BIO 161 Ch. 4 Nucleic Acids and RNA World

RNA Molecules Contain Information That Allows Them to Be Replicated

(1)provide a template that could be copied, and (2) catalyze polymerization reactions that would link monomers into a copy of that template

James Watson and Francis Crick

1953. Built first accepted DNA model explaining specific structure and properties of DNA.

Thymine

A component of nucleic acid that carries hereditary information in DNA in cells. is a pyrimidine base.

Cytosine

A component of nucleic acids that carries hereditary information in DNA and RNA in cells.is a pyrimidine base.

Three components of a nucleotide

A phosphate group, a five-carbon sugar, and a nitrogenous base

Nitrogenous bases in DNA

Adenine, Thymine, Cytosine, Guanine Pyrimidines: C,T Purines: G,A

Nitrogenous bases in RNA

Adenine, Uracil, Cytosine, Guanine Pyrimidines: C, U Purines: A, G (purines are larger than pyrimidines)

15. Watson and Crick met with Chargaff to discuss his work in 1952. Explain how Chargaff's observations helped Watson and Crick to propose the complementary base pairing in their model of double-stranded DNA. Would you expect similar ratios of nucleotides if Chargaff had used RNA instead? Explain why or why not.

Chargaff's data show that an approximately 1:1 molar ratio exists between adenine and thymine bases, and between guanine and cytosine bases. Watson and Crick used these data to come up with complementary base pair- ing, which requires that every adenine pairs with a thymine and every guanine pairs with a cytosine. In RNA, Chargaff's rules do not apply since RNA is single- stranded and the pairing is not consistent throughout the molecule.

16. PROCESS OF SCIENCE Now that you have learned a little more of the history behind the elucidation of the secondary structure of DNA, what does it tell you about the role of the scientific community in advancing science? Were Watson and Crick solely responsible?

Science is seldom advanced in isolation. Watson and Crick could not have arrived at their model of the double helix without Levene's discovery of the structure of nucleotides and how they are linked together, Franklin's X-ray crystallography data, or Chargaff's biochemical analysis of the molar proportions of nucleotides in double-stranded DNA

Tertiary structure in RNA

Secondary structures fold to form a wide variety of distinctive three-dimensional shapes

DNA's primary structure serves as a tem- plate for the synthesis of a complementary strand

Step 1 The two strands of a DNA double helix can be separated by breaking the hydrogen bonds that hold them together using either heat or enzyme-catalyzed reactions. Step 2 Free deoxyribonucleotides form hydrogen bonds with complementary bases on the original strand of DNA—also called a template strand. As they do, their sugar-phosphate groups form phosphodiester linkages to create a new strand— also called a complementary strand. Note that the 5∙ S 3∙ directionality of the complementary strand is the opposite to that of the template strand. Step 3 Complementary base pairing allows each strand of a DNA double helix to be copied exactly, producing two identical daughter molecules.

7. What would be the sequence of the strand of DNA that is made from the following template: 5∙-GATATCGAT-3∙? (Your answer must be written 5∙ S 3∙.) How would the sequence be different if RNA were made from this DNA template?

The DNA sequence of the new strand would be 5∙-ATCGATATC-3∙. The RNA sequence would be the same, except each T would be replaced by a U.

sugar-phosphate backbone

The alternating chain of sugar and phosphate to which the DNA and RNA nitrogenous bases are attached

13. Rosalind Franklin was the first person to obtain X-ray crystallographic data on the form of DNA that is most commonly found in cells. Other researchers, including Pauling, used data from DNA samples that were more concentrated than Franklin's samples. Why would you expect the amount of water to affect the helical structure of DNA?

The amount of water would affect the influence of hydrophobic inter- actions, which push the mostly nonpolar nitrogenous bases away from water and cause the DNA to twist into a double helix.

Guanine

The base that pairs with Cytosine in DNA and RNA, is a purine

Adenine

The base that pairs with Thymine in DNA Uracil in RNA

RNA secondary structures will form spontaneously

The bases are brought together by hydrophobic interac- tions and stabilized by hydrogen bonding and van der Waals interactions.

Three nucleotide components

The bond angles and measurements suggested that the dis- tance of 2.0 nm represented the width of the helix and that 0.34 nm was likely to be the distance between bases stacked in a spiral.

11. Phoebus Levene was the first to describe the structure of nucleotides and how they were bonded together with phosphodiester linkages. In 1919, he incorrectly proposed the tetranucleotide hypothesis, which stated that nucleic acids were polymers consisting of GCTA repeated over and over. If his model had been correct, then how would it affect the information that could be stored in the DNA?

