🏷️ LIMITED TIME OFFER: GET 20% OFF GRADE+ YEARLY SUBSCRIPTION →
Log in
HomeTextbook Notes300,000US110,000

BIOL 142 Chapter Notes - Chapter 20.4: Horizontal Gene Transfer, Genome Size, Dna Replication

57 views5 pages
bluemosquito338
30 Apr 2018
School
Emory University
Department
Biology
Course
BIOL 142
Professor
Patrick Cafferty

For unlimited access to Textbook Notes, a Class+ subscription is required.

20.4%Insights%from%Genome%Analysis%
!!
Genomics!
• Catalog!what!is!in!a!genome!
o Number,!type,!and!organization!of!genes!and!other!DNA!sequences!
• Patterns!within!and!between!different!genomes!
!!
The!natural!history!and!principles!of!prokaryotic!genomes!
• Prokaryotic!genomes!are!compact!
o Have!uninterrupted!coding!sequences!
o Little!space!between!genes!
o Make!extensive!use!of!operons!
o Have!relatively!few!regulatory!sequences!
o Genome!size!and!number!of!genes!increase!together!linearly!
• Does!not!happen!in!eukaryotic!genomes!
• Bacteria!species!that!live!in!a!variety!of!habitats!and!use!a!wide!array!of!molecules!for!food!have!
large!genomes!
o Parasitic!species!that!make!use!of!a!host's!biochemical!machinery!rather!than!synthesizing!
their!own!molecules!have!small!genomes!
• Most!of!the!genes!found!in!one!species!are!not!shared!widely!with!others!
o Only!a!small!set!of!genes!involved!in!fundamental!processes!such!as!DNA!replication,!
transcription,!and!translation!are!similar!across!a!wide!range!of!prokaryotes!
• Genome!size!and!content!vary!extensively,!even!within!species!
• Prokaryotic!genomes!are!frequently!rearranged!during!evolution!
o Even!closely!related!species!show!little!similarity!in!gene!order!
• A!significant!proportion!of!many!prokaryotic!genomes!has!been!acquired!from!other,!often!
distantly,!related!species!(lateral!gene!transfer)!
!!
Lateral'gene'transfer:!transfer!of!DNA!between!two!different!species!
• In!all!traditional!"species"!definitions,!members!of!one!species!cannot!exchange!genes!with!
members!of!another!species!
o Lateral!gene!transfer!counters!this!view!
• Instead(of(moving(vertically(from(generation(to(generation(within(a(species,(genes(move("laterally"(
between(different(species!
• A!major!force!in!the!evolution!of!prokaryotes!
• How!laterally!transferred!genes!are!identified:!
o The!gene!of!interest!is!much!more!similar!to!genes!in!distantly!related!species!than!to!those!
in!closely!related!species!!
o The!proportion!of!G-C!base!pairs!and!A-T!base!pairs!in!a!particular!gene!or!series!of!genes!is!
markedly!different!from!the!base!composition!of!the!rest!of!the!genome!
• The!proportion!of!G-C!base!pairs!in!a!genome!is!characteristic!of!the!particular!genus!
or!species!
• Can!occur!in!eukaryotes!
o Less!common!than!in!prokaryotes!
o Lateral!gene!transfer!plays!a!pivotal!role!in!eukaryote!evolution!
o Ex:!the!capture!of!bacterial!cells!that!were!predecessors!of!today's!mitochondria!and!
chloroplasts!and!the!subsequent!transfer!of!many!bacterial!genes!to!the!host!genome!
Unlock document

This preview shows pages 1-2 of the document.
Unlock all 5 pages and 3 million more documents.

