[ True or False ] A genome consists of only the DNA in an organism that codes for genes.
False
coding (5%) and non-coding (95%)
[ True or False ] The nitrogenous base of a nucleotide attaches to the C1 carbon of the sugar.
True
[True or False ] A polynucleotide strand is formed by joining the C3 phosphate group on the sugar of one nucleotide with the C5 hydroxyl group of another sugar
False
A phosphodiester bond exists between the phosphate of one nucleotide and the sugar 3' carbon of the next nucleotide.
[True or False ] Nucleotides are a nucleoside plus one or more phosphates
True
[ True or False ] The polarity of a single DNA polymer results from the polarity of the nucleotide subunits.
true
For a protein's [ tertiary / quaternary ] structure to be complete, non-linear associations can occur between R groups that are spaced far apart on the linear polymer sequence of the protein.
A) tertiary
B) quarternary
A) tertiary
Histones are an example of a [ sequence-specific / non-sequence specific ] DNA-binding protein.
A) non-sequence specific
B) sequence-specific
A) non-sequence specific
Interactions between atoms in the backbone (not the R groups) largely determine the [ secondary / tertiary ] structure of proteins.
A) secondary
B) tertiary
A) secondary
[True or False ] A-T base pairs are stronger than G-C base pairs.
False
[True or False ] All of the conserved regions in the genomes of divergent species are in the coding regions (in the areas within exons).
false
[ Condensation / hydrolysis ] reaction occurs when peptide bonds are formed.
A) hydrolysis
B) condensation
B) condensation
provide the name of the biomolecule that is made from that subunit.
Monosaccharide —>
amino acid —>
nucleotide —>
polysaccaharide or carbohydrate
protein
nucleic acid
The nitrogenous bases (and the two strands of the DNA double helix) are held together by ___________ bonds.
hydrogen
The nucleotides in a DNA polymer are held together by _________ bonds
phosphodiester
Amino acids are joined together in a protein polymer by ___________ bonds
peptide
Explain how polar and non-polar side chains (R groups) of amino acids inform the folding structure of polypeptides within a cell.
Non-polar side chains are hydrophilic and can be in regions that are exposed to aqueous surroundings. Polar side chains are hydrophobic and tend to cluster with other hydrophobic molecules to avoid the aqueous environments.
Name three ways RNA and DNA are different.
- RNA has a hydroxyl group at the C2 position while DNA has just a hydrogen
- RNA uses U while DNA uses T
- DNA is a double helix while RNA is a single polymer.
- DNA is genetic information and is very stable while RNA is a temporary copy of a gene region.
List the complementary base pairs found in DNA and RNA. Which bases are purines and which are pyrimidines?
DNA: A/T, G/C;
RNA: A/U, G/C.
Purines: A, G
Pyrimidines: T, U, C
What two factors about its structure makes the double helix structure energetically favorable?
Base-pair complementarity & anti-parallel structure ensures backbone is always equidistant.
Given the sequence of one strand of a DNA helix as :
5′-GCATTCGTGGGTAG-3′
5'-CTACCCACGAATGC-3'
is that correct^ jQuery11240792597413873878_1667147827299?
Name and describe the three regions (DNA sequence elements) needed to produce a stable eukaryotic chromosome. How many copies of these elements are found on a chromosome (you can say 1, 2 or many) ?
DNA replication origin -
many on a chromosome (ARS - autonomously replicating origin), AT rich region to allow less energy requirement to break apart DNA strands for replication machinery access to template
Centromere –
DNA repeat region bound by proteins that attach to the mitotic spindle and are important for the proper separation of chromosomes into each the daughter cells.
1 per chromosome.
Telomere –
DNA repeats at the ends of each chromosome (2 total per chromosome), prevents shortening of DNA with each round of replication.
For double-stranded DNA, consider the following base ratios:
A/G
C/T
C/G
(A+C)/(G+T)
(A+G)/(C+T)
(A+T)/(G+C)
Based on Chargaff’s rules, which of those ratios always equals 1?
B) 3,4, and 5
[ True or False ] Interphase chromosomes occupy specific regions within the nucleus
true
[ True or False ] Stepwise condensation of linear DNA happens in several different packing processes. Formation of the 30-nm chromatin fiber has a requirement for histone H1 to pull nucleosomes together into a regular repeating array.
true
[ True or False ] A nucleosome octomer core contains two molecules each of histones H1 and H2, H3 and H4.
false
Explain what would happen to the chromatin state of a gene that has undergone a mutation and is now positioned next to a telomere without a barrier sequence in-between?
Heterochromatin regions in the telomere will spread to the gene, ensuring that silencing of the gene expression occurs.
