BLY 121-101 Chapter 13

What does the genome sequence contain?

It contains, in coded form, the nucleotide sequence of all RNA molecules transcribed from the DNA as well as the amino acid sequence of all proteins; not all DNA is transcribed into RNA and not all of the RNA that is transcribed is translated into protein

What does it mean for a virus to have a narrow host range?

It means that the virus can only infest just a single species, like smallpox

What is comparative genomics?

The analysis of the similarities and differences in protein-coding genes and other types of sequence in the genomes of different species

What is the principle of molecular self-assembly that specifies how progeny particles are formed?

When the viral components are present in the proper relative amounts and under the right conditions, the components interact spontaneously to assemble themselves into the mature virus particle

What is a nucleosome?

a bead-like repeated unit of histone proteins wrapped with DNA makin gup the 10-nm chromatin fiber

What is a host cell?

a cell in which viral reproduction occurs

What is a nucleoid?

a cell structure with multiple loops formed from supercoils of DNA; supercoils in this can be relaxed by introducing nicks, or interruptions, in the DNA backbones by means of enzymes or chemicals

What is the 30-nm chromatin fiber?

a chromosomal conformation created by the folding of the nucleosome fiber of DNA and histones

What are supercoils?

a coil of coils; a circular molecule of DNA can coil upon itself to form this; it relieves the stress that the topoisomerase II causes; allows all of the base pairs to form, even though the molecule is underwound

What is a "hypothetical protein"?

a common annotation in large genomes; determined solely by the presence of an ORF in the genomic sequence, and not by the presence of actual mRNA or protein; indicates an ORF that could possibly code for a protein, but at that current time, its function is unknown

What is the sequence provided by the Human Genome Project?

a composite of sequences from different individuals

What is the pol in HIV?

a gene that encodes proteins needed for reverse transcription of the viral RNA into DNA and incorporation into the host genome: protease, reverse transcriptase, and integrase

What is the env in HIV?

a gene that encodes proteins that are embedded in the lipid envelope: surface glycoprotein and transmembrane glycoprotein

What is a lipid envelope?

a lipid structure that surrounds the capsids of some viruses

What is the 10-nm chromatin fiber?

a relaxed 30-nm chromatin fiber, the state of hte chromatin fiber in regions of the nucleus where transcription is currently taking place

What is an open reading frame (ORF)?

a sequence motif that is a long string of codons for amino acids with no stop codon; identifies the region as potentially protein coding; in an mRNA, it is the region that is actually translated into protein on the riosome

What is a non-coding RNA molecule?

a single-stranded molecule where the nucleotide sequence in one part of the RNA is complementary to that in another part causing it to fold back on itself and undergo base pairing to form a hairpin-shaped structure; the DNA from which this RNA is transcribed would have complementary sequences on either end as well

What is a virus?

a small infectious agent that contains a nucleic acid genome packaged inside a protein coat called a capsid

What is a Giemsa stain?

a stain that has a higher resoltution of human chromosomes where each chromosome has a unique pattern of bands and where homologous chromosomes can readily be identified by their identical banding patterns

What is a karyotype?

a standard arrangement of chromosomes, showing the number and shapes of the chromosomes rrepresentative of a species

What is the chromosome scaffold?

a supporting protein structure in a metaphase chromosome

What is a lentivirus?

a virus that has a long lag between the initial time of infection and the appearance of symptoms (lenti- means "slow")

What do the nicks in the supercoils allow the DNA to do?

allows the strands to rotate around each other to remove the supercoils, and the DNA molecule relaxes into the standard double helix; only relieves the supercoils in the loop that is nicked

What is topoisomerase II?

an enzyme that causes underwinding of the DNA double helix by breaking the double helix, rotating the ends, and then sealing the break

What is the gag in HIV?

an open reading frame gene that encodes protein components of the capsid: matrix, capsid, nucleocapsid, and vpr-binding protein

What makes simple-sequence repeats so hard to sequence?

an single-stranded fragment consisting of alternating nucleotides, such as AT, can fold back upon itself to form a double-stranded in which A is paired with T (such structures are more stable than single-stranded DNA and are harder to sequence)

Why is genome annotation an on-going process?