The capacity for storing information would be severely limited. It would be like trying to express ideas with a language that consisted of only one 4-let- ter word that is repeated over and over. According to this hypothesis, DNA would not serve as an effective information storage molecule

primary structure of protein

The order of the different nucleotides

Hydroxyl (OH-) group on the 2' carbon of ribose

This additional hydroxyl is much more reactive than the hydrogen atom on the 2' carbon of deoxyribose. When RNA molecules fold in certain ways, the hydroxyl group can attack the phosphate linkage between nucleotides, which would generate a break in the sugar-phosphate backbone. This -OH group makes RNA much less stable than DNA

To replicate a single-stranded RNA, first a complementary copy of the RNA is made

Using the original strand as a template, free ribonucleotides form hydrogen bonds with complemen- tary bases on the template. A new strand is polymerized when 3∙ hydroxyls and 5∙ phosphates on adjacent nucleotides are linked together via condensation reactions. The product is a double- stranded RNA molecule

12. In the 1950s, the race to solve the secondary structure of DNA became intense. In an uncharacteristic rush to publish, Linus Pauling erroneously proposed a triple-stranded structure in February 1953. This model had the nitrogenous bases on the exterior and the sugar-phosphate backbones clustered in the middle. How does the orientation of the sugar-phosphate backbone in this model compare with the one proposed by Watson and Crick? Do you think Pauling's structure could exist in cells? Why or why not?

Watson and Crick's model had the sugar-phosphate backbones oriented toward the exterior. Pauling's structure would not likely exist in cells because the sugar-phosphate backbones of nucleic acids are negatively charged and would repel one another.

Uracil

a nitrogen-containing base found in RNA (but not in DNA), is a pyrimidine

6. QUANTITATIVE If nucleotides from the DNA of a human were quantified and 30 percent of them contained the base adenine, what percentage of them would contain the base guanine? a. 20 percent b. 30 percent c. 40 percent d. 70 percent

a; if 30 percent is adenine, then 30 percent would be thymine, since they are base-paired together. This means that 40 percent consists of G-C base pairs, which would be equally divided between the two bases.

RNA

adenine forms two hydrogen bonds with uracil guanine forms three hydrogen bonds with cytosine.

nucleic acids(polymer)

are made up of monomers called nucleotides.

1. What are the four nitrogenous bases found in RNA? a. cytosine, guanine, thymine, uracil (C, G, T, U) b. adenine, cytosine, guanine, thymine (A, C, G, T) c. adenine, cytosine, guanine, uracil (A, C, G, U) d. alanine, cysteine, glycine, threonine (A, C, G, T)

c.

2. What determines the primary structure of a DNA molecule? a. hairpins and supercoils b. complementary base pairing c. deoxyribonucleotide sequence d. hydrophobic interactions and hydrogen bonding

c.

3. Which of the following describes the synthesis of nucleic acids? a. Nucleotides are added to the 5∙ end of a single nucleic acid strand. b. Nucleic acids are polymerized by the formation of peptide bonds between nucleotides. c. Strands in a double helix are synthesized in a parallel direction such that one end of the molecule has two 3∙ ends and other has two 5∙ ends. d. Complementary pairing between bases is required for copying nucleic acids.

d.

The polymerization reactions that join nucleotides into nucleic acids are catalyzed by...

enzymes

10. MODEL In the field of nanotechnology, DNA is used like Velcro to assemble tiny particles into structures that are 6 0.0001 mm in size. Draw a model to illustrate how two particles (a circle and a square) could be brought together by linking them to short single-stranded DNA molecules. If the DNA sequence linked to the circle is GGATC, then provide the sequence linked to the square and identify the 5∙ and 3∙ ends of each strand.

figure A4.5

RNA world hypothesis

ribonucleic acid (RNA) both stored the genetic information and catalyzed its own replication.

deoxyribonucleic acid (DNA)

stores genetic information and is rep- licated using proteins

double helix

the antiparallel strands were predicted to be twisted together to form a

Although, each base has polar groups involved in the hydrogen bonds....

the carbon-nitrogen ring structure is mostly nonpolar. This is a key point, because hydrophobic interactions cause double-stranded DNA to twist into a helix to minimize contact between the hydrophobic rings and surrounding water mole- cules. The paired strands are further stabilized by van der Waals interactions between the tightly packed bases. The negatively charged phosphate groups facing the exterior of the molecule make the double helix hydrophilic overall and thus soluble in aqueous solutions.

