Exam 1 Study Questions (Ch 1, 3, 6, 7) Flashcards
What are the structural differences between deoxyribose and ribose sugars?
What are the structural differences between purine and pyrimidine nitrogenous bases? (Ch 1)
Ribose is in RNA. Deoxyribose is in DNA. Ribose has a hydroxyl (OH) group on the 2’ carbon, while deoxyribose has just a hydrogen (H) at the 2’ carbon.
Purines have a double-ring structure. Adenine (A) and Guanine (G) are purines. Pyrimidines have a single-ring structure. Cytosine (C), Thymine (T), and Uracil (U) are pyrimidines.
What is supercoiling?
What is the difference between negatively and positively supercoiled DNA? (Ch 1)
Supercoiling is the coiling of a closed duplex DNA in space so that it crosses over its own axis. It creates tension in the DNA molecule. It occurs only in closed DNA with no free ends.
Positive supercoiling occurs if DNA is twisted in the same direction as the helix. Negative supercoiling occurs if DNA is twisted in the opposite direction as the helix. Negative supercoiling creates tension that can be relieved by denaturing the helix and promotes denaturing of helix.
What is a point mutation?
What are the differences between transitions, transversions, indels, and frameshift mutations? (Ch 1)
A point mutation is a mutation that changes a single base pair.
Transition mutation: Replaces a purine with a purine or a pyrimidine with a pyrimidine. A <—> G & C <—> T(U)
Transversion mutation: Replaces a purine with a pyrimidine or vice versa. A <—> T(U) & A <—> C & G <—> T(U) & G <—> C
Indel mutation: Insertions and deletions (can lead to frameshift).
Frameshift mutation: Shifts the reading frame
What is the relationship between DNA modification and mutation rate? (Ch 1)
At mutation hotspots, mutation frequency is increased by at least an order of magnitude. Many mutational hotspots result from the presence of modified bases.
Be able to define silent mutation, null mutation, loss of function mutation, gain of function mutation, and dominant negative. (Ch 1)
Silent mutation: Neutral substitutions. Substitution in a protein that cause changes in amino acids but does not affect activity. Change in nucleotide but no change in protein coding.
Null mutation: Completely eliminates function of gene.
Loss-of-function mutation: Prevents the normal gene product from being produced or renders it inactive.
Gain-of-function mutation: The altered gene product possesses a new molecular function or a new pattern of gene expression.
Dominant negative mutation: Results in a protein that interferes with the normal function of the wild-type protein.
What is a polymorphic locus? (Ch 1)
A polymorphic locus is a locus with multiple functional alleles.
What is the reading frame and how is it determined? (Ch 1)
The reading frame is all the ways that a nucleotide sequence can be translated into polypeptide. In DNA, there are 6 possible reading frames: 3 forward and 3 reverse. In mRNA, there are 3 possible reading frames.
Usually only one of the possible reading frames is used. Others are closed by frequent termination signals.
What is the relationship between the genetic code, codons, frameshift mutations, and the ORF? (Ch 1)
The genetic code is the relationship between a DNA sequence and the sequence of the corresponding polypeptide. It is read in triplet combinations of ribonucleotides called codons. The codons are nonoverlapping and are read from a fixed starting point.
The open reading frame (ORF) is a sequence of DNA consisting of triplets that can be translated into amino acids starting with an initiation codon and ending with a termination codon.
A frameshift mutation shifts the reading frame.
What is the general structure of an mRNA? (Ch 1)
Untranslated 5’ region (5’ UTR, leader)
Coding region
Untranslated 3’ region (3’ UTR, trailer)
What general steps are involved in RNA processing in eukaryotes? (Ch 1)
5’ cap
3’ poly A tail
removal of introns through splicing
What is the difference between cis- and trans-acting elements? (Ch 1)
Cis-acting elements: Affect only the contiguous stretch of DNA.
Trans-acting elements: Can act on any copy of a gene in the cell.
What are homologous genes?
How are the introns and exons of homologous genes related? (Ch 3)
Homologous genes: Genes that share a common ancestor. Should share common features that preceded their evolutionary separation.