Already have an account? Log in
• Effect!on!the!tree!of!life!
o If!lateral!gene!transfer!is!rare…!
• Then!evolutionary!paths!in!the!bacteria!and!archaea!form!a!set!of!branches!that!begin!
at!common!ancestors!and!branch!out!to!descendants!
o If!lateral!gene!transfer!is!widespread…!
• Then!evolutionary!paths!form!an!interconnected!network!that!links!species!in!a!web!
of!vertical!and!lateral!gene!transfers!
!!
Plasmids:!in!some!cases,!how!genes!move!from!one!species!to!another!
• In!lateral!gene!transfer,!genes!from!plasmids!become!integrated!into!the!main!chromosome!of!a!
bacterium!through!genetic!recombination!
• Can!occur!by!transformation!when!bacteria!and!archaea!take!up!raw!pieces!of!DNA!from!the!
environment!!
• Can!occur!by!infection!with!viruses!that!pick!up!DNA!from!one!cell!and!transfer!it!to!another!cell!
!!
Metagenomics'(environmental'sequencing):!the!inventory!of!all!the!genes!in!a!community!or!
ecosystem!created!by!sequencing,!analyzing,!and!comparing!the!genomes!of!the!component!organisms;!
often!refers!to!the!study!of!microbial!communities!!
• Cataloging!all!the!genes!present!in!a!complex!community!of!prokaryotes!
• In!the!past,!traditional!methods!of!species!identification!relied!on!growing!cells!in!the!lab,!but!only!
a!tiny!fraction!of!prokaryotes!can!be!successfully!grown!this!way!
• With!the!ability!to!analyze!DNA!sequences!now,!it!is!possible!to!learn…!
o The!genes!present!
o The!composition!of!species!
o Abundance!in!complex!prokaryotic!communities!
• Study!the!diversity!of!microbes!that!live!in!the!environments!in!and!on!us!
o The!roles!they!play!in!health,!disease,!obesity,!and!behavior!
o There!is!significant!variation!in!the!types!and!abundance!of!species!at!a!given!site!in!
different!people!
o The!composition!of!bacterial!communities!varied!widely!at!different!sites!in!the!same!
person!
!!
The!natural!history!of!eukaryotic!genomes!
• Genome!size!varies!widely,!but!the!number!of!genes!varies!relatively!little!
• Challenges!in!sequencing!eukaryotic!genomes:!
1. 'Big'genome'size'
2. 'Coping'with'sequences'that'are'repeated'many'times'
• Many'genomes'are'dominated'by'repeated'DNA'sequences'that'occur'between'
genes'or'inside'introns'
§ Do'not'code'for'products'used'by'the'organism'
• Complicate'aligning'and'interpreting'sequence'DNA'
!!
Repetitive!DNA!and!transposable!elements!
• Repeated!DNA!sequences!partially!explain!the!paradox!of!the!immense!variation!in!eukaryotic!
genome!sizes!
o About!50%!of!an!average!eukaryotic!genome!consists!of!repeated!sequences!
Unlock document

This preview shows pages 1-2 of the document.
Unlock all 5 pages and 3 million more documents.

Already have an account? Log in

Document Summary

Genomics: catalog what is in a genome, number, type, and organization of genes and other dna sequences, patterns within and between different genomes. The natural history and principles of prokaryotic genomes: prokaryotic genomes are compact, have uninterrupted coding sequences. Lateral gene transfer: transfer of dna between two different species. In all traditional species definitions, members of one species cannot exchange genes with members of another species. The proportion of g-c base pairs in a genome is characteristic of the particular genus or species: can occur in eukaryotes. Lateral gene transfer plays a pivotal role in eukaryote evolution: ex: the capture of bacterial cells that were predecessors of today"s mitochondria and chloroplasts and the subsequent transfer of many bacterial genes to the host genome. Then evolutionary paths in the bacteria and archaea form a set of branches that begin at common ancestors and branch out to descendants.

Get access

Grade+20% off
$8 USD/m$10 USD/m
Billed $96 USD annually
Grade+
Homework Help
Study Guides
Textbook Solutions
Class Notes
Textbook Notes
Booster Class
40 Verified Answers
Class+
$8 USD/m
Billed $96 USD annually
Class+
Homework Help
Study Guides
Textbook Solutions
Class Notes
Textbook Notes
Booster Class
30 Verified Answers

Related Documents

BIOL 142
Final Exam
Study Guide
BIOL 142 Midterm: BIOL 142 Study Guide Exam 2
indigominnow529
BIOL 142 Lecture Notes - Lecture 20: Dna Microarray, Dna Profiling, Tandem Repeat
bluemosquito338
BIOL 142 Lecture Notes - Lecture 26: Exon, Chromosome, Reverse Transcriptase
periwinklemouse682

Related Questions


Class 6: Viruses (and Cells, continued)


Making connections: viruses and microbes Match the cell biology concept (on page 1) with an important application of that concept (on page 2). Then answer the follow-up questions at the bottom of page 2.


