Biology - CH 4: Nucleic Acids and the RNA World

What early data provided clues for Watson and Crick?

-Knew that the molecule has a sugar-phosphate backbone. Knew that DNA polymerized through the formation of phosphodiester linkages. - # of purines = # of pyrimidines -the DNA molecule has an equal number of T's and A's, and it has an equal number of C's and G's -x-ray crystallography that inferred that DNA molecules had a regular and repeating structure

How are the secondary structures of RNA and DNA similar?

(like DNA) most RNA molecules have secondary structure that results from complementary base pairing between purine and pyrimidine bases. In RNA, adenine forms two H bonds with uracil, and guanine again forms three H bonds with cytosine.

Step 2 of making DNA copy

Free deoxyribonucleotides form hydrogen bonds with complementary bases on the original strand of DNA- called template strand. As they do, their do, their sugar-phosphate groups form phosphodiester linkages to create a new strand- called complementary stand. Note that the 5' to 3' directionality of the complementary strand is opposite to that of the template strand

What binding interaction is complementary base pairing based on?

Hydrogen Bonding

How do the secondary structures of RNA and DNA differ?

In most cases, the purine and pyrimidine bases in RNA undergo hydrogen bonding with complementary bases on the same strand (rather than H bonds w complementary bases on a different strand)

Who presented the the secondary structure of DNA?

James Watson and Francis Crick

What are the nitrogenous bases, and what structural group do they belong to?

Purines: adenine (A) and guanine (G) Pyrimidines: cytosine (C), uracil (U), and thymine (T) Ribonucleotides use uracil (U), while deoxyribonucleotides use thymine (T).

Important characteristics of RNA

RNA is highly versatile/widely diverse and can function as a catalytic molecule

How do the tertiary structures of RNA and DNA differ?

RNA molecules have a tertiary structure, which arises when secondary structures fold into more complex shapes. RNA molecules are much more diverse in size, shape, and reactivity than DNA molecules.

ribozymes

RNA that can catalyze reactions, similar to protein enzymes

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

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

Ribonucleic acid

Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes.

How are the primary structures of RNA and DNA similar?

Similar: Both have a primary structure consisting of four types of nitrogenous bases extending from sugar-phosphate backbone

By tinkering with helical configurations and using models, Watson and Crick began to realize..

That if the bases extending from each backbone are to fit within the interior of a 2.0-nm-wide structure, they they have to form purine-pyrimidine pairs (figure 4.5a) Purine-pyrimidine pairing allows hydrogen bonds to form between complementary bases. Adenine will form two H bonds with thymine and guanine will form three hydrogen bonds with cytosine. The third hydrogen bond in G-C pairs make them slightly stronger than A-T pairs. The patterns of hydrogen bonding (Figure 4.5b) could form only if the bases on opposite strands were flipped 180˚ relative to one another. For this to happen one strand runs 5' to 3' while the other runs 3' to 5', they run antiparallel. The antiparallel strands are twisted to form a double helix

Describe the secondary structure in RNA

The RNA folds over to align with bases on another part of the SAME strand. The two sugar-phosphate strands are antiparallel and the H bonding between complementary bases results in a helical structure

Compare the reactivity of DNA to RNA

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

Describe solubility of sugar-phosphate backbone

The negatively charged phosphate groups facing the exterior of the molecule base the double helix hydrophilic overall and thus soluble in aqueous solutions.

DNA grooves

The outside of the helical DNA molecule forms two grooves. A major and a minor groove. The groove asymmetry is vital for granting access to proteins that bind to particular base sequences in DNA.

What is the conventional written notation for a primary stretch of DNA or RNA?

The sequence of bases (in RNA or DNA) is always written in the 5' to 3' direction. This makes sense because in cells, RNA and DNA are always synthesized in this direction. Nucleotides are only added to the 3' end of the growing molecule.

How did Watson and Crick approach solving the mystery secondary structure of DNA?

They began by analyzing the size and geometry of the three nucleotide components : deoxyribose, phosphate, and base. The bond angles And measurements suggested that the distance of 2.0 nm was the width of the helix and that 0.34 nm was likely to be the distance between bases stacked in a spiral

What is the function of DNA?

To store information

How did researches test the RNA world hypothesis, and what did they discover?

