Principles of Biology Chapter 17: Gene Expression

What are the two steps to accurate translation?

1. Correct match of tRNA and an amino acid- done by aminoacyl- tRNA synthetase. 2. Correct match between mRNA codon and tRNA anti-codon.

What two things happen in eukaryotic cells after transcription and before translation?

1. End Modification These cells modify pre mRNA via RNA processing. The ends are modified- 5' end receives modified nucleotide 5' cap and 3' end receives poly-A tail 2. RNA Splicing Removes introns (non-coding regions) and joint exons from mRNA molecule to form one continuous coding sequence. Often done by spliceosomes/ snRNPs- whose RNA (ribozymes) can perform this process.

What are the three functions of mRNA processing by eukaryotes?

1. Facilitate the export of mRNA to the cytoplasm. 2. Protect mRNA from hydrolytic enzymes. 3. Help ribosomes attach to the 5' end.

In what direction are codons read and what exactly does that mean? Describe what the reading frame is. What happens when the reading frame is altered?

5' to 3' direction- each codon specifies the amino acid to be placed at the corresponding position. The reading frame is the correct order in which codons must be read in order for a specific polypeptide to be produced. A frameshift mutation (wrong polypeptide produced) happens when the reading frame is altered.

Elongation of translation and what are the three steps of the general process?

Amino acids are added one by one to C-terminus of growing chain- each addition requires three steps 1) codon recognition 2) peptide bond formation 3) translocation (energy is expended in 1st & 3rd steps) This occurs in 5' to 3' direction.

What are ribozymes? What is the significance of the discovery of ribozymes? What are the three properties of RNA that enable it to function as an enzyme?

Catalytic RNA molecule that can function as an enzyme and splice RNA. The discovery of ribozymes demonstrated that not all biological catalysts were proteins. 1. It can form a 3-D structure by base-pairing with itself. 2. Functional groups in RNA enable catalysis. 3. Can hydrogen bond w/ other nucleic acid molecules

What are mutations?

Changes in genetic material of a cell or virus

What are exons?

Coding regions of RNA- regions that are eventually expressed, usually translated into amino acid sequences

What are codons? Why are they important?

Codons are mRNA base triplets. Important because triplet code (series of non-overlapping, three-nucleotide words) determines flow of information from gene to nucleotide.

What is the central dogma?

DNA => RNA => polypeptide

Beadle & Tatum's experiment- what did it demonstrate? What did they hypothesize? How has modern research modified this hypothesis?

Demonstrated the link between genes and proteins and produced the one gene-one enzyme hypothesis. It has been revised because we now know that not all products of gene expression are enzymes- although all products are proteins. We call it the one gene- one polypeptide (or one protein) hypothesis now.

Describe elongation in transcription.

Elongation= means elongation of the RNA strand; As RNA polymerase moves along the DNA strand, it untwists the double helix. Nucleotides are added to the growing 3' end of the RNA molecule.

What is "wobble" and what is its significance?

Flexible pairing at the third base of mRNA codon- some tRNA anti-codons can bond with more than one codon. The first two nucleotides determine much of what protein will be synthesized- third nucleotide "subject to change".

What are indels and some examples of indel types?

Indels are insertions or deletions of nucleotide pairs in a gene. They may produce a frameshift mutation (alter the reading frame for mRNA), may be spontaneous mutations, may be due to mutagens (X-rays, gamma rays, UV light)

Difference between small-scale mutations (missense, nonsense, point) and indels (insertions and deletions).

Indels generally have a much more disastrous effect.

Define transcription on a basic level. Where does it occur?

Information from one copy of DNA is synthesized into many mRNA molecules. This occurs in the nucleus of the cell.

What is the primary transcript?

Initial RNA transcript from any gene prior to processing.

What are introns and what is their functional and evolutionary importance?

Introns are long noncoding regions of RNA that are present before RNA splicing, occur in most eukaryotic genes between coding regions. Some introns contain sequences that regulate gene expression- alternative RNA splicing. Alternative RNA splicing means that some genes can encode more than one kind of polypeptide (depends on which segments are exons during splicing).

Initiation of translation

Joins mRNA, tRNA with 1st amino acid and two ribosomal subunits.

What are spliceosomes and what are snRNPs?

Molecules whose RNA catalyzes RNA splicing; snRNPs are small nuclear ribonucleoproteins

What are nonsense mutations?

Mutations in which a stop codon is substituted for amino acid codon- leads to nonfunctional proteins.

What are missense mutations? give an example.

Mutations in which an amino acid is still produced but it is the wrong one. Example: Sickle cell disease- valine is produced instead of glutamic acid in primary structure of hemoglobin protein.

What are silent mutations? give an example

Mutations that have no effect on the amino acid produced because of redundancy in the genetic code. Example: When coding for proline, only the first two bases (CC) really matter. The third can be variable.

What happens in prokaryotic cells after transcription and before translation?

Nothing- the two processes can occur at the same time because they are not separated by the nuclear envelope, as in eukaryotes.

