DNA + RNA

DNA/RNA

polymers of nucleic acids

carriers of genetic info

nucleic acids

composed of a 5-carbon sugar, nitrogenous base, and phosphate group

RNA (ribonucleic acids)

contains the sugar ribose

DNA (deoxyribonucleic acid)

contains the sugar deoxyribose

nitrogenous bases

order of these along the length of DNA and RNA dictate the order of amino acids in the different proteins

pyrimidine or purine

types of nitrogenous bases

pyrimidine

single 6-membered ring, containing two nitrogen atoms and is planar

purine

contains two rings , and is not quite planar having a slight pucker between two rings

pyrimidine and purine

these are relatively insoluble in water (hydrophobic)

adenine

guanine

types of purines

cytosine

uracil (RNA)

thymine (DNA)

types of pyrimidine

adenine

guanine

cytosine

uracil

thymine

nucleosides

consist of a nitrogenous base and sugar (no phosphate group)

adding -idine to root name of pyrimidine (cytidine, uridine, thymidine) or -osine to purine (adenosine and guanosine)

if sugar is deoxyribose, deoxy- is added to the front

how nucleosides are named

glycosidic bond

nitrogenous base is attached to the C1 carbon of ribose/deoxyribose via a ? bond

nucleotides

have nitrogenous base, sugar, and phosphate group

C5 carbon of the sugar

where phosphate group is located on nucleotide

2 phosphates (diphospate)

3 phosphates (triphosphate)

1 phosphate

types of phosphate groups a nucleotide can have attached

nucleoside name + number and position of phosphate groups

how to name nucleotides (ex. adenosine-5’-triphosphate)

nucleotides with a triphosphate group

NTPs

nucleotide with a diphosphate

NDPs

NDPs and NTPs

nucleotides that are relatively strong polyprotic acids

can dissociate 3 and 4 protons from their phosphate groups

mononucleotides

can dissociate 2 protons from the phosphate group

stable complexes

resulting phosphate anions form ? with divalent cations such as Mg2+ and Ca2+

Mg2+

most nucleotides in the cell exist primarily as ? complexes

ATP (source of energy)

this molecule bonds between phosphates groups in nucleoside 5’-triphosphates

nucleic acids

polymers of nucleotides linked by phosphodiester bonds

phosphodiester bonds

bonds between nucleotides

nucleotides

have a phosphate bonded to C5 and OH on C3

nucleotides

bonded by phosphodiester bond between the C3 OH of one nucleotide to the C5 phosphate of the next nucleotide

phosphate group on C5 —> 5’ end

OH group on C3 —> 3’ end

direction of nucleic acids

structure of DNA or RNA strand

consists of sugar-phosphate backbone, with bases protruding from backbone

genetic info

the order of bases encodes the ?

5’—>3’ end

DNA and RNA sequences are always written down in the ? direction

order of bases

p

notations for DNA and RNA sequences can list the ? or can have a ? in between to designate phosphate groups

DNA

double stranded → made of sugar-phosphate backbones on the outside with bases buried in the center

hydrogen bonded

bases from each strand are ? bonded to each other

stacking (mostly Van der Waals)

each base pair in a double stranded DNA has ? interactions with top and bottom neighbors

thymine (T)

adenine (A) bases pairs with ?

guanine (G)

cytosine (C) base pairs with ?

Watson-Crick base pairs

A-T and C-G

three H bonds

number of H bonds between C and G

2 bonds

number of H bonds between A and T

helical structure

two strands of DNA form a ?

amino acid sequences

sequence of the bases along with the length of DNA encodes the ? of the protein

number of base pairs

DNA size is usually given by the ?

anti-parallel

two strands of DNA have a ? orientation

5’ end

3’ end

one strand of the ? (P) at the top and ? (OH) at the bottom, other strand is the opposite orientation

hydrogen bonding

hydrophobic effect

stacking forces

forces that stabilize the double helix

H bonds

large number of these bonds between all the bases that stabilize the double helix

hydrophobic effect

the bases are hydrophobic, so being “buried” in the core is energetically favorable which stabilizes helix

stacking forces

bases in double stranded helix are stacked on top of each other, leading to stabilization in helix due to attractive Van der Waals forces (induced dipole interactions)

major and minor grooves

types of grooves in DNA

antiparallel

in order for bases to pair in double stranded helix, the strands need to be ?, giving sugars on the two strands opposite orientations

angle

major and minor grooves

two sugar-phosphate backbones are not directly across the helix from each other, but are rather at an ? —> causes the backbones of the two strands to be closer together on one side and farther apart of the other strand —> results in ? and ?

