B: DNA and RNA structure

Question 1

–What is the difference between a protein coding gene and a non-coding RNA gene?

Answer 1

• Genes are transcribed to RNA, coding RNAs are translated into protein, coding RNAs code for proteins and are called mRNA.
• Non-coding RNAs do not encode proteins and are not translated

Question 2

–Name the bases in DNA, name the bases in RNA.

Answer 2

• DNA = Adenine, Thymine, Guanine, Cytosine
• RNA = same but Uracil instead of Thymine

Question 3

–What are the DNA base pairing rules?

Answer 3

A with T and G with C. As much A as T and as much G as C

Question 4

–Name the base pairs that occur in DNA, how many H-bonds in each pair?

Answer 4

Adenine-Thymine, Guanine-Cytosine. 2 H bonds for AT and 3 H bonds for GC

Question 5

—Draw the structure of ATP and dATP - what is the difference between the two molecules? which one is incorporated into RNA and which is incorporated into DNA?

Answer 5

Difference is the sugar: dATP has deoxyribose for DNA (missing OH on C2) and ATP has ribose for RNA (OH on C2)

Question 6

-What is the N-glycosyl bond?

Answer 6

• N-glycosyl bond links the N atom from the base with the C1 in the sugar group

Question 7

—Draw the structure of cytosine. What is the difference between cytosine and thymine? What is the difference between cytosine and uracil? What is the difference between cytosine and cysteine?

Answer 7

Question 8

–What is the difference between a purine and a pyrimidine?
-Which bases are pyrimidines and which are purines?

Answer 8

• Pyrimidines = A and G, Purines = C and T

Question 9

–What is the sugar molecule in DNA? what is the sugar molecule in RNA? how do they differ?

Answer 9

Deoxyribose for DNA (missing OH on C2) and ribose for RNA (OH on C2)

Question 10

—List the precursors of DNA, list the precursors of RNA, how do they differ?

Answer 10

• DNA precursors = dAMP, dTMP, dCMP, dGMP (deoxyribonucleotide 5’-triphosphates or deoxynucleotides).
• RNA precursors = AMP, UMP, CMP, GMP (ribonucleotide 5’- triphosphates or nucleotides).
• They differ because of their sugar group (deoxyribose vs ribose)

Question 11

—List the 12 key aspects of the structure of DNA and RNA.

Answer 11

1. DNA is made of two strands.
2. The two strands go in opposite directions, the strands are anti- parallel.
3. Base pairing occurs between A and T and between G and C.
4. Pairings are held together by hydrogen (H) bonds (2 between A and T, 3 between G and C)
5. The structure is a double helix.
6. The bases project to the middle of the helix.
7. The phosphates are on the outside like a backbone.
8. The double helix has a major groove and a minor groove.
9. One turn of the helix has approx 10.5 base pairs (bp).
10. The two strands of DNA are said to be complementary to each other.
11. If you know the sequence of one strand, you can tell the sequence and direction of the complementary strand because of base pairing rules.
12. The DNA structure as described by Watson and Crick is a right-handed helix. The helix winds in a clockwise manner as you look down its axis.

Question 12

–Describe the B form of DNA found in living cells.

Answer 12

• right-handed helix
• pitch 3.4nm
• 10 bps in one full turn DNA turn
• major groove 2.2nm wide
• minor groove 1.2nm wide
  (answer from master doc)

Question 13

–What is RNA secondary structure and explain how it can form.

Answer 13

• RNA secondary structures form when base pairing occurs in RNA molecules. They can form within an RNA strand and between 2 different RNA strands.
• Types of secondary structure: stem loops, pseudo knots, hairpins

Question 14

—Describe the differences between DNA and RNA.

Answer 14

DNA and RNA precursors- uracil and thymine
Ribose and deoxyribose
Single stranded and double stranded
RNA- intra base pairing
RNA- mRNA, rRNA, tRNA…
DNA- genes
(answer from master doc)