Biochemistry Test 2: Nucleic Acids Structures

Front 1

Reverse transcription

Back 1

Forming DNA from RNA using reverse transciptase, HIV does this.

Front 2

Exons

Back 2

Part of the mRNA that are translated into proteins

Front 3

Introns

Back 3

Parts of the mRNA in eukaryotes that must be excised before translation takes place.

Front 4

DNA base pairs, stabilization and structure

Back 4

A to T and G to C.

These bonds are hydrogen bonds that occur when the bases are inverted with respect to eachother.

Remember pyrimidines have a y in their names.

DNA is stabilized by keto-enol isomerization in the keto form because of H-bonding.

Purines have are a pyrimidine ring fused to an imadazole.

Front 5

Other DNA bases

Back 5

5-methylcytosine will shutdown transcription after a polymerase hits it.
Uracil is a thymine without a methyl group.

Front 6

Phosphodiester bonds

Back 6

Link base pairs together and are always polymerized in a 3-5 linkage.

Front 7

Energy for phosphodiester linkages

Back 7

Comes from the hydrolyis of phospates during poymerization.

Front 8

Direction of DNA synthesis

Back 8

Always 5-3 prime

Front 9

Oligonucleotide

Back 9

around 30 nucleotides long

Front 10

Polynucleotide

Back 10

longer than 30 nucleotides

Front 11

Difference between DNA and RNA structure

Back 11

RNA has a 2 prime hydroxyl group that makes it more susceptible to alkaline denaturation

Front 12

When writing a sequence

Back 12

It's always assumed to be RNA unless otherwise indicated, and 5-3 prime

Front 13

Endonuclease

Back 13

Severs a P-type linkage. Cleaves a phosphodiester bond within a nucleotide chain.

Front 14

Exonuclease

Back 14

Severs a D-type linkage
Hydrolyzes phosphodiester bonds from either the 3 or 5 prime terminus of a polynucleotide

Front 15

Chargaff's rule

Back 15

A-T and G-C always in a 1:1 ratio

Front 16

X-ray diffraction and DNA

Back 16

Shows that DNA is double stranded.

Front 17

Opposite polarity

Back 17

Means that DNA strands pairs bases upside down and different directions

Front 18

Forms of DNA

Back 18

A,B,Z

Front 19

A-form DNA

Back 19

Dehydrated
Wider, shorter, right-handed
Seen mostly in DNA/RNA hybrids like miRNA and siRNA

Front 20

B-form DNA

Back 20

Normal right handed helix with 10bp per turn

Front 21

Z-form DNA

Back 21

Zig-zag DNA is a left handed helix.
It is formed by dinucleotide repeats of purines and pyrimidines.
Only has one helical groove
Stabilized by methylation and hydrophobic interactions but is inherently unstable.

Front 22

DNA Grooves

Back 22

A and B have a major and minor groove.
Z form has one

Front 23

B-Z DNA

Back 23

Z forms are ustable and must be connected to B form on either end.
These are theorized to be points of x-somal breakage.

Front 24

Stabilizing DNA forces

Back 24

Hydrophobic interactions between bases
Electrostatic interactions of negative phosphate groups
H-bonds
Conterions that will counteract the negative groups to split and replicate DNA(Mg and basic proteins)

Front 25

Breathing of DNA

Back 25

The ability of DNA to open and close, denature and renature of the same complementary strands. Easy breathing occurs at A-T rich sites like the origin of replication and different promoters.

Front 26

DNA absorbance

Back 26

260-280nm

Front 27

What is the significance of the melting temperature of DNA(Tm)?

Back 27

Tm is where half of the DNA is denatured at about 80 degrees Celsius

Front 28

What is hyperchromicity?

Back 28

An increase in the absorbance of a certain material as you unwind it. DNA strands do this when they denature and unwind, will not do this with single strands.

Front 29

Hyperchromicity and Tm?