Cell Biology concepts
1. Bacteria that cannot construct new cell wall material become fragile and break down.
2. During influenza infection, the viral enzyme neuraminidase is required to release new viruses from the host cell in which they were made. Once released, the new viruses can infect many additional cells.
3. Thermus aquaticus is a bacterium found in hot springs and can live at temperatures up to ~80°C (175°F). It has adapted so that its enzymes are most functional at the elevated temperatures, compared with many organisms’ enzymes that function best ~37°C (98°F).
4. Until the isolation and investigation of retroviruses, scientists thought that RNA could be copied from DNA, but DNA could not be copied from RNA. Research on this class of viruses led to an update to this “Central Dogma” of biology.
5. Some bacteria have adapted, so that the enzymes involved in making cell wall materials have a slightly different shape and can no longer be bound by certain drugs.
6. Rhizobia are bacteria that colonize the roots of certain plants (legumes, including beans and peas). The host plant benefits from the prokaryotes’ ability to “fix” nitrogen, converting N2 from the atmosphere into a form that is usable by the plant.
7. Many species of bacteria contain the enzyme cellulase. More than 10 billion such bacteria and other symbiotic microbes may be found in a single milliliter of material from inside the digestive system of ruminant mammals.
8. Fungi, including those that cause athlete’s foot, use ergosterol to maintain healthy membranes. Animal cells do not make ergosterol, they use a similar lipid – cholesterol.
9. During retrovirus infection, a DNA copy is made of the virus’s RNA genome. A cut is made in the host cell’s DNA and the DNA copy of the viral genome is pasted into the host chromosome by a viral enzyme called integrase.
10. Prokaryotic cells contain smaller ribosomes (“70S” ribosomes) than eukaryotic cells (“80S” ribosomes). Both types of ribosomes synthesize proteins, but the macromolecules they use to do it are somewhat different.



2
Applications
_______ Oseltamivir, also called Tamiflu, binds and inhibits the viral protein neuraminidase.
_______ Clotrimazole is a drug that is used to treat certain infections. It interferes with synthesis of ergosterol, a lipid involved in phospholipid membranes.
_______ Penicillin is a drug that interferes with synthesis of peptidoglycans (these are biological molecules that are part protein and part carbohydrate) that are present in certain cell walls.
_______ HIV is often treated with several drugs that inhibit different parts of the viral replicative cycle. Raltegravir is an example of a drug that interferes with the integration of viral genes into the host cell’s chromosome.
_______ Cows, like other vertebrates, lack the ability to breakdown cellulose. Yet they are able to live on a diet of grass and other vegetation high in cellulose.
_______ Enzymes isolated from extremophiles have been very useful in laboratory research. For example, Taq polymerase facilitates PCR, a revolutionary technique for production of DNAs of particular sequences, which requires cycling reactions through high temperatures.
_______ Plants and animals require nitrogen to make biological macromolecules, however they’re unable to convert atmospheric nitrogen (N2) into a biologically useful form.
_______ Azithromycin is a drug that binds to 70S ribosomes and blocks synthesis of any new proteins.
_______ Methicillin-Resistant Staphylococcus aureus (MRSA) can cause life-threatening infections of the skin and bloodstream. One of the reasons MRSA infections are so serious is that they are resistant to treatment by many antibiotics, including methicillin and penicillin.
_______ The enzyme reverse transcriptase, isolated from retroviruses, is an important tool in molecular biology research. Scientists interested in learning what genes are turned on in particular cells use it to make DNA copies of RNAs they are studying (The DNA copies are useful because they are more stable).


When you have completed the matching activity, answer these follow-up questions:
• What types of infections can be treated with the following drugs?
o Penicillin
o Clotrimazole
o Azithromycin
o Tamiflu
o Raltegravir
• Why are these drugs (above) safe for you to take? That is, why don’t they kill your cells?
• Cancer cells are your own human cells that have become deregulated so that they divide and pile up in an uncontrolled way. Many chemotherapy drugs treat cancer by interfering with cell division and other cell processes.
o Why are there so many more side effects for individuals undergoing chemotherapy than for individuals taking antibiotics?