as macro-molecules and their functions and interactions become better understood, the annotations to the genome must be updated; the annotation of certain genomes will continue to change over time

Why are transposable elements referred to as "selfish" DNA?

because it seems that their only function is to duplicate themselves and proliferate in the genome, making them the ultimate parasite

What is it easier to isolate chromosomes in metaphase of mitosis?

because of the availability of chemicals that prevent the spindle from forming; these chemicals block the cell cycle at metaphase, so cells progress to metaphase and then stop

Why is infection of the host cell essential to viral reproduction?

because viruses use cellular ATP and hijack cellular machinery to replicate, transcribe, and translate their genome in order to make more viruses

What is a transcription factor?

binding to DNA initiates transcription;short sequence that are know binding sites for DNA-binding proteins; helps determine when the gene will be transcribed;

How were introns first discovered?

by comparing beta-globin mRNA with genomic DNA

How can a higher resoltution of human chromosomes be obtained?

by the use of stains that bind preferentially to certain chromosomal regions and produce a visible pattern of bands, or crosswise striations, in the chromosomes

What are the vif, vpr, vpu, and nef in HIV?

genes that encode accessory proteins that enhance virulence in organisms

What are tat and rev in HIV?

genes that encode proteins essential for the HIV life cycle

How are genome sizes measured?

genomes are measured in numbers of base pairs, and the yardsticks of genome size are a thousand base pairs (a kilobase, kb), a million base pairs (a megabase, Mb), and a billion base pairs (a gigabase, Gb).

What is the structure and function of the T4 bacteriophage?

has a complex structure that includes a head composed of protein surrounding a molecule of double-stranded DNA, a tail, and tail fibers; in infecting a host cell, the tail fibers attach to the surface, and the DNA and some proteins are injected into the cell through the tail

What is the structure and function of the tobacco mosaic virus?

has a helical shape formed by the arrangement of protein subunits entwined with a molecule of single-stranded RNA forming a helical shape; causes brown spots and discoloration of tobacco leaves so small that it could pass through the pores of filters that could trap even the smallest bacterial cells

What is polyploidy?

having more than two sets of chromosomes in the genome

What are the two main types of non-coding DNA found in most large eukaryotic genomes?

highly repetitive DNA and moderately repetitive DNA

What is the next step after genome sequencing?

identifying the locations and functions of the various types of sequence present in the genome

When is the sense of a nucleic acid negative?

if it is the complementary seqeunce

When is the sense of a nucleic acid positive?

if its sequence is the same as the sequence of mRNA that is used for protein synthesis

What is a nuclear genome?

in eukaryotic cells, the DNA in the chromosomes

What is a mitochondrial genome?

in eukaryotic cells, the DNA in the mitochondria

What is a chloroplast genome?

in plant eukaryotic cells, the genome of the chloroplast

Where does the genetic information in chromosomes reside?

in the DNA

How does the tobacco mosaic virus illustrate the process of self-assembly?

in the earliest stages, the coat-protein monomers assemble into two circular layers forming a cylindrical disk. This disk binds with the RNA, and the combined structure forms the substrate for polymerization of all the other protein monomers into a helical filament that incorporates the rest of the RNA as the filament grows.

What is the seventh Baltimore system major virus group?

incomplete double-stranded DNA, reverse transcriptase (Hepatitis B)

What happens in chromosome painting?

individual chromosome are isolated from cells in metaphase of mitosis; the DNA from each isolated chromosome if fragmented, denatured, and labeled with a unique combination of fluorescent dyes; they are then mixed and hybridized to intact metaphase chromosomes from another cell; each labeled fragment hybridizes to its complementary sequence in the metaphase chromosomes, "painting" each metaphase chromosome with dye-labeled DNA fragments

What are non-coding introns?

introns that are removed from the RNA transcript during RNA processing

What does genome annotation aim to identify?

it aims to identify all the functional and repeat sequences present in the genome

What does the process of chromosome painting illustrate?

it illustrates the nearly identical nature of the DNA molecules in each pair of homologs

What are the two main categories of complications in sequencing?

long repeating sequences and short repeating sequences

What is the sixth and final step of chromosomal condensation?

metaphase chromatid 1400 nm in diameter

What does it mean to say that the genomes of bacteria and archaeons are information dense?

