CHAPTER 21 LECTURE SLIDES - PBworks

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CHAPTER 21

LECTURE

SLIDES

Prepared by

Brenda Leady University of Toledo

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2

The unifying theme of biology is evolution

The genome of every living species is the

product of over 3.5 billion years of

evolution

All species evolved from an interrelated

group of ancestors

3

Prokaryotic genomes

Of interest because

Bacteria cause diseases

Can apply knowledge to more complex

organisms

Origin of first eukaryotic cell probably involved

the union between an archaeal and bacterial

cell

Venter, Smith, and Colleagues Sequenced the First

Complete Genome in 1995

Haemophilus influenzae causes a variety of human diseases

Relatively small genome – 1.8 Mb

One strategy for mapping large genomes is extensive mapping

Alternative is shotgun DNA sequencing

Randomly sequence fragments

Does not require extensive mapping but you may waste time sequencing the same DNA region

6

Eukaryotic genomes

Nuclear genome usually found in sets of

linear chromosome

Extranuclear DNA found in mitochondria

and chloroplasts

Entire nuclear genome sequenced for

several species

7

4 motivators to sequence genome

1. Great benefit from identifying and

characterizing genes in model organisms

2. More information to identify and treat

human diseases

3. Improved strains of agricultural species

4. Way to establish evolutionary

relationships

8

Genome size is not the same as the number of genes

In general, increases in the amount of DNA are correlated with increasing cell size, cell complexity and body complexity

However, major variations are observed between organisms with similar form and function

9

Eukaryotic genomes have repetitive sequences

Many copies of short DNA sequences

Moderately repetitive sequences

Few hundred to several thousand times

rRNA genes, multiple origins of replication, or role in gene transcription and translation

Highly repetitive sequences

Tens of thousands or millions of times

Most have no known function

Coding regions are only 2% of our genome

10


25

0 2%

24%

15%

59%

50

Perc

en

tag

e i

n t

he h

um

an

gen

om

e

Classes of DNA sequences

75

100

Regions of

genes that

encode

proteins

(exons) or

give rise to

rRNA or tRNA

Introns and

other parts

of genes

such as

enhancers

Unique

noncoding

DNA

Repetitive

DNA

Repetitive Sequences

Within a species,

sequences of repeat units

are conserved.

However, the number of

repeat units is variable

among individuals

DNA fingerpriniting

exploits differences in

DNA polymorphisms

11

13

Transposable elements

Transposition – short segment of DNA moves from original site to a new site

Transposable elements (TEs) – DNA segments that move

“Jumping genes”

Found in all species examined

First discovered by Barbara McClintock

1983, awarded Nobel Prize

14

DNA transposons

Both ends have inverted repeats (IRs), DNA

sequences that are identical (or very similar)

but run in opposite directions

TEs may contain a central region that

encodes transposase, an enzyme that

facilitates transposition

Cut-and-paste mechanism

Transposase recognizes IR and then removes sequence from original site

Complex moves to new location where transposase inserts it into the chromosome

15

16

RNA intermediates

Common only in eukaryotes

Retroelement contains reverse transcriptase and transposase

Reverse transcriptase

uses RNA as a template

to make a

complementary copy of

DNA

Retroelements may

accumulate rapidly in a

genome

Alu elements are 10% of

human genome

17

Role of transposable elements

Selfish DNA hypothesis

TEs exist solely because they have characteristics

that allow them to insert themselves into the host

cell DNA

Resemble parasites, can do harm

Others argue TEs may benefit a species

Promote genetic variation

Gene duplication

Provide raw material for the addition of more genes into a species’ genome

Create homologous genes

Two or more genes that are derived from the same

ancestral gene

Over the course of many generations, each version of the gene accumulates different mutations Genes with similar but not identical DNA sequences

18

20

Mechanism

Gene duplication caused by misaligned crossovers

2 homologous chromosomes have paired during meiosis but the homologs are misaligned

If a crossover occurs, one chromosome gets a gene duplication, one a gene deletion and 2 are normal

21


A

A A

A B

B

B

B C

C C

C D

D D

D

Following

meiosis

22


Misaligned crossover

between homologous

chromosomes

A

A A

A

A

A

A

A B

B

B

B

B

B

B C

C C

C

C

C C

C D

D

D

D

D D

D

Following

meiosis

B D Gene

duplication

Deletion

(b) Mechanism of gene duplication

Paralogs

Two or more homologous genes within a

single species

Gene family

Two or more paralogous genes that carry out

related functions

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24

Globin genes

Encode polypeptides that are subunits of

proteins that function in oxygen binding

14 paralogs derived from a single ancestral

globin gene

Duplications and rearrangements occurred

Mutations have created specialized globins

Hemoglobin, myoglobin, embryonic and fetal forms

Based on differences in oxygen transport needs

Pseudogenes

Genes that have been produced by gene duplication

but have accumulated mutations that make them

nonfunctional

Not transcribed into RNA

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Millio

ns o

f years

ag

o (

mya)

