Self Assessment Question 1 Which chemical group is at the 5' end of a single polynucleotide strand? Hydroxyl group      Diester group      Purine base      Phosphate group    Nitrogen group

Self Assessment Question 1 Answer Which chemical group is at the 5' end of a single polynucleotide strand? Hydroxyl group      Diester group      Purine base      Phosphate group CORRECT ANSWER    Nitrogen group

Structure of Nucleic Acid DNA and RNA consist of only four nucleotides Adenine (A) and guanine (G) are purines Cytosine (C), thymine (T) and uracil (U) are pyrimidines A nucleotides consist of an organic base linked to a five-carbon sugar with a phosphate group attached to carbon 5. In RNA, the sugar is ribose; in DNA, deoxyribose. Polynucleotide sequences are read in 5’ -> 3’ direction All nucleotides consist of an organic base linked to a five-carbon sugar with a phosphate attached to carbon 5. In RNA, the sugar is ribose; in DNA, deoxyribose. A single nucleic acid strand has a backbone composed of repeating pentose-phosphate units from which the purine and pyrimidine bases extend as side groups. The chemical linkage between adjacent nucleotides is a phosphodiester bond. The nucleic acid strand has an end-to-end chemical orientation; the 5’ end has a hydroxyl or phosphate group on the 5’ carbon of its terminal sugar; the 3’ end usually has a hydroxyl group on the 3’ carbon of its terminal sugar. This directionality, plus the fact that synthesis proceeds 5’ to 3’ has given rise to the convention that polynucleotides sequences are written and read in the 5’ to 3’ direction.

Self Assessment Question 2 Which chemical group is at the 3' end of a single polynucleotide strand? Phosphate group      Hydroxyl group    Purine base      Nitrogen group      Methyl group

Self Assessment Question 2 Answer Which chemical group is at the 3' end of a single polynucleotide strand? Phosphate group      Hydroxyl group CORRECT ANSWER    Purine base      Nitrogen group      Methyl group

Structure of Nucleic Acid DNA and RNA consist of only four nucleotides Adenine (A) and guanine (G) are purines Cytosine (C), thymine (T) and uracil (U) are pyrimidines A nucleotides consist of an organic base linked to a five-carbon sugar with a phosphate group attached to carbon 5. In RNA, the sugar is ribose; in DNA, deoxyribose. Polynucleotide sequences are read in 5’ -> 3’ direction All nucleotides consist of an organic base linked to a five-carbon sugar with a phosphate attached to carbon 5. In RNA, the sugar is ribose; in DNA, deoxyribose. A single nucleic acid strand has a backbone composed of repeating pentose-phosphate units from which the purine and pyrimidine bases extend as side groups. The chemical linkage between adjacent nucleotides is a phosphodiester bond. The nucleic acid strand has an end-to-end chemical orientation; the 5’ end has a hydroxyl or phosphate group on the 5’ carbon of its terminal sugar; the 3’ end usually has a hydroxyl group on the 3’ carbon of its terminal sugar. This directionality, plus the fact that synthesis proceeds 5’ to 3’ has given rise to the convention that polynucleotides sequences are written and read in the 5’ to 3’ direction.

Self Assessment Question 3 The purine bases are: Thymine and cytosine      Thymine and guanine      Cytosine and Adenine      Cytosine and guanine      Adenine and guanine   

Self Assessment Question 3 Answer The purine bases are: Thymine and cytosine      Thymine and guanine      Cytosine and Adenine      Cytosine and guanine      Adenine and guanine CORRECT ANSWER   

Self Assessment Question 4 The pyrimidine bases are: Thymine and cytosine    Thymine and guanine      Adenine and guanine      Cytosine and adenine      Cytosine and guanine

Self Assessment Question 4 Answer The pyrimidine bases are: Thymine and cytosine CORRECT ANSWER    Thymine and guanine      Adenine and guanine      Cytosine and adenine      Cytosine and guanine

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Self Assessment Question 5 Each new DNA strand is initiated by a: Short RNA primer    Single-stranded DNA-binding protein      Precursor fragment      Restriction fragment      Specific DNA primer

Self Assessment Question 5 Answer Each new DNA strand is initiated by a: Short RNA primer CORRECT ANSWER    Single-stranded DNA-binding protein      Precursor fragment      Restriction fragment      Specific DNA primer

Self Assessment Question 6 The phenomenon where the two complementary strands of duplex DNA have their 5’-to-3’ directions running in opposite directions is called: Antiparallel    Nucleic acid hybridization      Renaturation      Rolling-circle replication      Restriction fragment polymorphism  

Self Assessment Question 6 Answer The phenomenon where the two complementary strands of duplex DNA have their 5’-to-3’ directions running in opposite directions is called: Antiparallel CORRECT ANSWER    Nucleic acid hybridization      Renaturation      Rolling-circle replication      Restriction fragment polymorphism  

