NUCLEIC ACIDS AND DNA
Chargaff rule
# of purines = # of pyrimidines equal # of T's and A's and equal # of C's and G's
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
3 components of a nucelotide
1. Phosphate group 2. 5-carbon sugar 3. a nitrogenous base
characteristics of deoxyribonucleotides
1. are monomers of DNA 2. sugar: deoxyribose 3. H- group bonded to the 2' carbon
characteristics of ribonucleotides
1. are monomers of RNA 2. sugar: ribose 3. OH- group bonded to the 2' carbon
shape of DNA secondary structure
2 strands that twisted into a double helix
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?
20 percent (has to equal 50)
If a DNA double helix contains 28% T nucleotides, then what is the percentage of A nucleotides?
28%
end nucleotides are added to during polymerization
3 '
How many nitrogenous bases in DNA and RNA?
4
By convention, nucleotide sequences are always written from the...
5' end to the 3' end
DNA base pairing
A->T (double bonded w/ hydrogen bonds) G->C (triple bonded w hydrogen bonds)
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
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)
What is required for the synthesis of nucleic acids?
Complementary pairing between bases is required for copying nucleic acids
3 Pyrimidine bases
Contain 6 atoms in a single ring 1. Cytosine (C) 2. Uracil (U) only found in RNA 3. Tymine (T) only found in DNA
Central Dogma
DNA codes for RNA, RNA codes for proteins
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
Antiparallel
DNA strands that run in opposite directions- 3' to 5', 5' to 3'
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
True/False: New phosphodiester linkages always form at the 5' end of the existing polymer.
False- only form at 3'
tertiary structure of RNA
Folds that form distinctive three-dimensional shapes
Which statement best explains why G-T and A-C base pairs are not complementary?
G-T and A-C base pairs cannot form as many hydrogen bonds as A-T and G-C base pairs.
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
How are nucleotides linked together to form a polynucleotide chain?
In DNA and RNA, a phosphodiester linkage connects the 3' carbon of one nucleotide and the 5' carbon of another.
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.
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
Most biologists contend that the first life-form on Earth was a self-replicating RNA molecule, not DNA or protein. Why is that?
Only RNA can function as a catalyst and an information-containing entity.
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
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 accurately summarizes a difference between ribonucleotides and deoxyribonucleotides
Ribonucleotides have a hydroxyl group bonded to their 2' carbon; deoxyribonucleotides have an H at the same location.
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
How are the structures of RNA and DNA similar?
Their sugar-phosphate backbones are formed by phosphodiester linkages.
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.
What nitrogenous base is only found in deoxyribonucleotides (DNA)?
Thymine (T)
True/False: DNA can form primary, secondary and tertiary structures.
True
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
A double-stranded DNA must be heated to 95°C to cause the bonds between complementary base pairs break and produce single-stranded DNA. Considering this observation, is the formation of DNA's secondary structure spontaneous? Why or why not?
Yes. The energy present in the polar covalent bonds of the nitrogenous bases is sufficient to cause the hydrogen bonds to form.
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
DNA's and RNA's primary structure
a sequence of linked nucleotides
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
RNA's secondary structure includes
a variety of configurations including short regions of complimentary bases pairing that form double-helix stems and unpaired loops
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
What are the four nitrogenous bases found in RNA?
adenine, cytosine, guanine, uracil (A, C, G, U)
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
nucleic acids
are made up of monomers called nucleotides
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 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
purines
contain 9 atoms in their 2 rings adenine and guanine
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
What determines the primary structure of a DNA molecule?
deoxyribonucleotide sequence
stabilization of DNA secondary structure
done by hydrogen bonds, hydrophobic interactions, and Van der Waals interactions that form between complimentary bases stacked on the inside of the helix
Polymerization: endothermic or exothermic reaction?
endothermic reaction
formation of tertiary structure of DNA
formed by twisting the double helix into supercoils or wrapping around proteins
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.
Phosphodiester linkage
occurs between the phosphate group on the 5' carbon of one nucleotide and the -OH group on the 3' carbon of another.
backbone of nucleic acids
pentose sugar and phosphate group
The condensation reaction that forms nucleic acid polymers occurs between a _____ group on one nucleotide and a _____ group on a second nucleotide.
phosphate, hydroxyl
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
an RNA molecule that can catalyze chemical reactions is called a...
ribozyme
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
phosphidiester linkage
the connection between nucleotides that form when they polymerize via condensation reactions
What do cells do to activate nucleotides for incorporation into a polymer, and why?
they a dd phosphate groups to raise the potential energy of monomers
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
nucleotide polymerization
when condensation reactions join nucleotides together via phosphodiester linkages
