Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Review When the hydrogen...

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Review

When the hydrogen bonds are broken between amino acids in a protein:

1) What structure level are hydrogen bonds located?

2) When the hydrogen bonds are broken, the protein is called?

3) Do enzymes work when hydrogen bonds broken?


PowerPoint Lectures for Biology, Seventh Edition

Neil Campbell and Jane Reece

Lectures by Chris Romero

Chapter 16Chapter 16

The Molecular Basis of Inheritance


History of DNA

In 1953, James Watson and Francis Crick

Described the DOUBLIX HELIX STRUCTURE of DNA

Figure 16.1


What is DNA?

• DNA, the substance of inheritance

DNA directs the development of many different traits by using a chemical language

Terms

1. Chromosome – one molecule of DNA & associated protein

2. Genome – collection of ALL of the DNA in a given cell (Humans have 46 chromosomes in genome)

3. GENE – portion of DNA that encodes a single protein


Evidence that DNA is genetic material

Scientists first worked out by studying bacteria and the viruses that infect them

1. Griffith studied Streptococcus pneumoniae (bacteria that causes pneumonia in mammals)

– He used a pathogenic strain (called S b/c it’s encapsulated) and a nonpathogenic strain (called R b/c it’s not protected.


• Griffith found that when he mixed heat-killed remains of the pathogenic strain

– With living cells of the nonpathogenic strain, some of these living cells became pathogenic

– He called this phenomenon TRANSFORMATION Bacteria of the “S” (smooth) strain of Streptococcus pneumoniae are pathogenic because they have a capsule that protects them from an animal’s defense system. Bacteria of the “R” (rough) strain lack a capsule and are nonpathogenic. Frederick Griffith injected mice with the two strains as shown below:

Griffith concluded that the living R bacteria had been transformed into pathogenic S bacteria by anunknown, heritable substance from the dead S cells.

EXPERIMENT

RESULTS

CONCLUSION

Living S(control) cells

Living R(control) cells

Heat-killed(control) S cells

Mixture of heat-killed S cellsand living R cells

Mouse dies Mouse healthy Mouse healthy Mouse dies

Living S cellsare found inblood sample.

Figure 16.2



2. Viruses that infect bacteria, bacteriophages

– Are widely used as tools by researchers in molecular genetics

Figure 16.3

Phagehead

Tail

Tail fiber

DNA

Bacterialcell

100

nm



3. Chargaff analyzed the base composition of DNA

Concluded that DNA composition varies from one species to the next (evidence of diversity)

Chargaff’s ratio rule’s for HUMANS:

A: 30.3% G: 19.5%

T: 30.3% C: 19.9%


Evidence of the Structure of DNA

1. Wilkins & Franklin used a technique called

X-ray crystallography to study the structure

(a) Rosalind Franklin Franklin’s X-ray diffractionPhotograph of DNA

(b)Figure 16.6 a, b


• Franklin had concluded that DNA

– Composed of two antiparallel sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior

• The nitrogenous bases

– Are paired in specific combinations: adenine with thymine, and cytosine with guanine


O

–O O

OH

O

–OO

O

H2C

O

–OO

O

H2C

O

–OO

O

OH

O

O

OT A

C

GC

A T

O

O

O

CH2

OO–

OO

CH2

CH2

CH2

5 end

Hydrogen bond3 end

3 end

G

P

P

P

P

O

OH

O–

OO

O

P

P

O–

OO

O

P

O–

OO

O

P

(b) Partial chemical structure

H2C

5 endFigure 16.7b

O


Structure evidence cont.

Figure 16.7a, c

C

T

A

A

T

CG

GC

A

C G

AT

AT

A T

TA

C

TA0.34 nm

3.4 nm

(a) Key features of DNA structure

G

1 nm

G

(c) Space-filling model

T

2. Watson and Crick deduced that DNA was a double helix

– Through observations of the X-ray crystallographic images of DNA


• Watson and Crick reasoned that there must be additional specificity of pairing

– Dictated by the structure of the bases

• Each base pair forms a different number of hydrogen bonds

– Adenine and thymine form two bonds, cytosine and guanine form three bonds


N H O CH3

N

N

O

N

N

N

N H

Sugar

Sugar

Adenine (A) Thymine (T)