Answer must include discussion of heterochromatin spreading and silencing.
Which of the following sentences is false?
a. In eukaryotic cells, the DNA packaging state is potentially dynamic and reversible due to reversible covalent modifications to the histone tails.
b. In eukaryotic cells, the chromatin state is regulated by reversible histone tail modifications as well as proteins that bind directly to DNA sequences.
c. Some histone tail modifications will recruit proteins that will modify the adjacent histone tails to spread heterochromatin formation.
d. Information about the chromatin state is not transmitted to the daughter cells after DNA replication.
A) a
B) b
C) c
D) d
D) d
For each of the other models, explain what bands would have been seen in the Meselson-Stahl experiment if the other model was the most accurate model of DNA replication.
Dispersive model:
Conservative model:
Dispersive model: in both the heat treated and the unheated experiment there would be a single band. Would need to heat treat to separate strands
Conservative model: there would be two distinct bands that appear in the centrifuge tubes
Why is DNA replication rates of prokaryotes faster than eukaryotes (this is not asking about genome size).
Eukaryotes have DNA assembled in chromosomes. Have higher chromatin organization
_______ is the protein responsible for breaking hydrogen bonds, separating double-helix DNA strands during replication.
B) DNA helicase
Which of the following functions is NOT performed in the 5' to 3' direction?
A) Removal of a mispaired nucleotide by an exonuclease
[ TRUE or FALSE ] Replication bubble movement is referred to as bidirectional because nucleic acid synthesis can happen in both the 3' to 5' and 5' to 3' directions.
explain why if false
false.
replication only occurs 5’-3’ or that the bidirectional refers to the movement of the replication machinery with a fork going in each direction away from the origin of replication
[ TRUE or FALSE ] DNA replication relies on only one type of polymerase
false.
there are multiple types of polymerases required such as primase or dna repair polymerase.
Primase polymerases do not require a 3' hydroxyl to begin copying a template.
true
Primase is needed to initiate DNA replication on both the leading strand and the lagging strand.
true
only one primer is needed on the leading strand for continuous synthesis and many are needed on the lagging strand.
DNA replication in humans occurs at multiple locations within a single chromosome.
true
DNA polymerase uses ATP (Adenosine triphosphate) to link incoming deoxyribonucleotides to the 3’ end of the existing nucleic acid chain
false.
Deoxyribonucleotides provide the phosphates. We do not need ATP for this process
A specialized protein and RNA complex called telomerase is needed to prevent the shrinking of the chromosomes’ ends with each round of replication. Telomerase adds the repeats to the [ lagging DNA template strand / newly synthesized lagging strand ]
A) lagging DNA template strand
B) newly synthesized lagging strand
A) lagging DNA template strand
Telomerase uses [ an RNA strand / a DNA strand ] as the template to copy the repeats
A) an RNA strand
B) a DNA strand
A) an RNA strand
Telomerase synthesizes a [ ribonucleotide / deoxyribonucleotide ] polymer
A) deoxyribonucleotide
B) ribonucleotide
A) deoxyribonucleotide
If a telomere contains the repeat 5” TTGGGG 3” what would the corresponding telomerase RNA look like?
a. 5’ UUGGGG 3’
b. 3’ AACCCC 5’
c. 5’ CCCCAA 3’
d. 5’ CCCCUU 3’
e. 3’ CCCCUU 5
b or c
they are the same thing
What steps/enzymes with the excision repair process will be the same no matter which type of single strand DNA damage is being repaired?
To tie together the process, below is a brief description of how the process generally works:
1. recognize and cut
2. copy
3. seal
The Figure below shows a replication bubble. Label the image as directed below.
On the figure, draw a line to indicate where synthesis initiated at the origin of replication (label the line with O).
On each fork, label the leading-strand template and the lagging-strand template respectively.
For both forks, number the Okazaki fragments on each strand 1, 2, and 3 in the order in which they were synthesized (1 should be the first fragment made and 3 the most recent).
Just looking at the left hand fork: Indicate where the most recent DNA synthesis has occurred ( use S with a line pointing to where the most recent nucleotide would have been added to the leading and lagging strand on the left hand fork).
Indicate the direction of movement of the replication machinery complex on each replication fork with arrows.
protein-protein interaction is what level of structure
quaternary
is protein-lipid or protein-carbohydrate interaction also considered quarternary?
no
telomerase adds DNA nucleotides to which strand
it adds nucleotides to template strand of lagging strand
RNA template from telomerase
TTAGGG
AAUCCC
where is the RNA template added for telomerase to lagging template strand?
3'OH
what happens after telomerase adds RNA?
