Lecture 5: Nucleotides and Nucleic Acids Flashcards
What are the differences between Nucleotide and Nucleoside?
Same except for Nucleotide includes all (3) containing Phosphate Groups
What is the difference between ribose and deoxyribose?
Ribose is 2’ -> OH
Deoxyribose is 2’-> H (missing an oxygen on C2)
Where is the anomeric carbon?
C1. attachment of Nitrogenous Base
Is the phosphate group negative or positively charge at neutral pH?
Negatively
Can phosphate groups be attached to only C5 or other carbons as well?
C5 is not the only Carbon that phosphate groups can attach to.
Which of the following statements is true?
A. The 5’ carbon of a nucleoside is phosphorylated in a nucleotide.
B. The 5’ hydroxyl of a nucleoside is phosphorylated in a nucleotide.
C. The 1’ carbon of a nucleoside is phosphorylated in a nucleotide.
D. The 1’ hydroxyl of a nucleoside is phosphorylated in a nucleotide.
B
Which of the following statements is incorrect?
A. The nitrogenous base is attached to the 1’ carbon in both nucleotides and nucleosides.
B. The phosphate group of a nucleotide can only attached to the 5’ carbon.
C. The alpha phosphorus atom is the one closest to the 5’ carbon on a nucleotide.
D. Adenosine 5’ triphosphate includes 2 phosphoanhydride functional groups and can make 2 phosphodiester bonds with other nucleotides.
B
Which of the following is a nucleotide?
A. Cytosine
B. Guanosine
C. Adenylate
D. Uridine
C
Which of the following is a nucleoside?
A. Deoxythymidine
B. Uridylate
C. Guanine
D. Deoxyguanylate
A
Name the nucleotide that is only present in dna and not in rna.
DEOXYTHYMIDYLATE
What does cdp stand for?
cytosine 5’-diphosphate
what does dGMP stand for?
deoxyguanosine 5’-monophosphate
Which of the following statements is true?
A. The 2’ carbon in nucleotides and nucleosides is called the anomeric carbon.
B. The chiral center closest to the carbonyl carbon is used to determine the D or L configuration in sugars.
C. If the phosphate group of a nucleotide is above the plane of the sugar, then it is in the beta conformation.
D. The alpha and beta designation of sugars is made relative to the hydroxyl group on the 5’ carbon.
D
The N-glycosidic bond
How are N-bases attached to the sugar? To what carbon? In what configuration? To what Nitrogen atom in pyrimidines? To what Nitrogen in purines?
ANOMERIC
BETA
N1
N9
What is the normal syn/anti conformation in beta-dna? Why?
Anti!
So that H-bonds can occur between bases aka to allow for base-pairing
What are the syn and anti conformations assigned relative to?
Relative to the free rotation around the N-glycosidic bond in free nucleotides
difference between dna and rna
A. DNA includes a beta-D-ribofuranose and RNA includes a beta-2’-deoxy-D-ribofuranose.
B. RNA is more stable than DNA.
C. RNA includes uracil nitrogenous bases instead of thymine.
D. RNA is transcribed, DNA is translated.
Which of the following does not correctly indicated a parameter of what mendEl proposed?
A. Each adult only has 3 alleles for each gene.
B. Each gamete only carries 1 allele.
C. Each gene segregates equally into gametes.
D. There are hereditary determinants of particulate
A
What is Beta in reference to?
Nitrogenous Base & 5”OH attached in the same direction.
True or False;
Rotation is limited around the N-glycosidic bond
False; there is free rotation
Which type of Conformation is round in normal B-Dna
Anti-Conformation
What are the pH of Purines and Pyrimidines at ph of 7
both negative at a neutral pH
If Uridylate looses it’s phosphate what will it now be called?
Uridine
what do
- ate &
- ine refer to?
Tide
Side
What is the difference in syn/anti conformation?
Syn- Flag is flying in the same direction as sugar
Anti- Flag is flying in the opposite direction away from sugar
What type of bond attaches the pentose ring to the base?
N-glycosidic bond
Nitrogenous Base & 5’ Phosphate Group attached in the same direction of the plane of the sugar?
Beta
Nucleic Acids are build using 5’ tri phosphates
True
What is dTMP?
deoxy-thymidylate
What is AMP?
Adenosine monophosphate
What is dCMP
deoxy-cydidylate or deoxycytidylate monophosphate
What are purines?
Adenine
Guanine
What are pyrimidines?
Cytosine
Thymine
Uracil
How is inosine created?
delaminating adenosine
A pairs with T using how many hydrogen bonds?
2
C pairs to G using how many hydrogen bonds?
3
Why is RNA
2’ OH attack kicks off leaving group
weak/unstable bonds on RNA
O of the phosphate attacks OH of oxygen on C2.
