Chapter 7 and 8 - GCD 3033

What is the Central Dogma of molecular biology?

The Central Dogma states that information stored in the DNA sequence of chromosomes is transcribed into RNA, which is then translated into protein.

How do DNA and RNA differ in secondary structure and structural flexibility?

DNA generally adopts a double-stranded helical structure. RNA is single-stranded, allowing it to fold into specific shapes via short double helices formed between complementary stretches within the same molecule.

How do the sugars in the DNA and RNA sugar-phosphate backbones differ?

DNA contains deoxyribose, whereas RNA contains ribose. Ribose has a hydroxyl group (-OH) instead of a hydrogen atom (-H) at position 2 of the sugar ring.

What nitrogenous bases are found in DNA versus RNA?

DNA uses adenine (A), guanine (G), cytosine (C), and thymine (T). RNA uses adenine (A), guanine (G), cytosine (C), and uracil (U), which base-pairs with adenine.

How do DNA and RNA differ in cellular function?

DNA serves largely as a passive storage site for genetic information. Some RNA molecules carry out structural or enzymatic roles in addition to carrying information.

What is the molecular definition of a gene?

A gene is a segment of DNA that directs the production of a particular protein or functional RNA molecule, including both transcribed regions and non-transcribed regulatory sequences.

What is the functional difference between mRNA and non-coding RNAs?

Protein-coding genes produce mRNA as a template for protein synthesis. Non-coding RNAs (e.g., tRNA, rRNA, miRNA, snRNA) are final functional gene products that are never translated into protein.

What enzyme synthesizes RNA, and which specific class makes mRNA in eukaryotes?

RNA polymerase is the multi-subunit enzyme that synthesizes RNA. Eukaryotic mRNA is produced specifically by RNA polymerase II.

How does bacterial RNA polymerase recognize a promoter to initiate transcription?

Bacterial RNA polymerase uses a subunit called sigma factor to recognize and bind the promoter sequence.

How is transcription terminated in bacteria?

RNA polymerase moves along DNA until it encounters a transcription termination sequence (terminator), signaling the enzyme to detach and release the RNA transcript.

What is the role of general transcription factor TFIID during eukaryotic initiation?

TFIID contains the TATA Binding Protein (TBP) subunit, which binds to the promoter's TATA box and bends/kinks the DNA to help initiate transcription.

What two critical functions does TFIIH perform during transcription initiation?

TFIIH unwinds the DNA double helix at the promoter to expose the template strand and phosphorylates RNA polymerase II to release it from general transcription factors.

In what chemical direction is RNA synthesized, and how are new nucleotides linked?

RNA is always synthesized in the 5' to 3' direction. Incoming ribonucleotides form phosphodiester bonds with the 3' hydroxyl position of the ribose ring.

Do all genes on a chromosome use the same DNA strand as a template?

No, different genes use either one or the other DNA strand as a template, allowing transcription to occur in different directions along the chromosome.

Where do eukaryotic mRNA modifications occur, and what are the three major modifications?

mRNA processing occurs inside the nucleus. The three processing steps are 5' capping, polyadenylation (3' tailing), and RNA splicing.

What is 5' capping?

5' capping is the addition of a modified 7-methylguanosine cap to the 5' end of the mRNA transcript.

What is polyadenylation?

Polyadenylation is the enzymatic addition of a "poly-A tail" (100+ repeated adenine nucleotides) to the 3' end of the mRNA.

What are the functional benefits of 5' capping and 3' polyadenylation?

They increase mRNA stability, facilitate nuclear export, and promote efficient translation initiation.

What occurs during RNA splicing?

Non-coding intervening sequences (introns) are excised from pre-mRNA, and expressed sequences (exons) are joined together to form mature mRNA.

What is alternative splicing and why is it biologically important?

Alternative splicing combines different sets of exons from a single pre-mRNA, enabling a single gene to encode multiple distinct protein isoforms.

What is the spliceosome, and which component performs the catalytic activity?

The spliceosome is a large complex composed of proteins and small nuclear ribonucleoproteins (snRNPs). Its RNA component base-pairs with splice sites and catalyzes the splicing reaction.

What human genetic condition can result from a splicing error in the beta-globin gene?

Beta-thalassemia can be caused by aberrant splicing of the beta-globin mRNA transcript.

What is a codon, and why is the genetic code described as redundant?

A codon is a sequence of three mRNA nucleotides. The genetic code is redundant because 64 possible codons specify only 20 amino acids (plus stop signals), meaning multiple codons code for the same amino acid.

What is a reading frame, and what happens when a frameshift mutation occurs?

