Biochem Ii - Lecture 1

Front 1

T/F: Nucleotides are phosphate esters of a five-carbon sugar in which a nitrogenous base is covalently link to C1' of the sugar residue (carbons of the ribose are labeled with a prime, carbons of the nitrogenous base are not).

Back 1

True

Front 2

What is the name of a nucleotide with the phosphate group on the 3' carbon? 5' (normal)?

Back 2

3' nucleotide and a 5' nucleotide

Front 3

What is the name of a general nucleotide without a phosphate group?

Back 3

A nucleoside

Front 4

The names for the Nitrogenous bases are Adenine, Thymine, Cytosine, Guanine, and Uracil when they are independent. What are the names of these bases when they are in nucleoside form, i.e. when the "X" substituent is a ribose with no phosphate group?

Back 4

Adenosine, Guanosine, Cytidine, Uridine, Deoxythymidine

Front 5

The names for the Nitrogenous bases are Adenine, Thymine, Cytosine, Guanine, and Uracil when they are independent. What are the names of these bases when they are in nucleotide form, i.e. when the "X" substituent is a ribose with a phosphate group?

Back 5

Adenylic acid, Guanylic acid, Cytidylic acid, Uridylic acid, Deoxythymidylic acid

Front 6

T/F: There are derivatized nucleotides that contain extra methyl groups on their nitrogens and carbon rings and they obey Chargaff's rules just as their parent nucleotides do.

Back 6

True

Front 7

Why is it hypothesized that DNA evolved as the genetic material rather than RNA?

Back 7

Because it is not subject to base-catalyzed hydrolysis like RNA is because it lacks a 2' hydroxyl group!

Front 8

The term virulent means...

Back 8

Capable of causing disease

Front 9

Who did the R and S mouse experiment that led to the transformation principle?

Back 9

Frederick Griffith

Front 10

How did Oswald Avery eventually find that DNA was the transformation principle, i.e. the carrier of genetic information?

Back 10

Because he found that the transformation would still occur with enzymes that catalyzed the hydrolysis of RNA, and with proteases, but not with enzymes that cleaved DNA.

Front 11

How did the Hershey-Chase experiments show that DNA was the genetic material in phages?

Back 11

The first batch of phages was grown on radioactive Sulfur (mainly in proteins) and it was shown that the phage ghosts were ultimately the only radioactive material after transfection; the second was grown on radioactive Phosphorus (main component of DNA backbone) and after transfection it was shown that only the inside of the transfected bacteria was radioactive; viola

Front 12

What colleague of Watson and Crick showed them the correct tautomers of nucleotides, and which is the generally correct form?

Back 12

Donahue; the keto form is very dominant

Front 13

Whose experiment proved the semi-conservative model of DNA?

Back 13

Meselson and Stahl

Front 14

T/F: Ribonucleoproteins often participate in the post-transcriptional processing of other RNAs.

Back 14

True

Front 15

A variety of short RNA's participate in the control of eukaryotic gene expression and in protection against viruses in a phenomenon known as...

Back 15

RNA interference (RNAi)

Front 16

T/F: Base sequence does not so much confer a fixed conformation on a double helix as it established the deformability of the helix.

Back 16

True

Front 17

The phenomenon of Y-R, R-R steps and A-A steps having extensive ring-ring overlap keeping them parallel is important for what?

Back 17

Sequence-specific binding of DNA to proteins that process genetic information (these proteins often wrap their target DNA by bending them around, and the wrong sequence would resist the deformation)

Front 18

Which type of DNA increases the distance between successive pyrimidines?

Back 18

A-DNA

Front 19

T/F: The Z-DNA conformation is most readily assumed by DNA segments with alternating purine-pyrimidine base sequences.

Back 19

True

Front 20

Double stranded RNA usually takes the form of...

Back 20

A-DNA

Front 21

T/F: Many RNAs have well-defined tertiary structures.

Back 21

True

Front 22

What are the only two conformations available for the bases in their glycosidic linkages to the sugar? Which can purines and pyrimidines makes?

Back 22

Syn and anti; purines can do both and pyrimidines can only do anti

Front 23

Why does the ribose sugar ring in DNA pucker?

Back 23

So that all the substituents on the ring are not eclipsed, as they would be if the ring were flat

Front 24

Which carbons of ribose usually pucker, and what do the endo and exo conformations mean?

Back 24

C2 or C3 usually pucker to make the half chair conformation; the endo conformation means the pucker is on the same side of the ring as C5, exo is on the opposite side of the ring

Front 25

T/F: The ribose pucker is conformationally important in nucleic acids because it governs the relative orientations of the phosphate substituents to each ribose residue.

Back 25

True (C2 endo is most frequent)

Front 26

Which experiment showed that dead virulent bacteria could transform live nonvirulent bacteria, and thus further showed that DNA was the genetic material?

Back 26

Avery-McCarty

Front 27

The transforming substance of the previous experiment had what 3 characteristics that made it seem as though it was DNA?

Back 27

Inactivated by DNases, insensitive to proteases, and had the same molecular weight as theoretical DNA

Front 28

What are the purines?

Back 28

A and G

Front 29

What are the pyrimidines?

Back 29

C and T

Front 30

Which group is on the 5' end?

Back 30

A phosphate

Front 31

Which group is on the 3' end?

Back 31

A hydroxyl group

Front 32

Whose experiment showed, by radioactively labeling the proteins (S) on phages and then the DNA (P) on phages, that phage DNA entered the host cell and thus confirmed that DNA is the genetic material?

Back 32

Hershey-Chase blender experiment

Front 33

Who showed the X-ray diffraction patterns of DNA?

Back 33

Wilkins and Franklin

Front 34

T/F: In Chargaff's Ratios for Genomic DNA, he used Pauling's idea that there is always complementarity in biology in life.

Back 34

True

Front 35

Watson and Crick were initially using the wrong tautomers of bases; which is correct?

Back 35

Keto is the correct form; not enol

Front 36

How is the change from A-form to B-form DNA largely accomplished?

Back 36

By changing the sugar pucker of the sugar

Front 37

How does the major groove of DNA carry more information than the minor groove?

Back 37

Because in the major groove, T-A is differently recognized from A-T, and so sequence-specific recognition of DNA is usually accomplished by making a major groove interaction with the helix

Front 38

Which type of ring pucker does B-DNA usually take? A-DNA?

Back 38

B-DNA (normal DNA) C2' endo sugar

A-DNA (normal dsRNA) C3' endo sugar

Front 39

What does the shift from a C2' to C3' endo sugar pucker change about DNA?

Back 39

It changes the 3' oxygen from an axial to an equatorial position, changing P-P distances and thus making different helical geometries