Which type of configurations are found in DNA?
Syn or Anti
Anti
True or False;
Uracil will have deoxy.
False; Uracil will not have deoxy. Deoxy is only found in DNA and Uracil (N. Base) isn to found in DNA.
Which N on the N. Base is pyrimidine connected to?
N1
Which N on the N. Base is puring connected to?
N9
What is an epigenetic marker?
Way to make own DNA so that cells can degrade foreign DNA
AND
Way to mark which genes should be active
What position can the inosine be found?
“Wobble position” of the anticodon in tRNA
True or False
DNA is complementary and anti-parallel
True
True or False
Synthesis is catalyzed by enzymes known as DNA Polymerases
True
Newly made DNA molecule has one template strand and one daughter strand
False; one daughter strand and one parent strand
What is the fx. of mRNA
carry protein message
What sugar and n. base does mRNA carry that DNA does not?
ribose
uracil
True or False;
mRNA is polycistronic
True
What is the fx. of tRNA?
Matching Amino Acids with mRNA code
The most precise modern definition of a gene is a segment of genetic material that:
A) codes for one polypeptide. B) codes for one polypeptide or RNA product. C) determines one phenotype. D) determines one trait. E) that codes for one protein.
B
The DNA in a bacterial (prokaryotic) chromosome is best described as:
A) a single circular double-helical molecule.
B) a single linear double-helical molecule.
C) a single linear single-stranded molecule.
D) multiple linear double-helical molecules.
E) multiple linear single-stranded molecules
A
- Bacterial plasmids:
A) are always covalently joined to the bacterial chromosome.
B) are composed of RNA.
C) are never circular.
D) cannot replicate when cells divide.
E) often encode proteins not normally essential to the bacterium’s survival.
E
True or False
mRNA can only code for one protein?
False; it can code for more than one protein.
Which of these statements about nucleic acids is false?
A) Mitochondria and chloroplasts contain DNA.
B) Plasmids are genes that encode plasma proteins in mammals.
C) The chromosome of E. coli is a closed-circular, double-helical DNA.
D) The DNA of viruses is usually much longer than the viral particle itself.
E) The genome of many plant viruses is RNA.
B
B
Functional DNA is not found in:
A) bacterial nucleoids. B) chloroplasts. C) lysosomes. D) mitochondria. E) nuclei.
C
The DNA in a eukaryotic chromosome is best described as:
A) a single circular double-helical molecule.
B) a single linear double-helical molecule.
C) a single linear single-stranded molecule.
D) multiple linear double-helical molecules.
E) multiple linear single-stranded molecules
B
Introns:
A) are frequently present in prokaryotic genes but are rare in eukaryotic genes.
B) are spliced out before transcription.
C) are translated but not transcribed.
D) can occur many times within a single gene.
E) encode unusual amino acids in proteins
D
Approximately what fraction of the human genome is transposable elements?
A) 1.5% B) 5% C) 10% D) 45% E) 80%
D
The chromosomal region that is the point of attachment of the mitotic spindle is the:
A) centromere. B) endomere. C) exon. D) intron. E) telomere.
A
DNA in a closed-circular, double-stranded molecule with no net bending of the DNA axis on itself is:
A) a left-handed helix. B) a mixed right- and left-handed helix. C) relaxed. D) supercoiled. E) underwound.
C
It is correct to say that DNA supercoiling cannot:
A) be induced by strand separation.
B) be induced by underwinding of the double helix.
C) form if there is Z-DNA structure present.
D) occur if a closed circular double-stranded DNA molecule has a nick.
E) result in compaction of the DNA structure.
D
The linking number (Lk) of a closed-circular, double-stranded DNA molecule is changed by:
A) breaking a strand, then rejoining it.
B) breaking a strand, unwinding or rewinding the DNA, then rejoining it.
C) breaking all hydrogen bonds in the DNA.
D) supercoiling without the breaking of any phosphodiester bonds.
E) underwinding without the breaking of any phosphodiester bonds.
B
For a closed-circular DNA molecule of 10,000 base pairs in the fully relaxed form, the linking number (Lk) is about:
A) 10,000. B) 950. C) 100. D) 9.5. E) 2.
B
If the structure of a fully relaxed, closed-circular DNA molecule is changed so that the specific linking difference () is -0.05, the number of:
A) bases is decreased by 5%. B) bases is increased by 5%. C) helical turns is decreased by 5%. D) helical turns is increased by 5%. E) helical turns is unchanged.
C
Topoisomerases can:
A) change the linking number (Lk) of a DNA molecule.
B) change the number of base pairs in a DNA molecule.
C) change the number of nucleotides in a DNA molecule.
D) convert D isomers of nucleotides to L isomers.
E) interconvert DNA and RNA.
