MCB Chapter 13 Genomes

nucleoid .

In prokaryotes, a cell structure with multiple loops formed from supercoils of DNA

The α satellite DNA is essential for

attachment of spindle fibers to the centromeres during cell division

The level of DNA packaging brought about by the formation of _____ looks like beads on a string. nucleosomes scaffolds 30-nm chromatin fibers 2-nm chromatin fibers 1400-nm chromatin fibers

nucleosomes

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).

DNA is wrapped around histones, which contain many copies of the positive amino acids lysine and arginine. These positive amino acids neutralize the negative charge of the _____ of the DNA wrapped around the histone. nitrogenous base ribose sugar phosphate group hydroxyl group All of these choices are correct.

phosphate group

Most viral genomes range in size from

3 kb to 300 kb, but a few are very large. The largest viral genome, found in a virus that infects the amoeba Acanthamoeba polyphaga, is 1.2 Mb. This viral genome contains almost 1000 protein-coding genes, including some for sugar, lipid, and amino acid metabolism not found in any other viruses.

transposable element (TE)

A DNA sequence that can replicate and move from one location to another in a DNA molecule; also known as transposon. -they have the potential to increase their copy number in the genome over time. Transposable elements are sometimes 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. Transposable elements make up about 45% of the DNA in the human genome -hey can be grouped into two major classes based on the way they replicate. One class consists of DNA transposons, which replicate and transpose by DNA replication and repair. The other class consists of elements that transpose by means of an RNA intermediate. These are sometimes called retrotransposons because their RNA is used as a template to synthesize complementary strands of DNA, a process that reverses the usual flow of genetic information from DNA into RNA (retro- means "backward"). More than 40% of the human genome consists of various types of retrotransposons, whereas only about 3% of human DNA consists of DNA transposons.

chromatin

A complex of DNA, RNA, and proteins that gives chromosomes their structure; chromatin fibers are either 30 nm in diameter or, in a relaxed state, 10 nm.

karyotype

A standard arrangement of chromosomes, showing the number and shapes of the chromosomes representative of a species.

Transposable elements are: proteins that can move outside of the nucleus. proteins that can move into the nucleus. DNA sequences that can insert themselves into RNA. DNA sequences that can insert themselves into new positions within the genome. None of the answer options is correct.

DNA sequences that can insert themselves into new positions within the genome.

Each type of organelle has its own

DNA. meaning that eukaryotic cells have multiple genomes. Each eukaryotic cell has a nuclear genome consisting of the DNA in the chromosomes. Cells with mitochondria also have a mitochondrial genome, and those with chloroplasts also have a chloroplast genome.

first level of packaging

First, eukaryotic DNA is wrapped twice around a group of histone proteins called a nucleosome. A nucleosome is made up of eight histone proteins: two each of histones H2A, H2B, H3, and H4. The histone proteins are rich in the amino acids lysine and arginine, whose positive charges are attracted to the negative charges of the phosphates along the backbone of each DNA strand. - This first level of packaging of the DNA is sometimes referred to as "beads on a string," with the nucleosomes the beads and the DNA the string. It is also called a 10-nm fiber in reference to its diameter, which is about five times the diameter of the DNA double helix

Why are some eukaryotic genomes so large?

One reason is polyploidy, or having more than two sets of chromosomes in the genome. Polyploidy is especially prominent in many groups of plants. Humans have two sets of 23 chromosomes, giving us 46 chromosomes in total. But the polyploid bread wheat Triticum aestivum, for example, has six sets of seven chromosomes. -the principal reason for large genomes among some eukaryotes is that their genomes contain large amounts of DNA that do not code for proteins, such as introns and DNA sequences that are present in many copies.

what has been involved in the evolution of plants

Polyploidy - it is estimated that 30% to 80% of existing species have polyploidy in their evolutionary history, either because of the duplication of the complete set of chromosomes in a single species, or because of hybridization, or crossing, between related species followed by duplication of the chromosome sets in the hybrid

c value paradox

The disconnect between genome size and organismal complexity (the C-value is the amount of DNA in a reproductive cell).

homologous chromosomes

The members of each pair of homologous chromosomes have the same genes arranged in the same order along their length. If the DNA duplexes in each pair of homologs were denatured, each DNA strand could form a duplex with its complementary strand from the other homolog. There would be some differences in DNA sequence due to genetic variation, but not so many differences as to prevent DNA hybridization.

second level of packaging

The next level of packaging occurs when the chromatin is more tightly coiled, forming a 30-nm fiber - As the chromosomes in the nucleus condense in preparation for cell division, each chromosome becomes progressively shorter and thicker as the 30-nm fiber coils onto itself to form a 300-nm coil, a 700-nm coiled coil, and finally a 1400-nm condensed chromosome in a manner that is still not fully understood. The progressive packaging constitutes chromosome condensation, an active, energy-consuming process requiring the participation of several types of proteins. -Greater detail of the structure of a fully condensed chromosome is revealed when the histones are chemically removed. Without histones, the DNA spreads out in loops around a supporting protein structure called the chromosome scaffold. Each loop of relaxed DNA is 30 to 90 kb long and anchored to the scaffold at its base. Before removal of the histones, the loops are compact and supercoiled. Each human chromosome contains 2000-8000 such loops, depending on its size.

