Chapter 8: Genomes of Prokaryotes and Eukaryotic Organelles

Question 1

Module 7

traditional view has been that in a typical prokaryote the genome is contained in a _____, _____ DNA molecule, localized within the _____—the lightly staining region of the otherwise featureless prokaryotic cell

Answer 1

• single, circular
• nucleoid

Question 2

Module 7

genome packaging in prokaryotes is achieved with the help of _____ _____ that package the genome in an organized fashion

Answer 2

DNA-binding proteins

Question 3

Module 7

Supercoiling occurs when additional turns are introduced into the DNA double helix (_____ _____) or if turns are removed (_____ _____).

Answer 3

• positive supercoiling
• negative supercoiling

Question 4

circular molecules respond to torsional stress introduced by over- or underwinding by

Answer 4

winding around itself to form a more compact structure

Question 5

E. coli DNA molecule does not have unlimited freedom to rotate once a _____ is introduced.

The most likely explanation is that the bacterial DNA is attached to _____ that restrict its ability to relax, so that rotation at a break site results in loss of supercoiling from only a _____ _____ of the molecule.

This is supported by using trimethylpsoralen to distinguish between supercoiled and relaxed DNA. Explain

Answer 5

• break
• proteins
• small segment
• When trimethylpsoralen is photoactivated it binds to double-stranded DNA at a rate that is directly proportional to the degree of torsional stress possessed by the molecule
  
  • The degree of supercoiling can be assayed by measuring the amount of trimethylpsoralen that binds to a molecule in unit time
  • After E. coli cells have been irradiated to introduce single-strand breaks into their DNA molecules, the amount of trimethylpsoralen binding is proportional to the radiation dose

Question 6

Module 7

In E. coli, the supercoiling is thought to be generated and controlled by two enzymes:

Answer 6

DNA gyrase and DNA topoisomerase

Question 7

Module 7

The current model has the E. coli DNA attached to a protein core from which _____ supercoiled loops radiate out into the cell. Each loop contains approximately _____ kb of supercoiled DNA, the amount of DNA that becomes unwound after a _____ ______. The protein component of the nucleoid includes _____ _____ and _____ _____ __ as well as as well as a set of at least ____ _____ believed to have a more specific role in packaging, the most abundant being

Answer 7

• 40–50
• 100
• single break
• DNA gyrase and DNA topoisomerase I
• four proteins
• HU

Question 8

HU

Answer 8

• most abundant packaging protein in prokaryotes
• structurally very different to eukaryotic histones but acts in a similar way
• forms a tetramer
• 60 bp of DNA winds around the tetramer
• There are some 60,000 HU proteins per E. coli cell, enough to cover about one-fifth of the DNA molecule
• not known if the tetramers are evenly spaced along the DNA or restricted to the core region of the nucleoid

Question 9

archaea do not possess packaging proteins such as HU but instead have proteins that are much more similar to _____. These form a tetramer that associates with approximately ______ bp of DNA to form a structure similar to a _____ _____. Currently we have very little information on the archaeal nucleoid, but the assumption is that these histone-like proteins play a central role in DNA packaging.

Answer 9

• histones
• 80
• eukaryotic nucleosome

Question 10

Some bacteria have _____ or ______ genomes

Answer 10

• linear
• multipartite

Question 11

linear DNA molecules have free ends, which must be distinguishable from _____ ______, so they require terminal structures equivalent to the _____ of eukaryotic chromosomes. some ends are distinguishable because a covalent linkage is formed between the ___ and ___ ends of the polynucleotides in the DNA double helix, and in others the ends appear to be marked by special _____ ______

Answer 11

• DNA breaks
• telomeres
• 5’ and 3’
• binding proteins

Question 12

multipartite genomes

Answer 12

• genomes that are divided into two or more DNA molecules
  *

Question 13

a problem that arises with multipartite genomes is distinguishing genuine part of the ______ from a ______

Answer 13

• genome
• plasmid

Question 14

plasmid

Answer 14

• a small piece of DNA
• often but not always circular
• coexists with the main chromosome in a bacterial cell
• Some are able to integrate into the main genome
• others are thought to be permanently independent
• carry genes that are not usually present in the main chromosome, but in many cases these genes are nonessential to the bacterium, coding for characteristics such as antibiotic resistance, appearing dispensible

Question 15

many plasmids are able to ______ from one cell to another, and the same plasmids are sometimes found in bacteria that belong to different _____. These various features of plasmids suggest that they are ______ entities and that in most cases the plasmid content of a prokaryotic cell should not be included in the definition of its _____

Answer 15

• transfer
• species
• independent
• genome

Question 16

some plasmids contain essential _____ but also has certain features that are considered characteristic of plasmids, notably the presence of an _____—a set of genes and other DNA sequences that enable plasmids to capture genes from bacteriophages and other plasmids

Answer 16

• genes
• integron

Question 17

essential genes distributed among _____ and ______ leads to the possibility that some prokaryotes have highly ______ genomes, comprising a number of separate DNA molecules, more akin to what we see in the ______ nucleus rather than the “typical” prokaryotic arrangement

Answer 17

• chromosomes and plasmids
• multipartite
• eukaryotic

Question 18

prokaryotic genomes have very little _____ _____. There are theories that this compact organization is beneficial to prokaryotes, for example by enabling the genome to be replicated relatively quickly, but these ideas have never been supported by hard experimental evidence.

Answer 18

• wasted space

Question 19

operon

Answer 19

• a group of genes involved in a single biochemical pathway and expressed in conjunction with one another
• but in some species, like archaeon Methanococcus jannaschii and the bacterium Aquifex aeolicus, the genes in an individual operon rarely have any biochemical relationship
  
  • the belief that expression of an operon leads to the coordinated synthesis of enzymes required for a single biochemical pathway does not hold for these species

Question 20

prokaryotic genes are _____ than their eukaryotic counterparts, the average length of a bacterial gene being about _____-_____ that of a eukaryotic gene, even after the ______ have been removed from the latter. Bacterial genes appear to be slightly longer than ______ ones

Answer 20

• shorter
• two-thirds
• introns
• archaeal

Question 21

two main features of prokaryotic genomes

Answer 21

1. discontinuous genes are virtually absent in prokaryotes
   
   • few exceptions occurring mainly among the archaea
2. infrequency of repetitive sequences
   
   • Most prokaryotic genomes do not have anything equivalent to the high-copy-number genome-wide repeat families found in eukaryotic genomes
   • they have insertion sequences instead
     
     • transposable elements
     • sequences that have the ability to move around the genome
     • in the case of insertion elements, to transfer from one organism to another, even sometimes between two different species

Question 22

Most prokaryotic genomes are less than ___ Mb in size, but the overall range among sequenced genomes is from ___ kb to ___ Mb and a few unsequenced genomes are substantially larger. most are genome size is proportional to gene number, with an average of approximately _____ genes per ___ Mb of DNA

Answer 22

• 5
• 491
• 9.1
• 950
• 1

Question 23

The largest genomes tend to belong to _____ species that are found in the soil, the environment which is generally looked on as providing the broadest range of physical and biological conditions, to which the genomes of these species must be able to respond. At the other end of the scale, many of the smallest genomes belong to species that are _____ ______, these species are unable to synthesize many nutrients and hence must obtain these from their hosts. speculation about the smallest number of genes needed to specify a free-living cell is somewhere between ___- ___

Answer 23

• free-living
• obligate parasites
• 265-350