14: Nucleic acid structure Flashcards
What is the difference between thymine and uracil?
thymine - Ch3 grp
uracil - H
What are the characteristics of the ring structures of nitrogenous bases?
flat - relatively hydrophobic, edges have hydrogen bonding groups
How are nitrogenous bases categorized by structure?
purine: double ring of 5C and 6C - adenine and guanine
pyrimidine: 6C ring - thymine, uracil, cytosine
What is the purpose of the N in all nitrogenous bases?
makes N-glycosidic bonds to make nucleoside
What is the structure of a nucleoside?
sugar (ribose or deoxyribose) + base
N on base attached to 1’ C on sugar through N-glycosidic bond
difference between ribonucleoside and deoxyribonucleoside?
ribose - OH
deoxyribose - H (reduced ribose by O removal from 2’ carbon)
What is the structure of a nucleotide?
base + sugar + phosphate(s)
up to 3 phosphates
phosphate adds to 3’ C of sugar
What is the structure of a polynucleoside?
What is the bond used?
How is the sequence of polynucleotides written?
5’ end usually but not always has a phosphate group
phosphodiester bond of 3’ C of 1 sugar to phosphate group to the 5’ C of the next sugar (RNA and DNA)
written 5’ to 3’
What is B-DNA structure?
left hand or right hand, sugar phosphate backbone, antiparallel double helix
What is the evidence for B-DNA structure?
- char gaffs rule (amt of A=T, amt G=C to matter tissue or species)
- x-ray diffraction pattern
- structures of bases (enols vs ketone form)
What are the forces stabilizing the double helix?
- base stacking (important)
- flat nitrogenous bases stack protecting hydrophobic surface drives folding and stability - base pairing (HB) have constant width for each BP (10.85 A)
hydrophobic bases inside and sugar and phosphate (neg charge) are hydrophilic
What are the major and minor grooves? Why does this occur?
allows for proteins to interact with DNA by proteins sticking into correct grooves
major groove has more info and has more distance between backbone and base and this occurs bc the BP are not directly 180º from each over
What are the dimensions of B-DNA?
minor groove + major groove height = 10 BP = 34A
20A width
What is the effect of increasing temperature on nucleic acid?
How is this measured?
denaturation - separating strands
annealing (renature) reversible possible if temperature change is gradual so that BP will occur correctly
measured with absorbance of 260nm (absorbed better by single stranded DNA)
As length of BP increases, melting temperature…
increases
- more base stacking + pairing interactions = more difficult to pull strands apart
As %GC increases, melting temperature…
increases
- GC stand very well = more difficult to pull strands apart
As complementarity increases, melting temp…
increases
- mismatches in DNA = less HB, structure interrupted
[salt] increases, melting temp…,
increases
- phosphate group is negatively charged = phosphates repel each other ; salt = positive charge = protects/shields phosphates from each other = less likely to pull apart
water has lowest Tm
[organic solvent] increases, melting temp
decreases
- artificial environment, increases hydrophobic effect = makes DNA less stable = easy to pull apart
[urea] or [formamide] increase, melting temp…
decreases
- denaturing agents = easy to pull apart strands
extremes of pH cause Tm to
decreases
- increases DNA instability
What are 7 the main differences between DNA and RNA?
- deoxyribose vs ribose
- ribose allows different structures bc of OH group (OH can be deprotonated or act as nucleophile) = unstable in basic solutions bc backbone can degrade
- thymine vs uracil
- DNA is much longer in BP than RNA
- DNA = ds structure, RNA usually does not have complementary strand = can BP with it self = stem loop structures (tRNA)
- DNA fewer base modifications, RNA many base modifications for more structural variety (tRNA)
- RNA structure is sequence-dependent like proteins (can have distant regions BP), DNA structure will form double helix no matter the sequence (independent)
How long is human DNA?
102cm per strand (approx 2 meters for both)
3 billion BP
What is chromatin?
DNA + associated packaging proteins
heterochromatin: more packaged = harder to transcribe
euchromatic: less packaged = easier to transcribe
What are histones? What are its properties? What are the major subtypes?
relatively small proteins (100-200AA) that package DNA in eukaryotes
- higher Arg+Lys content = positively charged = attracts neg charge DNA phosphates
- conserved through evolution (even mutations dont’ change much - similar charge and structure in mutants)
H1, H2A, H2B, H3, H4 (from largest to smallest)
What are nucleosome core particles? What is the size and structure?
146 BP of DNA wrapped around histone octamer (2 of each histone H2A, H2B, H3, H4)
DNA wraps almost 2x around octamer
has N-terminus that can be covalently modified (phosphorylation, methylated) so that cell can determine where nucleosome core particle should be
What is a nucleosome? Size?
NCP (146 bp) + one linker (~50bp) = 200 bp
beads on a string
What are 30-nm chromatin fibres? Inhibits?
NCP packed together
H1 binds to core partible where DNA comes off N terminus - allows for regular structure
inhibits transcription
1 model: super helical structure: NCPs stack on top of each other so that DNA and linker region on inside and core particle histones are on the outside – 30 nm width
What is the order of levels of packing DNA?
- B-DNA (20A)
- nucleosome
- 30 nm fiber
- 30-200kbp loops of 30nm anchored to nuclear matrix (RNA and non-histone proteins)
