Bio 184 - Exam 2
Order the steps in chromatin immunoprecipitation (ChIP-Seq) from first to last.
1. Living cells are treated with formaldehyde, broken open, and treated with micrococcal nuclease. 2. Heavy beads attached to antibodies that recognize specific histones are added the nucleosome mixture. 3. The mixture is centrifuged to separate the immunoprecipitated material, crosslinks are reversed, and proteases partially digest core histones. 4. The remaining DNA is subject to gel electrophoresis. Fragments of 150 bp are saved. 5. Linkers are added to the DNA, then they are PCR amplified and subjected to DNA sequencing, DNA sequences are analyzed.
Select ways that nucleosomes can change.
Change in location; change in histones to variants with specialized roles; covalent modification to the amino-terminal tails of histones
Stretches of DNA of 1000-2000 bp in length containing a high number of CpG sites and found near gene promoters are called
CpG islands
Which of the following are examples of base pair mismatches?
Cytosine on parent strand and adenine on daughter strand; adenine in parent strand and cytosine on daughter strand; cytosine on parent strand and thymine on daughter strand
In a _______ cell, each type of chromosome is a member of a pair.
Diploid
A breakpoint refers to the region
Where two chromosome pieces break and rejoin with other chromosome pieces
In a natural population, a ____-____ genotype is the most common one.
Wild type
The gametes (sperm and egg cells or their precursors) are called ____ cells.
Germ
True or false: The function of regulatory transcription factors is modulated.
True
Activator proteins often increase transcription through an interaction with
Coactivators
The restoration of protein function by a second mutation in a different gene is known as a(n)
Intergenic suppressor
The restoration of function by a second mutation at a different site in the same gene is known as a(n)
Intragenic suppressor
Place these steps in a simplified model for transcriptional activation of a eukaryotic gene in order from first to last.
1. Binding of activator to an enhancer in the NFR. 2. Recruitment of a chromatin-remodeling complex and history- modifying enzyme 3. Recruitment of general transcription factors and RNA Pol II to the core promoter, allowing the formation of a preinitiation complex 4. Eviction or destabilization of histone octamers, allowing RNA pol II to pass, and elongation to occur.
Place the steps in glucocorticoid hormone and receptor action in order from first to last.
1. The glucocorticoid hormone diffuses through the plasma membrane. 2. The glucocorticoid hormone binds to the glucocorticoid receptors. 3. HSP90 is released from the glucocorticoid receptor. 4. Two glucocorticoid receptors form a homodimer and travel through a nuclear pore into the nucleus.
A normal human cell carries __ pairs of chromosomes for a total of __.
23; 46
DNA methyltransferase is an enzyme that attaches a methyl group to the _ position of the ________ base.
5; cytosine
A frameshift mutation is caused by what?
A base addition, a base deletion
What is chromatin?
A complex between DNA and proteins that are found in eukaryotic cells.
A motif
A domain that has a very similar structure in many different proteins
Which of the following best describes asexual reproduction?
A mother cell divides to produce two identical daughter cells.
An organelle is
A structure within the cytoplasm with a specific function
Which of the following base changes are transversion mutations?
A to C, G to C, A to T
_______ are different variations of the same gene.
Alleles
Unicellular organisms proliferate by _______ reproduction, in which a preexisting cell divided to produce two new cells.
Asexual
Prokaryotes, which include the ________ and the _______, are organisms that lack a membrane-bound nucleus.
Bacteria; archaea
A mutation that enhances the survival and/of reproduction success of an individual is referred to as a(n) __________ mutation.
Beneficial
Most bacterial cells divide by
Binary fission
What effect can ATP- dependent chromatin remodeling have on transcription?
Both activation and repression.
The region where two chromosome pieces break and re-attach to other chromosome pieces is called a chromosomal
Breakpoint
Mediator phosphorylates the _______-terminus of RNA polymerase II, stimulating progression to the __________ stage of transcription.
Carboxy; elongation
The two chromatids of a chromosome are joined together at a region of DNA called the
Centromere
After replication, each chromosome consists of two copies called
Chromatids
What is the term that can refer to either a dyad (pair of sister chromatids) or a monad (single chromatid)?
Chromosome
The structures within all living cells that contain the genetic material are called
Chromosomes
The phenomenon is which the combination of many factors determines the expression of a given gene is known as
Combinatorial control
Mutations that affect the phenotype only under certain circumstances are called
Conditional mutations
Select common factors that contribute to combinatorial control.
DNA methylation inhibits transcription; Repressor proteins inhibit the ability of RNA polymerase to initiate transcription; Activator proteins stimulate the ability of RNA polymerase to initiate transcription; Regulatory proteins alter the composition or arrangement of nucleosomes in the vicinity of a promoter; Activator and repressor activity is modulated by small effector molecules, protein-protein interactions, and covalent modifications.
The methylation of DNA that was previously unmethylated is called __ ____ methylation.
De novo
Transcription factors contain protein regions called _______ that have specific functions.
Domains
You are studying a transcription factor that binds to DNA near a gene of interest. You discover that once the transcription factor binds, transcription of your gene of interest becomes undetectable. This is an example of
Down regulation
What affect does acetylation have on lysine in core histone proteins?
Eliminates the positive charge on lysine, disrupting the electrostatic attraction between the histone and the negatively charged DNA backbone.
Activators bind to
Enhancers
A position effect can alter gene expression in cases when the gene is moved from a less condensed, or ___________ chromosome, where it is active, to a very highly condensed, or _______________ chromosome, where it's expression may be turned off.
Euchromatic; heterochromatic
Organisms, such as protists and fungi, that have a true nucleus are called
Eukaryotes
True or false: Most eukaryotic species are haploid or have such a phase to their life cycle.
