Chapter 8 - Nucleotides and Nucleic Acids

What are some early studies that demonstrated the informatio-carrying properties of DNA.

DNA extracted from a virulent (disease-causing) strain of the bacterium Streptococcus pneumoniae and injected into a nonvirulent strain of the same bacterium transformed the nonvirulent strain into a virulent strain. They concluded that the DNA from the virulent strain carried the genetic information for virulence. Then in 1952, experiments by Alfred D. Hershey and Martha Chase, in which they studied the infection of bacterial cells by a virus (bacteriophage) with radioactively labeled DNA or protein, removed any remaining doubt that DNA, not protein, carried the genetic information.

How do base structures result in base-pairing rules?

-This is consistent with there not being enough space (20 Å) for two purines to fit within the helix and too much space for two pyrimidines to get close enough to each other to form hydrogen bonds between them. -only with A & T and with C & G are there opportunities to establish hydrogen bonds (shown here as dotted lines) between them (two between A & T; three between C & G).

Describe example from lecture of spontaneous mutations?

1)Deamination: Very slow reactions, large number of resdues 2)Depurination: N-glycosidic bond is hydrolyzaed Depurination, in which a purine is lost by hydrolysis of the N-B- glycosyl bond. Loss of pyrimidines via a similar reaction occurs, but much more slowly. The resulting lesion, in which the deoxyribose is present but the base is not, is called an abasic site or an AP site 3)Oxidative damage:Hydroxylation of guanine, mitochondrial DNA is most susceptible Excited-oxygen species such as hydrogen peroxide, hydroxyl radicals, and superoxide radicals arise during irradiation or as a byproduct of aerobic metabolism. Of these species, the hydroxyl radicals are responsible for most oxidative DNA damage. 4)Chemical alkylation: Methylation of gunaine

Who were some important reasearhers involed in the search for the structure of DNA?

1)Levene and london discover strucure of DNA via hydrolysis of nuclein 2)Levene and tipson discovered structure via chemical anylsis to find pentsoe is ribofuranoside and the linkages 3)Watson and crick find double helix and base pairing 4)franklin and wilkins found out about the backbone

Describe examples from lecture of induced mutations?

1)UV light induces dimerization of pyrimidines; this may be the main mechanism for skin cancers 2)Ionizing radiation causes ring opening and strand breaking linked to aging and carcinogensis

Describe UV adsoprtion of Nucleobases.

Adsorption of UV light at 350-270nm is due to pi electronic transitions. Excited states of common nucleobases decay rapidly via radiationless transitions (effective photoprotection of genetic material and no fluorescence from nucleic acids. DNA can be detected around 260nm

Describe the helical configurations of double stranded DNA.

B form, the helix makes a turn every 3.4 nm, and the distance between two neighboring base pairs is 0.34 nm. Hence, there are about 10 pairs per turn. The intertwined strands make two grooves of different widths, referred to as the major groove and the minor groove, which may facilitate binding with specific proteins.

What are the major feature of B-form DNA?

B form, the helix makes a turn every 3.4 nm, and the distance between two neighboring base pairs is 0.34 nm. Hence, there are about 10 pairs per turn. The intertwined strands make two grooves of different widths, referred to as the major groove and the minor groove, which may facilitate binding with specific proteins.

Describe the structure of ATP and how it can be the "energy currency" of cells

Because of the highly charged phosphate groups that release a ton of energy when released due to repelling forces between them

What is chargaff's law?

Chargaff published a paper stating that in DNA of any given species, the ratio of adenine to thymine is equal, as is the ratio of cytosine to guanine. This is known as Chargaff's ratios and it was a crucial clue that helped solve the structure of DNA. Chargaff's ratios are universal: all forms of life obey this rule. Only the balance of A-T pairs and C-G pairs varies between species.

• What is cyclic AMP? How is it made, and what are some functions?

Cyclic adonine monophsophate, made from ATP and functions as an activator of kinases and signaling proteins like Epac

What are the major pyrimidine bases, and their structures?

Cytosine is found in both DNA and RNA, Thymine is found only in DNA, Uracil is found only in RNA. All are good H-bond donors and acceptors. Cytosine and Thymine. These are neutral molecules are pH of 7. Pyrimidines are generally restricted to the anti-conformation because f steric interference between the sugar and the carbonyl oxygen at C'-2

What is the relatonship between genes and DNA.

DNA is the material that is located in the cell's nucleus that makes up the chromosomes and genes

What is DNA methylation?

