Ls 3 Lecture 5

Front 1

What are nucleic acid monomers composed of?

Back 1

Base

Sugar

Phosphate

Front 2

Where does a ribose have hydroxyls?

Back 2

on the 2' and 3' position

Front 3

What are the two major types of bases?

Back 3

purines (adenine and guanine)
-attached to sugar at N9
pyrimidines (cytosine and thymine, (uracil) )
-attached to their sugar at N1

these are planar molecules

Front 4

What gives DNA polarity?

Back 4

hooking up monomers from 5' to 3'

5' has phosphate
3' a free OH

there is no OH at 2' because it helps with stability and you don't want cyclic bonding like in RNA

Front 5

What gives DNA it's distinctive 3D shape?

Back 5

bases can form H-bonds

G-C is stronger with 3 hydrogen bonds than A-T

Front 6

What is the most common form of DNA?

Back 6

right handed B DNA.

10 base paris in one 360 degree turn in B DNA

somewhat hydrophobic inside (bases are hydrophobic)
-stablizes

they are only held together by H bonds but there are a lot of them which gives it strength

like a zipper so it can be pulled apart easily

Front 7

What is a function of the grooves in DNA?

Back 7

proteins that regulate gene expression can fit into the grooves.

Front 8

Major and MInor Grooves

Back 8

present surfaces for major interactions with proteins

arise because of asymmetric attachment to sugar-phosphate backbone

grooves expose H-bond acceptors and donors and hydrophobic groups

binding is defines by the sequence of bases and grooves

Front 9

What bends DNA?

Back 9

binding of proteins (DNA binding proteins)

Front 10

Pitch

Back 10

distance between each base

Front 11

Residues (referring to a measure of DNA structure)

Back 11

number of bases per turn

Front 12

Supercoiling of DNA

Back 12

because it is helical, it has qualities like a rope
-design is perfect to make radical turns
-you can put it in small things

Front 13

Gel Electrophoresis of DNA

Back 13

DNA has large negative charge due to backbone phosphate
-DNA fragments will migrate to the + pole of a gel apparatus
-fragments can be visualized (fluorescent)

Front 14

Melting of DNA

Back 14

measure concentrations of DNA by UV absorbance at 260 nm.

absorbance:
free nucleotides>single stranded DNA>double stranded DNA

DNA melts to two separate strands and so it has a bigger absorbency

T = the temp at which 50% of the DNA is single stranded

T(m) increases as the number of GC pairs increases (they are harder to break)

DNA comes apart most readily at A-T pairs

Front 15

What component does RNA have?

Back 15

enzyme component

Front 16

where are small RNA's found?

Back 16

nucleus

nucleolus

cytoplasm

Front 17

Where is RNA regulatory?

Back 17

at points where it bends back on itself and goes from single to double stranded

Front 18

What structure does RNA commonly take on?

Back 18

complicated secondary structure

loops are used to regulate RNA function

structures are often regulatory