Chapter 4 - Nucleic Acids and the RNA World

Question 1

what are nucleic acids made of?

Answer 1

nucleotides (monomers)

Question 2

what are the 3 components of a nucleotide?

Answer 2

1) phosphate group
2) a five-carbon sugar
3) a nitrogenous base (contains nitrogen)

Question 3

what are two types of nucleotides?

Answer 3

1) ribonucleotides –> ribonucleic acid (RNA)

2) deoxyribonucleotides –> deoxyribonucleic acid (DNA)

Question 4

what is the sugar component of ribonucleotides?

Answer 4

ribose

Question 5

what is the sugar component of deoxyribonucleotides?

Answer 5

deoxyribose (deoxy means “lacking oxygen)

Question 6

purines

Answer 6

type of nitrogenous base

• adenine
• guanine

Question 7

pyrimidines

Answer 7

type of nitrogenous base

• cytosine
• uracil (RNA)
• thymine (DNA)

Question 8

what type of nitrogenous base does RNA use?

Answer 8

pyrimidine (uracil)

Question 9

what type of nitrogenous base does DNA use?

Answer 9

pyrimidine (thymine)

Question 10

DNA primary structure

Answer 10

the sequence of deoxyribonucleotides

-bases are A,T,G,C

Question 11

DNA secondary structure

Answer 11

2 DNA strands running in opposite directions held together by complementary base pairing, twisted into a double helix

• stabilized by hydrogen bonding between nitrogenous bases and hydrophobic interactions
• A = T
• G = C

Question 12

RNA primary structure

Answer 12

sequence of ribonucleotides

-bases are A,U,G,C

Question 13

RNA secondary structure

Answer 13

short regions of double helices and structures called “hairpins”

• -stabilized by hydrogen bonding between nitrogenous bases (complementary base pairing)
• RNA bases fold over and make hydrogen bond base pairings with bases on the SAME strand

Question 14

what is more easily made, sugars/purines or pyrimidines/ribose?

Answer 14

sugars and purines are easily made. pyrimidines and ribose are not

Question 15

what reaction occurs when nucleotides polymerize to form nucleic acids?

Answer 15

a condensation reaction

• this forms a phosphodiester bond
• between 5’ carbon and 3’ carbon of two different nucleotides

Question 16

qualities of the sugar-phosphate backbone of nucleic acid

Answer 16

-they are directional (one end has an unlinked 5’ carbon/one end has unlinked 3’ carbon)

Question 17

primary structure of nucleic acid

Answer 17

• the directional nucleotide sequence of the growing molecule
• goes from 5’ –> 3’ (only added to the 3’ end)

Question 18

qualities of the polymerization of nucleotides

Answer 18

• endergonic (requires energy input, not spontaneous)
• catalyzed by enzymes
• energy used in this process comes from the “phosphorylation” of nucleotides

Question 19

phosphorylation

Answer 19

• transfer of one or more phosphate groups to a substrate molecule
• raises the potential energy of the substrate
• enables endergonic reactions

Question 20

why can polymerization take place in cells?

Answer 20

the potential energy of the nucleotide monomers is raised by reactions that add two phosphate groups to either ribonucleotides or deoxyribonucleotides

• this creates nucleoside triphosphates (3 phosphate groups)

** the addition of one or more phosphate groups raises the potential energy of substrate molecules enough to make the reaction possible)

Question 21

ATP

Answer 21

adenosine triphosphate (“activated” nucleotide) with 3 phosphate groups

Question 22

2 empirical rules of DNA

Answer 22

• total number of purines and pyrimidines are the same
• the number of A’s = T’s
• the number of G’s = C’s

Question 23

describe the secondary structure of DNA

Answer 23

• antiparallel configuration, double helix
• hydrophilic sugar-phosphate backbone (exterior facing)
• nitrogenous base pairs (interior facing, A-T and G-C)
• two different sized grooves (major and minor)

Question 24

what nitrogenous base pairings exist in DNA?

Answer 24

purines always pair with pyrimidines

-complementary base pairs include A-T and G-C

Question 25

how many hydrogen bonds do A-T pairings have?

Answer 25

2

Question 26

how many hydrogen bonds do G-C pairings have?

Answer 26

3

Question 27

how is DNA stabilized?

Answer 27

- hydrophobic interactions in its interior | - hydrogen bonding between complementary base pairs

Question 28

how does DNA contain biological information?

Answer 28

- language of nucleic acids is contained in the sequence of the bases - DNA carries info for growth and reproduction of all cells

Question 29

what makes DNA replication possible?

Answer 29

complementary base pairing (A-T and G-C) | -each strand serves as a template for the formation of a new complementary strand

Question 30

steps of DNA replication

Answer 30

1) double helix separates 2) each existing strand of DNA serves as the template for a new strand to form. free nucleotides attach to existing 3' ends according to complementary base pairing 3) polymerization - new strands come together/forms a sugar-phosphate backbone (secondary structure is restored)

Question 31

is DNA stable? reliable? is it a good catalyst?

Answer 31

-DNA is extremely stable and reliable for storing information -HOWEVER is it not a good catalyst because it is so stable (because DNA is not a good catalyst, they think RNA composed the first life form, not DNA)

Question 32

what are the two functions that the first living molecule would have needed to carry out?

Answer 32

1) carry information | 2) catalyze reactions that promoted its own reproduction

Question 33

how are DNA and RNA similar?

Answer 33

-both have same primary structure (phosphodiester linkages --> sugar-phosphate backbone + sequence of 4 nitrogenous bases extending from the backbone)

Question 34

what are the two main differences between DNA and RNA?

Answer 34

1) RNA sugar = ribose DNA sugar = deoxyribose 2) RNA = pyrimidine base is uracil DNA = pyrimidine base is thymine

Question 35

is RNA more or less stable than DNA?

Answer 35

less stable! | -OH makes ribose much more reactive and less stable than DNA

Question 36

can RNA have tertiary and quaternary structures? if so, what are they?

Answer 36

tertiary- folds that form distinct 3 dimensional shapes | quaternary- associations between several RNA molecules

Question 37

what are some capabilities of RNA?

Answer 37

- intermediate between DNA and proteins - capable of storing information, self-replicating - can function as catalytic molecule

Question 38

ribozymes

Answer 38

enzyme-like RNA's

Question 39

RNA replicase

Answer 39

a type of ribozyme | -can catalyze the addition of ribonucleotides to a complementary RNA strand