Module 1 Quiz Review

Consensus sequence

Calculated order of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment.

Spliceosome

Cellular machine that removes introns from gene transcripts to generate mature messenger RNA

3' hydroxyl

Exists on 3' end of a DNA strand. 3'-hydroxyl group is on the lower side of a 5 carbon sugar

Polycistronic

mRNA corresponding to multiple genes whose expression is also controlled by a single promoter and a single terminator. Polycistronic mRNAs are also called operons. All eukaryotic mRNAs are monocistronic.

Out of A, T, C, and G, which are complementary and how do their percentages relate?

%A=%T and %G=%C

What is the difference between DNA and RNA?

(a) RNA contains the sugar ribose, while DNA contains the slightly different sugar deoxyribose (a type of ribose that lacks one oxygen atom) (b) RNA has the nucleobase uracil while DNA contains thymine.

What is the difference between prokaryotic and eukaryotic genes?

1. eukaryotic genes have introns whereas this is absent in the prokaryotic genes. 2. eukaryotic genes can show alternative splicing thus resulting in more than one type of protein from one gene. 3. prokaryotic genes have operons 4. prokaryotic genes can be polycistronic

Fill in the blank: the standard genetic code has ___ amino acids and ___ codons

20, 64

How many introns are present on a gene that consists of 4 exons?

3 introns

RNA polymerase moves along the template strand ___________ and synthesizes an RNA ____________.

3' to 5'; 5' to 3'

The Crick strand

5′-to-3′ bottom strand (3′←5′)

The Watson strand

5′-to-3′ top strand (5′→3′)

Template/non-coding/antisense strand

A cell uses antisense DNA strand as a template for producing messenger RNA (mRNA) that directs the synthesis of a protein

ncRNA = noncoding RNA

A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. (E.g. rRNAs, tRNAs, snoRNAs, microRNAs, LncRNA)

Element

A non-coding functional sequence of DNA

Locus (plural loci (pronounced low-sigh))

A particular location in a genome

Primer

A primer is a short nucleic acid sequence that provides a starting point for DNA synthesis. In living organisms, primers are short strands of RNA. RNA polymerase does not need a primer

What are the three sites of a ribosome and how do they differ?

A site Where the TRNA ribosome enters and is tested for a codon / anticodon match P site Then it is shifted here and the aa is added to the end of the aa chain E site Then finally the spent tRNA is moved here and ejected to be recycled

Residue

After a peptide bond is formed, it is attached to something on either side. A residue is what is left over after peptide bond formation

Exon

An exon is any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts

What is the central dogma of molecular biology?

DNA -> RNA -> Protein

What are transcription factors?

DNA binding proteins that bind to DNA that facilitate the activation or repression of transcription

Which double-stranded DNA sequence requires the most amount of heat to "melt" (=denature)?

GC rich

What are housekeeping genes?

Genes whose products are needed at all times in all cells

A new nucleotide can be added to a nucleic acid strand provided there is a ______ at the strand's end.

Hydroxyl group

What does polar mean in biology?

In Biology, polar means having two distinct ends (not necessarily different by charge)

What is a silencer and what binds to it?

In genetics, a silencer is a DNA sequence capable of binding transcription regulation factors, called repressors. Thus, silencers prevent genes from being expressed as proteins.

What is a TATA box? What does a TATA box do?

It is a short region of DNA that contains a sequence of T and A base pairs. The protein that binds to this site helps position RNA polymerase.

Does DNA/RNA polymerase join incoming phosphate to the 5' or 3' end?

It joins it at the 3'OH of a growing nucleic acid chain

What is a mediator protein and what is it a part of?

It stimulates activator-independent (basal) transcription. Furthermore, Mediator can act as a co-repressor that facilitates transcriptional silencing. transcription initiation complex

Which term is used for RNAs that code for proteins?

Messenger (mRNA)

Every polypeptide that is synthesized must begin its life with _______________ at its amino terminus. (Many proteins are processed by removal of one or more amino-terminal residues).

Met (Methionine)

Phosphodiester bond

Nucleotides are joined by phosphodiester bonds to form nucleic acids. Phosphodiester bond is formed when exactly two hydroxyl groups in phosphoric acid react with a hydroxyl group on other molecules forming ester bonds

Nucleotide

Nucleotides are organic molecules consisting of a nitrogenous base, a 5 carbon sugar, and a phosphate. They serve as monomeric units of the nucleic acid polymers deoxyribonucleic acid and ribonucleic acid

What is the difference between an open reading frame and a reading frame?