N

N

N

N

Sugar

O H N

H

NH

N OH

H

N

Sugar

Guanine (G) Cytosine (C)Figure 16.8

H


DNA REPLICATION

1. Definition – manufacture of an EXACT copy of DNA molecule

2. Process of DNA replication

A. Parts

1. DNA to be replicated (called parent)

2. Enzymes

1. DNA polymerase (adds nucleotides)

2. Helicase (unwinds the double helix)

3. Single stranded binding proteins (hold DNA open)

4. Primase (begins replication by laying down small “RNA primer”)

5. Ligase (seals the gaps in DNA)


Other Proteins That Assist DNA Replication

• Helicase, topoisomerase, single-strand binding protein

– Are all proteins that assist DNA replication

Table 16.1


• In DNA replication

– The parent molecule unwinds, and two new daughter strands are built based on base-pairing rules

(a) The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C.

(b) The first step in replication is separation of the two DNA strands.

(c) Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand.

(d) The nucleotides are connected to form the sugar-phosphate backbones of the new strands. Each “daughter” DNA molecule consists of one parental strand and one new strand.

A

C

T

A

G

A

C

T

A

G

A

C

T

A

G

A

C

T

A

G

T

G

A

T

C

T

G

A

T

C

A

C

T

A

G

A

C

T

A

G

T

G

A

T

C

T

G

A

T

C

T

G

A

T

C

T

G

A

T

C

Figure 16.9 a–d


DNA REPLICATION

B. Steps

1. Open the complementary DNA strands to expose the nucleotide nitrogenous bases

Requires enzyme HELICASE (unwind) & SSB’s (to keep strands apart)

2. Prime the DNA strands

Enzyme PRIMASE – forms a very small piece of RNA called RNA primer (DNA polymerase grabs the 3’ OH end of RNA primer)


DNA REPLICATION

3. Polymerize DNA

DNA polymerize aligns appropriate nucleotides across from the template strand (must have RNA primer to use free –OH to start)

Rules:

1. NEW strands are built in 5’ to 3’ direction

2. All strands that form pairings must be in opposite direction

3. Leading strand is built continuously & needs only 1 primer

4. Lagging strand is built in segments & needs primer for each individual segment


Overall direction of replication

3

3

3

35

35

35

35

35

35

35

3 5

5

1

1

21

12

5

5

12

35

Templatestrand

RNA primer

Okazakifragment

Figure 16.15

Primase joins RNA nucleotides into a primer.

1

DNA pol III adds DNA nucleotides to the primer, forming an Okazaki fragment.

2

After reaching the next RNA primer (not shown), DNA pol III falls off.

3

After the second fragment is primed. DNA pol III adds DNAnucleotides until it reaches the first primer and falls off.

4

DNA pol 1 replaces the RNA with DNA, adding to the 3 end of fragment 2.

5

DNA ligase forms a bond between the newest DNAand the adjacent DNA of fragment 1.

6 The lagging strand in this region is nowcomplete.

7


DNA REPLICATION

4. Lagging Strand

1. Helicase opens DNA

2. SSB’s hold them apart

3. Primase lays down RNA primer

4. DNA polymerase forms new DNA strands in segments called OKAZAKI FRAGMENTS (5’ to 3’)


Parental DNA

DNA pol Ill elongatesDNA strands only in the5 3 direction.

1

Okazakifragments

DNA pol III

Templatestrand

Lagging strand3

2

Templatestrand DNA ligase

Overall direction of replication

One new strand, the leading strand,can elongate continuously 5 3 as the replication fork progresses.

2

The other new strand, thelagging strand must grow in an overall3 5 direction by addition of shortsegments, Okazaki fragments, that grow5 3 (numbered here in the orderthey were made).

3

DNA ligase joins Okazakifragments by forming a bond betweentheir free ends. This results in a continuous strand.

4

Figure 16.14

35

53

35

21

Leading strand

1

• Synthesis of leading and lagging strands during DNA replication


DNA REPLICATION

5. Fill in the gaps

a. Second DNA polymerase “chews out” the RNA primer and fills those areas with DNA

b. DNA ligase “seals” the gaps

FINAL RESULT

2 double stranded DNA molecules identical to each other & identical to their parental molecule

SEMICONSERVATIVE REPLICATION – each daughter is ½ old & ½ new


Figure 16.10 a–c

Conservativemodel. The twoparental strandsreassociate after acting astemplates fornew strands,thus restoringthe parentaldouble helix.

