BIO 331 Final Exam 2025

What are mutations - -Mutations are an alteration in the genome resulting in altered nucleotide sequence that may cause a change in phenotype depending on the type of and location of mutation. How and when do mutations arise? - -Mutations occur during DNA replication if the DNA polymerase attaches a nucleotide that is not complementary to the nucleotide of the original strand. Can also occur due to spontaneous changes in the DNA which can happen during replication or when replication not occurring. Ectopic recombination events and transposition event can causes mutations. And an addition of DNA in a genome via lateral gene transfer are also type of mutations. DNA replication - -1 double stranded molecule is duplicated and occurs during mitosis and meiosis. DNA poly incorporates nucleotides that are complementary to those on the template strand. Occurs in 5'-3' direction and nucleotides added to 3' OH. Mistakes made sometimes. DNA damage - -is defined as any modification of DNA that changes its coding properties or normal function in transcription or replication %GC content - -average GC-content in human genomes ranges from 35% to 60% across 100-Kb fragments, with a mean of 41% Types of mutations - -Point, insetion/deletion, duplication, transposition, inversion, translocation Point mutation - -A single nucleotide change. Within an open reading frame, point mutations can be missense or non-synonymous -- change in DNA sequence causes codon to encode amino acid that is different from the original amino acid that was supposed to be encoded. Within orfs/CDS sequences such changes are called non sense mutations when the alteration causes a stop codon to be encoded. Silent/synonymous mutation is when the change in DNA doesn't change the amino acid that is encoded. Transitions and trans version - -Descriptors for point mutations occurring anywhere within the genome. Transition: pyrimidine (Cytosine or thymine) replaced with the other pyrimidine or when a purine (adenine or guanine) is replaced with the other purine. Transversion: pyrimidine replaced with purine or vis versa. Transition more common than transversion. Insertion or deletion - -aka indel mutation: when nucleotides are removed or added. If this mutation occurs within OFR, it will cause a frameshift if indel is not a multiple of 3bp BIO 331 BIO 331 and if the indel doesn't fall between existing codons. Frameshifts drastically alter reading frame and hence the encoded proteins. Duplication - -some sort of DNA is copied more than it is supposed to be Transposition - -piece of DNA is moved to another part of the genome by a 'selfish' piece of DNA that has evolved to make copies of itself Inversion - -piece of DNA is placed into chromosome in the opposite orientation than it is supposed to be in Translocation - -a large piece of DNA breaks off and moves to a new place in the genome Which mutations are most likely to impact phenotype - -Missensse and nonsense due to the changes in what is being encoded for by the codon. Also frameshift mutations because they are likely to change phenotype because the reading frame is being altered a way that will change the amino acids being encoded for. Mutations that occur within regulatory regions can also impact phenotype. This is because mutations may cause the genes to be expressed more or less than they were originally supposed to be expressed. Gene - -A specific sequence of nucleotides in DNA or RNA which is transcribed and coded for an RNA molecule. They can be protein coding or non-protein coding. Represents a full unit of information that controls a specific trait or characteristic. Humans have ~20,000 protein coding genes while some bacteria have only a few hundred. In all cells/genomes of all organisms. (hereditary determinants) Recombination - -shuffling of genetic material mediated by crossing over between chromosomes Allele - -different types of single gene Genotype - -combination of alleles within an individual Phenotype - -physical characteristics of individuals Mendel's laws - -1st- law of segregation- during gamete formation, the paired hereditary determinants segrate such that each gamete is equally likely to contain either one 2- independent assortment- segrgation of members of a pair of alleles is inde. Of the segregation of other pairs in the formation of reprod. Cells Mendel's law apply: - -to diploid organism (loci), dominance/recessive relationships and a simple gene (phenotype correspondence), 2 genes are not close together BIO 331 BIO 331 Genome - -Sum of genetic info an organism contains and is made of DNA or for some