RNA is removed and DNA polymerase synthesizes 5'-3'
What form of chromatin is more compact?
heterochromatin
Chromatin vs. chromosome?
Chromatin is the complex of nuclear DNA w/ histone and nonhistone proteins (euchromatin and heterochromatin)
Is the repair polymerase used during excision repair the same enzyme used during DNA replication? If different, what are the similarities/difference between the excision repair and replication polymerases?
The repair polymerase used during excision is not the same enzyme used during DNA replication on the leading strand or to make the Okazaki fragments. It is the same enzyme used to fill in the sequences missing once the RNA primer has been removed.
DNA repair polymerase and DNA replication polymerase both synthesize the strands in the same way. They both elongate chains in the 5'-to-3' direction, require a 3’OH to initiate the synthesis and have the same type of proofreading activity.
What are two mechanisms of DNA double strand break repair?
Nonhomologous End- Joining
Homologous Recombination
In nonhomologous end-joining you will have a loss of some of the nucleotides.
true
In homologous end-joining when one DNA helix is broken in a homologous pair, the other DNA helix can act as a template to repair the damage
true
In homologous end-joining there is some loss of genetic information
false
explain
XX chromosome inheritance – calico cats
Coat color for cats is on X chromosome. Females with XX, then developmental stage will shut down one of the chromosomes (mom or dad copy). So all cells thereon inherit that chromosome/chromatin state that was chosen. All progeny have same information of the chosen chromatin state.
describe the effects of a single nucleotide change and protein functionality.
A single base change of nucleotides can cause an amino acid change that prevents protein that is targeted to the correct location in the cell which in turns causes a failure for that protein to function
example: cystic fibrosis.
(missense mutation)
Silent mutations
codes for the same amino acid, therefore, no impact on protein function
Neutral mutations
results in a different amino acid but no impact on protein function
Nonsense mutations
create a code to stop making the protein (truncated protein – depending on location possible no protein activity)
Missense mutations
results in an amino acid substitution that alters protein function.
A permanent change in DNA ((MUTATION)
can be either (3 options)
advantageous (positively selected)
disadvantageous (negatively selected)
neutral/ “silent” (no selection).
heterozygote advantage*
heterozygote phenotype has a higher relative fitness than either homozygote states
ex: sickle cell anemia and malaria
Majority of DNA damage comes from
spontaneous
induced
There are unique enzymes for each unique type of damage?
true
Excision Repair is used when only one strand of the helix has mutations
true
Types of damage corrected by DNA excision repair
a.Spontaneous DNA damage
b.Induced DNA damage
c.mismatch repair targets incorrect Watson-Crick base pairs
3 different types of DNA excision repair:
nucleotide excision repair (NER): used to remove pyrimidine dimers and modified nucleotides that cause a significant distortion in the DNA helix
base excision repair (BER): recognizes damaged bases that do not cause a significant distortion to the DNA helix (removes uridines)
mismatch repair: non-watson crick pairs (right after replication). Distortion.
Consequence of thymine dimers
they stall the replication machinery
examples of Induced DNA damage
(UV radiation, chemicals) based on exposure
- thymine dimers
A frame shift (truncated or incorrect a.a. coding rest of protein) could not effect every amino acid after this nucleotide
false
Unrepaired depurination will cause replication machinery to “skip” a nucleotide and shift how all the remaining information will be read during translation.
types of spontaneous DNA damage
Depurination
deamination
How can the cell recognize a DNA mismatch?
Enzyme can distinguish normal base pairs from those resulting from misincorporation.
Specific enzymes recognize different errors and recruit additional machinery to region
How can the cell differentiate the new strand from the template strand?
Cells mark the newly synthesize strand to ensure that they repair the correct strand
prok = methylation
euk = Nicks in the sugar-phosphate backbone from okazaki frags
sticky ends have overhangs?
true
last two examples have sticky ends
Which statement is false:
A) DNA ligase can readily join two DNA fragments produced by the same restriction enzyme
(B) DNA ligase can also be used to join DNA fragments produced by different restriction enzymes—for example, EcoRI and HaeIII.
C) DNA ligase does not require ATP to reseal the sugar–phosphate backbone of the DNA.
D)The fragments joined by DNA ligase can be from different cells, tissues, or even different organisms.
C
DNA ligase needs ATP
RE sites must be added to primers for PCR
true
Dideoxy (Sanger) method: older method used for
sequencing small pieces of DNA (such as a plasmid!)
These ddNTPs are derivatives of the normal deoxyribonucleoside triphosphates that lack the 5′ phosphate group. When incorporated into a growing DNA strand, they block further elongation of that strand.
