exam 4 bio

DNA

Deoxyribonucleic acid, genetic material. variation gives rise to different traits and species. information storage and expression

Nucleic acids

DNA & RNA

gemome

complete compliment of DNA. in nucleus, chloroplasts and mitochondria

nucleotide structure

phosphate group, pentose (DNA is deoxyribose, RNA is ribose), nitrogenous base (purine or pyrimidine)

purines

Adenine + guanine. double ring

pyrimidines

cytosine, thymine, uracil. single ring

DNA strand

phosphodiester linkage, sugar-phosphate backbone, directionality is based on sugar orientation (5’ end or 3’end). bases on inside.

5’ end

start of DNA; everything goes 5’ to 3’. can tell difference because of phosphate at the end

3’ end

end of dna; everything goes 5’ to 3’. has OH sticking out at the end

adenine matches to

thymine / uracil

thymine matches to

adenine

guanine matches to

cytosine

cytosine matches to

guanine

are dna strands complementary?

yes, antiparallel as well (in opposite directions)

erwin chargaff

1950, found out A=T and C=G.

Rosalin Franklin and Maurice Wilkins

X-ray diffraction suggested that DNA strand is a double helix. 1950s

James Watson and Francis Crick

Figured out DNA structure using rosalind franklins model

template strand

when replicating the sequence of dna is figured out from these strands

replication forks

DNA double helix goes straight but when it unwinds it goes diagonally left or right

Does DNA direct its own duplication?

Yes, using AT/GC rule

how does DNA replication begin?

origin of replication (ori) → replication bubble & forks → bidirectional replication

DNA strand unwinds → DNA replication begins outward from two replication forks → DNA replication continues in bith directions

Parental strands

original DNA strands

daughter strands

new DNA after being replicated is called daughter strand

semiconservative method

actual way of dna replication; each DNA helix has has one parental and one daughter strand

prokaryote vs eukaryote replication

prokaryote: 1 circular chromosome, one origin of replication

eukaryote: multiple linear chromosomes, multiple origins of replication

helicase

recognizes ori and denatures DNA; breaks hydrogen bonds; moves from 5’ to 3’ (everything DNA related moves 5’ → 3’); causes supercoils in DNA

single strand binding proteins

coats the DNA strand to prevent them from reforming a double helix

topoisomerase

travels slightly ahead of replication fork and alleviates supercoils caused by helicase by cutting, untwisting, and reattaching DNA together.

primase

reads the DNA and adds a corresponding RNA nucleotide, travels from 5’ → 3’, makes the 3’ end for polymerase to bind to

primers

RNA strand thats about 10 nucleotides long, complementary to DNA

DNA pol III

actually makes DNA, needs a phosphodiester bond AND hydrogen bond (which is why we have primer), needs a free 3’ end to bond to

deoxynucleotide triphosphates (dNTPS)

energy

leading strand

continuous DNA replication

lagging strand

moving away from replication fork, makes okazaki fragments and connects them together afterwards (DNA pol III makes a short fragment moving away from fork, then goes back to the beginning of the fork and makes a new fragment then connects the two and repeats), DNA is made in pieces

DNA pol I

finds the RNA primers, rips them out, replaces them with DNA

ligase

looks for gaps in DNA, makes a bond

are DNA mismatches rare?

yes

mismatch repair

rips out nucleotide and adds a new one

nucleotide excision repair

repairs problems caused by UV, uses nuclease and cuts out bad nucleotides; DNA pol goes back in then to repair DNA and ligase adds the phosphodiester bond

thymine dimers

2 thymine binding to eachother instead of to corresponding adenine

telomeres

end of linear chromosomes, gets shorter with each cell division. once used up cells can no longer divide

why do we need telomeres

the ends of linear chromosomes cant be perfectly replicated since there is no 3’ end for DNA pol when removing final

primer, so chromosomes get shorter and shorter

telomerase

protein and RNA cell complex, prevents chromosomes from shortening. only active in germ (sperm & egg) cells

germ cells

reproductive cells

somatic cells

non reproductive cells

chromosome

packaged for cell division, most compact version of DNA

chromatin

normal DNA packaging, loosely compacted

nucleosome

way or shortening DNA by wrapping it up

euchromatin

DNA is accessible, expressed

heterochromatin

DNA is not accessible or expressed

histone proteins

in eukaryotes

eukaryotic chromosomes

1 chromosome is hundreds of millions of base pairs long