transport specific amino acids to the ribosome during protein synthesis, matching its anticodon with the corresponding codon on the mRNA.

What is the genetic code?

A set of rules that defines how the sequence of nucleotides in DNA is translated into the sequence of amino acids in proteins. It consists of codons, which are groups of three nucleotides that correspond to specific amino acids or stop signals during protein synthesis.

What is a codon?

A sequence of three nucleotides in mRNA that corresponds to a specific amino acid or stop signal during protein synthesis.

How many codons are in the genetic code?

There are 64 codons in the genetic code, including 61 that specify amino acids and 3 stop codons.

What other amino acid does the start codon code for?

Methionine, which is the first amino acid in protein synthesis.

What does it mean when we say the genetic code is degenerate?

It means that multiple codons can code for the same amino acid, allowing for redundancy in the genetic code.

What does it mean when we say a start codon sets the reading frame?

It establishes the sequence of codons that will be read during translation, determining how the ribosome interprets the mRNA sequence. Since the codons are read in triplets.

What are the important aspects of tRNA’s?

Crucial for translating mRNA into proteins. They carry specific amino acids to the ribosome, matching their anticodons with codons on the mRNA during protein synthesis.

1.) Every tRNA has a specific amino acid attached to it.

2.) Every tRNA has a single anticodon that pairs (is complementary) with a corresponding codon on the mRNA.

What would the anticodon for 5’-GCU-3’?

3’-CGA-5’ is the complementary sequence that pairs with the mRNA codon during translation.

What are aminoacyl-tRNAs?

Aminoacyl-tRNAs are tRNA molecules that have an amino acid covalently attached to them. They play a key role in protein synthesis by bringing the correct amino acid to the ribosome, matching with the appropriate mRNA codon.

What is a Ribosome?

A molecular machine found within all living cells that facilitates the translation of mRNA into proteins by linking amino acids together in the order specified by the mRNA.

What are ribosomes made of?

Ribosomes are made of ribosomal RNA (rRNA) and proteins, forming two subunits that come together during protein synthesis.

What does the r in rRNA stand for?

Ribosomal

What is the job of the small ribosomal subunit?

Responsible for binding to the mRNA and ensuring the correct translation of the genetic code into a polypeptide chain during protein synthesis.

What is the large ribosomal subunit responsible for?

Responsible for catalyzing peptide bond formation between amino acids and facilitating the assembly of the polypeptide chain during protein synthesis.

What are the three sites of ribosomes used by tRNAs?

The three sites are the A (aminoacyl), P (peptidyl), and E (exit) sites, which play crucial roles in the translation process.

What is the job of the peptidyl Site (P-site)?

Responsible for holding the tRNA that carries the growing polypeptide chain during translation, facilitating peptide bond formation with the amino acid at the A-site.

What is the job of the Exit site (E site)?

Responsible for releasing the uncharged tRNA after it has donated its amino acid to the growing polypeptide chain, allowing for the next tRNA to enter the ribosome.

When do the large subunit and small subunits of ribosomes unit?

During the initiation phase of translation, forming a complete ribosome ready for protein synthesis.

Translation also has what (the same stages of transcription)?

Initiation, elongation, and termination.

The initiation stage of translation consists of?

The assembly of the ribosome, mRNA, and the initiator tRNA.

The elongation stage of translation consists of?

The sequential addition of amino acids to the growing polypeptide chain, facilitated by the ribosome as it moves along the mRNA. It synthesizes the protein from the N-terminus to the C-terminus.

The termination of translation consists of?

The release of the completed polypeptide chain from the ribosome, along with the disassembly of the ribosomal complex. A protein called the stop factor binds to the A site resulting in the protein being released from the ribosomal units (large and small).

What is a stop factor?

A protein that recognizes stop codons on the mRNA during translation termination, prompting the release of the polypeptide chain from the ribosome.

Define Polyribosome

A complex formed by multiple ribosomes translating the same mRNA strand simultaneously, allowing for the efficient synthesis of proteins.

