Chapter 16

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This might be on the optional exam and will be on the final

Unlike organisms, viruses are ________; that is, they are not cells, do not consists of cells, and do not carry out many of the processes characteristic of life

1) Acellular

Most virus particles, called _________, are composed of only nucleic acid and a few proteins.

1) Virions

Viruses do not carry out two of the basic functions of cellular life; what is it that they don't do specifically?

1) They do not regulate the transport of substances into and out of themselves by membranes
2) They do not perform metabolic functions involved with taking in nutrients, refashioning them, and expelling wastes

In a genome with many genes, not all promoters are active at a given time-there is _________ ______ ____________.

1) Selective Gene Transcription

The decision regarding which genes to activate involves two types of regulatory proteins that bind to DNA: _________ proteins and _________ proteins. In both cases, these proteins bind to the promoter to regulate the gene.

1) Repressor Proteins
2) Activator Proteins

In __________ regulation, the gene is normally transcribed. Binding of a repressor protein prevents transcription

1) Negative Regulation

In ________ regulation, the gene is normally not transcribed. An activator protein binds to stimulate transcription

1) Positive Regulation

The ________ _______ is a viral reproductive cycle in which the virus takes over a host cell's synthetic machinery to replicate itself, then bursts (lyses) the host cell, releasing the new viruses.

1) The lytic cycle

The ____________ are viruses that infect bacteria

1) Bacteriophage

At the molecular level, the reproductive cycle of a lytic virus has two stages....what are they?

1) Early
2) Late

During the lytic cycle some bacteriophage package their DNA in ________( the outer shell of a virus that encloses it nucleic acid).

1) Capsids

In rare cases, a bacterial DNA fragment is inserted into a capsid instead of, or along with, the phage DNA. When such a virion infects another bacterium, the bacterial DNA is injected into the new host cell, a mechanism of gene transfer called __________.
What is the effect of this?

1) Transduction
2) The viral infection does not produce new viruses. Instead, the incoming DNA fragment can recombine with the host chromosome, replacing host genes with genes from the virus's former host.

Some viruses have evolved an advantageous process called _________ that postpones the lytic cycle.

1) Lysogeny

1) In lysogeny, the viral DNA becomes integrated into the host DNA and becomes a ____________.
2) Give a brief definition of what exactly this term means...

1) Prophage
2) In lysogeny, it is the noninfectious units of a virus that are linked with the chromosomes of the host bacteria and multiply with them but do not cause dissolution of the cell.

Many eukaryotes are susceptible to infections by various kinds of viruses...what are the 3 types?

1) DNA Viruses
2) RNA Viruses
3) Retroviruses

The retroviral genome is RNA, and the _________ encodes a protein that makes a DNA strand that is complementary to the RNA.

1) Retrovirus

HIV is an _________ _______; it is enclosed within a phospholipid membrane derived from its host cell

1) Enveloped Virus

A distinctive feature of the retroviral life cycle is ______ _________ ___ __________

1) RNA-directed DNA synthesis

The viral enzyme __________ ______ uses the RNA template to produce a complementary DNA (cDNA) strand, while at the same time degrading the viral RNA

1) Reverse Transcriptase

A _________ is the double-stranded DNA made by a virus that is integrated into the host's chromosome and contains promoters that are recognized by the host cell's transcription apparatus

1) Provirus

There are several ways in which a prokaryotic cell can shut off the supply of an unneeded protein. The cell can do what?
Which one is the method that most prokaryotes use?
Why?

1) Downregulate the transcription of mRNA for that protein
2) Hydrolyze the mRNA after it is made, thereby preventing translation
3) Prevent translation of the mRNA at the ribosome
4) Hydrolyze the protein after it is made
5) Inhibit the function of the protein
6) They downregulate the transcription of mRNA for that protein
7) Because it conserves energy and is a more efficient process

Three enzymes are involved in the initial uptake and metabolism of lactose by E.Coli...they are?

1) B-galactoside permease
2) B-galactosidase
3) B-galactosidase Transacetylase

Compounds that, like lactose, stimulate the synthesis of a protein are called _________.

1) Inducers

The proteins that are produced (due to inducers) are called _________ _______, whereas proteins that are made all the time at a constant rate are called ___________ ________

1) Inducible Proteins
2) Constitutive Proteins (think of the constitution of a country, a document that does not change under normal circumstances)

The genes that encode the three enzymes for processing lactose in E. Coli are _________ ______; they specify the primary structure (the amino acid sequence) of a protein molecule. These are the genes that can be transcribed into mRNA..

