Biochem Exam 4
What is the central dogma of molecular biology? - ANSWER:
What are ways in which the central dogma has evolved? - ANSWER:
How are transcription and translation held in time and space in prokaryotes?
Eukaryotes? - ANSWER: prokaryotes - no nucleus, so transcription and translation
occur at the same time and place in cytoplasm
eukaryotes - nucleus present, transcription occurs first in nucleus and translation occurs
next in cytoplasm
Describe Oswald Avery's experiment. What did he prove and how did he prove it? -
ANSWER: - Avery proved that DNA held genetic material
- he removed the capsule forming DNA of the "killed" pathogenic S (smooth) strain of
Streptococcus pneumoniae and allowed the nonpathogenic R (rough) strain to
incorporate it
- the R strain then turned into the pathogenic S strain because it developed a capsule
- he repeated this experiment with proteinases and RNases (which destroyed all
proteins and RNA) and the results proved the same
- however the experiment changed once DNases were included (which proved his point)
What are Chargaff's base pairing rules? - ANSWER: *A=T and C=G
*pairings vary with species (humans have 59% AT and 41% GC)
*constant and not changed by cell type, age, nutrition, environment, etc
Describe Watson and Crick base pairs. - ANSWER: A and T:
*H-O hydrogen bond is 2.8 A
*N-N hydrogen bond is 3.0 A
*entire pairing is 11.1 A
G and C:
*O-H hydrogen bond is 2.9 A
*N-N hydrogen bond is 3.0 A
*N-O hydrogen bond is 2.9 A
*entire pairing is 10.8 A
Describe the double helix model of DNA. - ANSWER: - two unbranched polynucleotide
chains in an antiparallel formation
- only interaction is between base pair hydrogen bonds
- phosphodiester linkage between each nucleotide
,- read in the 5'→3' direction (phosphate to hydroxyl)
- glycosidic bonds between base and ribose sugar
What are the terms used when describing the separation and pairing of DNA strands? -
ANSWER: denaturing (heat to 95 degrees) and annealing
What is the structure of B-DNA? - ANSWER: - right-handed helix
- 10.5 base pairs per turn
- base pairs lie flat and perpendicular to the axis
- hydrated
- major and minor grooves expose base pairs (so proteins can access them)
What is A-DNA and Z-DNA? - ANSWER: A-DNA:
*dehydrated
*double stranded RNA or DNA and RNA hydrids
Z-DNA:
*less than 1% of all DNA
*left-handed
What 3 forms of DNA are seen in very small amounts? - ANSWER: cruciform, triplex,
quadruplex
Describe the structure of RNA. - ANSWER: - linear single-stranded polynucleotide chain
- ribose sugar-phosphate backbone
- uracil (U) in place of thymine (T)
- read in the 5'→3' direction (phosphate to hydroxyl)
What are the primary, secondary, and tertiary structures of RNA? How do they
contribute to more complex structures? - ANSWER: primary: stem, loop, stem
secondary: stem-loop, internal loop, single stranded, double stranded, hairpin loop,
open ends
tertiary: stem loop structures interact with each other
What is a gene? Where are they located? - ANSWER: a heredity unit that includes the
DNA encoding a function RNA or protein and the regulatory elements controlling its
expression
**all genes have fixed locations within the genome
Describe the genome of E.coli. - ANSWER: a single circular chromosome with all 4500
genes in fixed positions
Describe the human genome. - ANSWER: - 46 linear chromosomes
- positions of genes are characteristic of species
- 29,000 genes
- 3,070,128,600
, What is the position of the EDN1 gene? - ANSWER: 6p24.1
What is chromatin? Nucleosomes? - ANSWER: - DNA molecules that are tightly coiled
around proteins call histones
- histones +DNA = nucleosomes
What is the packaging order of DNA in eukaryotic nuclei? - ANSWER: two chromatids >
one coil (30 rosettes) > one rosette (6 loops) > one loop (75000 bp) > 30 nm fiber >
beads of a string form of chromatin > DNA
What are the three polymerases and their function? What do they require to function? -
ANSWER: *DNA polymerase - adds one dNMP to the 3' end, requires a DNA template
chain and a primer
*RNA polymerase - adds one NMP to the 3' end, require DNA template chain
*Reverse transcriptase - adds one dNMP to the 3' end of a growing DNA chain, requires
a RNA template chain and primer
What are the three nucleases (DNase or RNase) and their function? - ANSWER:
*Endonuclease - breaks a phosphodiester bond within a polypeptide chain
*Excinuclease - breaks two phosphodiester bonds within a single polynucleotide chain
*Exonuclease - removes nucleotides from one end of the polynucleotide chain
What is DNA ligase and what does it do? - ANSWER: links two existing DNA chains
together end-to-end by catalyzing formation of a phosphodiester bond
What are the basic concepts of polynucleotide synthesis? - ANSWER: - synthesis is
always 5'→3' direction
- addition of dNMPs are always to existing strands
- pyrophosphate is kicked off the dNMP
How do endonucleases work? - ANSWER: - cut at specific sites
- cause a nick (one strand) or a double strand break (both strands)
- are either sequence-independent (DNase1) or sequence-specific (EcoRI)
How do exonucleases work? - ANSWER: - remove nucleotides from one end or the
other
- DNase or RNase
- exonuclease I is 3' to 5' for example
How do DNA ligase work in vivo? - ANSWER: - joins the end of DNA nucleotide chains
to make a continuous 5' to 3' strand by forming phosphodiester linkages
- AMP from ATP or NAD+ (E.coli) is linked to DNA ligase
- phosphate from ligase-AMP links to the open phosphate in a DNA nick, donating an O
to seal the nick
What is the central dogma of molecular biology? - ANSWER:
What are ways in which the central dogma has evolved? - ANSWER:
How are transcription and translation held in time and space in prokaryotes?