1.

__________ are fairly small organelles that provide a safe place within the cell to carry out certain biochemical reactions that generate harmful, highly reactive oxygen species. These chemicals are both generated and broken down in the same location.

Lysosomes
Endosomes
Peroxisomes

Nucleosomes

2.

Biologists cannot possibly study all living species. Instead, they try to understand cell behavior by studying a select subset of them. Which of the following characteristics are useful in an organism chosen for use as a model in laboratory studies?

rapid rate of reproduction
all of the above
ability to grow under controlled conditions

amenability to genetic manipulation

3.

By definition, prokaryotic cells do not possess __________.

ribosomes.
a nucleus.
membrane bilayers.

replication machinery.

4.

Cell biologists employ targeted fluorescent dyes or modified fluorescent proteins in both standard fluorescence microscopy and confocal microscopy to observe specific details in the cell. Even though fluorescence permits better visualization, the resolving power is essentially the same as that of a standard light microscope because the resolving power of a microscope is limited by the __________ of light.

intensity
absorption
wavelength

filtering

5.

Choose the phrase that best completes this sentence: Microtubules ____________ and are required to pull duplicated chromosomes to opposite poles of dividing cells.

generate contractile forces
can rapidly reorganize
are found in especially large numbers in muscle cells

are intermediate in thickness

6.

Despite the differences between eukaryotic and prokaryotic cells, prokaryotes have proteins that are distantly related to eukaryotic actin filaments and microtubules. What is likely to be the most ancient function of the cytoskeleton?

cell division
cell motility
vesicle transport

membrane support

7.

DNA and RNA are different types of nucleic acid polymer. Which of the following is true of DNA but not true of RNA?

It contains thymine.
It has 5'-to-3' directionality.
It is single-stranded.

It contains uracil.

8.

Double covalent bonds are both shorter and stronger than single covalent bonds, but they also limit the geometry of the molecule because they ____________________.

prevent additional bonds from being formed with the bonded atoms.
limit the rotation of the bonded atoms.
create a new arrangement of electron shells.

change the reactivity of the bonded atoms.

9.

Drosophila melanogaster is a/an __________. This type of animal is the most abundant of all animal species, making it an appropriate choice as an experimental model.

mammal
amphibian
bird

insect

10.

If the isotope 32S has 16 protons and 16 neutrons, how many protons, neutrons, and electrons will the isotope 35S have, respectively?

16, 19, 17
16, 19, 15
16, 19, 16

16, 20, 15

11.

Living systems are incredibly diverse in size, shape, environment, and behavior. It is estimated that there are between 10 million and 100 million different species. Despite this wide variety of organisms, it remains difficult to define what it means to say something is alive. Which of the following can be described as the smallest living unit?

cell
organelle
protein

DNA

12.

Macromolecules in the cell can often interact transiently as a result of noncovalent interactions. These weak interactions also produce stable, highly specific interactions between molecules. Which of the factors below is the most significant in determining whether the interaction will be transient or stable?

the concentration of each molecule
the size of each molecule
surface complementarity between molecules

the rate of synthesis

13.

Many of the mechanisms that cells use for maintenance and reproduction were first studied at the molecular level in bacteria. Which bacterial species had a central role in advancing the field of molecular biology?

E. coli
S. pombe
C. elegans

D. melanogaster

14.

Many types of cells have stores of lipids in their cytoplasm, usually seen as fat droplets. What is the lipid most commonly found in these droplets?

cholesterol
isoprene
triacylglycerol

palmitic acid

15.

Mitochondria contain their own genome, are able to duplicate, and actually divide on a different time line from the rest of the cell. Nevertheless, mitochondria cannot function for long when isolated from the cell because they are __________________.

anaerobes.
viruses.
parasites.

endosymbionts.

16.

Mitochondria perform cellular respiration, a process that uses oxygen, generates carbon dioxide, and produces chemical energy for the cell. Which answer below indicates a correct pairing of material “burned” and the form of energy produced during cellular respiration?

fat, protein
sugar, fat
sugar, ATP
fat, ADP

17.

Polar covalent bonds are formed when the electrons in the bond are not shared equally between the two nuclei. Which one of these molecules contains polar bonds?

propane
methane
molecular oxygen
water