Anthill 2

Name three sources of DNA mutations.

- When an error occurs during DNA replication - When we're exposed to environmental factors, such as UV radiation - Spontaneous mutations can be passed down through generations (inheritance)

What is a gene? Does it always need to be translated? Approximately how many genes are in the genomes of A) humans; B) E. coli; C) SARS-CoV-2?

A gene is a small section of DNA that is arranged on a structure called a chromosome. They are the basic unit of hereditary. Humans have approximately 20,000 genes in their genome. The E. coli genome consists of about 4,000 genes. The SARS-CoV-2 genome hasn10 genes.

What is the difference between a nonsense and a missense mutation? Which type is more likely to have a bigger impact on the function of the resulting protein?

A missense mutation occurs when one base is changed in a nucleotide sequence, resulting in a different amino acid incorporated in the polypeptide chain. A nonsense mutation also involves an alteration to one base in the sequence; however, the resulting codon is turned to a STOP codon, terminating any further synthesis of proteins. This type of mutation may shorten the protein significantly and is more likely to have a larger impact on its function.

What are transitions and transversions (regarding base substitutions)? How many possible transitions are there? How many possible transversions? Which type is more common in nature?

A transition is a type of substitution mutation in which a purine (A and G) or a pyrimidine (C and T) is replaced by a base of the same kind; an adenine replaced by a guanine is an example of a transition. In a transversion mutation, a purine or a pyrimidine is replaced by a base of the opposite kind, such as a thymine that is replaced by a guanine. There are two possible transitions and there are four possible transversions. Although there are twice as many possibilities for transitions to occur, transitions are more common in nature.

Create a nucleotide sequence that codes for four amino acids (show the DNA sequence and the polypeptide sequence). Then show a point mutation in the sequence that would not affect the polypeptide sequence.

DNA sequence: 5' TACGTATTAGGG 3' RNA sequence: 5' AUGCAUAAUCCC3' Polypeptide sequence: N- Met His Asn Pro -C Point mutation in DNA sequence: 5' TACGTATTAGGA 3' (this does not affect the polypeptide sequence because GGG as well as GGA both code for pro)

Imagine you're a ribosome. How do you know where to begin translating? Where to end translating?

During the initiation of translation, the small ribosomal subunit binds to the start codon on the mRNA strand. Then a tRNA with an anti- codon and cooresponding amino acid binds to the start codon on the mRNA strand, initiating translation. Translation will end when the ribosome reaches a stop codon on the mRNA strand.

What are some differences in the way genes are structured (their components) in prokaryotes compared with eukaryotes? Think of regulatory regions and coding regions.

Eukaryotic genes have far more regulatory elements for gene expression than prokaryotes do. For example, eukaryotic genes have exon and intron regions while prokaryotes only have an open reading frames that are grouped in operons. Eukaryotes have splicing to get rid of the introns during the pre-mRNA stage. However, the prokaryotes have an open reading frame where operons are fully transcribed into mRNA on one strand then translated. Another difference is that prokaryotic gene expression happens in the cytoplasm only while the eukaryotic gene expression happens in both the nucleus and the cytoplasm.

In what two locations in eukaryotic cells is DNA found? In which location is the DNA circular? Where is DNA found in prokaryotic cells?

In eukaryotic cells, the mitochondrial DNA is found in the mitochondria and the nuclear DNA is found in the nucleus. The nuclear DNA is linear while the mitochondrial DNA is circular. In a prokaryotic cell, the DNA is in the central part of the cell, called the nucleoid. The nucleoid is not surrounded by a membrane. Some prokaryotes also have plasmids, which are small, circular DNA molecules.

What are "indels"? What is their connection to frameshift mutations? Which type of indel will NOT result in a frameshift mutation?

Indels are a molecular biology term to describe the process of genetic variation which specific nucleotide sequences are inserted (present) or deleted (absent). Their ability to influence genetic mutation through changing the reading frame of any number of nucleotides in DNA sequence not divisible by three is what connects them to frameshift mutation. This results in a completely different translation from the original. If an indel is in the non-coding or regulatory regions of the genome, it will not have a direct effect on the sequences; thus, not resulting in a frameshift mutation.

Describe each of these terms: exon, intron, 5'UTR and 3'UTR.

Introns are sequences in DNA that don't code for an amino acid in the protein that is being translated. These introns are removed in the pre-mRNA stage by RNA splicing. Exons are sequences (regions) in the DNA that contain genetic information that is needed in the translation of a protein. These exons are not removed during RNA splicing and continue to exist while making the mature mRNA. 5'UTR is the untranslated part of the mRNA that goes from the 5' cap to the first codon. 3' UTR is the untranslated part of the mRNA that goes from the last codon coded to the 3' poly A tail end.

From whom did you inherit your mitochondrial DNA (mtDNA)? What types of problems can occur from mutations in mtDNA? What types of organs or tissues are most likely to be affected?

Mitochondrial DNA (mtDNA) is almost exclusively inherited from mother to offspring. Mitochondrial genetic disorders can be caused by mutations in mitochondria DNA or nuclear DNA, which leads to mitochondria dysfunctions such as the following: muscle weakness, movement difficulties, diabetes, kidney failure, heart disease, dementia, hearing loss, and abnormalities involving the eyes and vision. Furthermore, high-energy tissues/organs like the muscle, brain, or heart are most likely to be affected by mitochondrial disorders.

What are three types of point mutations? Which type is responsible for most cases of sickle-cell anemia?

Substitution - a base it changed Insertion - a base is added Deletion - a base is deleted Substitution mutations are responsible for most cases of sickle-cell anemia. It is caused when the GAG codon is accidently converted into the GUG codon -which translates the amino acid Valine instead of Glutamic Acid.

Imagine you're a molecule of RNA polymerase knocking about in a nucleus. How would you know where to bind DNA to start transcribing?

The RNA polymerase knows where to bind and start transcribing when it finds the promoter sequence at the beginning of gene. This can be found directly from the RNA polymerase or with the help of a protein. The promoter is a recognition site so when the RNA polymerase finds this promoter sequence in the DNA, it attaches and then continues to start transcribing.

What is the approximate size (in bases or base-pairs) of each of these genomes? A) humans; B) E. coli; C) SARS-CoV-2. Since human cells are diploid, how many base-pairs of DNA are in each human cell nucleus?

The human genome has a total length over 3 billion base pairs. E. coli genome consists of about 4.6 million base pairs. SARS-CoV-2 has approximately 25-32 kilobases. Since a haploid human genome has about 3 billion base pairs, a diploid human cell would have about 6 billion base pairs in each cell.

What are trinucleotide repeats, and how do they occur (briefly)?

Trinucleotide repeats (also known as microsatellite expansion diseases) are a kind of mutation in, which repeats of three nucleotides increase in copy numbers until they cross a threshold above which they become unstable and produce a set of over 50 genetic diseases.

Briefly describe these three types of DNA repair: a) proofreading; b) mismatch repair; c) nucleotide excision repair

a) Proofreading is a process in which DNA polymerases can detect and fix any errors they come across during DNA synthesis. If a nucleotide has been paired incorrectly, the polymerase can remove and replace it prior to continuing with replication. b) Mismatch repair is a process that occurs after DNA synthesis to "double-check" the proofreading changes and to correct any errors that the polymerase may have caused by cutting and replacing a section of DNA where the mismatch was. c) In nucleotide excision repair, a patch of nucleotides is removed and replaced by undamaged DNA.