viruses, RNA. Human genome contains 3 billion nucleotide base pairs. All organisms have. Chromosome - -A single thread like structure made of tightly packed DNA and proteins that store the organisms's genetic material. Linear chromosomes in eukaryotes have a central point called centromere with histones helping to pack the long DNA molecules. Humans have 23 pairs of chromosomes. Not all organisms have chromosomes. Open reading frame (CDS or ORF) - -A sequence of genetic material that can be read by cellular machinery to create protein through translation. Begins with a start codon (AUG in RNA) and end with a stop codon (UAA, UAG, or UGA). Consist of a multiple of 3 nucleotides as the codons determining the amino acid. Present in all organisms. Locus - -a specific physical site of a particular gene or non-coding DNA segment located on a region of chromosome. Loci are present in the cells/genomes of all organisms. Codon - -A trinucleotide DNA or RNA sequence that encodes a specific amino acid or acts as an signal that starts or stops protein synthesis. Each codon is representativeof a single amino acid of a protein eventually forming a unit of genomic information.Codons are present in the cells/genomes of all organisms as they play a crucial role in the process of protein synthesis. During the translation process, the codon sequence determines the amino acid order in theprotein. Intron - -A non-coding sequence/region that is situated within a gene that is not included in thefinal mature RNA molecule. After transcription, introns are 'spliced' out of the mrna molecule and, hence, do not contribute to the final functional RNA product. Not all organisms have introns. Eukaryotic organisms (with nucleus) tend to have introns in their genes whereas prokaryotic organisms tend to not. Exon - -A region that remains in an RNA after splicing/maturation. While some portions of exons are regulatory in nature (i.e. 5' and 3' utrs), and hence do not code for proteins (or even remain in the final structures of ncrna molecules), the majority of nucleotides within exons of protein coding genes are 'coding', comprising the ORF/CDS. Eukaryotes contain exons and introns. Technically, most prokaryotic genes contain only exons. Promoter - -A regulatory element/sequence of DNA that proteins bind to, when initiating transcription of a nearby gene. Promoters typically are at the 5' end of the transcription initiation site. Promoters can be found in every gene in eukaryotes; but prokaryotic genes found within a single operon may have just one promoter for the entire operon. Promoters are much more complex in eukaryotes. Enhancers - -A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes. BIO 331 BIO 331 Low complexity filtering - -identify and remove regions of low complexity from nucleotide or protein sequences. Low complexity regions are sequences that contain repetitive or simple patterns, such as long stretches of a single nucleotide or amino acid, tandem repeats, or sequences with biased compositions. Non-coding DNA - -This region of DNA does not code for proteins. With the exceptions of ncrna genes, most non-coding DNA is not transcribed. It may contain regulatory elements. Non-coding DNA is found in all organisms, but can comprise over 95% of the genome cin eukaryotes with large genomes.In prokaryotes, non-coding DNA is much rarer and makes up a much smaller percentage of the prokaryotic genome. What is DNA made up off and where is it found - -DNA is made up of nucleotides, which are composed of a sugar, phosphate, and a nitrogenous base (purine or pyrimidine), in which the bases differ in structure. Complementary DNA bases are held together by H bonds and form a double stranded helix. Strands of DNA are then organized and packed into chromosomes. DNA is strictly found in the nucleus of the cell for eukaryotes and in the nucleoid of prokaryotes. DNA does not leave the nucleus at any time. It is also found in the mitochondria of eukaryotes (and in chloroplasts of organisms like plants). Note that prokaryotes do not have a nucleus. What is RNA made up of and where is it found - -RNA is made up of transcribed genes, which are regions of DNA that encode something, such as RNA or a protein. DNA can encode for RNA or proteins with codons, which are triplet sets of DNA. RNA polymerase reads DNA and incorporates nucleotides which complement the template DNA to create an RNA strand. Codons then determine the information used to synthesize proteins. RNA can be found in the nucleus (for eukaryotes), ribosome, and cytoplasm of a cell. They are able to leave the nucleus during the translation po