Back 29

At the Tm there is 50% absorbance of light because half of the DNA is unwound. 100% absorbance would be totally denatured.

Front 30

Melting temperature and base pairs

Back 30

Tm is proportional to the GC content because 3 H bonds are harder to break than the 2 between AT.

Front 31

Single copy DNA

Back 31

Code for proteins and spaces. They are DNA that are only present in 1 copy.

Front 32

Moderately repetitive DNA

Back 32

Sequences that are repeated 100-1000 times, usually non-coding.

Front 33

Highly repetitive DNA

Back 33

Short sequences repeated a million times. This is the make up of satellite DNA, and is located in the centromeres and are non coding.

Front 34

Satellite DNA

Back 34

Have a different density from bulk DNA and form a second band of DNA when separated because of a different bp ratio.

Front 35

Types of DNA symmetry

Back 35

Inverted repeat
Mirror repeat
Direct repeat

Front 36

Palindrome

Back 36

Sequences that be read the same forwards and backwards. Can be mirror repeats or inverted.

Front 37

Cruciform structure

Back 37

The hairpin structure that can be created by endonuclease activity on inverted repeats.

Front 38

Histones

Back 38

Proteins that have evolved to compact and supercoil DNA. They have a high Lys-Arg content.

Front 39

Nucleosomes

Back 39

DNA wrapped around histone proteins in left handed superhelical turns.

Front 40

Histone charcteristics

Back 40

Highly conserved across species
Expressed during S-phase
Have no introns and occur in tandem repeats
Not in mitochondrial or bacterial DNA
No poly A tail on their mRNA

Front 41

Function of a poly A tail

Back 41

They protect the protein from degradation by exonucleases in the cytoplasm.

Front 42

Topoisomerases

Back 42

Facilitate the unwinding of DNA for transcription

Front 43

Nucleofilaments

Back 43

The regular spacing of histone/DNA associations into a fiber. Beads on a string

Front 44

DNA Replication, steps

Back 44

1. Begins at origins, one only in prokaryotes
2. Each 5-3 initiated by an RNA primer made by RNA primase. That means that leading strand has one, and lagging strand has multiple.
3. Nucleotides added 5-3 prime
4. Phosphodiester linkages happen 3-5 prime
5. Okazaki fragments are used to add to the lagging strand

Front 45

3 modes of DNA replication

Back 45

Conservative, dispersive, semiconservative

Front 46

Semiconservative replication

Back 46

Strand spilts in two and each parent strand has a new daughter strand.

Front 47

Why do eukaryotes have multiple origins?

Back 47

Because their DNA is so large if they didn't they would never finish replication.

Front 48

Telomerase

Back 48

A reverse transcriptase that carries it's own RNA.
It's function is to add the telomere to DNA that prevents shortening.
The sequence is TTACGGG

Front 49

Prokaryotic Polymerases

Back 49

Pol 1 = primer removal
Pol 2 = DNA repair
Pol 3 = DNA synthesis

Front 50

Eukaryotic Polymerases

Back 50

Pol alpha = Initiator and primer
Pol beta = DNA repair
Pol sigma = synthesis

Front 51

Why does alkaline denature RNA and not DNA?

Back 51

The 2 prime hydroxyl of RNA will form a keto-enol structure that can break the strands under alkaline conditions.

Front 52

Acceptor stem of tRNA

Back 52

Region of tRNA that will carry the AA necessary for protein synthesis

Front 53

Ribozyme

Back 53

A modified RNA with enzymatic activity. RNase P, and D cut the ends of the 5 and 3 prime respectively.

Front 54

Nucleotidal transferase

Back 54

Puts the CCA onto the 3' end of all tRNAs, the 5' has GG

Front 55

45s RNA transcript in eukaryotes

Back 55

Made from the 28s, 5.8s, and 18s rRNAs. Makes mature rRNA. The s= sedimentation coefficient.