Biology 202 Midterm Study Guide 2025

Finding particular function of a gene - -reducing expression (knock out) and increasing gene expression How can we manipulate dna? - -restriction enzymes after heating Separating dna fragments - -gel electrophoresis (sds-page) Small dna fragments separated in .... - -polyacrylamide gels Larger dna fragments separated in ... - -arose gels Dna possesses what charge? - -negatively charged Why does dna possess a negative charge? - -due to the phosphate backbone What travels further in electrophoresis large molecules or small? - -smaller dna fragments due to smaller and more polar How can dna be detected in a gel ? - -staining with ethidium bromide How does ethidium bromide fluoresce dna? - -under uv light, also acts as a mutagenic agent (intercalating agent) Pulsed-field electrophoresis - -used to separate/resolve larger dna fragments with two electric fields that run opposite directions Restriction endonuclease (restriction enzymes) - -cut dna molecules at an internal site recognizing a specific sequence Restriction site - -specific recognition sequence Recombinant dna - -2 different sources dna mixed together Bacteriophages - -able to cut dna of viruses and cut viruses out (attacks bacteria) What was the first genome fully sequenced? - -e. Coli Dna strands run ... - -antiparallel (5' to 3' and 3' to 5') Staggered cut dna - -sticky ends, able to cohesively integrate into a new dna sequence (recombination) Biology 202 Biology 202 Biology 202 Blunt ends of dna - -where strands are cut at the same point (same fragment lengths) Restriction enzyme sites are ... - -palindromic (sequences read same forwards and backwards) When dna is cut with one restriction enzyme and combinations of enzymes can result in ... - -creating a restriction map What does methylation do? - -inhibits transcription (inactivating it) Many restriction enzymes won't cut dna strands if it is ... - -methylated Unmethylated genes are - -active or potentially active Process of souther blotting - -digested with restriction enzyme, separated by gel electrophoresis, transfers dna from gel to paper, nucleic acid probe added, made visible through autoradiography What is autoradiography? - -x-ray film makes bound nucleic acid probe visible Cloning vector - -can replicate inside a cell grown in culture and adding dna of interest into element What seals dna fragments together? - -dna ligase Pcr (polymerase chain reaction) - -amplifies a region of dna insert What do you need to know before running a pcr? - -you must know the sequence of the dna you wish to amplify What is taq polymerase? - -heat resistant dna polymerase used for primers to stick to the ends Genomic library - -represents most or all of that genome (includes junk dna) (coding, regulatory, and junk) Cdna library - -only expressed (coding region) part of the genome not the regulatory region, produced from reverse transcriptase Eukaryotic cells have ... While prokaryotes have ... - -introns and exons, neither When splicing occurs ... Is removed - -introns (only in eukaryotic cells) In pcr the dna must be ... To work - -double stranded (cdna is double stranded) Biology 202 Biology 202 Whole genome sequencing - -determines the order of the nucleotide sequences (helps diagnose diseases eg. Sanger sequencing The sanger method - -chain termination method, uses dideoxynucleotides (ddntp) to interfere with normal enzymatic synthesis of dna eg. No hydroxyl group present on 3' end to add to Genome - -a complete copy of all genetic information of that organism Mitochondrial and chloroplast dna is ... - -circular unlike eukaryotic dna which is linear Diploid - -2 sets of chromosomes (one from each parent) Map-based cloning - -for genomic library and maps for different fragments Contigs - -overlapping dna sequences Shot gun sequencing - -rapidly sequencing and assembling a genome (ends of random fragments are put together with overlapping contigs) The complexity of an organism and genome is not properly reflected by ... - -the size of the genome C-value paradox - -that the genome size for not seem to reflect the number of genres in eukaryotes Mutations in the dna sequences may alter ... And why? - -the lengths of the restriction fragments, due to the restriction enzymes possibly not recognizing the sequences and cuts in different areas of the gene sequence Single nucleotide polymorphisms - -found greater in non coding region and are closer to each other on the same chromosome tend to be inherited in blocks (haplotypes) When single nucleotide polymorphisms are found more in coding region what may happen to the organism? - -"less fit" organisms Variable number tandem repeats - -variable numbers of copies of particular repeat sequences (small sequences that are repeated) What are the different types of variable number tandem repeats - -minisatellite dna and microsatellite dna What are so useful of vntr's? - -could help narrow down a criminal, everybody has different vntr's so it helps crime solving Biology 202 Biology 202 Northern blotting - -rna sample is subjected to electrophoresis and transferred to a special blotting paper, paper exposed to radioactive labeled dna probe containing gene sequence of interest Mrna has a - -poly a tail, why beads of ttttt are present to separate mrna and rna from eachother Cdna can be made from - -isolated mrna with reverse transcriptase Cdna can be amplified by - -primers that correspond to known sequences In situ hybridization (fish) - -fluorescent dna probe is used to detect the position of a gene on a chromosome Dna microarrays - -tiny microscope slides or silicon chips that are spotted with dna fragments Two-dimensional gel electrophoresis - -separates proteins first based on charge then by size Isoelectric point - -charge at a specific protein, from r groups