Open reading frame (ORF) is a set of uninterrupted codons beginning with a start codon and ending with a stop codon while a reading frame can be any sets of three

Peptidyl transferase reaction

Peptidyl transferase is an enzyme that catalyzes the addition of an amino acid residue in order to grow the polypeptide chain in protein synthesis. It is located in the large ribosomal subunit, where it catalyzes the peptide bond formation

The term "5' end" refers to the end of a nucleic acid strand with _________.

Phosphate

Open reading frame (ORF)

Set of codons starting with the start codon and ending with the the stop codon

Fill in the blank: The start codon is _____. The stop codons are ___, ____, ____

Start: AUG Stop: UAA, UAG, UGA

Non-template/coding/sense strand

The DNA strand whose base sequence is identical to the base sequence of the RNA transcript produced (although with thymine replaced by uracil).

Degeneracy

The ability of elements that are structurally different to perform the same function or yield the same output, a well known characteristic of the genetic code

Denaturation

The breaking of many of the weak linkages, or bonds (e.g., hydrogen bonds), within a protein molecule that are responsible for the highly ordered structure of the protein in its natural (native) state.

5' cap = 5-methylguanosine(5 Me-G)

The cap is a modified guanine (G) nucleotide, and it protects the transcript from being broken down. It also helps the ribosome attach to the mRNA and start reading it to make a protein.

Collinearity

The concept that nucleotide sequences in genes dictate amino acid sequences in proteins.

polyA tail = polyadenosine tail

The poly-A tail is a long chain of adenine nucleotides that is added to a messenger RNA (mRNA) molecule during RNA processing to increase the stability of the molecule.

Hybridization

The process of combining two complementary single-stranded DNA or RNA molecules and allowing them to form a single double-stranded molecule through base pairing

5' UTR = 5' untranslated region

The region of an mRNA that is directly upstream from the initiation codon.

Reading frame

The register of sets of threes that are read as codons

Complementarity

The relationship between two structures each following the lock-and-key principle. In nature complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other,the nucleotide bases at each position in the sequences will be complementary

3' UTR = 3' untranslated region

The section of messenger RNA (mRNA) that immediately follows the translation termination codon

What is the difference between transcription and translation?

Transcription is the synthesis of RNA from a DNA template where the code in the DNA is converted into a complementary RNA code. Translation is the synthesis of a protein from an mRNA template where the code in the mRNA is converted into an amino acid sequence in a protein.

Is RNA double or single stranded? What structures does it form?

Unlike DNA, RNA is generally single stranded (due to the 2' OH) and often forms secondary and tertiary structures

What do the terms upstream and downstream describe?

Upstream of gene Anything before the promoter Downstream of gene Anything after the terminator

What does polyadenylation of a pre-mRNA entail?

addition of a bunch of A nucleotides to the 3' end

Colinearity refers to the correspondence of a nucleic acid's 5' to 3' sequence to a protein's ________________ sequence

amino terminus to carboxyl terminus

Which is likely to contain multiple open reading frames? a. A bacterial protein b. A eukaryotic mRNA c. A bacterial mRNA d. A eukaryotic protein

c. A bacterial mRNA

What three processes does pre-mRNA undergo?

capping, splicing, and polyadenylation

Operon

genetic regulatory system found in bacteria and their viruses in which genes coding for functionally related proteins are clustered along the DNA. This feature allows protein synthesis to be controlled coordinately in response to the needs of the cell

What are the parts of a ribosome?

large and small subunit

What does capping a pre-mRNA entail?

modifying the pre-mRNA at its 5' end with a 5-methylguanosine

Is DNA reactive?

no it is generally inert

Intron

non-coding sections of an RNA transcript, or the DNA encoding it, that are spliced out before the RNA molecule is translated into a protein.

Is a TATA box a promoter or enhancer?

promoter

A ___________ building blocking is required for addition of a new nucleotide subunit to a growing RNA chain.

ribonucleotide triphosphate

Terminator

section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription

Promoter

sequence of DNA to which proteins bind that initiate transcription of a single RNA from the DNA downstream of it.

Enhancer

short region of DNA that can be bound by proteins to increase the likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors

What does splicing a pre-mRNA entail?

the intron sequences are removed and the exons are joined

Is the promoter sequence upstream (before with respect to the coding sequence) or downstream (after with respect to the coding sequence) of the start codon for a gene? (Consider the "direction" of a gene the direction in which it would be transcribed.)

upstream