most of the genome has a defined function

How can the host range of a virus change?

mutation and other mechanisms

What does a virus consist of?

nucleic acid, capsid, and, sometimes, a lipid envelope

The genomes of mitochondria and chloroplasts are organized into...

nucleiods

What is the second level of chromosome condensation?

nucleosome fiber 10 nm in diameter; often referred to as "beads on a string"

What is the Baltimore system?

one of the most useful types of classification of viruses based on the type of nucleic acid the virus contains and how the messenger RNA, which produces viral proteins, is synthesized

How can viruses reproduce?

only by infecting living cells and subverting cellular metabolism and protein synthesis to produce more viruses

What are three examples of sequence motifs?

open reading frame, non-coding RNA molecule, and transcription factor binding sites

What are homologous chromosomes?

pairs of chromosomes, matching in size and appearance, that carry the same set of genes; one of each pair was received from the mother, the other from the father

What are some reasons for large differences in genome size among species?

polyploidy and the fact that most eukaryotic genomes contain large amounts of non-coding DNA

Where are transcription factors present?

present in multiple copies and in either strand of DNA; sometimes, they are located near the region of a gene where transcription is initiated; can also be located far upstream of the gene, downstream of the gene, or in introns

What are the different types of sequences in genomes?

protein-coding regions, noncoding regions, and regions that are transcribed into RNA but never translated into protein

How do viruses gain entry into cells?

proteins on the surface of the capsid or envelope (if present) bind to proteins on the surface of host cells; these proteins interact in a specific manner, so the presence of the host protein on the cell surface determines with host cells a virus can infect

What is a genome?

refers to all of the genetic material of an organism that is transmitted from parents to their offspring

What are the different regions in protein-coding genes?

regulatory elements, non-coding introns, and protein-coding exons

What are dispersed repeats?

repeated sequences that are several thousand nucleotides in length and are dispersed throughout the genome; long repeated sequence

What are tandem repeats?

repeated sequences that are several thousand nucleotides in length occurring one after the other; long repeated sequence

What was the goal of the Human Genome project?

sequencing the human genome as well as the genomes of certain key organisms used as models in genetic research; the model organisms chosen are the mainstays of laboratory biology-- a species of each bacteria, yeast, nematode worm, fruit fly, and mouse

According to the Baltimore system, how many major groups of viruses?

seven

What are exceptions to the rule that chromosomes come in pairs?

sex chromosomes and polyploids

What is the second Baltimore system major virus group?

single-stranded DNA, (+) sense (canine parvovirus)

What type of strand is the genome of HIV?

single-stranded RNA

What is the fourth Baltimore system major virus group?

single-stranded RNA, (+) sense (polio)

What is the fifth Baltimore system major virus group?

single-stranded RNA, (-) sense (influenza)

What is the sixth Baltimore system major virus group?

single-stranded RNa, (+) sense, reverse transcriptase (HIV)

How many levels of chromosome condensation are there?

six levels

What does the annotation of a single-copy gene specify?

specifies any nearby regulatory regions that control transcription, the intron-exon boundaries in the gene, and any known or predicted alternative forms in which the introns and exons are spliced

What do regulatory elements in the protein-coding genes do?

specify when and where an RNA transcript will be produced

What are positive supercoils?

supercoils that result from overwinding

What are negative supercoils?

supercoils that result from underwinding; in most organisms, DNA is this; serves to compress the molecule into a compact volume

What is the structure and function of the adenovirus?

surrounded by a glycoprotein envelope composed of a lipid bilayer with embedded proteins and glycoproteins that recognize and attach to host cell receptors forming a icosahedron; a common cause of upper respiratory infections in humans

What are three principal types of sequence repeats found in eukaryotic genomes?

tandem repeats, dispersed repeats, and simple-sequence repeats

What is the C-value and what is the "paradox"?

the C-value is the amount of DNA in a reproductive cell and the "paradox" is the apparent contradiction between genome size and organismal complexity, and hence the difficulty of predicting one from the other

What is the C-value paradox?

the disconnect between genome size and organismal complexity

What is a sequence motif?

the first step in genome annotation; indicates what type of sequence it is; can be found in the DNA itself or in the RNA sequence inferred from the DNA sequence; typically confirmed by experimental methods