To test, researchers are attempting to synthesize new ribozymes in the laboratory. Using artificial selection strategies, they have succeeded in identifying RNAs that catalyze several different reactions. Ribozymes that catalyze reactions necessary for the production of nucleotides may have preceded the evolution of RNA replicases.

DNA's tertiary structure

Two tertiary structures of DNA are found in cells. When DNA becomes would too tightly or loosely wound with respect to to their number of base pair per helical turn, it can twist on itself to form compact, 3D structures called supercoils. Additionally, DNA often forms highly organized tertiary structures by wrapping around certain proteins. These DNA-protein complexes compact the DNA into discrete, moveable units during cell division and they also contribute to DNA's ability to store and transmit information.

Is the polymerization of active nucleotides spontaneous or non spontaneous?

When activated nucleotides polymerize, the energy released from the condensation reaction compensates for the decrease in entropy, making the reaction spontaneous.

Summarize the findings of Watson and Crick

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 bonding between the complementary base pairs A-T and G-C

What is an example of an activated ribonucleotide?

adenosine triphosphate, ATP

What is the secondary structure of DNA?

antiparallel double helix

Nucleic acids

are polymers, nucleic acids are made up of monomers called nucleotides

Deoxyribonucleotides (& draw its sugar)

are the monomers of deoxyribonucleic acid (DNA). In deoxyribonucleotides, the sugar is deoxyribose. Deoxyribonucleotides can use A, G, C, and T as a nitrogenous base. Only deoxyribonucleotides can use Thymine (t).

Ribonucleotides (& draw its sugar)

are the monomers of ribonucleic acid (RNA). In ribonucleotides, the sugar is ribose. Ribonucleotides can use A, G, C, and U as a nitrogenous base. Only ribonucleotides can use Uracil (U)

Deoxyribonucleic acid

stores genetic information and is replicated using proteins

Step 1 of making DNA copy

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.

Describe the bonding between base pairs

Although each base has polar groups involved in the hydrogen bonds, the carbon-nitrogen ring structure (nitrogenous base) is mainly non-polar. This is key because hydrophobic interactions cause the double-stranded DNA to twist into a helix to minimize the contact between the hydrophobic rings and surrounding water molecules. The paired strands are further stabilized by van der Waals interactions between the tightly paced bases.

Step 3 of making DNA copy

Complementary base pairing allows each strand of DNA double helix to be copied exactly, producing two identical daughter molecules

What are the three components of a nucleotide (draw)

1) phosphate group 2) a five-cabon sugar 3) a nitrogenous (nitrogen containing) base

How do the primary structures of RNA and DNA differ?

1. The sugar-phosphate backbone of RNA is ribose, not deoxyribose as in DNA 2. The pyrimidine base thymine does not exist in RNA. Instead, RNA contains the closely related pyrimidine base uracil.

Describe the general make-up of DNA

DNA molecules have a sugar-phosphate backbone, created by phosphodiester linkages, and a sequence of any four nitrogenous bases that extend from it.

Can DNA perform catalysis? Why/why not?

No, because of DNA's orderliness, stability, and dependence as an information repository. The structure of DNA is simple and nonreactive. It has never been observed to catalyze any reaction in an organism.

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. The reaction forms a new covalent bond, called a phosphodiester linkage/phosphodiester bond between the nucleotides and a water molecule is released. When phosphodiester linkages join ribonucleotides together, the polymer that is produced is RNA. Phosphodiester linkages between deoxyribonucleotides produce DNA.

Draw the complementary base pairing that's based on hydrogen bonding

Occurs between A-T and G-C bases

How can polymerization take place in cells?

Polymerization can take place in cells because the potential energy of the nucleotide monomers is first raised by reactions that add two phosphate groups to the ribonucleotides/deoxyribonucleotides, creating nucleoside triphosphates. Nucleoside triphosphate are referred to as "activated nucleotides".

Are DNA and RNA strands directional?

Yes! Like the peptide-bonded backbone of a polypeptide, 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.

Does polymerization require energy?

Yes, polymerization requires an energy source. In cells, the polymerization reaction that joins nucleotides into nucleic acids are catalyzed by enzymes. As with other polymerization reactions, the joining of nucleotides dramatically decreases entropy and thus is not spontaneous. An input of energy is needed to tip the energy balance in favor of polymerization.