False
The eukaryotic cell cycle is composed of
Four phases called: G1, G2, S, and M
Gene regulation means that
Gene expression can be controlled so that genes can be expressed at high or low levels
The transactivation domain of coactivators promotes the activation of RNA polymerase, often by interacting with
General transcription factors
A mutation that occurs directly in a sperm or egg cell, or in one of their precursors, is referred to as a(n) ____-____ mutation.
Germ line
Cells that give rise to eggs and sperm are called
Germ line
Select the histones in which variants have been identified.
H1; H2A; H2B; H3
A genetic mosaic is an individual that
Has regions of the body that are genotypically different from each other
The dimerization of two identical proteins results in a
Homodimer
Each type of chromosome in a diploid cell is found in a homologous pair. Each chromosome in such a pair is referred to as a(n)
Homolog
In general, the chromosome number of a particular species
Is the same for all individuals of the species
What is the effect of a suppressor mutation?
It suppresses the phenotypic effect of another mutation.
A mutation that results in the death of an organism is known as a(n) ______ mutation.
Lethal
A(n) _____ refers to the physical location of a gene.
Locus
If chromatin is in a closed confirmation, nucleosome position and histone composition
Make it difficult for transcription factors to gain access to and bind their target sequences in the promoter DNA
Most eukaryotic genes are regulated by
Many facitrs
The protein complex that mediates the interaction between RNA polymerase II and regulatory transcription factors is called
Mediator
If fully methylated DNA is introduced into a plant or animal cell, in subsequent generations the DNA will be __________. If the same sequence of nonmethylated DNA is introduced into a cell, it will be _____________ in daughter cells.
Methylated; nonmethylated
A base substitution in DNA that ultimately leads to a change in the encoded amino acid is called a(n) ________ mutation.
Missense
An individual that has somatic regions with different genotypes is known as a genetic
Mosaic
Which of the following statements about eukaryotes is true?
Most eukaryotic species are diploid or have a diploid phase to their life cycle.
An allele that has a DNA sequence different from that one or the wild-type is called a(n) ______ allele.
Mutant
A heritable change in the genetic material is called a(n)
Mutation
A(n) ______ mutation is a missense mutation that has no detectable effect in protein function.
Neutral
A silent mutation is a mutation that results in
No change to the amino acid sequence of the polypeptide
What type of mutations involve a change from a normal codon to a stop codon?
Nonsense mutations
A(n) _____ mutation refers to a mutation in which just one base is changed within the DNA sequence.
Point
The expression of an intact gene may be altered when it is moved to a new location. That is due to a(n)
Positive effect
Rank the phases of mitosis in order, starting with the earliest at the top.
Prophase; prometaphase; metaphase; anaphase; telophase
If gene regulation acts to prevent translation, which molecule will not be produced?
Protein
DNA sequences in eukaryotes that can be bound by regulatory transcription factors, which then affect the ability of RNA polymerase to transcribe a particular gene are called
Regulatory sequences; regulatory elements; control elements
Regulatory transcription factors that prevent transcription from occurring are called __________.
Repressors
A _______ mutation is one that converts a mutant allele back to the wild-type form.
Reverse
Repressors bind to
Silencers
Muscle cells, nerve cells, skin cells are examples of
Somatic cells
A second mutation that occurs in a different site than the first mutation, and which converts the mutant back to the wild-type phenotype, is best referred to as a(n) _______ mutation.
Suppressor
Coactivators often contain a _______________ domain that promotes the activation of RNA polymerase.
Transactivation
A _____________ ______ is a protein that influences the ability of RNA polymerase to transcribe a given gene.
Transcription factor
The cytosines in CpG islands near housekeeping genes are
Unmethylated
When a fully methylated DNA segment of DNA is replicated, the newly made daughter strand contains ____________ cytosines. This DNA is said to be ______________.
Unmethylated; hemimethylated
Which of the following statements about promoter mutations is true?
Up promoter mutations cause the promoter sequence to be more like the consensus sequence; down promoter mutations decrease the affinity of transcription factors to the promoter
DNA sequences that are analogous to the operator sites found near bacterial promoters are called ______ elements or __________ sequences.
Control; regulatory
Transcription factors that affect the ability of RNA polymerase to begin the transcription process may work by
Controlling the switch from the initiation to the elongation stage of transcription; regulating the binding of the transcriptional complex to the core promoter
Mutations that occur in a promoter sequence can be divided into two types: __ promoter mutations increase the transcription rate, while ____ promoter mutations decrease it.
Up; down
Which of the following base changes is a transition mutation?
A to G
Select all the events that occur during prophase.
The nuclear membrane begins to dissociate into small vesicles; the mitosis spindle begins to form; the nucleolus becomes less visible, the chromatids become condensed
Which of the following are eukaryotes?
Plants, protests, fungi
The function of TFIID is to
Bind to the TATA box and recruit RNA polymerase II to the core promoter
When chromatin is accessible to transcription factors and RNA polymerase, it is referred to as being in the
Open confirmation
Mutations in body cells that do not go on to form gametes are known as
Somatic mutations
Errors in DNA replication are examples of ___________ mutations, while mutations caused by ultraviolet light are _______ mutations.
Spontaneous; induced
An enhancer is a DNA element that is bound by a regulatory transcription factor, which leads to
Up regulation
Select the organism with the highest amount of DNA methylation.
Vertebrates
The _______ of a eukaryote is the organelle that contains most of the genetic material found in the cell.
Nucleus
Prokaryotes usually have a single type of circular chromosome in a region of the cytoplasm called the
Nucleoid
Some errors create bulky distortions of the double helix. These errors are removed primarily by a DNA repair system called NER, which stands for _________ ________ repair.
Nucleotide excision