Bio 233 exam two
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111 Terms
What is a gene?
A DNA sequence transcribed into an RNA molecule.
What is the central dogma?
Genetic information generally flows from DNA to RNA to protein.
What is the difference between the abstract and molecular definitions of a gene?
Abstract: inherited factor affecting a trait. Molecular: DNA sequence transcribed into RNA.
What is the epigenome?
Chemical modifications and chromatin features that regulate gene activity without changing DNA sequence.
What is a nucleosome?
DNA wrapped around a core of histone proteins.
What is open chromatin?
Chromatin that allows relatively easy access to DNA.
What is closed chromatin?
Chromatin that restricts access to DNA.
Why do most cells have the same genome but different identities?
They express different subsets of genes.
What is the DNA coding strand?
The strand with the same sequence as the RNA transcript, except DNA uses T instead of U.
What is the DNA template strand?
The strand RNA polymerase reads 3′ to 5′ to synthesize RNA 5′ to 3′.
In what direction does RNA polymerase synthesize RNA?
5′ to 3′.
In what direction does RNA polymerase read the DNA template?
3′ to 5′.
How does the mRNA sequence compare with the coding DNA strand?
It matches the coding strand except RNA has U instead of T.
What is the transcription start site?
The DNA position corresponding to the first nucleotide transcribed into RNA.
What is a promoter?
A DNA sequence where transcription machinery assembles.
What is a TATA box?
A promoter DNA sequence that can help recruit transcription machinery.
What is an enhancer?
A regulatory DNA sequence that can increase transcription.
What is an activator?
A protein that binds regulatory DNA and helps stimulate transcription.
Are promoters proteins or nucleotide sequences?
Nucleotide sequences.
Are enhancers proteins or nucleotide sequences?
Nucleotide sequences.
Are activators proteins or nucleotide sequences?
Proteins.
What are general transcription factors II (GTF-IIs)?
Proteins required to assemble and initiate RNA polymerase II transcription.
What is TFIIH's role in transcription initiation?
It helps unwind DNA at the transcription start site using helicase activity.
What is the correct basic order of transcription initiation?
GTF-IIs bind promoter; RNA polymerase II is recruited; TFIIH unwinds DNA; activators stimulate transcription.
What is transcription elongation?
The stage when RNA polymerase extends the RNA strand.
Does RNA polymerase II require a primer?
No. RNA polymerase can initiate RNA synthesis without a primer.
What is pre-mRNA?
The initial RNA transcript before processing is complete.
What are the three major eukaryotic pre-mRNA processing steps?
5′ capping, splicing, and 3′ cleavage with poly-A tail addition.
What is the function of the 5′ cap?
It protects mRNA and helps with nuclear export and translation initiation.
What does RNA splicing do?
Removes introns and joins exons.
What is an intron?
A transcribed RNA region removed during splicing.
What is an exon?
A region retained in mature RNA after splicing.
What is alternative splicing?
Processing one pre-mRNA in different ways to produce different mature RNA transcripts.
What is the spliceosome?
A protein–RNA complex that removes introns and joins exons.
What is the 5′ splice site?
The boundary at the beginning of an intron.
What is the 3′ splice site?
The boundary at the end of an intron.
What is the branch point of an intron?
A nucleotide involved in forming the lariat intermediate during splicing.
What is the AAUAAA signal?
An RNA sequence that helps direct cleavage and polyadenylation.
What happens downstream of the AAUAAA signal?
Cleavage occurs upstream of a downstream GU-rich region.
What does poly-A polymerase do?
Adds adenine nucleotides to the 3′ end of RNA.
What are poly-A binding proteins?
Proteins that bind the poly-A tail and help regulate RNA stability, export, and translation.
Is the promoter included in mature mRNA?
No. The promoter is DNA that directs transcription.
Is the start codon included in mature mRNA?
Yes. It signals where translation begins.
Is the stop codon included in mature mRNA?
Yes. It signals where translation ends.
Is an intron normally present in mature spliced mRNA?
No. It is removed during splicing.
What is the 5′ UTR?
The mRNA region before the start codon.
What is the 3′ UTR?
The mRNA region after the stop codon.
What percentage of the human genome is protein-coding sequence?
Approximately 2%.
Why can a hair follicle cell avoid expressing the insulin gene?
Closed chromatin can block access, or the cell may lack the necessary activators.
What is another mechanism that can prevent insulin gene expression?
A repressor protein can inhibit transcription.
