Chapter 1: Nucleic Acids and Proteins
Molecular Diagnostics Lela Buckingham
Verified
What makes up a nucleotide? - Answer sugar, phosphate, nitrogen base
What kind of bond is between two nucleotides on a DNA strand - Answer Phosphodiester bond
Bonds between the complementary nucleotide strands (sense and antisense strands) are - Answer
Hydrogen Bonds
The addition of nucleotides to form a complementary strand of DNA occurs in what direction - Answer
5'->3'
What part of the nucleotide can change - Answer nitrogenous base (Adenine, Cytosine, Guanine,
Thymine, and Uracil in RNA)
What does the ribose sugar have that deoxyribose sugar does not have - Answer a Oxygen on the 2'
Carbon
What is deoxyribose? - Answer -Pentose sugar found in DNA nucleotides, missing an oxygen on 2'
Carbon
What do purines look like? - Answer They have 2 ring structures
What do pyrimidines look like? - Answer They have 1 ring structure
What causes the spiraling in a Double helix DNA/RNA - Answer Polarity (nucleotides are negatively
charged)
,What can affect the DNA double helix - Answer Order of nucleotides, surrounding chemical micro
envirornment (heat, acid, alkalinity)
What is the difference between a nucleotide and a nucleoside - Answer Nucleotides have a phosphate
group, sugar and base. Nucleosides only have a sugar and base
DNA structure considered to be - Answer Complementary and antiparallel
Nucleoside examples - Answer Adenosine, Guanosine, Cytidine, Thymidine
nucleotide examples - Answer Adenosine Triphosphate, Guanosine Triphosphate, Cytidine Triphosphate,
Thymidine Triphosphate
What is the key to specificity of most nucleic acid based tests in the molecular laboratory - Answer
Hydrogen bonds in DNA
modified bases - Answer mutation or change (on purpose) that affects gene expression. Used by viruses
or bacteria to distinguish self from host
Which way is DNA read/ are parallel bases added - Answer 5' to 3'
anti-parallel strands - Answer 3' end of one strand aligns with 5' end of other. This is the complementary
strand, and the strand that okazaki fragments are added
DNA addition (polymerization) is done using - Answer DNA Polymerase and DNA template as a guide
Helicase - Answer An enzyme that untwists the double helix at the replication forks, separating the two
parental strands and making them available as template strands.
Gyrase - Answer Part of Topermerase II subclass that produces a double strand break "DNAgate" that
can cause the double helix to pass through break, reseal break and disassociate from DS DNA. This needs
ATP.
, Topoisomerase I - Answer produces a transient single strand nick allowing the phosphodiester bonds to
rotate freely releasing tension (Doesn't need ATP). Relieves the tension created by helicase
DNA replication - Answer 1.) DNA is unwound/unzipped by the enzyme helicase and single strand
binding proteins keep the strand exposed
2.) Helicase and accessory proteins such as DNA primase, DNA polymerase, & sliding clamp loader
produce a replication fork
3.) each strand produces a template which can produce a new strand of DNA
4.) DNA polymerase binds to the primer and makes new strands of DNA using the original template
strand (semi-conservative)
5.) Exonuclease removes all of the primers from DNA strands once the new strands have been made
6.) DNA polymerase then fills the gaps of the strand that had the primer removed
7.) DNA ligase seals up the nicks and fragments in both strands of the DNA to form a continuous double
strand
Leading strand - Answer The new continuous complementary DNA strand synthesized along the
template strand in the mandatory 5' to 3' direction. DNA polymerase-primer-accessory protein complex
synthesizes it in one continuous motion.
