DNA Structure
Given that DNA is a double-stranded helix, state how many strands of DNA are in a single DNA molecule.
The DNA molecule consists of two strands.
State which end (5’ or 3’) of a DNA strand that new nucleotides are always added to.
New nucleotides are added in the 5’ to 3’ direction (added to the 3’ end)
Differentiate between RNA and DNA.
Dna contains the sugar deoxyribose and has the nucleobase thymine.
RNA contains the sugar ribose and has the nucleobase uracil.
Identify where transcription occurs in prokaryotes and eukaryotes
Eukaryotes- Transcription occurs in the nucleus
Prokaryotes- Transcription occurs in the cytoplasm
State the functions of mRNA, tRNA, and rRNA.
mRNA: Carries genetic code from DNA in a cell’s nucleus to ribosomes (the cell's protein making machinery).
tRNA: Translate genetic information into protein sequence by delivering amino acids to the protein synthesis machinery during translation.
rRNA: Molecule in cells that forms part of the protein-synthesizing organelle known as a ribosome and that is exported to the cytoplasm to help translate the information in messenger RNA into protein.
State what James Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins contributed to our knowledge of DNA structure.
James Watson and Francis Crick discovered the double-helix structure of DNA.
Rosalind Franklin discovered the density of DNA and established that the molecule existed in a helical formation.
Maurice Wilkins crystallized DNA in a form suitable for quantitative X-ray diffraction work and obtained the best quality X-ray images seen at that time.
Identify the three parts of a nucleotide given a nucleotide structure.
Nitrogenous Base: Two categories purines and pyrimidines. In DNA, the bases are Adenine and Guanine (purines), Cytosine, Thymine and Uracil (pyrimidines).
Pentose Sugar: In DNA, the sugar is 2’ deoxyribose. In RNA, the sugar is ribose. Both are 5-carbon sugars. The difference is 2’ deoxyribose has one less oxygen atom attached to the second carbon.
Phosphate Group
Differentiate between template strand and coding strand.
The template strand only serves as the template for transcription.
The coding strand contains the exact same sequence of nucleotides in the mRNA except thymine.
Identify where translation occurs in prokaryotes and eukaryotes
Eukaryotes- Translation occurs in the cytoplasm
Prokaryotes- Translation occurs in the cytoplasm
Discuss why transcription and translation can be nearly simultaneous in prokaryotes, but not in eukaryotes.
Bacteria do not have a distinct nucleus that separates DNA from ribosomes, so there is no barrier to immediate translation.
State the functions of key proteins involved in DNA replication.
Single-stranded binding proteins: stabilize single-stranded DNA to help hold the replication bubble open.
Explain how the definition of antiparallel
Two bipolymers are antiparallel if they run parallel to each other but with opposite directionality (alignments). For example DNA is parallel but if one end is 5’ on top and 3’ on bottom, then the other end is 3’ on top and 5’ on bottom.
Determine the DNA sequence and directionality (5’/3’) when given a transcribed RNA sequence.
RNA polymerase synthesizes an RNA strand complementary to a template DNA strand. It synthesizes the RNA strand in the 5’ to 3’ direction, while reading the template DNA strand in the 3’ to 5’ direction.
Differentiate between the promoter sites for prokaryotic and eukaryotic promoters (e.g. TATA box).
Prokaryotes only carry three promoter elements, -10,-35, and the UP elements, whereas eukaryotes carry a wide variety of promoter elements.
State the 3 things that occur during eukaryotic RNA processing.
5’end capping.
Splicing
3’ end polyadenylation (The addition of a poly-a tail)
Describe the process of semiconservative DNA replication.
The two original DNA strands separate during replication; each strand then serves as a template for a new DNA strand, which means that each newly synthesized double helix is a combination of one old (or original) and one new DNA strand.
Predict the consequence if a key protein involved in DNA replication were mutated or could not function.
If there was a problem with the single-stranded binding protein then the replication bubble would destabilize and possibly close, causing the replication process to be halted or replicated incorrectly.
Differentiate between the functions of RNA polymerase and DNA polymerase.
The main difference between DNA and RNA polymerase is that DNA polymerase produces a double-stranded DNA molecule during polymerization whereas RNA polymerase produces a single-stranded RNA molecule during transcription. Also DNA polymerase requires a primer while RNA polymerase does not.
