chapter 4

What are the three components of a nucleotide?

1) A phosphate group 2) A five-carbon sugar 3) A nitrogenous (nitrogen-containing) base

What did Watson and Crick determine of DNA's secondary structure?

1) DNA strands run in an antiparallel configuration. 2) DNA strands form a double helix 3) Purines always pair with pyrimidines 4) DNA has two different-sized grooves

What are the two groups of nitrogenous bases? What nucleic acids are in each?

1) Purines (Adenine & guanine) 2) Pyrimidines (Cytosine, uracil, & thymine)

What about RNA's primary structure differs from DNA's?

1) RNA contains uracil instead of thymine 2) RNA contains ribose instead of deoxyribose

What were Erwin Chargaff's two established, empirical rules for DNA?

1) The total number of purine and pyrimidines is the same 2) The number of A's and T's are equal and the number of C's and G's are equal

The nucleotide sequence for the sugar-phosphate backbone is written in the _ -> _ direction. This reflects the order that nucleotides are added to a growing molecule. What is the nucleotide sequence in the nucleic acid?

5' -> 3' direction the nucleic acid's primary structure

This is a polymer of nucleotide monomers

A nucleic acid

A molecule consisting of an adenine base, a sugar, and three phosphate groups that can hydrolyzed to release energy. Universally used by cells to store and transfer energy

Adenosine triphosphate (ATP)

In both ribose and deoxyribose, what group and what carbon are bonded?

An -OH group is bonded to the 3' carbon

Suppose that Bartel's research group succeeded in producing a molecule that could make a copy of itself. Which of the five fundamental characteristics of life would support the claim that this molecule is alive?

An RNA replicase would undergo replication and be able to evolve. It would process information in the sense of copying itself, and it would use energy to drive polymerization reactions. It would not be bound by a membrane and considered a cell, however, and it would not be able to acquire energy. It would best be considered as an intermediate step between non-life and true life.

Describing the opposite orientation of nucleic acid strands that are hydrogen bonded to one another, with one strand running in the 5' -> 3' direction and the other in the 3' -> 5' direction

Antiparallel

For RNA's ____ structure, the RNA strand folds over, forming a hairpin structure. The bases are on one side of the fold. The bases align with an ____ RNA segment on the other side of the fold.

Antiparallel

Purine and pyrimidine strands form this type of base pair... What nucleic acids bond & what type of/how many bonds?

Complementary base pair. A-T have two hydrogen bonds; C-G have three hydrogen bonds

The association between specific nitrogenous bases of nucleic acids stabilized by hydrogen bonding. Adenine pairs only with thymine (in DNA) or uracil (in RNA), and guanine pairs only with cytosine

Complementary base pairing (Watson-Crick pairing)

A newly synthesized strand of RNA or DNA that has a base sequence complementary to that of the template strand

Complementary strand

A major theme in this chapter is that the structure of molecules correlates with their function. Explain how DNA's secondary structure limits its catalytic abilities compared with that of RNA. Why is it expected that RNA molecules can catalyze a modest but significant array of reactions?

DNA has limited catalytic ability because it (1) lacks functional groups that can participate in catalysis and (2) has a regular structure that is not conducive to forming shapes required for catalysis. RNA molecules can catalyze some reactions because they (1) have exposed hydroxyl functional groups and (2) can fold into shapes that then can function in catalysis

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, and because the two sugar-phosphate backbones are held together by many hydrogen bonds between nitrogenous bases

This aspect of DNA makes it a reliable store for genetic information, it's less reactive than RNA, and it is more resistant to chemical degradation

DNA's stability

A nucleic acid composed of deoxyribonucleotides that carries the genetic information of a cell. Generally occurs as two intertwined strands, but these can be separated

Deoxyribonucleic acid (DNA)

The sugar-phosphate backbone of a nucleic acid is ____, which means it has polarity. One end has an unlinked 5' carbon; the other end has an unlinked 3' carbon

Directional

The secondary structure of DNA, consisting of two antiparallel DNA strands wound around each other

Double helix

T/F? The bases of RNA typically form hydrogen bonds with complementary bases on new strands.

FALSE with complementary bases on the SAME strand

tertiary structure of RNA

Folds that form distinctive three-dimensional shapes

A secondary structure in RNA consisting of a stable loop formed by hydrogen bonding between purine and pyrimidine bases on the same strand

Hairpin

Based on Watson & Crick's determining the double helix formation of DNA strands, what structures face where?