DNA methylation is an epigenetic mechanism used by cells to control gene expression. A number of mechanisms exist to control gene expression in eukaryotes, but DNA methylation is a commonly used epigenetic signaling tool that can fix genes in the "off" position

Can DNA sequences be determined? Can DNA be artificially synthesized?

Detection of a specific DNA in complex ixtures via radioactive detection and fluroscent DNA chips. Amplification of specific DNA via PCR and site-directed mutagenesis.

In addition to carrying infromation or energy. what are some biological functions of nucleic acids and nucletodies?

Enrgy source via AMP, ADP, ATP, GMP, GDP, GTP, CMP, CDP, CTP etc -Conenzymes like NAD+ and FAD -Regulatory molecules like cAMP

Describe Pseudouridine.

Found widely in tRNA and rRNA More common in eukaryotes but found also in ubacteria -made from uridine by enzymatice isomerization after RNA synthesis -May stabalize the structure of tRNA and may help folding of rRNA

Describe nucleic acid hybridization

However, some strands of the mouse DNA will associate with human DNA strands to yield hybrid duplexes, in which segments of a mouse DNA strand form base-paired regions with segments of a human DNA strand. This reflects a common evolutionary heritage; different organisms generally have many proteins and RNAs with similar functions and, often, similar structures. In many cases, the DNAs encoding these proteins and RNAs have similar sequences. The closer the evolutionary relationship between two species, the more extensively their DNAs will hybridize.

Describe the phopsodieter bond that forms polynucleotides?

In DNA and RNA, the phosphodiester bond is the linkage between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another, deoxyribose in DNA and ribose in RNA. Strong covalent bonds form between the phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds.

What factors affect DNA melting and annealing?

In DNA denaturation covalent bonds remain intact (Genetic code), the hydrogen bonds are broken (resulting in two separate strands) and the base stacking is lost (resulting in increased UV absorbance's) DNA exists as double helix at normal temperatures, two strands dissociate at elevated temperatures. Two strands re-anneal when temperature is lowered. The reversible thermal denaturation and annealing form basis for the polymerase chain reaction. DNA denaturation is commonly monitored by UV spectrophotometry at 260 nm. AT rich regions melt at lower temperatures than CG rich regions

Describe beta-N-glycosidic bond.

In nucleotides the pentose ring is attached to the nucleobase via N-glycosidic bond. The bond is formed to the anomeric carbon of the sugar in beta configuration. The bond is formed to position N1 in pyrimidines and to position N9 in purines. This bond is quite stable toward hydrolysis, especially in pyrimidines.

Describe Minor nucleotides in DNA.

It is when modification is done after DNA synthesis i.e. 5-Methylcytosine for eukaryottes and N-methyladensosine in bacteria -They are epigentic markes, ways to mark own DNA so that call can degrade foreing DNA

Distinguish between nucleosides, nucleotides and nucleic acids.

Nucleotides (Nitrogenous base, Pentose and phosphated) Nucleoside (Nitrogenous base and pentose) Nucleobase(nitrogenous base)

What are some of the important functions of nucleotides and nucleic acids in biological systems?

Nucleotides: Energy for metabolism via ATP; Enzyme cofactors (NAD); Signal transduction (cAMP) Nucleic Acid: Storage of genetic information (DNA); Transmission of genetic infromation (mRNA); Processing of genetic information (ribozymes);Portein synthesis (tRAN and rRNA)

What is base-catalyzed RNA hydrolysis, and is it a problem for DNA?

RNA is unstable under alkaline conditions and hydrolysis is catalyzaed by enzyme (RNase) -RNA is hydrolyzed rapidly under alkaline condition, but DNA is not as RNA contains 2'-hydroxyl groups that are directly involved with the process.

Describe inosine

Sometimes found in the "wobble position" of the anticodon in tRNA. made by deaminating adenosine, provides richer genetic code and base pairs with A, C or U. Also a minor nucleobase

Describe the A-form DNA

The DNA is still arranged in a righthanded double helix, but the helix is wider and the number of base pairs per helical turn is 11, rather than 10.5 as in B-DNA. The plane of the base pairs in A-DNA is tilted about 20º relative to B-DNA base pairs, thus the base pairs in A-DNA are not perfectly perpendicular to the helix axis. These structural changes deepen the major groove while making the minor groove shallower. The reagents used to promote crystallization of DNA tend to dehydrate it, and thus most short DNA molecules tend to crystallize in the A form.