How do you make karyotype?

the images of the homologous chromosomes are arranged in pairs from largest to shortest, with the sex chromosomes placed at the lower right

What is genome annotation?

the process by which researchers identify the various types of sequence present in genomes; an exercise in adding commentary to a genome sequence tat identifies which types of sequence are present and where they are located; a form of pattern recognition, where the patterns are regularities in sequence that are characteristic of protein-coding genes or other types of sequence

What is molecular self-assembly?

the process by which, when conditions and relative amounts are suitable, viral components spontaneously interact and assemble into mature virus particles

What is chromosome condensation?

the progressive coiling of the chromatin fiber, an active, energy-consuming process requiring the participation of several types of proteins

What is a capsid?

the protein coat that surrounds the nucleic acid in a virus

What are simple-sequence repeats?

the repeating sequence is short, even as short as two nucleotides, repeated over and over again in a stretch of DNA; short repeated sequences

What is horizontal gene transfer?

the transfer of genetic material between organisms that are not parent and offspring

What was the first genome ever sequenced?

the viral genome

What is host specificity relate to?

the way that viruses gain entry into cells

What makes tandem repeats and dispersed repeats so hard to sequence?

they are typically much longer than the short sequences obtained by automated sequencing; thus, the repeat may not be detected at all

What are the DNA transposable elements?

transposable elements that replicate and transpose via DNA replication and repair

What are LINEs?

transposable elements that transpose by means of an RNA intermediate and are characterized by long interspersed nuclear elements or about 1000 base pairs

What are LTR elements?

transposable elements that transpose by means of an RNA intermediate and are characterized by long repeated sequences, called long terminal repeats (LTRs), at their ends

What are SINEs?

transposable elements that transpose by means of an RNA intermediate and are characterized by short interspersed nuclear elements with about 300 base pairs

What are bacteriophages?

virus that infects bacterial cells

When causes a viral genome to enter the cell?

when viruses bind to the surface receptor molecules on the cells of the host organism

What are protein-coding exons?

exons that contain the codons that specify the amino acid sequence of a polypeptide chain

What are the known functional elements of HIV?

gag, env, and pol

What percentage of the genome actually codes for proteins?

2.5%

The human genome consists of...

22 pairs of chromosomes and 2 sex chromosomes

What is the definition of personalized medicine?

An approach in which the treatment is matched to the patient, not the disease; examination of an individual's genome sequence, by revealing his or her disease susceptibilities and drug sensitivities, allows treatments to be tailored to that individual

What is the first level of chromosome condensation?

DNA duplex 2 nm in diameter

What are transposable elements?

DNA sequences that can replicate and insert themselves into new positions in the genome; they have the potential to increase their copy number in the genome over time

What is shotgun sequencing?

DNA sequencing method in which the sequenced fragments do not originate from a particular gene or region but from sites scattered randomly across the molecule

What is moderately repetitive DNA?

DNA that consists of dispersed repeated sequences

What is highly repetitive DNA?

DNA that consists of sequences present in more than 100,000 copies per genome; corresponds to short sequence repeats

What is the alpha satellite DNA?

DNA that consists of tandem copies of a 171-bp sequence repeated near each centromere an average of 18,000 times; essential for attachment of spindle fibers to the centromeres during cell division

What are the different classes of transposable elements?

DNA transposable elements (DNA TEs), LTR elements, LINEs, and SINEs

Who discovered the enzyme reverse transcriptase?

David Baltimore

What is sequence assembly?

The process in which short nucleotide sequences of a long DNA molecule are arranged in the correct order to generate the complete sequence

What is the third level of chromosome condensation?

chromatin fiber 30 nm in diameter

What is the fourth level of chromosomal condensation?

coiled chromatin fiber 300 nm in diameter

What is the fifth level of chromosomal condensation?

coiled coil 700 nm in diameter

What does it mean for sequences to be conserved?

describes sequences that are similar in different organisms

What is the first Baltimore system major virus group?

double-stranded DNA (adenovirus)

Whereas the genome of all cell consists of double-stranded DNA, what can the genome of viruses be?

double-stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded RNA

What is the third Baltimore system major virus group?

double-stranded RNA (Rotavirus)