A
Topoisomerases:
A) can change the linking number in increments of 1 or 2.
B) can act on single-stranded DNA circles.
C) change the degree of supercoiling of a DNA molecule but not its linking number of DNA.
D) occur in bacteria, but not in eukaryotes.
E) always require energy from ATP.
A
A commonality between type I and type II topoisomerases is that they both:
A) change the linking number in increments of 1 or 2.
B) require ATP.
C) go through a mechanism using a covalent enzyme-substrate intermediate.
D) are inhibited by quinoline antibiotics.
E) All of the above
C
Plectonemic supercoils in a negatively supercoiled DNA molecule:
A) are always left-handed. B) are always right-handed. C) are balanced by solenoidal supercoils D) can be either right- or left-handed. E) never occur.
B
Histones are _______ that are usually associated with _________.
A) acidic proteins; DNA B) acidic proteins; RNA C) basic proteins; DNA D) basic proteins; RNA E) coenzymes derived from histidine; enzymes
C
Which of the following does not contribute to the octameric histone core?
A) H1 B) H2A C) H2B D) H3 E) H4
C
The fundamental repeating unit of organization in a eukaryotic chromosome is the:
A) centrosome. B) lysosome. C) microsome. D) nucleosome. E) polysome.
D
Which of the following contributes to the structure of nucleosomes?
A) Plectonemic supercoiled DNA B) Relaxed closed-circular DNA C) Solenoidal supercoiled DNA D) Spacer DNA E) Z (left-handed) DNA
C
Nucleosomes:
A) are important features of chromosome organization in eukaryotes and bacteria.
B) are composed of proteins rich in acidic amino acids, such as Asp and Glu.
C) are composed of protein and RNA.
D) bind DNA and alter its supercoiling.
E) occur in chromatin at irregular intervals along the DNA molecule.
D
A condensed eukaryotic chromosome is known to be associated with all of the following proteins, except for:
A) core histones H2A, H2B, H3, and H4. B) histone H1. C) SMC proteins. D) topoisomerase I. E) topoisomerase II
D
The SMC proteins (for structural maintenance of chromosomes) include cohesins and condensins, and are known to have all of the following properties except:
A) a complete ATP binding site. B) a hinge region. C) topoisomerase activity to produce positive supercoils. D) the ability to condense DNA. E) two coiled-coil domains.
C
Bacterial chromosomes:
A) are highly compacted into structures called nucleoids.
B) are seen in electron microscopy as “beads on a string.”
C) are surrounded by a nuclear membrane.
D) contain large numbers of nucleosomes.
E) when fully extended are as long as the bacterial cell.
A
What is the charge of the DNA backbone?
Negative
Does an A to T or G to C bond melt easier?
A to T melts easier. This bond only contains 2 hydrogen bonds while a G to C contains 3, so an A to T is easier to break.
_______ is a type of RNA that translates mRNA into specific sequence of amino acids for protein use.
tRNA (Transfer)
What does ribosomal RNA (rRNA) do?
- Catalyzes synthesis of proteins and contains specially modified bases
- Complex 3D shape (globular) associated with proteins for ribosome use only
The compound that consists of ribose linked by an N-glycosidic bond to N-9 of adenine is:
A) a deoxyribonucleoside. B) a purine nucleotide. C) a pyrimidine nucleotide. D) adenosine monophosphate. E) adenosine.
E
A major component of RNA but not of DNA is:
A) adenine. B) cytosine. C) guanine. D) thymine. E) uracil.
E
The difference between a ribonucleotide and a deoxyribonucleotide is:
A) a deoxyribonucleotide has an —H instead of an —OH at C-2.
B) a deoxyribonucleotide has alpha configuration; ribonucleotide has the beta configuration at C-1.
C) a ribonucleotide has an extra —OH at C-4.
D) a ribonucleotide has more structural flexibility than deoxyribonucleotide.
E) a ribonucleotide is a pyranose, deoxyribonucleotide is a furanose.
A
Which one of the following is true of the pentoses found in nucleic acids?
A) C-5 and C-1 of the pentose are joined to phosphate groups.
B) C-5 of the pentose is joined to a nitrogenous base, and C-1 to a phosphate group.
C) The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond.
D) The pentoses are always in the -furanose forms.
E) The straight-chain and ring forms undergo constant interconversion.
D
A) always link A with T and G with C.
B) are susceptible to alkaline hydrolysis.
C) are uncharged at neutral pH.
D) form between the planar rings of adjacent bases.
E) join the 3’ hydroxyl of one nucleotide to the 5’ hydroxyl of the next.
E
The phosphodiester bond that joins adjacent nucleotides in DNA:
A) associates ionically with metal ions, polyamines, and proteins.
B) is positively charged.
C) is susceptible to alkaline hydrolysis.
D) Links C-2 of one base to C-3 of the next.