What is the difference between an exonuclease and an endonuclease?
Exonucleases cut from a nucleic acid end; endonucleases cut within a strand.
What is one similarity between exonucleases and endonucleases?
Both break phosphodiester bonds in nucleic acids.
What is the genetic code?
The rules relating mRNA codons to amino acids or stop signals.
What is a codon?
A three-nucleotide sequence in mRNA read during translation.
What is a tRNA anticodon?
A three-nucleotide sequence that pairs antiparallel with an mRNA codon.
What is the usual start codon?
AUG, which encodes methionine.
What does a stop codon do?
Signals translation termination rather than encoding an amino acid.
What is genetic-code degeneracy?
Multiple codons can specify the same amino acid.
What is tRNA wobble pairing?
Flexible pairing at the third codon position that lets some tRNAs recognize multiple codons.
What is an aminoacyl-tRNA synthetase?
An enzyme that attaches the correct amino acid to its corresponding tRNA.
What is a charged tRNA?
A tRNA carrying its amino acid.
If an anticodon is 5′-CGU-3′, what is the corresponding mRNA codon?
5′-ACG-3′.
Which amino acid does ACG encode?
Threonine.
What is messenger RNA's role?
Carries coding information used to make a polypeptide.
What is ribosomal RNA's role?
Contributes to ribosome structure and catalyzes peptide bond formation.
What is a ribosome?
A molecular complex that translates mRNA into a polypeptide.
What does the small ribosomal subunit do?
Helps bind mRNA and decode codon–anticodon pairing.
What does the large ribosomal subunit do?
Contains the peptidyl transferase center that catalyzes peptide bond formation.
What is the A site of a ribosome?
The aminoacyl site that receives incoming charged tRNAs.
What is the P site of a ribosome?
The peptidyl site that holds the tRNA carrying the growing chain.
What is the E site of a ribosome?
The exit site through which uncharged tRNAs leave.
Which ribosomal site receives release factors?
The A site.
What is peptidyl transferase activity?
Ribosomal catalysis of peptide bond formation by an rRNA-containing catalytic center.
What initially recognizes the mRNA 5′ cap during translation initiation?
Cap-binding proteins within the translation initiation machinery.
Which ribosomal subunit is recruited during eukaryotic translation initiation?
The small ribosomal subunit.
What are the three major stages of translation?
Initiation, elongation, and termination.
What happens during translation initiation?
The ribosome, mRNA, and initiator tRNA assemble at the start codon.
What happens during translation elongation?
Charged tRNAs enter, peptide bonds form, and the ribosome translocates.
What happens during translation termination?
A stop codon recruits a release factor, and the completed polypeptide is released.
What are the three main recurring events during translation elongation?
Charged tRNA entry, peptide bond formation, and ribosome translocation.
What is translocation?
Movement of the ribosome along mRNA by one codon.
In what direction does a ribosome read mRNA?
5′ to 3′.
In what direction does a polypeptide grow?
From the N-terminus toward the C-terminus.
What is a peptide bond?
The covalent bond linking amino acids in a polypeptide.
What is the N-terminus?
The end of a polypeptide with the free amino group.
What is the C-terminus?
The end of a polypeptide with the free carboxyl group.
What is primary protein structure?
The linear amino acid sequence.
What is secondary protein structure?
Local structures such as alpha helices and beta sheets.
What is tertiary protein structure?
The overall three-dimensional structure of one polypeptide chain.
What is quaternary protein structure?
The arrangement of multiple polypeptide subunits.
What is a post-translational modification?
A chemical or structural change to a protein after translation.
What is proteolytic processing?
Cleavage of peptide bonds to remove part of a protein.
What happens to the insulin signal peptide?
It directs the precursor into the secretory pathway and is subsequently removed.
What is the insulin C-peptide?
The connecting peptide removed during insulin maturation.
What are insulin's A-chain and B-chain?
The two polypeptide chains of mature insulin.
What is the LMNA gene?
The gene that produces Lamin A and Lamin C.
What is the primary transcript difference between Lamin A and Lamin C?
Lamin C is translated from a shorter mRNA.
What is farnesylation?
Addition of a hydrophobic farnesyl group to a protein.
Why is farnesylation important for prelamin A?
It helps the protein associate with membranes, including the nuclear envelope.
What is Lamin A proteolytic processing?
Maturation involving cleavage of the precursor, including removal of its farnesylated C-terminal region.