molecular bio exam 1

Major groove

site of most protein-DNA interactions

minor groove

site of fewer, but very specialized and critical protein-DNA interactions

Molecular weight of DNA

660 daltons

Common amino tautomer

imino

common keto tautomer

enol

Base flipping

process where one nucleotide flips outside of the double helix

why would you base flip?

could be used for chemical modification, base excision repair, or recombination

which groove of DNA has more chemical information?

The major groove, hence why it is more likely to be important in protein-DNA interactions

right vs left handed helices

right = cw, purines are in anti

left = ccw, purines are in syn

B DNA

• normal watson-crick DNA

• right handed

• favored at high water concentrations

A DNA

• can be RNA-RNA or DNA-RNA

• right-handed helix

• hole in center of helix

• happens under dehydrating conditions

• happens in high temp

Z DNA

• important in some transcriptional regulation

• zig-zagged

• left-handed helix

  • areas with high salt

S DNA

• slipped strand mispairing

  • happens when there are lots of repeats in sequences

propeller twist

• when base pairs twist

• too much twist can lead to strand separation

covalently closed circular DNA properties

• linking number

• twist

• writhe

linking number

number of times one strand would have to pass through the other to separate two strands

twist

number of times one strand wraps around another

writhe

number of times a double helix crosses over itself

methods of denaturation

• heat

• increase base solubility

• decrease salt concentration

• high pH

Tm

• the point where 50% of DNA is single stranded

• A260 of 1.8 means all phosphodiester bonds are broken

• Tm goes up with ionic strength and in GC regions

• Tm goes down with ionic strength and in AT regions

DNA renaturation

• higher concentration higher renaturation rate

• higher copy number higher renaturation rate

Topoisomerases

can change linking number of supercoiled DNA

Topoisomerase type I

• can only make a single stranded break and change linking number by one

• don’t require ATP

Topoisomerase type II

• can change linking number by two

• require ATP

• DNA gyrase is an example in prokaryotes that can introduce negative supercoils

catenanes

“links of chain”

types of II isomerases

• IIA has 2 homodimers and can only relax supercoils

• IIB has a similar enzyme that removes knots after replication in bacteria (type IV)

• type VI decatenates dna during replication and relaxes positive supercoils

slow to fast moving through electrphoresis

slow:

• Nicked (DS)

• Linear (DS)

• Supercoiled (DS)

• Circular (SS)

fast

Unique sequences

primarily protein coding genes (1 copy)

slightly repetitive

generally protein coding, (1-10 copies)

Middle repetitive

clustered or dispersed genes in multiple copies to increase the amt of product (10- ~400 copies) like rRNA gene clusters or transposable elements

highly repetitive

(1000 to millions of copies) centromere repeats, coding for miRNAs, or regulatory genes that have a lot of copies

Direct repeat

• simple repeat that is identical in orientation

• ex:

• A-B-C-D-E-F

• A’-B’-C’-D’-E’-F’

inverted repeats

A-B-C-D-E-F

F’-'E’-D’-C’-B’-A’

G-U pairing

it is tolerated in RNA and critical in tRNA-mRNA binding

free energy and stability

• if free energy is negative = stable form

• if free energy is positive - unstable form

• between +1 and -1 structure might form and will dissociate pretty quickly

delta GTotal = delta Gi + delta Gsym + delta Gx + delta Gu

delta Gi and delta Gsym together are 3.8

delta Gx = sum of all rxns forming H bonds

delta Gu = sum of all situations in secondary struct where opposite bases arent complementary

RNAseP

ribonucleoprotein that processes precursor transfer RNA (tRNA)

leadzyme

cleaves RNA at phosphodiester bond when there’s lead

hammerhead ribozyme

catalyzes reversible cleavage and joining rxns forming a 3D tertiary structure

twister ribozyme

can self-cleave, fastest rate of all ribozymes

mitochondrial DNA diseases

• Kearns-Sayre syndrome (KSS)

  • salt & pepper retinal pigmentation

• leigh syndrome & maternally inherited leigh syndrome

  • causes brain abnormalities resulting in seizures

• mitochondrial DNA depletion syndrome (MDS)

  • leads to muscle weakness and/or liver failure

• mitochondrial neurogastrointestinal encephalomyopathy (MNGIE)

  • droopy eyelids, weak limbs, digestive problems

why is yeast mtDNA larger than human and why might there be more recombination?

• more recombination bc theres more mtDNA

• larger bc there are more repeated secuences

Hu

analog to histones, resembles H2B,can introduce negative supercoils

circular vs linear chromosomes

linear telomeres can degrade, if telomeres degrade the chromosomes could fuse together, circular has more dense coding gene

why do prokaryotes have a higher gene coding density than eukaryotes?

prokaryotes have less introns

chi site

site where recombination can take place (the majority of repetitive sequences)

avg human genome length

27kb long

ways to splice RNA

• normal

• exon skipped

• exon extended

• intron retained

• alt exons

functional repeats

• centromeres

• telomeres

• origins of replication

conserved DNA elements (CDE)

regions that are highly observed

pseudogenes

• unique components of intergenic DNA

  • rarely have any readily apparent function and often many repeats

Structural maintenance of chromosomes (SMC proteins)

• cohesins

• condensins

nucleosome

basic repeating unit of chromatin in the nucleus

histone vairants

• H2Az

• H3.3

• CENP-A

histone chaperones

• CAF-1

  • H3-H4

• HIRA

  • H3-H4

• RCAF

  • H3-H4

• NAP-1

  • H2A-H2B