E) links C-3 of deoxyribose to N-1 of thymine or cytosine.
A
The alkaline hydrolysis of RNA does not produce:
A) 2'- AMP. B) 2',3'-cGMP. C) 2'-CMP. D) 3',5'-cAMP. E) 3'-UMP.
D
The nucleic acid bases:
A) absorb ultraviolet light maximally at 280 nm.
B) are all about the same size.
C) are relatively hydrophilic.
D) are roughly planar.
E) can all stably base-pair with one another.
D
In a double-stranded nucleic acid, cytosine typically base-pairs with:
A) adenosine. B) guanine. C) inosine. D) thymine. E) uracil.
B
In the Watson-Crick model for the DNA double helix (B form) the A-T and G-C base pairs share which one of the following properties?
A) The distance between the two glycosidic (base-sugar) bonds is the same in both base pairs, within a few tenths of an angstrom.
B) The molecular weights of the two base pairs are identical.
C) The number of hydrogen bonds formed between the two bases of the base pair is the same.
D) The plane of neither base pair is perpendicular to the axis of the helix.
E) The proton-binding groups in both base pairs are in their charged or ionized form.
A
Chargaff’s rules state that in typical DNA:
A) A = G. B) A = C. C) A = U. D) A + T = G + C. E) A + G = T + C.
E
In the Watson-Crick structure of DNA, the:
A) absence of 2’-hydroxyl groups allows bases to lie perpendicular to the helical axis.
B) adenine content of one strand must equal the thymine content of the same strand.
C) nucleotides are arranged in the A-form.
D) purine content (fraction of bases that are purines) must be the same in both strands.
E) two strands are parallel.
A
In the Watson-Crick model of DNA structure:
A) both strands run in the same direction, 3’ to 5’; they are parallel.
B) phosphate groups project toward the middle of the helix, where they are protected from interaction with water.
C) T can form three hydrogen bonds with either G or C in the opposite strand.
D) the distance between the sugar backbone of the two strands is just large enough to accommodate either two purines or two pyrimidines.
E) the distance between two adjacent bases in one strand is about 3.4 Å.
E
Which of the following is not true of all naturally occurring DNA?
A) Deoxyribose units are connected by 3’,5’-phosphodiester bonds.
B) The amount of A always equals the amount of T.
C) The ratio A+T/G+C is constant for all natural DNAs.
D) The two complementary strands are antiparallel.
E) Two hydrogen bonds form between A and T.
C
In the Watson-Crick model of DNA structure (now called B-form DNA):
A) a purine in one strand always hydrogen bonds with a purine in the other strand.
B) A-T pairs share three hydrogen bonds.
C) G-C pairs share two hydrogen bonds.
D) the 5’ ends of both strands are at one end of the helix.
E) the bases occupy the interior of the helix.
E
In nucleotides and nucleic acids, syn and anti conformations relate to:
A) base stereoisomers. B) rotation around the phosphodiester bond. C) rotation around the sugar-base bond. D) sugar pucker. E) sugar stereoisomers.
C
B-form DNA in vivo is a ________-handed helix, _____ Å in diameter, with a rise of ____ Å per base pair.
A) left; 20; 3.9 B) right; 18; 3.4 C) right; 18; 3.6 D) right; 20; 3.4 E) right; 23; 2.6
D
In double-stranded DNA:
A) only a right-handed helix is possible.
B) sequences rich in A-T base pairs are denatured less readily than those rich in G-C pairs.
C) the sequence of bases has no effect on the overall structure.
D) the two strands are parallel.
E) the two strands have complementary sequences.
E
Triple-helical DNA structures can result from Hoogsteen (non Watson-Crick) interactions. These interactions are primarily:
A) covalent bonds involving deoxyribose.
B) covalent bonds involving the bases.
C) hydrogen bonds involving deoxyribose.
D) hydrogen bonds involving the bases.
E) hydrophobic interactions involving the bases.
D
Double-stranded regions of RNA:
A) are less stable than double-stranded regions of DNA.
B) can be observed in the laboratory, but probably have no biological relevance.
C) can form between two self-complementary regions of the same single strand of RNA.
D) do not occur.
E) have the two strands arranged in parallel (unlike those of DNA, which are antiparallel).
C
When double-stranded DNA is heated at neutral pH, which change does not occur?
A) The absorption of ultraviolet (260 nm) light increases.
B) The covalent N-glycosidic bond between the base and the pentose breaks.
C) The helical structure unwinds.
D) The hydrogen bonds between A and T break.
E) The viscosity of the solution decreases.
B
The “energy carrier” ATP is an example of a(n):
A) deoxyribonucleoside triphosphate B) di-nucleotide C) peptide D) ribonucleotide E) ribonucleoside triphosphate
E
