Chapter 9

order of bases, 3-D conformation of backbone, supercoiling of the molecule

Name the primary, secondary, and tertiary structure of Nucleic acids

ribosomes

the sites of protein synthesis in all organisms consisting of RNA and protein

nucleotides

monomers of nucleic acids, purine or pyrimidine bases bound to sugars (ribose or deoxyribose) which in turn are bonded to phosphate groups (base, sugar, phosphate group)

nucleic acid bases

nitrogen containing aromatic compounds that make up the coding portion of nucleic acids

pyrimidine bases

nitrogen containing aromatic compounds that make up the coding portion of nucleic acids (Cytosine and thymine)

purine bases

N-containing aromatic compounds that contain a 6-membered ring, parent compounds of several nucleobases (Adenine and Guanine)

unusual bases

bases with different structures typically modified by methylation commonly found in t-RNA

nucleoside

purine or pyrimidine base bonded to a sugar (ribose or deoxyribose) with NO phosphate group

ribonucleoside

compound formed when a nucleobase forms a glycosidic bond with ribose (beta- D- ribose)

deoxyribonucleoside

compound formed with a nucleobase forms a glycosidic bond with ribose

3’ 5’ phosphodiester bond

a covalent linkage in which phosphoric acid is esterified to the 3’ hydroxy; of one nucleoside and the 5’ hydroxy; of another nucleoside; it forms the backbone of nucleic acid

• deoxyribose lacks the 2’ OH unlike ribose

• only RNA uses Uracil

  • some RNA has thymine

how does DNA structure differ from RNA

left, 5’, right, 3’

If p (phosphate) is to the ___ of the base letter like (pA) then it is a ___ nucleotide and to the ___ is a ___ nucleotide

Double helix

2 polynucleotide chains wrapped around each other, the fundamental structural motif of DNA

amount of A in DNA must be = to T and C to G because of complementary base pairing since one must always bind to the other the amounts must be equal

what is Chargaff’s rule

antiparallel, complementary

sugar phosphate backbone of each chain run in _____ directions (one 3’ to 5’ and the other 5’ to 3’). And because bases are complementary ____ must be complementary as well

3

how many H-bonds are between adenine and thymine

3

How many h-bonds are between cytosine and guanine

11 Armstrong (1.1nm)

the inside diameter of the sugar phosphate backbone of the double helix as well as distance between complementary bases (AT and CG) is _____

backbone may bulge

What happens to the backbone when noncomplementary base pairing occurs(AC or GT)

34 armstrong (3.4nm) and 10 base pairs

what’s the length of one complete turn of helix along axis

major groove

the larger of 2 empty spaces in an imaginary cylinder that encloses the DNA double helix (22A)

minor groove

the smaller of the 2 empty spaces in an imaginary cylinder that encloses the DNA double helix (12A)

B-DNA

most common form of DNA helix (right handed)

A-DNA

• form of DNA double helix characterized by having fewer residues per turn and major/minor grooves with dimensions that are more similar to each other than of B-DNA

• 11 base pairs per tern

• bases 20 degree perp to helix axis compared to 90 perp for B-DNA

• right handed

• found in dehydrated DNA samples or RNA/DNA hybrids

Z-DNA

• a form of DNA that is left-handed helix which has been seen to occur naturally under certain circumstances

• found in alternating purine-pyrimidine (CGCGCG)

• found in sequences with C methylated at numbers 5 position of pyrimidine ring

• can become B form by flipping 180 degrees without breaking backbone or H-bond

base stacking

interactions between bases that are next to each other in DNA chain

• bases can also slide sideways allowing for between contact with bases aove and below them on the same chain

• ring potions are hydrophobic and interact with each other vis van der waals

base, overlap, minor

B-DNA is optimal for ___ pairing but not for maximal ____. Because bases in the ___ groove are exposed/ come in contact with water

propeller twist

base pairing less optimal but overlap from base stacking is. It also eliminates contact in the minor groove with water

Step

dinucleotide pair + complementary bases

• Ex) AG/CT has a different structure than GC/GC

supercoils

extra twists (over and above the double helix) in closed circular DNA

negative supercoils

circular DNA with fewer than the normal number of turns of the helix (counterclockwise)

positive supercoils

circular DNA with more than the normal number of turns in the helix (clockwise)

topoisomerases

enzymes that relax supercoiling in closed circular DNA

Class I topoisomerases

cut phosphodiester backbone of 1 strand of DNA, ass the other end through and then reseal backbone