Semiconservativemodel. The two strands of the parental moleculeseparate, and each functionsas a templatefor synthesis ofa new, comple-mentary strand.

Dispersivemodel. Eachstrand of bothdaughter mol-ecules containsa mixture ofold and newlysynthesizedDNA.

Parent cellFirstreplication

Secondreplication

• DNA replication is semiconservative

– Each of the two new daughter molecules will have one old strand, derived from the parent molecule, and one newly made strand

(a)

(b)

(c)


Getting Started: Origins of Replication

• The replication of a DNA molecule

– Begins at special sites called origins of replication, where the two strands are separated


• A eukaryotic chromosome

– May have hundreds or even thousands of replication origins

Replication begins at specific siteswhere the two parental strandsseparate and form replicationbubbles.

The bubbles expand laterally, asDNA replication proceeds in bothdirections.

Eventually, the replicationbubbles fuse, and synthesis ofthe daughter strands iscomplete.

1

2

3

Origin of replication

Bubble

Parental (template) strand

Daughter (new) strand

Replication fork

Two daughter DNA molecules

In eukaryotes, DNA replication begins at many sites along the giantDNA molecule of each chromosome.

In this micrograph, three replicationbubbles are visible along the DNA ofa cultured Chinese hamster cell (TEM).

(b)(a)

0.25 µm

Figure 16.12 a, b


Figure 16.16

Overall direction of replication Leadingstrand

Laggingstrand

Laggingstrand

LeadingstrandOVERVIEW

Leadingstrand

Replication fork

DNA pol III

Primase

PrimerDNA pol III Lagging

strand

DNA pol I

Parental DNA

53

43

2

Origin of replication

DNA ligase

1

5

3

Helicase unwinds theparental double helix.1

Molecules of single-strand binding proteinstabilize the unwoundtemplate strands.

2 The leading strand issynthesized continuously in the5 3 direction by DNA pol III.

3

Primase begins synthesisof RNA primer for fifthOkazaki fragment.

4

DNA pol III is completing synthesis ofthe fourth fragment, when it reaches theRNA primer on the third fragment, it willdissociate, move to the replication fork,and add DNA nucleotides to the 3 endof the fifth fragment primer.

5 DNA pol I removes the primer from the 5 endof the second fragment, replacing it with DNAnucleotides that it adds one by one to the 3 endof the third fragment. The replacement of thelast RNA nucleotide with DNA leaves the sugar-phosphate backbone with a free 3 end.

6 DNA ligase bondsthe 3 end of thesecond fragment tothe 5 end of the firstfragment.

7

• A summary of DNA replication


Proofreading and Repairing DNA

• DNA polymerases proofread newly made DNA

– Replacing any incorrect nucleotides

• In mismatch repair of DNA

– Repair enzymes correct errors in base pairing


Figure 16.17

Nuclease

DNApolymerase

DNAligase

A thymine dimerdistorts the DNA molecule.1

A nuclease enzyme cutsthe damaged DNA strandat two points and thedamaged section isremoved.

2

Repair synthesis bya DNA polymerasefills in the missingnucleotides.

3

DNA ligase seals theFree end of the new DNATo the old DNA, making thestrand complete.

4

• In nucleotide excision repair

– Enzymes cut out and replace damaged stretches of DNA


Replicating the Ends of DNA Molecules

• The ends of eukaryotic chromosomal DNA

– Get shorter with each round of replication

Figure 16.18

End of parentalDNA strands

Leading strandLagging strand

Last fragment Previous fragment

RNA primer

Lagging strand

Removal of primers andreplacement with DNAwhere a 3 end is available

Primer removed butcannot be replacedwith DNA becauseno 3 end available

for DNA polymerase

Second roundof replication

New leading strand

New lagging strand 5

Further roundsof replication

Shorter and shorterdaughter molecules

5

3

5

3

5

3

5

3

3


• Eukaryotic chromosomal DNA molecules

– Have at their ends nucleotide sequences, called telomeres, that postpone the erosion of genes near the ends of DNA molecules

Figure 16.19 1 µm


• If the chromosomes of germ cells became shorter in every cell cycle

– Essential genes would eventually be missing from the gametes they produce

• An enzyme called telomerase

– Catalyzes the lengthening of telomeres in germ cells

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Review When the hydrogen...

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