4.2

Front 1

nucleic acid

Back 1

biopolymer of nucleotides held together by phosphodiester bonds;

5' end to 3' end; has A,U(T),C,G

Front 2

complex bonds

Back 2

slide 5

Front 3

nucleic acid strand

Back 3

phosphodiester linkages hold nucleosides together

Front 4

strand polarity

Back 4

running from 5'C atom of sugar to the 3'C atom at the other end;

5' --> 3'

Front 5

syn-bases

Back 5

nitrogenous base goes with the sugar

Front 6

anti-bases

Back 6

nitrogenous base goes against the sugar;

highly preferred in order to avoid steric clashes;

slide 7

Front 7

double helix

Back 7

diameter of 20A;

two strands run antiparallel

Front 8

sugar-phosphate backbone

Back 8

sugars linked by phosphate groups;

stack against each other perpendicular to the helical axis and pointing inwards into the core

Front 9

minor groove

Back 9

12A;

therapeutic drugs target this groove

Front 10

major groove

Back 10

22A;

transcription factors bind to this groove

Front 11

double helix physical parameters

Back 11

base pairing: A/T and G/C;

helical diameter is 20A

helical pitch is 34A

helical rise is 3.4A

10 base pairs per turn

helical twist is 36 degrees

base tilt is 6 degrees

Front 12

Left handed vs. Right handed

Back 12

the fingers curl in the direction the helix turns

Front 13

Adenine with Thymine

Back 13

paired with 2 hydrogen bonds

Front 14

Guanine with Cytosine

Back 14

paired with 3 hydrogen bonds;

higher melting point because of the enhanced stacking interactions

Front 15

Watson-Crick Base Pairs

Back 15

combinations of pairs can be interchanged, allowing for a perfect symmetry;

DNA symmetry is independent of base composition

Front 16

Base mismatching

Back 16

results in DNA distortion and bending

Front 17

Helix thermodynamic stability

Back 17

(1) Hydrogen bonding - only weakly stabilize the DNA; loss of H-bonds is caused by bases interacting with water molecules

(2) Stacking Interactions - bases stack due to dipoles in aromatic rings forming a sheet; special case of van der Waals forces

(3) Ionic interactions - metal ions engage in ionic bonds with the charged phosphate groups, causing stabilization

Front 18

DNA denaturation

Back 18

when heated past melting temp the structure collapses;

viscosity - decreases due to loss of rigid double helix

hyperchromicity - light absorbance is enhanced due to the disruption of interactions between bases

Front 19

hyperchromic effect

Back 19

when denatured, there is an increase in the absorbance maximum wavelength

Front 20

DNA melting curve

Back 20

denaturation occurs over a narrow temp range, making a sigmoidal curve;

mid point is the melting temp;

its a cooperative process, such that when one finally gives it, they all fall rapidly

Front 21

stability of DNA

Back 21

dependent on solvent, pH and base composition;

GC rich has higher melting temp

Front 22

DNA renaturation

Back 22

lowering the temp to about 50 C fully restores the double helix;

if rapidly cooled, it attains a partially base-paired structure;

DNA is incubated at a temp no more than 25 C below melting temp

Front 23

DNA conformations

Back 23

A-DNA, B-DNA, Z-DNA;

B --> most common;

Front 24

A-DNA

Back 24

has C3'-endo deoxyribose;

C3' atom is on the same face as C5';

right handed;

diameter of 26A;

major groove - narrow and deep;

minor groove - wide and shallow;

hollow core

wide

Front 25

B-DNA

Back 25

has C2'-endo deoxyribose;

C2' atom is on the same face as C5';

right handed

diameter of 20A

major groove - wide and deep

minor groove - narrow and deep;

semi-solid core;
thin and elongated;
dehydration of this goes to A-DNA;
chemical modifications go to Z-DNA

Front 26

Z-DNA

Back 26

left handed;

diameter of 18A

major groove is flat

minor groove - narrow and deep;

solid core;

thin and compact

Front 27

Single-stranded RNA (ssRNA)

Back 27

has ribose and uracil;

single stranded due to steric clashes between 2'-OH on the sugar of ribonucleotides prevents the formation of a double helix

Front 28

double-stranded RNA (dsRNA)

Back 28

A-U and G-C base pairs come together;

formation of a hairpin loop fold

Front 29

RNA-DNA helix

Back 29

RNA can attach to a complementary DNA in a double helix formation;

Front 30

restriction enzymes

Back 30

enzymes that cleave dsDNA at specific sequences

Front 31

restriction endonucleases

Back 31

cleave DNA at palindromes

Front 32

palindromes

Back 32

sequences that are identical on both strands and are related by a two-fold symmetry;

same forward as they are backwards

Front 33

agarose gel electrophoresis

Back 33

separates DNA fragments on the basis of their size;

stained with DNA-binding fluorescent dyes

Front 34

DNA polymerase

Back 34

converts single-stranded DNA into double-stranded DNA;

adds nucleotides to the 3' end of a chain paired to the complementary strand (primer)

Front 35

primer

Back 35

short polynucleotide complementary to the 3' end of the ssDNA

Front 36

DNA template is incubated with:

Back 36

DNA polymerase, complementary primer, 4 dNTPs, 4 ddNTPs;

chain growth is terminated due to the lack of free 3'-OH group

Front 37

gel electrophresis

Back 37

separates differentially tagged fluorescent DNA fragments on the basis of size