BSCI222 Exam 2

Key characteristics of genetic material

• contain complex info

• compact

• stable

• replicate accurately

• capacity to vary

• easily/quickly retrieved

Supercoiling

coiling of DNA by overwinding or underwinding

Positive supercoiling

DNA is over-rotated and twists on itself

Negative supercoiling

DNA is under-rotated and twists on itself in opposite direction

Topoisomerase

Enzyme that adds or removes rotations by breaking strands then rotating and rejoining the ends

How many bps per rotation in DNA

10

Role of supercoiling

used to compact DNA in bacteria

chromatin

genetic material made of 1/3 DNA, 1/3 histone proteins, and 1/3 non-histone proteins

euchromatin

dispersed form of chromatin, often involved in active transcription

heterochromatin

condensed form of chromatin

relationship between differentiation and chromatin

as cells differentiate, they tend to have a higher percentage of heterochromatin

polytene chromosome

huge chromosome made of many aligned DNA strands as a result of DNA replication without division

chromosomal puff

euchromatin region of polytene chromosome where active transcription is taking place

constitutive heterochromatin

permanently condensed, transcriptionally inactive regions of DNA typically in centromeres and telomeres

nucleosome

eukaryotic unit of DNA, made of 8 histone proteins with a strand of DNA wrapped around it

H1 protein role

clamps DNA to nucleosome

nucleosome core protiens

2 of each: H2A, H2B, H3, H4

condensin

protein complex which folds DNA and forms loops that encircle DNA loops

protein kinase

transfer phosphate group from ATP to protein in a process called phosphorylation

phosphatase

enzyme which removes phosphate group from enzyme

Topoisomerase II

Enzyme which untangles DNA strands by cleaving one strand and pulls the other through the gap

Topoisomerase I

cuts one strand of the duplex, relaxes and reaneals it

chromosome location during interphase

chromosomes segregate into distinct territories when uncondensed

transcription factories

regions where loops of chromatin extend outside their chromosomal region to meet where transcription enzymes are concentrated

C value

amount of DNA per cell

C value paradox

in eukaryotes there is no correlation between c value and complexity of organism

gene family

similar but not identical genes that arose from duplication of the same genes

tandem repeat sequences

region where nucleotides patterns are repeated adjacent to one another

Nucleolus Organizer Regions (NORs)

chromosomal regions consiting of tandem repeat sequences that encode rRNA

Telomere function

act as chromosomal caps made of repeating noncoding DNA that can be sacrificed in replication

centromere function

binding site of spindle fibers that is composed of tandem repeats

satellite DNA

repeated pattern between 1 to 1000s of bps

Micro satellites (or short tandem repeats: STR)

tandem repeats 2-5 bps in length in specific regions of genome

CODIS

Combined DNA Index System which uses 13 STRs to build a DNA profile on individuals

microevolution

gradual change in allele frequencies in a population over short period of time

macroevolution

large scale evolutionary change that occurs over long period of time

transposable elements

sequences that can move around the genome

DNA (Class II) Transposons

cut out DNA and move it to another part of the genome

Retro (class I) transposons

Use RNA intermediaries to copy DNA and paste it into another part of the genome

Class I & II transposons commonalities

• flanking direct repeats

• terminal inverted repeats

insertion sequence

two inverted repeats surrounding a sequence contains encoding information for transposase which recognizes the flanking inverted repeats, cleaves the insertion sequence, then inserts it elsewhere

composite transposon

genetic sequence flanked by two insertion sequences that allows the whole sequence to transpose

plasmid

small circular extrachromosomal double stranded DNA molecules which replicate independently and primarily present in prokaryotes

conjugation

transfer of genetic material through a pilus. Ex: plasmids with antibiotic resistance are transferred

V(D)J recombination

shuffling, cutting and recombination of the VDJ genes to produce millions of different permutations of antibodies

Mosaic species

a species built from multiple different genomes

endogenous retrovirus (ERV)

viral DNA that has inserted itself into germline DNA and is inheritable

HERV-W

most studied ERVs. They have been domesticated. The proteins they encode allow mother and daughter cells to fuse in the placenta and transfer nutrients

selfish/junk DNA

parasitic DNA that exists because it is good at getting itself replicated

integrase

enzyme produced by retroviruses that allows it to insert DNA into its host

LINE

Long interspersed nuclear elements. class of retrotransposon. Streamlined retrovirus genomes that are highly repeated that copy and pastes itself throughout the genome

Most common LINE

LINE-1, only LINE that’s still active

SINE

short interspersed nuclear elements. retrotransposons class that does not encode protein and must rely on other retrotransposons for endonuclease and reverse transcriptase

endonuclease

Enzyme encoded by LINEs which makes a double-stranded cut in DNA and allows the LINE to insert itself

reverse transcriptase

Enzyme encoded by LINEs which turns the LINE’s RNA transcript back into DNA to be inserted

Mutagenetic effects of transposons

Inserts into another gene, disrupting function. promotes DNA rearrangements

Significance of Fugu fish

its genome is “dewormed”, it has a normal amount of genes but much smaller genome size

Central Dogma

genetic information is transferred from DNA to RNA to proteins

3 groups of amino acids

Amino group, carboxyl group, R group

Alphafold 3 significance

Able to predict the structure of proteins from their amino acid sequence which allows understanding of their function

Watson and Crick significance

discovered the 3d structure of DNA

Paleogenetics

Extraction and analysis of DNA from ancient specimens, possible due to the stability of DNA

eDNA and its significance

environmental DNA, genetic material released by an organism into its environment. Can be used to tally new and ancient ecosystems

3 Nucleotide components

Phosphate groups, sugar, nitrogen containing base

Structural difference between DNA and RNA

RNA contains ribose which DNA contains deoxyribose

Purine vs Pyrimidine

Purines have two ring structures, pyrimidine has one

purines

Adenine and guanine

pyrimidine nucleotide

cytosine, thymine, and uracil

Chargaff’s rule

There is an equal amount of A as there is T, and C as there is G in DNA

Maurice Wilkins and Rosalind Franklin

Took an x-ray crystallography that suggested helical structure of DNA

Watson and Crick

proposed the double helix shape for DNA

Anti-parallel

The strands in the double helix of the DNA run opposite directions of one another

Phosphodiester bond

Phosphate groups forming the backbone of DNA, joins the 3’ end of one sugar to the 5’ end of another

DNA melting temperature rule

2C for each A/T pair, 4C for each G/C pair

B-DNA

Right handed DNA, predominant in cells