Explain the difference between silent, missense, and nonsense mutations.
Missense- Occurs when there is a mistake in the DNA code and one of the DNA base pairs is changed, for example, A is swapped for C.
Nonsense- Similar to a missense mutation except for the result is a stop codon.
Silent- A form of mutation that does not cause a significant change in the amino acid.
Explain why RNA processing occurs in eukaryotes, but not prokaryotes.
Eukaryotic protein-coding sequences are not continuous, as they are in prokaryotes. The coding sequences (exons) are interrupted by non coding introns, which must be removed to make a translatable mRNA.
Explain why DNA polymerase needs a primer, but primase (aka, RNA polymerase) does not.
No known DNA polymerase is able to begin a new chain. DNA polymerase can add a nucleotide onto only a preexisting 3’-OH group, and, therefore needs a primer at which it can add the first nucleotide.
Describe the process of DNA replication in bacteria (circular vs. linear).
Circular DNA: RepA knicks one strand of the DNA and holds on to the 5’ end, while the 3’ end serves as a primer for a host DNA polymerase III to begin to replicate the intact complementary strand. The helicase is called in to start unwinding the DNA, as it becomes unwound it is coded by single-stranded binding proteins. This process continues until replication of the intact strand is complete. The two ends of the nicked single strand are rejoined by RepA and released. DNA ligase seals the knick in the double stranded protein, remember at this point the replicated DNA is only single stranded. A region of the single stranded DNA becomes looped allowing access for RNA polymerase to form a primer DNA polymerase then uses this primer as a starting point for the synthesis/creation of DNA. DNA ligase then comes in to seal the final knick.
Linear DNA: Helicase unzips the DNA, resulting in the formation of a replication fork. Single-stranded binding proteins hold and stabilize the unzipped DNA open. Primase makes a small piece of RNA called a primer on a piece of the unzipped DNA. DNA polymerase III binds to the primer and starts adding DNA bases in the 5’ to 3’ direction. DNA polymerase I removes the primer and replaces it with DNA nucleotides. DNA ligase joins the backbones together (the split between the DNA added from DNA polymerase III and the new nucleotides from DNA polymerase I). Topoisomerase breaks, twists, and rejoins DNA ahead of the replication fork to relieve strain caused by the helicase unwinding.
Define Central Dogma, reading frame, codon, anticodon, triplet, and spliceosomes.
Central dogma- The process of DNA>RNA>Protein.
Reading frame- A reading frame is one of three possible ways of reading a nucleotide sequence. Codons must be read in the correct reading frame, in a non-overlapping fashion.
Codon- A sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule.
Anticodon- A trinucleotide sequence complementary to that of a corresponding codon in a messenger RNA (mRNA) sequence. Basically 3 nucleotides in tRNA that pair to a codon.
Triplet- A three base codon of the genetic code.
Spliceosome- Found in eukaryotic nuclei, they assemble on RNA polymerase II transcripts from which they excise RNA sequences called introns and splice together the flanking sequences called exons.
State the function of each component of a gene (promoter, TSS, terminator, 5’UTR, 3’UTR, protein coding region, intron, exon, start codon, stop codon), what enzyme “reads” it, and what process it is involved in (e.g. ribosome reads the start and stop codon in translation).
5’ UTR: Critical for ribosome recruitment to the mRNA and start codon choice, and plays a major role in the control of translation efficiency and shaping cellular proteome.
3’UTR: Influences the localization, stability, export, and translation efficiency of an mRNA.
Intron: Used as a faster pathway to assemble new genes.
Exon: A coding region of a gene that contains the information required to encode a protein.
State what occurs during initiation, elongation, and termination of translation.
Initiation- The ribosome gets together with the mRNA and the first tRNA so translation can begin.
1. Small ribosomal subunit binds to mRNA.
2. Large ribosomal subunit completes the initiation complex.
Elongation- Amino acids are brought to the ribosome by tRNAs and linked together to form a chain.
1. Codon recognition.
2. Peptide bond formation.
3. Translocation.
Termination- The ribosome reaches a stop codon (UAA,UAG, or UGA), since there are no tRNA molecules that can recognize these codons, the ribosome recognizes that translation is complete. The new protein is then released, and the translation complex comes apart.
1. Ribosomes reach a stop codon on mRNA.
2. Release factor promotes hydrolysis.
3. Ribosomal subunits and other components dissociate.