DNA forms a Double Helix The presence of thousands of such hydrogen bonds in a DNA molecule contributes greatly to the stability of the double helix. Hydrophobic and van der Waals interactions between the stacked adjacent base pairs further stabilize the double-helical structure. Two DNA strands where nucleotides form base pairs are said to be complementary. The DNA forms a right-handed helix. The two strands form two helical grooves of different widths described as the major groove and the minor groove. The atoms on the edge of each base within these grooves are accessible from outside the helix, forming two types of binding surfaces. DNA binding proteins can “read” the sequence of bases in duplex DNA by contacting atoms in either the major or the minor grooves. The bases are projected inward whereas the sugar phosphate backbone is on the outside The two strands are antiparallel A is paired with T through two hydrogen bonds G is paired with C through three hydrogen bonds

Self Assessment Question 7 The Meselson-Stahl experiment showed that a single round of DNA replication produces: One DNA molecule made of two parental strands and a second DNA molecule made of two daughter strands.      Two duplex DNA molecules where all of the strands are partly parental and part new DNA.      Two duplex DNA molecules each with one parental strand and one daughter strand.    Many duplex DNA molecules, all with two new daughter strands.

Self Assessment Question 7 Answer The Meselson-Stahl experiment showed that a single round of DNA replication produces: One DNA molecule made of two parental strands and a second DNA molecule made of two daughter strands.      Two duplex DNA molecules where all of the strands are partly parental and part new DNA.      Two duplex DNA molecules each with one parental strand and one daughter strand. CORRECT ANSWER    Many duplex DNA molecules, all with two new daughter strands.

DNA Replication: Meselson-Stahl Experiment Results ** Important points: The conservative mechanism never generates H-L DNA. The semiconservative mechanism never generates H-H DNA, but does generate H-L DNA during the second and subsequent doublings. DNA replicates by which mechanism? In this experiment, E. coli cells were grown in a medium containing ammonium salts prepared with “heavy” nitrogen (N15) until all the cellular DNA was labeled. After the cells were transferred to a medium containing the normal “light” isotope N14. Samples were periodically removed and the DNA in each was measured by density-gradiant centrifugation. This technique can separate H-H, H-L, and L-L duplexes into distinct bands.

Self Assessment Question 8 DNA fragments migrate in an electric field because DNA molecules: Are positively charged      Are neutral in charge      Are negatively charged Are double stranded      Contain numerous covalent bonds

Self Assessment Question 8 Answer DNA fragments migrate in an electric field because DNA molecules: Are positively charged      Are neutral in charge      Are negatively charged CORRECT ANSWER    Are double stranded      Contain numerous covalent bonds

Self Assessment Question 9 Endonucleases: Break internal phosphodiester bonds in a single- or double-stranded nucleic acid molecule.   Remove amino acids from the carboxyl end of a polypeptide chain.      Connect two DNA fragments.      Remove terminal nucleotides from the 3'-end of a polynucleotide chain.      Connect two oligopeptides.

Self Assessment Question 9 Answer Endonucleases: Break internal phosphodiester bonds in a single- or double-stranded nucleic acid molecule. CORRECT ANSWER    Remove amino acids from the carboxyl end of a polypeptide chain.      Connect two DNA fragments.      Remove terminal nucleotides from the 3'-end of a polynucleotide chain.      Connect two oligopeptides *Note: restriction enzymes are endonucleases produced by bacteria

Self Assessment Question 10 A palindrome is a sequence that: reads differently when read from either direction      can be found in multiple origins of replication      is the same when read from either direction is used as a primer in DNA replication      contains only purines

Self Assessment Question 10 Answer A palindrome is a sequence that: reads differently when read from either direction      can be found in multiple origins of replication      is the same when read from either direction CORRECT ANSWER    is used as a primer in DNA replication      contains only purines websters-dictionary-online.com

Self Assessment Question 11 Which of the following sequences are palindromes? 5'-CCAG-3'      5'-CCCC-3'      5'-CCAGG-3'      5'-ACCGGA-3'      5'-CCATGG-3'   

Self Assessment Question 11 Answer Which of the following sequences are palindromes? 5'-CCAG-3'      5'-CCCC-3'      5'-CCAGG-3'      5'-ACCGGA-3'      5'-CCATGG-3' CORRECT ANSWER   

Self Assessment Question 12 Which of the following is a characteristic of restriction enzymes? Most restriction enzymes recognize a single site.      The restriction site is recognized regardless of the source of the DNA.      The number of times a piece of DNA is cut is determined by the number of times the restriction site is present in the DNA.      Most restriction sites are palindromes.      A, B, C, and D    A and C      B and D

Self Assessment Question 12 Answer Which of the following is a characteristic of restriction enzymes? *Most restriction enzymes recognize a single site.      * The restriction site is recognized regardless of the source of the DNA.      * The number of times a piece of DNA is cut is determined by the number of times the restriction site is present in the DNA.      * Most restriction sites are palindromes.      A, B, C, and D CORRECT ANSWER    A and C      B and D

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