What are the nitrogenous bases?

The Nucleobases are derivatives of pyrmidine or purine. They are nitrogen-containing heteroaromatic molecules. Planar or almost planar structures. Absorb UV light around 250-270nm

What pentoses?

The Pentose in nucleotides can be beta-D-ribofuranose in RNA or B-2'-deoxy-D-ribofuranose in DNA. Different puckered conformations of the sugar ring are possible

What are phosphates?

The Phosphate group is negatively charged at neutral pH, typically attached at 5' position (nucleic acids are built using 5'- triphosphates (ATP, GTP, TTP, CTP). The nucleic acids contain one phosphate moiety per nucleotide and may be attached to other positions or even in cyclic conformation.

What are factors affecting DNA denaturation?

The midpoint of meltin (Tm) depends on base compoition (High CG increases Tm) Tm dependeing on DNA length (Longer DNA has higher Tm) Tm depends on pH and ionic strength (high salt increases Tm)

What allows RNA to take on diverse 3-D forms?

The single strand of RNA tends to assume a right handed helical conformation dominated by base-stacking interactions which are stronger between a purine and pyrimidine or two pyrimidines. RNA can base-pair with complementary regions of either RNA or DNA.

What are the two main types of nucleic acid? compare and contrast them.

The two main types of nucleic acids are DNA and RNA DNA contains the sugar deoxyribose, while RNA contains the sugar ribose. The only difference between ribose and deoxyribose is that ribose has one more -OH group than deoxyribose, which has -H attached to the second (2') carbon in the ring. DNA is a double stranded molecule while RNA is a single stranded molecule. DNA is stable under alkaline conditions while RNA is not stable. DNA and RNA perform different functions in humans. DNA is responsible for storing and transferring genetic information while RNA directly codes for amino acids and as acts as a messenger between DNA and ribosomes to make proteins. DNA and RNA base pairing is slightly different, since DNA uses the bases adenine, thymine, cytosine, and guanine; RNA uses adenine, uracil, cytosine, and guanine. Uracil differs from thymine in that it lacks a methyl group on its ring.

Describe rotation about the N-glycosidic bond.

There is relatively free rotation that can occur around the N-glycosidic bond in free nucleotides. The torsion angle about the N-glycosidic bond (N-C1') is denoted by the symbol c. The sequence of atoms hosen to define this angle is O4'-C1'-N9-C4 for purine, and 04'-C1'-N1-C2 for pyrimidine derivatives. Angle near 0 degrees corresponds to syn conformation, angle near 180 degrees corresponds to anti conformation (anti conformation is found in normal B-DNA)

Describe the structure of hydrogen bond in polynucleotides

Two bases can ydrogen bond to form a base pair for monomers, large number of base pairs is possible in polynucletoide only a few are possible. Watson-Crick base pairs preodminate in DS DNA

Describe Z DNA

Z-form DNA is a more radical departure from the B structure; the most obvious distinction is the left-handed helical rotation. There are 12 base pairs per helical turn, and the structure appears more slender and elongated. The DNA backbone takes on a zigzag appearance. Certain nucleotide sequences fold into left-handed Z helices much more readily than others. Prominent examples are sequences in which pyrimidines alternate with purines, especially alternating C and G or 5-methyl-C and G residues. To form the left-handed helix in Z-DNA, the purine residues flip to the syn conformation, alternating with pyrimidines in the anti conformation. The major groove is barely apparent in Z-DNA, and the minor groove is narrow and deep.

What are the majore purine bases, and thier structures?

are adenine and guanine and are found both in RNA and DNA. Good H-bond donors and acceptors. Adenine and Guanine. The molecules are neutral at a pH of 7. Because of steric constratins, purines in purine nucleotides are restricted to two stable conformations with respect to deoxyribose called syn and anti

What are the major categories of RNAs

mRNA transcribes the genetic code from DNA into a form that can be read and used to make proteins. mRNA carries genetic information from the nucleus to the cytoplasm of a cell. rRNA is located in the cytoplasm of a cell, where ribosomes are found. rRNA directs the translation of mRNA into proteins. tRNA Like rRNA, tRNA is located in the cellular cytoplasm and is involved in protein synthesis. Transfer RNA brings or transfers amino acids to the ribosome that correspond to each three-nucleotide codon of rRNA. The amino acids then can be joined together and processed to make polypeptides and proteins.