1,000

800

600

400

200

0

Ancestral globin

Myoglobin

Chromosome 16 Chromosome 11

β-globins

Hemoglobins

α-globins

Chromosome 22

Mb

Nonfunctional

pseudogenes

α2 α1 α2 α1 e gG Cβ β gA

26

Human Genome Project

Officially began October 1, 1990

Largely finished by end of 2003

Goals

Identify all human genes

Sequence entire human genome

Develop technology

Analyze genomes of model organisms

Develop legal, ethical and social programs

addressing the results

27

Proteomes

Relative abundance of proteins

Abundance in genome Number of genes that encode a particular type of

category of protein

Abundance in cell Amount of a given protein or protein category

actually made by a living cell

Liver/muscle cell example

Same genes so % in genome identical

Cellular abundance very different

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Abundance in cell

Abundance in genome

Abundance in cell

Abundance in genome

Liver cell Skeletal muscle cell

Genes for metabolic 25%

enzymes

Genes for structural 5%

proteins

Genes for motor < 2%

proteins

Metabolic enzymes > 50%

Structural proteins < 10%

Motor proteins < 5%

Genes for metabolic 25%

enzymes

Genes for structural 5%

proteins

Genes for motor < 2%

proteins

Metabolic enzymes < 10%

Structural proteins 20–30%

Motor proteins 25–40%

29

Proteomes are larger than genomes

Due to…

Alternative splicing

A single pre-mRNA can be spliced into more than

one version

Often cell specific or related to environmental

conditions

Post-translational covalent modification

Permanent or reversible

Involved in assembly and construction of protein

Phosphorylation, methylation, acetylation

30


Permanent modifications

Reversible modifications

Phosphorylation

Phospholipid

Sugar

Heme

group

Acetylation

Methylation

(b) Post-translational covalent modification

CH 3

C

O

PO 4 2–

CH 3

SH SH S S

(a) Alternative splicing

pre-mRNA

Exon 1 Exon 2 Exon 3 Exon 4 Exon 5 Exon 6

Exon 1 Exon 2

Exon 4 Exon 5

Exon 6

Exon 1 Exon 3

Exon 4 Exon 5

Exon 1 Exon 2

Exon 4 Exon 6

Exon 6

Translation

Alternative splicing

or

or

Attachment

of prosthetic

groups, sugars,

or lipids

Proteolytic

processing

Disulfide bond

formation

Phosphate

group

Acetyl

group

Methyl

group

31

Bioinformatics

Use of computers, mathematical tools, and

statistical techniques to record, store, and

analyze biological information

More than just DNA sequences

Highly interdisciplinary, incorporating

principles from mathematics, statistics,

information science, chemistry, and

physics

Issues of size and speed in analyzing

huge volumes of data

Computational molecular biology

Uses computers to characterize the molecular

components of living things

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33

First step is to collect and store data

Then write programs to analyze

sequences in particular ways

Translate DNA sequence into amino acid

sequence – results for all 3 reading frames

May also not know which strand is coding

strand so results for both strands

35

Databases

Collect large numbers of files and store

them in one place for rapid search and

retrieval

Additional descriptive information included

Research community has collected

genetic information from thousands of

research labs and created several large

databases

36

Identify homologous sequences

Can use computer to identify genes that

are evolutionarily related

Closely related organisms tend to have

genes with similar DNA sequences

Ortholog – homologous genes in different

species

Helps us understand evolutionary

relationships

37


Random mutations

Mus musculus Rattus norvegicus

Mouse

Rat

X X X X X T

ime

GGGCAGGTTGGTATCCAGGTTACAAGG C AGCTC AC AAGTAGAAG C T G GGTGCTTGGAGAC

GGGCAGGTTGGTATCCAGGTTACAAGG T AGCTC CT AAGTAGAAG T T T GGTGCTTGGAGAC

(a) A comparison of one DNA strand of the mouse and rat -globin

genes

-globin gene in common

ancestor to mice and rats

(b) The formation of homologous -globin genes during evolution

of mice and rats

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A matrix can be used to compare 2

sequences

DNA sequences are long so use more

complex dynamic programming methods

39

BLAST

Homologous genes usually carry out similar

or identical functions

First indication of function for a new

sequence is through homology to known

sequences

Basic Local Alignment Search Tool

(BLAST)

Uses particular genetic sequence to find

homologous sequences in a large database

40

Sample BLAST

Order follows

evolutionary

relatedness of various

species to humans

Main power of the

BLAST program is its

use with newly

identified sequences,

in which a researcher

does not know the

function of a gene or

an encoded protein

CHAPTER 21 LECTURE SLIDES - PBworks

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