1) Structural Genes

A cluster of genes with a single promoter is called an ________, and the one that encodes the three lactose-metabolizing enzymes in E.Coli is called the ______________.

1) Operon
2) Lac Operon

The _________ is a short stretch of DNA that lies between the promoter and the structural genes

1) Operator

There are numerous mechanisms to control the transcription of operons; what are the 3 main examples?

1) An inducible operon regulated by a repressor proteins
2) A repressible operon regulated operon regulated by a repressor protein
3) An operon regulated by an activator protein

The lac operon contains a promoter, to which RNA polymerase binds to initiate transcription, and an operator, to which a _________ protein can bind. When it is bound, transcription of the operon is blocked.

1) Repressor

In contrast to the inducible system of the lac operon, other operons in E. Coli are repressible; that is, they are represented when molecules called _________ bind to their repressors.

1) Co-Repressors

E. Coli can also use positive control to increase transcription through the presence of an ____________ protein.

1) Activator Protein

__________ __________, is a system of gene regulation in which the presence of the preferred energy source represses other catabolic pathways

1) Catabolite Repression

The _______ ________ is the sequence recognized by RNA polymerase

1) Recognition Sequence

The _____ ___ (so called because its rich in AT base pairs), where DNA begins to denature so that the template strand can be exposed

1) TATA box

________ _________ are various regulatory proteins

1) Transcription factors

The combination of factors present determines _________________.

1) The rate of transcription

_______ _______ consist of different combinations of structural elements (protein conformations) and may include special components such as zinc

1) Structural Motifs

The four common structural motifs in DNA binding domains are...? What does each one regulate?

1) Helix-Turn-Helix- Regulate genes involved in development
2) Leucine Zipper- These proteins regulate cell division genes
3) Zinc Finger- These proteins are steroid hormone receptors
4) Helix-Loop-Helix-These proteins regulate immune system genes

An intact DNA double helix can be recognized by a protein motif whose structure:

1) Fits into the major or minor groove
2) Has amino acids that can project into the interior of the double helix
3) Has amino acids that can form hydrogen bonds with the interior bases

_________ refers to changes in the expression of a gene or a set of genes that occur without changing the DNA sequence

1) Epigenetics

_____ ___________ is the addition of methyl groups to bases in DNA, usually cytosine or guanine.

1) DNA Methylation

______ __________ is an enzyme that catalyzes the methylation of DNA

1) DNA methyltransferase

DNA regions rich in these doublets are called ______ _________, and are especially abundant in promoters.

1) CpG Islands

When DNA is replicated, a ________ _________ catalyzes the formation of 5 methylcytosine in the new DNA strand

1) Maintenance Methylase

The pattern of cytosine methylation can also be altered, because methylation is reversible: a third enzyme, appropriately called __________, catalyzes the removal of the methyl group from cytosine

1) Demethylase

The form of a gene's expression is determined by parental source (i.e, whether the gene is inherited from the male or female parent)...this is the definition of...?

1) Genomic Imprinting

_________ __________ can be a deliberate mechanism for generating a family of different proteins with different activities and functions from a single gene

1) Alternative Splicing

The noncoding RNAs are often very small and therefore difficult to detect. These tiny RNA molecules are called _________

1) microRNA (miRNA)

Certain proteins can be targeted for destruction in a chain of events that begins when an enzyme attaches a 76-protein called __________ to a lysine residue of the protein to be destroyed

1) Ubiquitin

The protein-polyubiquitin complex then binds to a huge protein complex called a __________

1) Proteasome (from protease and soma body)

What happens in the early stage of the lytic stage?

The viral genome has a promoter that binds host RNA polymerase. In this early stage viral genes that lie adjacent to this promoter are transcribed. Three minutes after DNA entry, viral nuclease enzymes digest the host's chromosome, providing nucleotides for the synthesis of viral genomes. (Pg. 345)

What happens in the late stage of the lytic cycle?

Viral late genes are transcribed; they encode the viral caspid proteins and enzymes that lyse the host cell to release the new virions.

What is the difference between the lytic and lysogenic cycles?

1) In the lytic cycle, infection of a bacterium by viral DNA leads to the multiplication of the virus and lysis (bursting) of the host cell
2) In the lysogenic cycle, an inactive prophage is integrated into the host DNA where it is replicated during the bacterial life cycle.

If the tat protein is present, HIV expression is observed (T/F)...why?