Hydrophilic sugar-phosphate backbone faces the exterior; nitrogenous base pairs face the interior

Explain how Chargaff's rules relate to the complementary base pairing seen in the secondary structure of DNA. Would you expect these rules to apply to RNA as well? Explain why or why not

In DNA, the secondary structure requires that every guanine pairs with a cytosine and every thymine pairs with an adenine, resulting in consistent ratios between the nucleotides. Chargaff's rules do not apply to RNA, since it is single-stranded and the pairing is not consistent throughout the molecules

Before Watson and Crick published their model of the DNA double helix, Linus Pauling offered a model based on a triple helix. If the three sugar-phosphate backbones were on the outside of such a molecule, would hydrogen bonding or hydrophobic interactions be more important in keeping such a secondary structure together?

In a triple helix, the bases are unlikely to align properly for hydrogen bonding to occur, so hydrophobic interactions would probably be more important

What are the two groove sizes of DNA?

Major and minor groove

secondary structure of RNA

Most common are hairpins, formed when a single strand folds back on itself to form a double helix "stem" and a single-stranded "loop"

To replicate a ribozyme, a complete complementary copy must be made. Would you expect the double-stranded intermediate to maintain its catalytic activity? Justify your answer with an explanation.

No. Catalytic activity in ribozymes depends on the tertiary structure generated from single-stranded molecules. Double-stranded nucleic acids do not form tertiary structures.

A macromolecule composed of nucleotide monomers. Generally used by cells to store or transmit hereditary information. Include ribonucleic acid and deoxyribonucleic acid

Nucleic acid

A molecule consisting of a five-carbon sugar (ribose or deoxyribose), a phosphate group, and one of several nitrogen-containing bases. DNA and RNA are polymers of nucleotides containing deoxyribose (deoxyribonucleotides) and ribose (ribonucleotides), respectively. Equivalent to a nucleoside plus one phosphate group

Nucleotide

Nucleic acids are directional, meaning that there are two different ends. What functional groups define the two different ends of a DNA 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

Chemical linkage between adjacent nucleotide residues in DNA and RNA. Forms when the phosphate group of one nucleotide condenses with the hydroxyl group on the sugar of another molecule

Phosphodiester linkage (bond)

Only these pairs fit inside the double helix...

Purine-pyrimidine pairs

A class of double-ringed bases (guanine, adenine) found in nucleotides

Purines

A class of single-ringed bases (cytosine, uracil, thymine) found in nucleotides

Pyrimidines

What's similar about DNA and RNA's functionality?

RNA can function as an information-containing molecule capable of self-replication

Proposal that chemical evolution produced RNAs that could catalyze key reactions involved in their own replication and basic metabolism, which led to the evolution of proteins and the first life-form

RNA world hypothesis

A nucleic acid composed of ribonucleotides that usually is single stranded. Functions include structural components of ribosomes (rRNA), transporters of amino acids (tRNA), and messages of the DNA code required for protein synthesis (mRNA), among others

Ribonucleic acid (RNA)

What two types of nucleotides are involved in condensation reaction?

Ribonucleotides & deoxyribonucleotides

Any RNA molecule that can act as a catalyst, that is, speed up a chemical reaction

Ribozymes

Who calculated the distances between groups of atoms in the DNA molecule by bombarding DNA with x-rays and analyzing how it scattered the radiation (called 'x-ray crystallography')?

Rosalind Franklin and Maurice Wilkins

primary structure of DNA

Sequence of deoxyribonucleotides; bases are A, T, G, C

primary structure of RNA

Sequence of ribonucleotides; bases are A, U, G, C

An original nucleic acid strand used to make a new, complementary copy based on hydrogen bonding between nitrogenous bases

Template strand

RNA's ___ structure forms when secondary structures fold into more complex shapes

Tertiary structure

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' -> 3'.) How would this 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 the T would be replaced by a U

Ribozymes

These are enzyme-like RNAs

What about RNA's structure is similar to DNA's?

They have a primary structure consisting of a sugar-phosphate backbone formed by phosphodiester linkages, extending from that backbone, a sequence of four types of nitrogenous bases.

How do nucleic acids form?

Through condensation reaction

What nitrogenous base is only found in deoxyribonucleotides (DNA)?

Thymine (T)

secondary structure of DNA

Two antiparallel strands twist into a double helix, stabilized by hydrogen bonding between complementary bases (A-T, C-G) and hydrophobic interactions.

