Nucleic Acids
The end in which the final phosphate in the strand is bound to the 5 carbon on the final sugar at that end of the strand
Define semi-conservative replication
The original strands of DNA in a given double helix serve as templates for the new strands during replication, and the original strands of DNA simultaneously participate as components of the new double helices.
What is a transcript composed of?
messenger RNA, which is composed of nucleotides A, G, U, C. Each nucleotide is base, sugar, phosphate.
What is a stop codon (not the sequence, but the functional definition)?
A codon for which no amino acid is coded, and which when encountered causes the growing polypeptide chain to stop being translated as the polypeptide is released from the ribosome.
If an RNA primer is present in front of DNA nucleotides, which process is taking place?
DNA replication
This data suggests that humans and cows may have a more recent common ancestor than humans and yeast, given the seemingly closer genetic similarity.
What do the enzymes
A) Topoisomerase and
B) Helicase
do?
Helicase unwinds and separates the DNA strands which are being replicated
Topoisomerase breaks, unwinds, and then rejoins the original double helix so as to relieve torsional strain
Where are the codons located, as oriented from 5' to 3'
on the messenger RNA transcript, such that the "codon chart" refers to the 5' -> 3' sequence on the mRNA transcript
Where does translation take place in eukayotes vs. in prokaryotes? What functional consequence does this have for the timing of transcription and translation in these two cell types?
In prokaryotes, transcription and translation can occur at the same time given that they both occur in the cytoplasm and no splicing is required prior to translation. This allows for faster gene expression.
In eukaryotes, the pre-mRNA must be completed and processed in the nucleus prior to being moved to the cytoplasm for translation on ribosomes. Therefore in eukaryotes, transcription and translation (of the same physical transcript) cannot occur simultaneously.
Production efficiency and production complexity have a trade-off.
What are plasmids and where can they be found?
plasmids are small circular double-stranded DNA fragments located in the cytoplasm of bacterial cells
They typically contain genes for traits that aid in bacterial survival under various forms of environmental stress
A gene is isolated and studied. It is found that Guanine makes up 15% of the nucleotides in the gene. What % of the nucelotides are made up of Adenine?
35%
Why must the lagging strand be synthesized in fragments rather than continuously, given that the leading strand is synthesized continuously?
Feel free to draw a visual aid to help the explanation.
New DNA must be synthesized from 5' to 3', and structurally this means that as parent DNA is continually unwound at the replication fork, one strand of new DNA, the "lagging strand," must start at the portion of the newly exposed portion of parent DNA furthest from the origin of replication in order to start the new fragment at the new fragment's 5' end.
Define RNA processing and describe its timing with respect to transcription and translation
5' cap, poly-A tail. splicing. Occurs in eukaryotes, in nucleus, after transcription of primary transcript, and prior to translation of processed transcript.
If a strand of mRNA is 5'-UGG-3', what will the anticodon sequence be when read from its own 5' end toward its own 3' end?
5'-CCA-3'
If a new nucleic acid strand is being synthesized and contains uracil, what can be said?
The new strand is a strand of RNA, given that RNA uses uracil instead of Thymine
Describe the location and structure (all locations and structures) of primary hereditary information in
A) Eukaryotic Cells
B) Prokaryotic Cells
Both types of cells use double-stranded DNA to carry hereditary information.
In eukaryotes, DNA is located in linear chromosomes found within the nucleus of cells. In eukaryotic cells, specific membrane-bound organelles (mitochondria, chloroplasts) also contain hereditary information (in the sequence of double-stranded DNA) pertinent to the function of those organelles.
In prokaryotes, there is usually a single circular "bacterial chromosome" composed of double-stranded DNA, along with small plasmids of double-stranded DNA containing traits often aiding in survival under environmental stress.
While possible for plasmids exist in some types of eukaryotic cells and archae, plasmids are typically associated with, and more prevalent throughout, bacterial cells.
ligase and RNA primase
1) what type of macromolecule are they
2) what is each of their roles in the process of DNA synthesis
ligase and RNA Polymerase are enzymes, and therefore proteins
RNA primase adds new nucleotides to the growing mRNA strand during transcription. Primase, rather than RNA polymerase, synthesizes RNA primers for DNA replication (therefore RNA polymerase has no role in DNA replication).
DNA ligase joins the Okazaki fragments together by facilitating bonds between sugar and phosphate along the sugar-phosphate backbone of the lagging strand.
What must be true with respect to the number of codons and the number of amino acids?
There are more codons than amino acids, therefore there are multiple codons that code for given amino acids in many cases.
If an mRNA has 350 bases, and the first 5'-AUG-3' sequence on the mRNA begins 20 bases from the beginning of the mRNA, and the first stop codon is completed 30 bases from the end of the mRNA, how many amino acids will be present in the protein coded for by the gene that was transcribed to create this mRNA?
99
Describe WHY we must have triplet (three nucleotide) codons rather than having one amino acid specified by a given nucleotide or by two nucleotide sequences?
single base codons could differentiate between 4 amino acids
double base codons could differentiate between 16 amino acids
In short, triplet codons allow for more amino acid "words" to be present in any set of instructions specified by the DNA.
The nitrogenous bases Adenine and Guanine have two rings in their structure, while the nitrogenous bases Cytosine and Thymine have one ring in their structure. What is the significance of this in terms of the structure of the DNA double helix?
describe the biochemistry of elongation of a new DNA strand, including the presence and manipulation of nucleoside triphosphates
A nucleoside triphosphate (a nucleoside = sugar + base, triphosphate = 3 phosphates) is the conduit and starting molecule in the addition of a new nucleotide to the growing strand of DNA. A nucleoside triphosphate containing the complimentary base to the parent strand's base is brought in, and cleaving pyrophosphate (2P) as well as subsequent hydrolysis of pyrophosphate, supplies energy for the addition of the nucleotide to the new strand of DNA.
Use the terms "transcription factors", "RNA polymerase", "TATA box" and "promoter" properly to SPECIFICALLY describe the process of transcription.
Define
Template strand vs. nontemplate strand
Coding strand vs. noncoding strand
The template strand is the DNA strand that is read from 3' to 5' (DNA) in order for complimentary RNA to be synthesized from 5' to 3' (RNA). The nontemplate strand is the other strand of the original DNA.
The coding strand is the original strand of DNA the ends up being identical to the newly synthesized RNA strand (save for U subbed for T). The noncoding strand is the other strand of the original DNA.
The noncoding strand IS the template strand.
How many different proteins can be synthesized from a pre-mRNA containing 4 exons and 3 introns, assuming any combinations must be arranged in positive numerical order (i.e. E3 must be after E1 in the final transcript)
15
see below
E1-E2-E3-E4
E1-E2-E3
E1-E2
E1-E3
E1
E2-E3-E4
E2-E3
E2
E3-E4
E3
E4
E1-E3-E4
E1-E2-E4
E1-E4
E2-E4