Lagging Strand - Answer A discontinuously synthesized DNA strand that elongates by means of Okazaki
fragments, each synthesized in a 5' to 3' direction away from the replication fork. DNA polymerase can
only read one fragment at a time and primase continually forms primers because the 3' lagging strand
doesnt have the 3'OH needed to form the DNA because it starts at the 5' end
DNA Polymerase I and II function - Answer responsible to fix gaps and discontinuities in previously
synthesized DNA. DNA Pol I proofreads and has exonuclease II activity
DNA polymerase III - Answer Main polymerizing enzyme in replication
Includes a holoenzyme that works with other proteins required for priming, initiation, regulation, and
termination of the replication process. 20% of the subunits are used for synthesis of leading and lagging
strand via DNA polymerizing enzymes. Can build up and break down simultaneously (add nucleotides at
3' end while reading 5' end). Nick translation simultaneously synthesis and hydrolysis of DNA and then
moving strand forward until polymerize is Discharged
Molecular Diagnostics Lela Buckingham
Verified
What makes up a nucleotide? - Answer sugar, phosphate, nitrogen base
What kind of bond is between two nucleotides on a DNA strand - Answer Phosphodiester bond
Bonds between the complementary nucleotide strands (sense and antisense strands) are - Answer
Hydrogen Bonds
The addition of nucleotides to form a complementary strand of DNA occurs in what direction - Answer
5'->3'
What part of the nucleotide can change - Answer nitrogenous base (Adenine, Cytosine, Guanine,
Thymine, and Uracil in RNA)
What does the ribose sugar have that deoxyribose sugar does not have - Answer a Oxygen on the 2'
Carbon
What is deoxyribose? - Answer -Pentose sugar found in DNA nucleotides, missing an oxygen on 2'
Carbon
What do purines look like? - Answer They have 2 ring structures
What do pyrimidines look like? - Answer They have 1 ring structure
What causes the spiraling in a Double helix DNA/RNA - Answer Polarity (nucleotides are negatively
charged)
,What can affect the DNA double helix - Answer Order of nucleotides, surrounding chemical micro
envirornment (heat, acid, alkalinity)
What is the difference between a nucleotide and a nucleoside - Answer Nucleotides have a phosphate
group, sugar and base. Nucleosides only have a sugar and base
DNA structure considered to be - Answer Complementary and antiparallel
Nucleoside examples - Answer Adenosine, Guanosine, Cytidine, Thymidine
nucleotide examples - Answer Adenosine Triphosphate, Guanosine Triphosphate, Cytidine Triphosphate,
Thymidine Triphosphate
What is the key to specificity of most nucleic acid based tests in the molecular laboratory - Answer
Hydrogen bonds in DNA
modified bases - Answer mutation or change (on purpose) that affects gene expression. Used by viruses
or bacteria to distinguish self from host
Which way is DNA read/ are parallel bases added - Answer 5' to 3'
anti-parallel strands - Answer 3' end of one strand aligns with 5' end of other. This is the complementary
strand, and the strand that okazaki fragments are added
DNA addition (polymerization) is done using - Answer DNA Polymerase and DNA template as a guide
Helicase - Answer An enzyme that untwists the double helix at the replication forks, separating the two
parental strands and making them available as template strands.
Gyrase - Answer Part of Topermerase II subclass that produces a double strand break "DNAgate" that
can cause the double helix to pass through break, reseal break and disassociate from DS DNA. This needs
ATP.
, Topoisomerase I - Answer produces a transient single strand nick allowing the phosphodiester bonds to
rotate freely releasing tension (Doesn't need ATP). Relieves the tension created by helicase
DNA replication - Answer 1.) DNA is unwound/unzipped by the enzyme helicase and single strand
binding proteins keep the strand exposed
2.) Helicase and accessory proteins such as DNA primase, DNA polymerase, & sliding clamp loader
produce a replication fork
3.) each strand produces a template which can produce a new strand of DNA
4.) DNA polymerase binds to the primer and makes new strands of DNA using the original template
strand (semi-conservative)
5.) Exonuclease removes all of the primers from DNA strands once the new strands have been made
6.) DNA polymerase then fills the gaps of the strand that had the primer removed
7.) DNA ligase seals up the nicks and fragments in both strands of the DNA to form a continuous double
strand
Leading strand - Answer The new continuous complementary DNA strand synthesized along the
template strand in the mandatory 5' to 3' direction. DNA polymerase-primer-accessory protein complex
synthesizes it in one continuous motion.
Lagging Strand - Answer A discontinuously synthesized DNA strand that elongates by means of Okazaki
fragments, each synthesized in a 5' to 3' direction away from the replication fork. DNA polymerase can
only read one fragment at a time and primase continually forms primers because the 3' lagging strand
doesnt have the 3'OH needed to form the DNA because it starts at the 5' end
DNA Polymerase I and II function - Answer responsible to fix gaps and discontinuities in previously
synthesized DNA. DNA Pol I proofreads and has exonuclease II activity
DNA polymerase III - Answer Main polymerizing enzyme in replication
Includes a holoenzyme that works with other proteins required for priming, initiation, regulation, and
termination of the replication process. 20% of the subunits are used for synthesis of leading and lagging
strand via DNA polymerizing enzymes. Can build up and break down simultaneously (add nucleotides at
3' end while reading 5' end). Nick translation simultaneously synthesis and hydrolysis of DNA and then
moving strand forward until polymerize is Discharged