What nitrogenous base is only found in ribonucleotides (RNA)?

Uracil (U)

With the nature of DNA's secondary structure, who knew that the molecule had a sugar-phosphate backbone?

Watson and Crick

A technique for determining the three-dimensional structure of large molecules, including proteins and nucleic acids, by analysis of the diffraction patterns produced by X-rays beamed at crystals of the molecule

X-ray crystallography

Viruses are particles that infect cells. In some viruses, the genetic material consists of two strands of RNA, bonded together via complementary base pairing. Would these antiparallel strands form a double helix? Why or why not?

Yes - if the complementary bases lined up over the entire length of the two strands, they would twist into a double helix analogous to a DNA molecule. The same types of hydrogen bonds and hydrophobic interactions would occur as observed in the "stem" portion of hairpins in single-stranded RNA

DNA attains a secondary structure when hydrogen bonds form between the nitrogenous bases called purine and pyrimidines. What are the complementary base pairs that form in DNA? a) A-T and G-C b) A-U and G-C c) A-G and T-C d) A-T and G-U

a

Ribose and deoxyribose differ by a single _ atom. Ribose has an _ group bonded to the _ _. Deoxyribose has an _ instead at the same location

a single oxygen atom. -OH; 2' carbon; H

If nucleotides from the DNA of a human were quantified and 30 percent of them consisted of adenine, what percentage of guanine nucleotides would be present? a) 20% b) 30% c) 40% d) 70%

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

DNA's secondary structure consists of two ___ strands twisted into a double helix. The molecule is stabilized by ___ interactions in its interior. ___ bonding occurs between the complementary base pairs: ___-T & ___-C

antiparallel; hydrophobic; hydrogen; A-T; G-C

How would you expect the structure of ribozymes in organisms that grow in very hot environments, such as hot springs or deep sea vents, to differ from those in organisms that grow in cooler environments? a) These ribozymes would have more hairpin secondary structures. b) The hairpins would have more G's and C's in the primary structure. c) The hairpins would have more A's and U's in the primary structure. d) These ribozymes would exhibit no tertiary structure.

b; the high temperature would make it more likely that the secondary and tertiary structures would be denatured in the ribozymes. To overcome this effect, you would expect the hairpins to possess more G-C pairs, since they consist of three hydrogen bonds compared to the two found in A-T pairs

The language of nucleic acids is contained in the sequence of the ___

bases

DNA can store and transmit ___ information. DNA carries the information required for the organism's ___ and ___ of all cells.

biological. growth; reproduction

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

c

What determines the primary structure of a DNA molecule? a) the sugar-phosphate backbone b) complementary base pairing and the formation of hairpins c) the sequence of deoxyribonucleotides d) the sequence of ribonucleotides

c

RNA can function as a ___ molecule

catalytic

RNA's secondary structure results from...

complementary base pairing

Which of the following rules apply to the synthesis of nucleic acids? a) Nucleotides are added to the 5' end of nucleic acids. b) The synthesis of nucleic acids cannot occur without the presence of an enzyme to catalyze the reaction. c) Strands are synthesized in a parallel direction such that one end of the double-stranded product has the 3' ends and other has the 5' ends. d) Complementary pairing between bases is required for copying nucleic acids.

d

Nucleic acids

form from polymerized nucleotides

With the nature of DNA's secondary structure, chemists had worked out the structure of ___; they knew that ___ polymerized through the formation of phosphodiester linkages

nucleotides; DNA

Phosphodiester linkage

occurs between the phosphate group on the 5' carbon of one nucleotide and the -OH group on the 3' carbon of another.

Stable molecules such as DNA make ____ catalysts.

poor

With DNA replication, the ___ structure serves as a template for the synthesis of a complementary strand, containing the information required for a copy of itself to be made.

primary

Structurally/chemically, RNA is intermediate between the complexity of ____ and the simplicity of ____

proteins; DNA

Complementary base pairing

provides a simple mechanism for DNA replication. Each strand can serve as a template for the formation of a new complementary strand

In a nucleotide, the phosphate is bonded to the _ molecule, which is bonded to the _ base

sugar; nitrogenous base

With RNA's structure, the presence of this group on ribose makes RNA much more reactive and less stable than DNA

the -OH group

T/F? Biologists think that the first life-form was made of RNA, not DNA. DNA does not appear to catalyze any chemical reaction.

true