Define Polycistronic mRNA

mRNA that encodes multiple proteins, typically found in prokaryotes, allowing for the coordinated expression of genes.

Are activators positive or negative regulators?

Activators are positive regulators that enhance the transcription of specific genes by binding to regulatory regions of DNA.

Are repressors positive or negative regulators?

Repressors are negative regulators that inhibit the transcription of specific genes by binding to regulatory regions of DNA.

If a small effector molecule is present and bound to the repressor, can a repressor bind to the operon? Why?

The repressor cannot bind to the operon. The binding of the small effector molecule causes a conformational change in the repressor, preventing it from attaching to the operon.

Where does the repressor bind?

The repressor binds to the operator region of the operon, blocking RNA polymerase from initiating transcription of downstream genes.

Where does an activator bind?

Binds to the promoter region or enhancer (CAP) sequences of the operon, facilitating the recruitment of RNA polymerase to initiate transcription.

What is a regulator transcription factor?

A regulator transcription factor is a protein that modulates the transcription of specific genes by binding to nearby DNA.

An operator acts as what?

An on/off switch for gene expression in an operon.

What is the lac operon?

A set of genes in E. coli that are involved in the metabolism of lactose, regulated by the presence or absence of lactose and glucose.

Is the lacI gene considered apart of the lac operon?

No, the lacI gene is not part of the lac operon; it encodes the lac repressor, which regulates the operon.

What is the CAP site in the lac operon?

The CAP site is a region in the lac operon where the catabolite activator protein (CAP) binds, enhancing transcription of the operon in the presence of cAMP and low glucose levels.

Which genes are under the control of the lac promoter?

The genes lacZ, lacY, and lacA, which are responsible for lactose metabolism.

If the lac repressor is bound can RNA polymerase transcribe any proteins?

No, when the lac repressor is bound to the operator region of the lac operon, it prevents RNA polymerase from transcribing the genes responsible for lactose metabolism.

Can RNA polymerase bind to the promoter if the repressor is bound?

Yes but if the lac repressor is bound to the operator region, RNA polymerase cannot effectively bind to the promoter and initiate transcription of the lac operon genes. It cannot move past the repressor to initiate transcription.

What is a merozygote?

A bacterial cell that is partially diploid, containing two copies of some genes due to the presence of an F' plasmid. This allows for the study of gene expression and genetic interactions.

What is the CAP activator controlled by?

The availability of cyclic AMP (cAMP) in response to glucose levels.

If allolactose is bound to the repressor then…

The repressor cannot bind to the operator and therefore it cannot inhibit transcription.

If allolactose is not bound to the repressor then…

the repressor binds to the operator, therefore inhibiting transcription.

The presence of lactose means…

that allolactose will be formed, which binds to the repressor and prevents it from inhibiting transcription of the operon.

The absence of lactose means…

that allolactose is not formed, allowing the repressor to bind to the operator and inhibit transcription of the operon.

How is cAMP produced?

cAMP is produced from ATP by the enzyme adenylyl cyclase, which is activated when glucose levels are low.

CAP and cAMP are examples of what kind of control?

Positive control in gene regulation.

When CAP and cAMP are bound to the CAP site near the lac promoter, what happens?

They enhance the binding of RNA polymerase, increasing transcription of the lac operon.

What is the key function of CAP?

Allows E.coli to use different sugars as an energy source.

What is catabolite repression?

A regulatory mechanism in bacteria that prevents the use of secondary carbon sources when a preferred source, like glucose, is available. It involves the inhibition of the lac operon and other operons.

Transcription of the lac operon is inhibited by what sugar?

Glucose

Glucose inhibits the production of cAMP and in turn…

Prevents the activation of CAP, reducing transcription of the lac operon. Prevents the binding of CAP to the DNA by inhibiting cAMP.

When cAMP is bound to CAP what is the result?

The complex enhances the binding of RNA polymerase to the promoter of the lac operon, increasing transcription.