To make a copy of the original single-stranded RNA

the hydrogen bonds between the double-stranded product must first be broken by heating or by a catalyzed reaction (step 3). The newly made complementary RNA molecule now exists independently of the original template strand. If steps 1-3 were repeated with the new strand serving as a template (steps 4-6), the resulting molecule would be a copy of the original

Activated Monomers Drive Polymerization Reactions.

the potential energy in activated nucleotides, such as atp, is primarily stored in the bonds between the phosphates. When atp reacts with water, one of the bonds between two phosphates is replaced with a lower potential energy bond, resulting in the release of energy, and either a single phosphate (pi) or a pyrophosphate (p-pi). a similar release of potential energy occurs when activated nucleotides are used as substrates for polymerization of nucleic acids.

Secondary structure of RNA

the purine and pyrimidine bases in RNA undergo hydrogen bond- ing with complementary bases on the SAME strand Most common are hairpins, formed when a single strand folds back on itself to form a double-helix "stem" and an unpaired "loop"

The Secondary Structure of DNA Is a Double Helix

the schematic diagrams illustrate complementary base pairing (yellow bands represent hydrogen bonding) and how strands are twisted into a double helix. (b) the spacefilling model shows tight packing of the bases inside the double helix. the doublehelix structure explains the measurements inferred from Xray analysis of Dna molecules.

Tertiary structure of DNA

two forms: When DNA becomes wound too tightly or loosely with respect to the number of base pairs per helical turn, it can twist on itself to form compact, three-dimensional structures called supercoils highly organized tertiary structures by wrapping around certain proteins

8. According to the RNA world model, a ribozyme would replicate by creating a double-stranded RNA intermediate. Would you expect the intermediate to have the same catalytic activity as the original ribozyme? Justify your answer with an explanation.

No. Catalytic activity in ribozymes depends on the tertiary structure gener- ated from folding single-stranded molecules. Fully double-stranded forms of the RNA would not form the same tertiary structure.

How do nucleotides polymerize to form nucleic acids?

Nucleotides polymerize via condensation reactions between the hydroxyl on the sugar component of one nucleotide and the phosphate group of another nucleotide this reaction forms a new covalent bond

4. Single strands of nucleic acids are directional, meaning that there are two different ends. What functional groups define the two different ends of a strand?

One end has a free phosphate group on the 5∙ carbon; the other end has a free hydroxyl group bonded to the 3∙ carbon.

adenosine triphosphate, or ATP

Polymerization can take place in cells because the poten- tial energy of the nucleotide monomers is first raised by reac- tions that add two phosphate groups to the ribonucleotides or deoxyribonucleotides, creating nucleoside triphosphate

Ribozymes

RNA molecules that function as enzymes -ribozymes are responsible for the catalytic activity of the ribosomes that polymerize amino acids to form polypeptides.

How do added phosphate groups raise the potential energy of a molecule?

Recall that phosphates are negatively charged and that like charges repel (Chapter 2). Linking two or more phos- phates together generates a covalent bond that carries a large amount of potential energy due to the strong repulsive forces. The energy is released when the phosphates form new, more stable bonds with other atoms

X-ray crystallography

Rosalind Franklin and Maurice Wilkins had calculated the distances between groups of atoms in the molecule. The technique they used is called

5. What is responsible for the increased stability of DNA compared to RNA?

DNA is a more stable molecule than RNA because it lacks a hydroxyl group on the 2∙ carbon and is therefore more resistant to cleavage

How is DNA put together?

DNA is put together like a ladder. The antiparallel sugar-phosphate backbones form the supports of the ladder, and the base pairs form its rungs. The helical twist- ing of the strands allows the bases to line up in a way that makes hydrogen bonding between them possible.. The physical restraints posed by these interactions result in a full helical turn every 10 bases—the 3.4-nm distance observed by Franklin and Wilkins

DNA secondary structure

DNA's secondary structure consists of two antiparallel strands twisted into a double helix. • The double helix is shaped and stabilized by hydrophobic interactions, van der Waals interactions, and hydrogen bond- ing between the complementary base pairs A-T and G-C.

phosphodiester linkage

Forming of a new covalent bond in a nucleic acid strand, formed by linking two nucleotides via condensation reaction (water molecule released)

the sugar-phosphate backbone of a nucleic acid is directional

In a strand of RNA or DNA, one end has an unlinked 5' phosphate while the other end has an unlinked 3' hydroxyl—meaning the groups are not bonded to another nucleotide. written in 5 --->3 direction

The DNA double helix is highly structured

It is regular, sym- metric, and held together by phosphodiester linkages, hydrogen bonding, and hydrophobic interactions