Class II topoisomerase

cut both strands of DNA, pass some of the remaining DNA helix between the cut ends and then resealD

DNA Gyrase

bacterial topoisomerases that introduces supercoiling into closed circular DNA

positive charged side chains on proteins (like Histones) and negatively charged groups of DNA at pH 7 allow for electrostatic interactions that favor the form of complexes

How does supercoiling take place in Eukaryotic DNA

chromatin

a complex of DNA and protein found in the Eukaryotic nucleus

histones

basic proteins found complexed to eukaryotic DNA (help form chromatin)

nucleosome

a globular structure in chromatin in which DNA is wrapped around an aggregate of histone molecules or core

• 150 base pairs of DNA in contact

protein core

octamer; contains 2 molecules of each histone EXCEPT H1 (H2A, A2B, H3, H4)

• H-bonds between complementary bases

• stacking of bases in native confirmation of DNA (largest contributor to stabilization)

For DNA to be denatured what must break

melting

heat denaturization of DNA

hyperchromicity

bases once stacked on top of each other in native DNA become unstacked as DNA denatures causes the bases to become more exposed they still absorb the same wavelengths (260nm) of light just MORE of it

• amount of G/C vs A/T pairs

  • G/C has 3 H-bonds which takes more energy to break than the 2 A/T has as a result if the DNA has more G/C pairs it will take more heat to denature

• aromatic ring shapes allow the pi clouds from base stacking to overlap more efficiently= more van der waals interactions

what effects melting point of DNA

transcription

order of bases passed from DNA to RNA (mRNA)

translation

process of protein synthesis which the amino acid sequence of the mRNA codes for a protein

• prokaryotes: no nuclear membrane= transcription and translation can happen at the same time

• eukaryotes: mRNA synthesized in the nucleus and undergoes processing including splicing out introns so that the expressible parts (exons) are next to each other

explain how and where transcription and translation occur in prokaryotes and eukaryotes

RNA interferece

a process where short pieces of RNA effect gene expression

transfer RNA (tRNA)

• transports AA’s to site of protein synthesis (reads 3 bases at a time)

• single polypeptide chain folded over

• intrachain bonding between AU and GC

• secondary structure= cloverleaf

stems

H-bonded portions of the molecule

leafs

non- H-bonded portions of the molecule

protein synthesis

both tRNA and mRNA are bound to the ribosome

L-shaped confirmation

tertiary structure needed for tRNA to interact with the enzyme that covalently attaches the AA to the 2’ or 3’ end

CAA

tRNA nucleotidyl transferase adds sequence ___ to 3’ end without it the molecule can’t pick up the correct amino acid or will degrade the molecule if it has structural deficiencies

Ribosomal RNA (rRNA)

• combines with proteins to form ribosomes, the site of protein synthesis

• small and large subunit

  • small: 1 large RNA molecules and around 20 different proteins

  • large subunit: 2 RNA molecules and around 35 different proteins in prokaryotes and 50 in eukaryotes

sedimentation coefficient (S)

S value increases with the molecular weight of the sedementing particle (not totally directly proportional)

messenger RNA (mRNA)

• sequence of bases in mRNA that specify the order of AAs in proteins

  • formed when needed—> direct protein synthesis—> degrade afterwards and nucleotides recycled h

heterogenous RNA (hnRNA)

eukaryotic RNA that is initially produced by transcribing DNA, contains intervening sequences that do not code for proteins

introns

intervening sequences in DNA that do not appear in the final sequence of mRNA

small nuclear RNA (snRNA)

• processes initial mRNA to its mature form in eukaryotes (only found in nucleus)

small nuclear ribonucleoprotein particles (snRNPs)

snRNA + protein= protein/ RNA complex found in the nucleus that aid in processing mRNA molecules for export to cytosol

small interfering RNA (siRNA)

• affects gene expression; used by scientists to knock out a gene being studied

• binds to mRNA and cleaves it

• 20-30 nucleotides

  • used in RNA interference

antisense RNA

short piece of RNA complementary to the mRNA produced by a gene of interest and keeps mRNA from being translated and eventually degraded by a nonspecific nuclease (RNase)

micro RNA

• affects gene expression important to growth and development

• bind to mRNA to prevent translation

Long noncoding RNA

do not code for protein, function still under debate but appears to affect development and be related to certain disease states

CRISPR

• clustered regularly interspaced short palindromic repeats repetitive structures of DNA found in bacteria and archaea

• uses proteins that are guided to a specific DNA sequence and then cut the DNA into 2

  • uses short-stranded RNA from invading organism to targe invader DNA