Given our knowledge of genome sizes in different organisms, would you predict that Homo sapiens or the two-toed salamander (Amphiuma means) has the larger genome?

You can't tell. The C-value paradox means that you cannot predict genome size from the complexity of the organism. In fact, the genome size of the two-toed salamander is 30 times larger than that of the human genome.

The C-value paradox is the disconnect between genome size: and organismal complexity. and gene ratio. and protein ratio. and gene size. within the same species.

and organismal complexity.

postive supercoils

are a result from overwinding

negative supercoils

are a result from underwinding. - this is found in most organisms

what shape are Bacterial genomes

circular. and the DNA double helix is underwound, which means that it makes fewer turns in going around the circle than would allow every base in one strand to pair with its partner base in the other strand.

Complete genome sequencing has allowed the

different types of noncoding DNA to be specified more precisely in a variety of organisms

David has a lab assignment where he must cut out shapes of chromosomes and place two chromosomes of the same shape and size together. Two chromosomes of the same size and shape are termed a(n) _____ pair. antiparallel template and a daughter complementary transposable homologous

homologous

the mechanism of packing DNA differs

in bacteria, archeaons, and eukarotyes

William has a lab assignment where he must cut out shapes of chromosomes and place two chromosomes of the same shape and size together. He lines up all of the chromosome pairs from largest to smallest and glues them to a piece of paper. William has created a: karyotype. chromosome paint. Southern blot. phenotype. DNA scaffold.

karyotype.

The two organelles that contain their own genome are: Golgi apparatus and mitochondria. endoplasmic reticulum and mitochondria. chloroplast and vacuole. Golgi apparatus and endoplasmic reticulum. mitochondria and chloroplast.

mitochondria and chloroplast.

a single gene may yield

multiple proteins, either because of alternative splicing (different exons are spliced together to make different proteins) or posttranslational modification (proteins undergo biochemical changes after they have been translated).

Once the histones are removed from a metaphase chromosome, one can see DNA spreading out in loops around the supporting protein structure, called the: beads on a string. 300 nm fiber. 1400 nm fiber. scaffold. 2 nm fiber.

scaffold.

underwinding creates strain on DNA which is relieved by the formation of

supercoils. there is where the dna molecule coils on itself allowing all the base pairs to form, even though the molecule is underwound.

The bigger genomes have more genes, allowing these bacteria to

synthesize small molecules that other bacteria have to scrounge for, or to use chemical energy in the covalent bonds of substances that other bacteria cannot. Archaeons, whose genomes range in size from 0.5 to 5.7 Mb, have similar capabilities.

Because the genome organization and mechanisms of protein synthesis in these organelles resemble those of bacteria, most biologists subscribe to the theory that

the organelles originated as free-living bacterial cells that were engulfed by primitive eukaryotic cells billions of years ago

Differential gene expression allows

the same protein-coding genes to be deployed in different combinations to yield a variety of distinct cell types. In addition, proteins can interact with one another so that, even though there are relatively few types of protein, they are capable of combining in many different ways to perform different functions.

Two major types of transposable elements are those that transpose via a DNA intermediate and those that transpose via an RNA intermediate. true false

true

This enzyme is responsible for breaking the backbone on the DNA double helix. ligase transcriptase polymerase topoisomerase II supercoilase

topoisomerase II

underwinding of the bacterial DNA is caused by

topoisomerase II, an enzyme that breaks the double helix, rotates the ends to unwind the helix, and then seals the break.

Among flowering plants, 30 percent to 80 percent of existing species are polyploidy somewhere within their evolutionary history. true false

true

In eukaryotes, just as the number of genes does not correlate well with organismal complexity, the size of the genome is

unrelated to the metabolic, developmental, and behavioral complexity of the organism

Retrotransposons are a class of transposable elements that: replicate and transpose via DNA replication and repair. uses RNA as an intermediate. uses DNA as an intermediate. uses protein as an intermediate. uses ribosomes as an intermediate.

uses RNA as an intermediate.