Molecular Biology Exam 2 Flashcards
The structure in a prokaryotic cell that contains the genome. The DNA is bound to proteins and is not enclosed by a membrane.
Nucleoid
The state of nuclear DNA and its associated proteins
Chromatin
A discrete unit of the genome carrying many genes. Each consists of a very long molecule of duplex DNA and an approximately equal mass of proteins. It is visible as a morphological entity only during cell division.
Chromosome
True or False: DNA primarily exists as condensed units rather than loose, double helices.
True.
The actual state of DNA is highly compacted genetic material via proteins.
Active process in which DNA is driven into the head of a virus by an adenosine triphosphate (ATP) dependent mechanism.
Translocation
An enzyme that cleaves multimers of a viral genome and then uses hydrolysis of ATP to provide the energy to translocate the DNA into an empty viral capsid with the cleaved end,
Terminase
True or False: The bacterial genome is a supercoiled nucleoid
True
In reference to a chromosome, this refers either to a discrete structural entity defined at a region within which supercoiling is independent of other regions, or to an extensive region including an expressed gene that has a heightened sensitivity to degradation by the enzyme DNase.
In a protein, it is a discrete continuous part of
the amino acid sequence that
can be equated with a particular
function
Domain
Most domains in terms of of a chromosome are __ kb (kilobases) in length.
- Recent research suggests they may be 10kb in length, however.
NAPs stands for
Nucleoid-associated proteins
Interphase chromatin consists of a tangled mass with topologically isolated domains which average around ________ kb (kilobases)
85kb
DNA attached to proteinaceous structures in interphase nuclei are called ____ _____ ______.
Matrix attachment regions (MARs) or Scaffold attachment regions (SARs)
MARs sequences are usually ___ rich.
A-T rich
The form of chromatin that comprises most of the genome in the interphase nucleus, which is less tightly coiled than heterochromatin and contains most of the active or potentially active single-copy genes.
Euchromatin
Regions of the genome that are highly condensed, less transcribed, and late replicating. It is divided into two types, constitutive and facultative.
Heterochromatin
The common form of heterochromatin that always remains heterochromatic is called _____ _____.
Constitutive chromatin
It is near permanently condensed, replicated late in S phase and has a reduced frequency of genetic recombinations.
Consists of multiple repeats.
Type of chromatin in which regions of euchromatin are converted to a heterochromatic state.
Heterochromatin
Bands generated on eukaryotic chromosomes by staining techniques that appear as a series of lateral striations.
They are used for karyotyping (identifying chromosomes and chromosomal regions by the banding pattern)
Stained with Giemsa dye.
G-bands
Densely staining granules visible in chromosomes under certain conditions, especially in meiosis.
Chromomeres
True or False: Telomeres do not have simple repeating sequences.
False. Telomeres DO have simple repeating sequences.
We know that telomeres must be a special structure because chromosome ends generated by breakage are “sticky”, and tend to react with other chromosomes, whereas natural ends are stable.
The single stranded ___ rich tail of the telomere can form a G-quadruplex because ______ bases have the ability to associate with one another.
G-rich
Guanine
The human centromere consists of _____ satellites or ____ satellite repeats.
Alpha, alpha
How do eukaryotes resolve the telomere shortening problem?
With telomerase, which is an enzyme that adds repeating units to the 3’ end of the telomere. Primarily active only in germ cells and stem cells.
Telomerase is a special ______ _____, or reverse transcriptase.
DNA polymerase.
Unusually large chromosomes in diptera in certain tissues. Dark bands represent ______ while lighter bands represent _______.
Dark bands = chromomeres, inactive
Light Bands = interbands, active
Polytene chromosomes undergo ______, which arises from multiple rounds of replication, but sister chromatids remain synapsed (adhered) to each other.
Endoreduplication
In terms of polytene chromosomes, what physical change occurs that signifies gene expression being induced.
Puffs, or rather when the bands expand in response to gene expression. They quite literally “puff” up.
Replication of DNA involves the stages of ____, _____, and, _____.
Initiation, elongation, and termination.
Before initiation can occur, the replication origin region of the chromosome must be negatively supercoiled or _____.
Unwound
What enzyme is responsible for the negative supercoiling at the replication origin and the subsequent relaxation of positive supercoils ahead of the moving replication fork?
Topoisomerase
Read: Initiation involves recognition of an origin via a large protein complex. Before DNA synthesis can begin, the parental strands must be separated and transiently stabilized in the single-stranded state, creating a replication bubble.