Template strand

One of the two DNA strands that provides a template for ordering the sequence of complementary nucleotides in an mRNA transcript.

What are point mutations? When is a point mutation considered a genetic or hereditary disease? what is an example of a point mutation?

Point mutations are substitutions in a single base pair of a gene. This eventually leads to the wrong polypeptide being produced. If this mutation has abnormal effect on phenotype of an organism, it is called a genetic disorder or hereditary disease. Results in diseases like sickle-cell anemia (substitution of valine instead of glutamic acid in primary structure of hemoglobin protein).

Define gene expression.

Process by which DNA directs protein synthesis in order to give the organism certain traits

Differences between gene expression in prokaryotes/ eukaryotes.

Prokaryotes: Transcription & translation can occur simultaneously, which makes the process much more efficient and quick. Eukaryotes: Transcription occurs first, then translation. They are separated by the nuclear envelope.

What is a "promoter" in transcription and what is an example that we discussed in class? What is the significance of this promoter?

Promoter is the sequence of DNA where RNA polymerase attaches; TATA (Thymine/Adenine/Thymine/Adenine) box. The TATA box is vital to form the transcription-initiation complex in eukaryotes.

Describe initiation of transcription.

Promoters signal the transcription "start point" and extend nucleotide pairs. Transcription factors mediate the binding of RNA polymerase and the initiation of transcription.

What happens after translation and why is this often necessary? What are three things that can occur?

Protein must be targeted and completed because often translation is not enough to make a functional protein. 1) Protein folding/ change in shape 2) targeting polypeptides to specific locations- those destined for ER versus those that are not 3) Making multiple polypeptides via polyribosome

Why is the number of proteins that can be produced much greater than the number of genes? Why is this important to evolution?

Proteins have discrete regions called domains. Different exons can code for different domains in a protein-exon shuffling can result in production of different proteins (this can lead to evolution).

What links the genotype with the phenotype?

Proteins that are produced via gene expression

What is the bridge between genes & proteins?

RNA

What catalyzes RNA synthesis? What does this molecule exactly do? What is the effect of this process?

RNA polymerase; pulls apart strands of DNA so that they can be copied and joins together the RNA nucleotides. RNA produced is complementary to the DNA strand.

Job of ribosomes in translation and describe both subunits' role. What are the three binding sites in large subunit, and give them in correct order? Describe the function of each.

Ribosomes facilitate coupling of codons and anti-codons during protein synthesis. Small subunit holds mRNA by sugar-phosphate backbone to allow protein synthesis to occur in large subunit. Large subunit acquires energy to bring the whole complex together. 1) " A" site- aminoacyl binding complex- holds tRNA and carries next amino acid back to the chain, 2) "P" site holds tRNA and holds growing polypeptide chain, 3) "E" site where discharged RNA molecules leave the ribosome

Which is more conserved, stems or loops?

Stems because of hydrogen bonding- stronger.

Termination of translation- what is the "signal" for translation to stop? What happens when this is received- substitution, etc.?

Stop codon of mRNA (3 of 64 are stop codons) reaches A site of ribosome. Site accepts release factor (protein) instead of mRNA which causes hydrolysis- the assembly comes apart.

What is the transcription-initiation complex?

The completed assembly of transcription factors and RNA polymerase II bound to a promoter

Define translation on a basic level. Where does it occur?

The mRNA molecules produced by transcription travel to the cytoplasm into ribosomes (in eukaryotes) where this information is translated into directions for protein synthesis.

What is the terminator? How does the process of termination differ in prokaryotes vs. eukaryotes?

The sequence of DNA that signals the end of transcription in bacteria; In bacteria RNA polymerase II stops transcription at the end of the terminator. In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence which stops the process.

What is the information content of genes?

The sequence of nucleotides

How are polypeptides produced by ribosomes targeted for specific locations?

There are two types of ribosomes- free and bound (to endoplasmic reticulum). They can move easily from one state to another. Polypeptide synthesis always begins in the cytosol, but if the polypeptide being produced needs to be used in the nucleus it is marked by a signal peptide. After part of synthesis has occurred, the signal recognition particle brings partially synthesized protein and ribosome to endoplasmic reticulum where it will bind.

How are multiple polypeptides made in bacteria and in eukaryotes? What are the advantages of polyribosomes?

This occurs when multiple ribosomes translate a single mRNA simultaneously- forms polyribosome/ polysome. Polyribosomes allow many polypeptides to be synthesized simultaneously, which makes the process more efficient. In bacteria, transcription and translation are coupled to make the process more streamlined, while in eukaryotes the two processes are separated by the nuclear envelope.

How does tRNA help a cell translate mRNA message into protein? How is this aided by its structure?

tRNA transfers amino acids to growing polypeptide in ribosome. Molecules of tRNA consist of specific amino acid on one end and an anti-codon (which base-pairs with codon on mRNA) at the other. Beside the ends, it is a single strand of RNA with 80 nucleotides.