BIOL 325 DNA STUDY GUIDE

exam 1

describe the structure of DNA monomers and polymers, including the DNA double helix

• DNA is composed of nucleotides (monomers) that consist of a deoxyribose sugar, negatively charged phosphate group, and one of four nitrogenous bases (adenine, cytosine, guanine, and thymine)

• nucleotides are joined together via phosphodiester bonds (strong covalent bond) to form a long polymer chain resulting in the DNA backbone

• the DNA double helix is then formed by the twisting of the long polymer chains and the strands run anti-parallel to each other (5’ to 3’)

what is a nucleoside?

a molecule that only contains the deoxyribose sugar and a nitrogenous base

what is a nucleosome?

packaged DNA + histone (protein)

what is chromatin?

unwound DNA

what is a chromosome?

wound DNA

what is methylation?

the process to not express/silence certain genes?

what is cytosine methylation?

a methyl group is added onto a cytosine, preventing the expression of the gene and prevents restriction (MOST COMMON)

what are the purpose of linkers?

to give space

what is deamination?

the removal of an amine group (R-NH₂) which means that the DNA is being degraded

what is dideoxy?

the process of terminating a chain by taking away the oxygen that allows nucleotides to stick

how does DNA replication conserve AND protect the sequence?

• DNA replication is conserved and protected through the DNA polymerase enzyme. DNA polymerase creates the daughter strand, adds the correct complementary base, and also proofreads the DNA strand

• DNA replication is also protected from degrading through telomeres

what are the various enzymes needed for DNA replication?

• DNA polymerase 1 = removes RNA primer and replaces RNA primer with DNA on an older okazaki fragment

• DNA polymerase 3 = creates daughter strand and proofreads by cutting out the incorrect sequence and putting in the correct sequence

• primer (RNA) = makes the first few nucleotides

• primase = makes RNA primer

• DNA ligase = creates the last phosphodiester bond

what is telomerase?

an enzyme that has an RNA template that continues telomere sequence by helping continue DNA sequence

what do telomeres do?

protect the chromosomal ends and tells how old a cell is

contrast VGT and HGT

• VGT: DNA in genome (parent) —> offspring (natural)

• HGT: genetic transfer between two entities (genes and plasmids) and has three methods of transferring in prokaryotes (natural and artificial)

name and describe three ways in which DNA can be transferred between bacterial cells

1. conjugation: transfer of genetic material between two bacteria via sex pilus

2. transformation: one bacteria takes up DNA from the environment

3. transduction: transfer genetic material via virus (bacterial phage); infects bacteria and gives them their DNA

what is the lytic cycle?

viral DNA takes over host DNA and the cell lyses/breaks/explodes open to release the phages but kills host cell in turn

what is the lysogenic cycle?

• viral DNA stays in host cell/integrates itself w/ the host DNA which means when the host cell divides, the viral DNA in the host cell divides too

• virus is not often expressed but when expressed, prophage is cut out and begins a lytic cycle

how does HGT compare between eukaryotic and prokaryotic organisms?

• eukaryotes cannot perform conjugation because they have no conjugation bridge unlike prokaryote

• viruses can affect both eukaryotes and prokarytoes via transduction

• eukaryotes cannot take up DNA from environment unlike prokaryotes due to being a single celled organism

explain how transposable elements affect the genomes of organisms

TEs affect the genomes of organisms because they can cut themselves out and randomly insert themselves into a genome that can cause cancer or permanent location that they cannot jump out of

what are the types of DNA damage?

• replication mismatches/insertions/deletions

• deamination

• depurination

• base alkylation

• pyrimidine dimers

• interstrand crosslinks

• ssDNA breaks

• dsDNA breaks

what DNA damage is pyrimidine dimers?

when pyrimidines doubly covalently bond with each other and do not interact with the other strand

what are some DNA repair pathways?

• base excision repair (BER)

• nucleotide excision repair (NER)

• mismatch repair (MMR)

• homologous recombination (HR)

• nonhomologous end joining (NHEJ)

what are the enzymes that modify DNA?

• polymerase

• helicase

• primase

• methylases

• deaminases

• exonucleus

• endonuclase

• ligase

what is the purpose of DNA polymerase?

promotes the formation of phosphodiester bonds

what is the purpose of helicase in DNA modification?

unwinds/untangles DNA double helix

what is the purpose of primase?

initiates DNA synthesis by synthesizing RNA

what is the purpose of exonucleases?

removes ends of linear DNA

what is the purpose of endonucleases?

cuts interior DNA (RE, DNase 1)

what is the purpose of DNA ligase?

promotes the formation of a single phosphodiester bond

what is the purpose of a restriction endonuclease in a bacteria?

it acts as its immune system and cuts out any foreign DNA

how are restriction endonucleases named?

bacteria, strain, what enzyme it is cut at

what is the purpose of DNA ligase when a Pst 1 enzyme is present?

puts the cut strand back together

what is a plasmid?

used to move genes from cell to cell, test tube to cell, virus to cell

what are the five classes of naturally occurring plasmids in prokaryotes?

1. resistance plasmids (R plasmids)

2. fertility plasmids (F plasmids)

3. virulence plasmids

4. degradative plasmids

5. col plasmids

what is the role of a naturally occurring plasmid?

gives beneficial factors to bacteria such as antibiotic resistance

what is the role of artificial plasmids?

to drive the replication of recombinant DNA

what are the various tools used to make new genetic combinations in vitro?

• plasmid vectors (bacteria)

• viral vectors (plants and animals)

• artificial chromosome vectors use electroporation (the use of electric pulses to introduce DNA into the cells)

• restriction enzymes (cut DNA)

• DNA ligase (paste DNA)

• CRISPR-Cas9

what is recombination?

the process of exchanging genetic material in vitro or in vivo

how are new combinations of genes generated in sexual reproduction?

during meiosis, two homologous chromosomes line up next to each other and cross over to create variability in the gametes

how are new combinations of genes generated in asexual reproduction?

through either of the three methods of HGT (prokaryotes) and TEs (in eukaryotes)