A reading frame is one of three possible ways to group nucleotides into triplets. Inserting or deleting nucleotides in numbers not divisible by three shifts the reading frame, typically ruining protein structure and function.

What are the two critical functional regions of a tRNA molecule?

The anticodon loop, which base-pairs with complementary mRNA codons. 2) The 3' end, which covalently attaches to a specific amino acid.

What is "wobble" base pairing in translation?

Wobble occurs when non-standard or relaxed base pairing is permitted between the third position of an mRNA codon and the tRNA anticodon.

Which enzyme attaches amino acids to their corresponding tRNA molecules?

Aminoacyl-tRNA synthetases covalently attach each amino acid to its correct tRNA molecule.

What is the subunit structure of a eukaryotic ribosome?

It consists of a large subunit (49 proteins + 3 rRNAs) and a small subunit (33 proteins + 1 rRNA).

What are the three tRNA binding sites on a functional ribosome?

The A site (Aminoacyl), P site (Peptidyl), and E site (Exit).

What are the four steps in the ribosomal elongation cycle?

1) Charged tRNA entry into the A site, 2) peptide bond formation, 3) large and small subunit translocation, and 4) uncharged tRNA exit from the E site.

What distinct function does each of the three main RNA types perform during protein synthesis?

mRNA carries genetic information; tRNA acts as the code reader matching amino acids to codons; rRNA catalyzes peptide bond formation.

How is translation initiated in eukaryotes?

An initiator tRNA attached to methionine binds the P site of the small ribosomal subunit, which scans mRNA to identify the start codon (AUG).

How do release factors terminate translation?

Release factor proteins bind to stop codons (UAA, UAG, UGA) in the A site instead of tRNA, causing the completed polypeptide chain to be released.

What are the 5' UTR, 3' UTR, and Open Reading Frame (ORF)?

The 5' UTR is non-translated mRNA upstream of AUG; the 3' UTR is non-translated mRNA downstream of stop codons; the ORF is the protein-coding sequence between start and stop codons.

What is polycistronic mRNA, and where is it commonly found?

Polycistronic mRNA is a single mRNA molecule that encodes multiple distinct proteins; it is common in prokaryotes but absent in eukaryotes.

What is a polyribosome (polysome)?

A polyribosome is a complex formed when multiple ribosomes simultaneously translate a single mRNA molecule

What molecules help newly synthesized polypeptides fold correctly?

Molecular chaperones assist newly produced polypeptide chains in folding into their proper 3D structure

How are unwanted or damaged proteins targeted and destroyed in eukaryotic cells?

Enzymes covalently attach ubiquitin tags to target proteins, directing them to the proteasome where proteases break them down.

What is the “central dogma”?

Genetic information flows from DNA to RNA to protein.

Which base is not present in RNA?

T

In RNA, which base pairs with the base A?

U

An RNA molecule can fold into complex three-dimensional shapes because:

it is a single-stranded.

All of the RNA in a cell is made by what process?

Transcription

What determines the nucleotide sequence of an RNA strand?

Complementary base pairing with the DNA template during transcription

RNA polymerases join nucleotides through what kind of bond?

Phosphodiester

An RNA chain elongates in what direction?

5’ to 3’

Some genes do not encode proteins, but instead encode functional RNA.

True

At which site on the DNA of a gene does RNA polymerase release its newly made RNA?

Terminator

What is the name of the subunit of bacterial RNA polymerase that recognizes the promoter of a gene?

Sigma factor

In eukaryotes, what must assemble at a promoter before RNA polymerase can transcribe a gene?

General transcription factors

The assembly of general transcription factors to a eukaryotic promoter begins at what site in a promoter?

The TATA box

Bacterial mRNAs:

are transcribed and translated simultaneously.

Eucaryotic mRNAs:

are translated after they are exported from the nucleus

Which of the following does not increase the stability of eucaryotic mRNAs?

An intron

In bacteria, most protein-coding genes lack introns.

True

Introns are removed by:

RNA splicing in the nucleus

In eukaryotes, which parts of a gene are transcribed into RNA?

Introns and exons

Unlike the coding sequence of an exon, most of the nucleotide sequence of an intron is unimportant.

True

What structure is responsible for selecting and transporting only properly processed eucaryotic mRNAs into the cytoplasm?

The nuclear pore complex

Which of the following statements is NOT true?

In a eukaryotic mRNA, the poly-A tail promotes degradation of the molecule.

Each nucleotide in an mRNA encodes one amino acid in a protein.

False

How many nucleotides are necessary to specify a single amino acid?

3

In principle, how many reading frames in RNA can potentially be translated into proteins?