Eukaryotes? - ANSWER: prokaryotes - no nucleus, so transcription and translation
occur at the same time and place in cytoplasm
eukaryotes - nucleus present, transcription occurs first in nucleus and translation occurs
next in cytoplasm
Describe Oswald Avery's experiment. What did he prove and how did he prove it? -
ANSWER: - Avery proved that DNA held genetic material
- he removed the capsule forming DNA of the "killed" pathogenic S (smooth) strain of
Streptococcus pneumoniae and allowed the nonpathogenic R (rough) strain to
incorporate it
- the R strain then turned into the pathogenic S strain because it developed a capsule
- he repeated this experiment with proteinases and RNases (which destroyed all
proteins and RNA) and the results proved the same
- however the experiment changed once DNases were included (which proved his point)
What are Chargaff's base pairing rules? - ANSWER: *A=T and C=G
*pairings vary with species (humans have 59% AT and 41% GC)
*constant and not changed by cell type, age, nutrition, environment, etc
Describe Watson and Crick base pairs. - ANSWER: A and T:
*H-O hydrogen bond is 2.8 A
*N-N hydrogen bond is 3.0 A
*entire pairing is 11.1 A
G and C:
*O-H hydrogen bond is 2.9 A
*N-N hydrogen bond is 3.0 A
*N-O hydrogen bond is 2.9 A
*entire pairing is 10.8 A
Describe the double helix model of DNA. - ANSWER: - two unbranched polynucleotide
chains in an antiparallel formation
- only interaction is between base pair hydrogen bonds
- phosphodiester linkage between each nucleotide
,- read in the 5'→3' direction (phosphate to hydroxyl)
- glycosidic bonds between base and ribose sugar
What are the terms used when describing the separation and pairing of DNA strands? -
ANSWER: denaturing (heat to 95 degrees) and annealing
What is the structure of B-DNA? - ANSWER: - right-handed helix
- 10.5 base pairs per turn
- base pairs lie flat and perpendicular to the axis
- hydrated
- major and minor grooves expose base pairs (so proteins can access them)
What is A-DNA and Z-DNA? - ANSWER: A-DNA:
*dehydrated
*double stranded RNA or DNA and RNA hydrids
Z-DNA:
*less than 1% of all DNA
*left-handed
What 3 forms of DNA are seen in very small amounts? - ANSWER: cruciform, triplex,
quadruplex
Describe the structure of RNA. - ANSWER: - linear single-stranded polynucleotide chain
- ribose sugar-phosphate backbone
- uracil (U) in place of thymine (T)
- read in the 5'→3' direction (phosphate to hydroxyl)
What are the primary, secondary, and tertiary structures of RNA? How do they
contribute to more complex structures? - ANSWER: primary: stem, loop, stem
secondary: stem-loop, internal loop, single stranded, double stranded, hairpin loop,
open ends
tertiary: stem loop structures interact with each other
What is a gene? Where are they located? - ANSWER: a heredity unit that includes the
DNA encoding a function RNA or protein and the regulatory elements controlling its
expression
**all genes have fixed locations within the genome
Describe the genome of E.coli. - ANSWER: a single circular chromosome with all 4500
genes in fixed positions
Describe the human genome. - ANSWER: - 46 linear chromosomes
- positions of genes are characteristic of species
- 29,000 genes
- 3,070,128,600
, What is the position of the EDN1 gene? - ANSWER: 6p24.1
What is chromatin? Nucleosomes? - ANSWER: - DNA molecules that are tightly coiled
around proteins call histones
- histones +DNA = nucleosomes
What is the packaging order of DNA in eukaryotic nuclei? - ANSWER: two chromatids >
one coil (30 rosettes) > one rosette (6 loops) > one loop (75000 bp) > 30 nm fiber >
beads of a string form of chromatin > DNA
What are the three polymerases and their function? What do they require to function? -
ANSWER: *DNA polymerase - adds one dNMP to the 3' end, requires a DNA template
chain and a primer
*RNA polymerase - adds one NMP to the 3' end, require DNA template chain
*Reverse transcriptase - adds one dNMP to the 3' end of a growing DNA chain, requires
a RNA template chain and primer
What are the three nucleases (DNase or RNase) and their function? - ANSWER:
*Endonuclease - breaks a phosphodiester bond within a polypeptide chain
*Excinuclease - breaks two phosphodiester bonds within a single polynucleotide chain
*Exonuclease - removes nucleotides from one end of the polynucleotide chain
What is DNA ligase and what does it do? - ANSWER: links two existing DNA chains
together end-to-end by catalyzing formation of a phosphodiester bond
What are the basic concepts of polynucleotide synthesis? - ANSWER: - synthesis is
always 5'→3' direction
- addition of dNMPs are always to existing strands
- pyrophosphate is kicked off the dNMP
How do endonucleases work? - ANSWER: - cut at specific sites
- cause a nick (one strand) or a double strand break (both strands)
- are either sequence-independent (DNase1) or sequence-specific (EcoRI)
How do exonucleases work? - ANSWER: - remove nucleotides from one end or the
other
- DNase or RNase
- exonuclease I is 3' to 5' for example
How do DNA ligase work in vivo? - ANSWER: - joins the end of DNA nucleotide chains
to make a continuous 5' to 3' strand by forming phosphodiester linkages
- AMP from ATP or NAD+ (E.coli) is linked to DNA ligase
- phosphate from ligase-AMP links to the open phosphate in a DNA nick, donating an O
to seal the nick