1) True
2) Under normal circumstances, the host cell regulates viral gene expression using proteins that may have originated as a defense mechanism against invaders. However, HIV can counteract this regulation with a virus-encoded protein called "tat", which binds to the terminator proteins and blocks their action. (pg. 347)

What does a typical operon consist of?

1) A promoter, an operator, and two or more structural genes

Inducible system vs. repressible system. Explain/ Verbally Summarize...

1) In inducible systems, the substrate of a metabolic pathway (the inducer) interacts with a regulatory protein (the repressor), rendering the repressor incapable of binding to the operator and thus allowing transcription.
2) In repressible systems, the product of a metabolic pathway (the co-repressor) binds to a regulatory protein, which is then able to bind to the operator and block transcription.

What are the two important sequences in a eukaryotic promoter?

1) The recognition sequence-the sequence recognized by RNA
2) TATA Box- Where DNA begins to denature so that the template strand can be exposed

(T/F) RNA polymerase II binds only after several other proteins have bound to this complex.

1) True

Some DNA elements are positive regulators termed ________ (explain what they do.) and others are negative regulators termed ________(explain what they do.)

1) Enhancers- Bind activator proteins
2) Silencers-Bind repressor proteins

DNA methylation adds a methyl group to _________ to form ___________.

1) The 5'-carbon
2) 5-methylcytosine

(T/F) DNA methylation is a heritable process

1) True

(T/F) Methylated genes are expressed

1) False; Methylated genes are "silenced"; their transcription is repressed

(T/F) Demethylated genes are not expressed

1) False; Demethylation allows genes that are normally inactive to become expressed...it acts as an enhancer

If the cell is a ________ _______ _______ that forms gametes, the epigenetic changes can be passed on to the next generation

1) Germ Line Cell

(T/F) The environment plays an important role in epigenetic modifications and, therefore, in the regulation of genes that these modifications affect

1) True

Some phenotypic characteristics acquired during the lifetime of an organism might be __________, contrary to biologists' long-held views.

1) Heritable

In mammals specific patterns of methylation develop for each sex during gamete formation. This happens in two stages: what are they?

1) The existing methyl groups are removed from the 5-methylcytosines by a demethylase
2) A DNA methylase adds methyl groups to the appropriate cytosines

(T/F) Males and females may be the same genetically (except for the X and Y chromosomes), but they differ epigenetically

1) True

_______ ________ may be a key to the differences in levels of complexity among organisms

1) Alternative Splicing

Several hundred miRNAs have now been described in many eukaryotes. Each one is about ______ bases long and usually has _______ or mRNA targets.

1) 22
2) Dozens

A ________ _______ guides the miRNA to its target mRNA, where translation is __________ and the mRNA is degraded.

1) Protein Complex
2) Inhibited

What must be done to access DNA tightly coiled by histones?

1) Enzymes called histone acetyltransferases can add acetyl groups to these positively charged amino acids, thus changing their charges. Since DNA is negative and has an affinity for positive charges this change will cause the compact chromosomes to recoil and get off of the DNA. Histone acetyltransferases can thus activate transcription.

Can males have Barr Bodys? Why or why not?

1) The average male (XY chromosomal representation) only has one X-chromosome, so it is automatically active; there is no option for another to be active. There are some men with XXY (an X from the father, and one from the mother; like a woman) chromosomal representation and they will have one Barr Body. The Barr Body is simply the transcriptionally inactivated X chromosome, since only one of the two X chromosomes in women (and a few men) can be active.

Is the amount of a protein in a cell determined by its mRNA?

1) Not exactly. The concentrations of a protein in a cell is determined by factors after the mRNA is made.

There are three known ways in which the translation of mRNA can be regulated. What are they?

1) Inhibit translation with miRNAs
2) Modification of the guanosine triphosphate cap on the 5' end of the mRNA. An mRNA that is capped with an unmodified GTP molecule is not translated
3) Repressor proteins directly block translation

What two major things do cells do after mRNA is made that effect the amount of protein or mRNA?

1) Block the translation of mRNA
2) Altering how long newly synthesized proteins persist in the cell

The proteasome is a powerful structure where proteins are digested by several powerful __________. Basically the proteasome can break down proteins, thus affecting _________ ________.

1) Proteases
2) Protein Longevity

What are four ways the eukaryotic gene expression can be regulated after transcription?

1) Alternative splicing of pre-mRNA can produce different proteins
2) MicroRNAs are small RNAs that do not code for proteins, but regulate the translation and longevity of mRNA.
3) Translational repressors can regulate the translation of mRNA to proteins.
4) The proteasome can break down proteins, thus affecting protein longevity.

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