3

What is NOT true about codons in mRNA molecules?

Some codons code for more than one amino acid.

Amino acids are attached to their tRNA molecules by:

aminoacyl-tRNA synthetase.

An RNA message is decoded by:

ribosomes.

Within the ribosome, the formation of peptide bonds is catalyzed by:

an RNA molecule in the large ribosomal subunit.

At which end of an mRNA molecule do ribosomal subunits first bind?

The 5’ end

The translation of an mRNA begins at the start codon:

AUG

In eucaryotes, the initiator tRNA always carries which amino acid?

Methionine

Which part of a protein is synthesized by a ribosome first?

The N-terminus

At what site does the charged initiator tRNA first bind on the ribosome?

P site

At what site do all charged tRNAs (with the exception of the initiator tRNA) first bind on the ribosome?

A site

Which statement is false?

Stop codons are recognized by a stop tRNA.

What is a polyribosome?

A cluster of ribosomes translating the same mRNA, but positioned at different sites along the mRNA .

Where in a cell are most damaged proteins broken down?

Cytosol

Proteasomes act primarily on proteins that have been marked for destruction by the covalent attachment of which small protein?

Ubiquitin

RNA in cells differs from DNA in that ___________________.

it is single-stranded and can fold up into a variety of structures

Which of the following statements is false?

Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.

You have a piece of DNA that includes the following sequence:
 
5′-ATAGGCATTCGATCCGGATAGCAT-3′
3′-TATCCGTAAGCTAGGCCTATCGTA-5′
 
Which of the following RNA molecules could be transcribed from this piece of DNA?

5′-AUAGGCAUUCGAUCCGGAUAGCAU-3′

You have a segment of DNA that contains the following sequence:
 
5′-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3′
3′-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5′
 
If you know that the RNA transcribed from this segment contains the following sequence:
 
5′-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA–3′
 
Which of the following choices best describes how transcription occurs?

The bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′.

Imagine that an RNA polymerase is transcribing a segment of DNA that contains the following sequence:
 
5′-AGTCTAGGCACTGA-3′
3′-TCAGATCCGTGACT 5′
 
If the polymerase is transcribing from this segment of DNA from left to right, which strand is the template?

the bottom strand is the template

The sigma subunit of bacterial RNA polymerase ___________________.

recognizes promoter sites in the DNA

Which of the following might decrease the transcription of only one specific gene in a bacterial cell?

a mutation that introduced extensive sequence changes into the DNA that precedes the gene’s transcription start site

You have a bacterial strain with a mutation that removes the transcription termination signal from the Abd operon. Which of the following statements describes the most likely effect of this mutation on Abd transcription?

The Abd RNA from the mutant strain will be longer than normal.

Transcription in bacteria differs from transcription in a eukaryotic cell because __________________________.

RNA polymerase (along with its sigma subunit) can initiate transcription on its own

Which of the following does NOT occur before a eukaryotic mRNA is exported from the nucleus?

The ribosome binds to the mRNA.

“Since introns do not contain protein coding information, they do not have to be removed precisely (meaning, a nucleotide here and there should not matter) from the primary transcript during RNA splicing.”

False

Which of the following statements about the genetic code is correct?

The genetic code is redundant.

The piece of RNA below includes the region that codes the binding site for the initiator tRNA needed in translation.
 
5′-GUUUCCCGUAUACAUGCGUGCCGGGGGC-3′
 
Which amino acid will be on the tRNA that is the first to bind to the A-site of the ribosome?

arginine

Which amino acid would you expect a tRNA with the anticodon 5′-CUU-3′ to carry?

lysine

Which of the following pairs of codons might you expect to be read by the same tRNA as a result of wobble?

CAC and CAU

Below is the sequence from the 3′ end of an mRNA.
 
5′-CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3′
 
If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA in the P-site of the ribosome when release factor binds to the A-site?

5′-CCA-3′

Which of the following statements is TRUE?

rRNA contains the catalytic activity that joins amino acids together.

In eukaryotes, but not in prokaryotes, ribosomes find the start site of translation by ____________________________.

scanning along the mRNA from the 5′ end

Which of the following statements about prokaryotic mRNA molecules is FALSE?

Ribosomes must bind to the 5′ cap before initiating translation.

Which of the following methods is NOT used by cells to regulate the amount of a protein in the cell?

Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm.

What is gene expression?

The process of selective synthesis of proteins and RNA molecules encoded in a cell’s genome

What is differentiation?

The process of specialization that cells undergo to acquire particular functions, behaviors and morphologies.

How does differentiation occur in a cell?

The select expression of different genes.