When two genes are related, the similarities in sequence between their exons is greater than between their introns. Changes in exon sequence are constrained by selection against mutations that alter the function of the polypeptide (negative selection). Introns change more rapidly than exons.
What will happen to the sequences of exons and introns when they are under negative or positive selection? (Ch 3)
Negative selection: Changes in exon sequence are constrained by selection against mutations that alter the function of the polypeptide. Exon sequence is under selective pressure to produce a polypeptide with a specific function. Introns change more rapidly than exons.
Positive selection: Under positive selection an individual with an advantageous mutation in an exon has a greater fitness relative to those without the mutation. Introns may be more highly conserved than exons if the gene is under positive selection.
What is the relationship between complexity of a species and the structure of introns and exons? (Ch 3)
Introns are short in unicellular eukaryotes but can be many kb in multicellular eukaryotes. The overall length of a eukaryotic gene is determined largely by the length of its introns.
What is alternative splicing and what are the evolutionary advantages and disadvantages associated with this process? (Ch 3)
Alternative splicing: Production of different polypeptides by including or excluding individual exons or choosing between alternative exons.
Describe the relationship between interrupted gene structure and the structure of the protein encoded by the gene. (Ch 3)
Interrupted genes: Genes for which the coding sequence is not continuous due to the presence of introns.
What is a gene family?
What is a gene superfamily? (Ch 3)
Gene family: A set of genes within a genome that encode related or identical RNA or proteins. Derived by duplication of an ancestral gene followed by accumulation of changes in sequence between the copies.
Superfamily: A set of genes all related by presumed descent from a common ancestor. Now show considerable variation.
What are orthologous genes? (Ch 3)
Orthologous genes: Related genes in different species. Special type of homologue. Gene diverges after speciation.
What are the differences between repetitive and nonrepetitive DNA?
What types of sequences would you find contained within each?
Where is each type found in the genome? (Ch 6)
Highly repetitive DNA has a very short repeating sequence and no coding function (Satellite DNA). Short repeating sequence units.
Satellite DNA is located in large blocks that can have distinct physical properties.
Satellite DNA is often the major constituent of centromeric heterochromatin.
What are pseudogenes? (Ch 6)
Pseudogenes: Inactive but stable components of the genome derived by mutation of an ancestral active gene.
Usually inactive because of mutations that block transcription, translation, or both
What is a gene cluster and how are they created via unequal recombination? (Ch 6)
Gene cluster: A group of adjacent genes that are identical or related (rRNA and histone proteins).
Duplication and expansion into clusters often begins with unequal crossover (recombination that occurs between sites that are similar but not perfectly aligned).
– Increases the number of repeats on one chromosome and decreases on the other.
What are the similarities and differences between satellite, minisatellite, VNTR, and microsatellite regions? (Ch 6)
Satellite DNA: Highly repetitive DNA has a very short repeating sequence and no coding function (not transcribed).
Minisatellites: Repeating unit length is 10-100 bp. Greater number of repeats than microsatellites. Rate of crossover at minisatellite loci is 10X that of other parts of the genome.
Microsatellites: Repeating unit length is <10 bp
Variable Number of Tandem Repeats (VNTR): Microsatellites that have < 20 repeats and a 2-6 bp repeat
Microsatellite and minisatellite loci can be used for gene mapping and DNA fingerprinting
Describe how the result of an unequal crossing over event between genes (or exons) is different than the result when unequal crossing over occurs within a gene (or exon). (Ch 6)
Unequal crossing over within a gene cluster, but between genes, results in:
– Increase in the number of repeats on one chromosome
– Decrease in the number of repeats on the other.
If crossing over occurs within a gene, the result depends on the similarity of the genes:
– If the genes are nearly identical, there is little change in the sequence of either gene
– If the genes are not identical, then the recombinant genes will be different from either of the original genes.
What effect does the presence of interrupted genes have on the rate of unequal crossing over?
Why does it have this effect? (Ch 6)
Interrupted genes are an obstacle to unequal crossing over. Exons of adjacent genes are similar. Introns have diverged and are not similar enough for pairing.
Restriction of pairing to the exons limits the continuous length of DNA that can cross over. Lowers the chances of unequal crossing over.