What is a multiprotein structure that assembles at the bacterial replication fork to undertake synthesis of DNA?
It contains DNA polymerase and other enzymes.
Replisome (It’s in the name, dummy)
After initiation begins, ____ can begin. It is undertaken by another complex of proteins known as ______.
Elongation
Replisome
The replisome exists as a persistent protein unit OR de novo and reassembled at the origin for each replication cycle.
Choose one.
The replisome exists de novo and is reassembled at the origin for each replication cycle.
DNA Polymerases are the enzymes which make _______.
DNA
Some DNA polymerases involved in replication have nuclease activity in addition to the ability to synthesize DNA. Which way do they excise DNA?
3’ to 5’ exonuclease activity or 5’ to 3’ exonuclease?
Both. DNA polymerase 1 has a unique 5’ to 3’ exonuclease activity in addition to its 5’ to 3’ synthetic and 3’ to 5’ exonuclease activities.
How many subclasses of errors exist that DNA polymerases can make during replication?
2.
- Substitutions: improperly paired nucleotide incorporation. The error frequency is determined by the efficiency of proofreading.
- Frameshifts: When an extra nucleotide is inserted OR one is omitted.
A site in the genome of which the frequency of mutation (or recombination) is very much increased, usually by at least an order of magnitude relative to neighboring sites.
Mutation hotspots
DNA polymerases replicate ____ to ____ (direction).
5’ to 3’
In MAMMALS, the origin of replication does or does not have an identifiable sequence?
In mammals, the origin of replication does not have an identifiable sequence.
The region or unit of DNA or RNA that replicates from a single origin of replication.
Prokaryotes typically have one.
Eukaryotes typically have multiple.
The Replicon
Replication strand growth can be unidirectional, bidirectional, or both?
Both
DNA replication requires priming. Therefor, DNA polymerase requires a ______ to initiate DNA synthesis.
3’-OH
Primase is needed for primer synthesis —> Short RNA primer is synthesized —> DNA is synthesized by DNA polymerase.
What are other mechanisms of priming? Name three.
- A preformed RNA (tRNA) can be used common to some retroviruses.
- A nick is introduced in DNA –rolling circle
- A protein covalently linked to a nucleotide (this is used by some viruses, it’s called a priming protein)
Once unwound, DNA strands have different modes of synthesis.
One, is _______ while the other is ______.
Discontinuous
Continuoius
Topisomerase 1 is involved in cutting one strand of DNA.
Topoisomerase 2 cuts 2 strands.
Recombinase is similar to _____________.
Topoisomerase 1
attB/attP, the b = bacteria, the p = phage
Lysogenic cycle leads to
Genome integration prophage
Lytic cycle leads to
Replication, packaging and cell lysis
Integrase is an enzyme involved in
Phage integration
Xis factor involved in integrated genome does what?
Excises the gene placed there (or target gene)
Knockout
Somatic recombination
Eukaryotic recombination that occurs in non-germ cells (not in meiosis)
Yeast mating type switching
V(D)J recombination of immunoglobulin genes in immune system
Must be two different types of yeast cells to mate. One is ___ and the other is ___.
a
alpha
Two a cells cannot mate. Two alpha cells cannot mate. They have receptors on their surface which recognize the other variant.
In yeast, the mating type information is encoded at the ______.
Mating Type Locus
With yeast cells, each subsequent generation becomes the opposite type. a to alpha, alpha to a, etc.
True
Three loci in yeast for mating information, HMLalpha, MAT, HMLa.
Which expresses identity?
MAT.
In yeast, the mating type switching occurs by replacement of _______ locus with opposite ______ cassette. This is non reciprocal.
MAT, MAT
HO endonuclease used for cutting open two strands, just like SPOI11 for switching mechanism in
Yeast
Because MATa/alpha is not identical, HMLa and HMLalpha are found via flanking (side) genes of the middle MATa/alpha
What happens to a yeast cell of mating type “a” when its HO gene is mutated?
It will remain as mating type “a”.
Fragmented pieces of DNA part of the discontinuous strand
Okazaki Fragments
What is used to link okazaki fragments?
DNA Ligase
What is the name of the E. coli origin?
oriC
On the leading strand, or forward strand, DNA synthesis can proceed (continuously or in fragments) toward the 5’ to 3’ direction.
However, on the lagging strand, synthesis can proceed (continuously or in fragments).
Continuously
in fragments
Fragments of DNA that must be annealed back together with ligase enzymatic activity.
Okazaki fragments