B, A, and Z

different double-stranded conformations of DNA

B-DNA

most prevalent form of DNA in solution

simple right-handed helix

helix repeats every 10 bp

forms major and minor groove

A-DNA

usually forms when DNA is dehydrated

found in double-stranded RNA and in some RNA-DNA hybrids

forms right-handed helix, making 1 turn every 11 bp

shorter and wider compared to B-DNA

bases are tilted and not perpendicular to the helix axis as in B-DNA

major groove: extremely narrow and deep

minor groove: very broad and shallow

Z-DNA

forms left-handed helix

was discovered using DNA that has the sequence CGCGCG

phosphates of the backbone form a “zigzag” pattern

methylation of C can favor changing DNA from B to Z form

major groove: flattened out

minor groove: extremely narrow and deep

role is still uncertain —> there are some viral proteins that bind Z-DNA and are necessary for pathogenesis

stem-loop structures

single-stranded nucleic acid can fold back on itself

stem-loop structures

ssDNA can form these types of structures but it is more often found in DNA, which is usually single stranded

stem-loop structures

bases in single stranded RNA pair to form ?

mismatched or unmatched bases

loops or bulges in stem-loop structures are made of ? bases that loop out

ribosomal RNA

found in ribosomes forms many stem-loop structures

denaturation by heat

heat disrupts base-pairing in DNA (melting)

as DNA melts and the bases unstack, the UV absorbance increases

melting temp (Tm)

increase in midpoint of absorbance

Tm

is dependent on the % GC and % AT content

denaturation by pH extremes

at pH values >10, bases become unprotonated, destroying their base pairing ability and denatures the DNA

low pH (<2.3) also denatures and depurinates DNA

reannealing

when strands reassociate after denatured DNA is removed from the denaturing conditions

process consists of strands finding the complementary strand and base pairing with it

renaturation rate

dependent of DNA concentration and time

a lot of times reassociation is imperfect and the sequences must dissociate again and pair properly

renaturation

the process occurs more quickly if the temp is warm enough to promote diffusion of the DNA molecules, but not hot enough to cause melting

rate of renaturation

an indication of sequence complexity

faster

DNA with more repeated DNA will renature ? than DNA with more unique sequences

faster

shorter strands of DNA (less bair pairs) will renature ? than longer strands of DNA (more base pairs)

hybrid duplexes

DNA from different species can form ?

DNA sequence or relatedness of two species

the amount of hybridization between two species is a measure of ?

messenger RNA (mRNA)

synthesized during transcription when an RNA copy is made of a sequence of DNA bases, which then directs the synthesis of a polypeptide chain (protein)

ribosomal RNA and transfer RNA

synthesized by transcription of DNA but they are not translated into proteins

rRNA and tRNA

types of RNA that fold into complex secondary and tertiary structures by intramolecular base-pairing interactions

prokaryotic mRNA

may encode several polypeptides

eukaryotic mRNA

encodes only one polypeptide which can be spliced into several versions

more complex than prokaryotic ones

have intervening non-coding regions (introns) that must be spliced out before translation + polyA tails and 5’ cap

synthesized in nucleus and move out to the cytoplasm for translation

introns

non-coding regions in mRNA that must be spliced out before translation

introns

polyA tail

5’ cap

components of eukaryotic mRNA

nucleus

where eukaryotic mRNA is synthesized

cytoplasm

where eukaryotic mRNA is translated

ribosomes

translate mRNA into proteins

composed of 2 subunits of different sizes (large and small) that can dissociate from each other

proteins and rRNA

each subunit in ribosomes consist of an assembly of ? and ?

rRNA

more than 80% of total cellular RNA is ?

tRNA

small RNAs that carry amino acids to the growing polypeptide chain on the ribosome

anticodon

determines which amino acid a tRNA carries

amino acids

these are attached to tRNAs by aminoacyl-tRNA syntheases

aminoacyl-tRNA syntheases

enzymes that attach tRNAs to amino acids

tRNA molecules

form a cloverleaf secondary structures with 4 or 5 segments

acceptor stem

structure on tRNA where the amino acid is linked to the tRNA

loop and stem of anticodon

stem-loop segment on tRNA

seven unpaired bases are on the ? and 3 are on the ?

acceptor stem

anticodon stem and loop

D-stem and loop

T-stem and loop

variable loop

structures on tRNA