23/4/18

Li Xiaoling

Office: M1623

QQ: 313320773

E-MAIL: 313320773 @qq.com

ContentChapter 1 Introduction

Chapter 2 The Structures of DNA and RNA

Chapter 10 Regulation in Eukaryotes

Chapter 4 DNA Mutation and Repair

Chapter 5 RNA Transcription

Chapter 6 RNA Splicing

Chapter 7 Translation

Chapter 8 The Genetic code

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Chapter 9 Regulation in prokaryotes

Chapter 3 DNA Replication

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To learn effectively

To preview and reviewProblem-base learningMaking use of class time effectively

Active participationBi-directional question in classGroup discussionConcept map

Tutorship To call for reading, thingking and discussing of investigative

learning

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Question in-class and attendance : 10 pointsGroup study and attendance: 20 pointsFinal exam: 70 pointsBonus

The Structures of DNA and RNA The Structures of DNA and RNA

How do the structures of DNA and RNA account for their functions?

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OUTLINE

1.DNA Structure

2.DNA Topology

3.RNA Structure

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DNA STRUCTURE

1.1. The building blocks and The building blocks and base pairing.base pairing.

2.2. The structure: The structure: two two polynucleotide chains are polynucleotide chains are twisting around each twisting around each other in the form ofother in the form of a a double helixdouble helix.. 23/4/18

DNA building DNA building blocksblocks

Base Base

Nucleoside Nucleoside

Nucleotide Nucleotide is the is the fundamental building fundamental building block of DNA.block of DNA.

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Purines

pyrimidines

Adenine (A)

Guanine (G)

Cytosine (C)

Thymine (T)

N9

N1

Bases in DNABases in DNABases in DNABases in DNA

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Each bases has its preferred Each bases has its preferred tautomeric form tautomeric form (Related to (Related to Ch 9)Ch 9)

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The strictness of the rules for “Waston-Crick” pairing derives from the complementarity both of shape and of hydrogen bonding properties between adenine and thymine and between guanine and cytosine.

““Waston-Crick” Waston-Crick” pairingpairing

Maximal hydrogen bonding

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A:C incompatibility

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glycosidic bond

phosphoester bond

NucleosideNucleosides Nucleosides & &

NucleotidesNucleotides

Nucleosides Nucleosides & &

NucleotidesNucleotides

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3’

5’

Asymmetric

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A DNA molecule is A DNA molecule is composed of two composed of two

antiparallel antiparallel polynucleotide chains polynucleotide chains

A DNA molecule is A DNA molecule is composed of two composed of two

antiparallel antiparallel polynucleotide chains polynucleotide chains

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DNA polarity: DNA polarity: is defined by the asymmetry of the nucleotides and the way they are joined.

Phosphodiester linkagesPhosphodiester linkages: repeating, sugar-phosphate backbone of the polynucleotide chain

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The two strands are held together by base pairing in an antiparallelantiparallel orientation: a stereochemical ( 立立立立立 ) consequence of the way that A-T and G-C pair with each other. (Related to replication and transcription)

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DNA structureDNA structure

two antiparallel two antiparallel polynucleotide chains are polynucleotide chains are twisting around each twisting around each other in the form ofother in the form of a a double helixdouble helix..

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1. The Two Chains of the Double 1. The Two Chains of the Double Helix Have Complementary Helix Have Complementary SequencesSequences

1. The Two Chains of the Double 1. The Two Chains of the Double Helix Have Complementary Helix Have Complementary SequencesSequences

Example: If sequence 5’-ATGTC-3’ on one chain, the opposite chain MUST have the complementary sequence 3’-TACAG-5’

Watson-Crick Base Pairing

(Related to replication and transcription)

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2. Hydrogen Bonding 2. Hydrogen Bonding determines the Specificity of determines the Specificity of Base Pairing, while stacking Base Pairing, while stacking interaction determines the interaction determines the stability a helix.stability a helix.

2. Hydrogen Bonding 2. Hydrogen Bonding determines the Specificity of determines the Specificity of Base Pairing, while stacking Base Pairing, while stacking interaction determines the interaction determines the stability a helix.stability a helix.

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Hydrogen bonding also contribute to the thermodynamic stability of the helix (?)

Stacking interactions () between bases significantly contribute to the stability of DNA double helix

H2O molecules lined up on the bases are displaced by base-base interactions, which creates disorder/hydrophobicity.

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3. Two different models 3. Two different models illustrate structure a DNA illustrate structure a DNA double helix.double helix.

3. Two different models 3. Two different models illustrate structure a DNA illustrate structure a DNA double helix.double helix.Schematic

modelSpace-filling model

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4. DNA is usually a right-handed 4. DNA is usually a right-handed double helix. double helix. 4. DNA is usually a right-handed 4. DNA is usually a right-handed double helix. double helix.

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(See the Structural Tutorial of this chapter for details)

It is a simple consequence of the geometry of the base pair.

5. The double helix has Minor 5. The double helix has Minor and Major grooves (What & and Major grooves (What & Why)Why)

5. The double helix has Minor 5. The double helix has Minor and Major grooves (What & and Major grooves (What & Why)Why)

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The Major groove is rich in chemical information

(What are the biological relevance?)

The edges of each base pair are exposed in the major and minor grooves, creating a pattern of hydrogen bond donors and acceptors and of van der Waals surfaces that identifies the base pair.

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A: H-bond acceptors D: H-bond donors

H: non-polar hydrogens M: methyl groups23/4/18

The B form (10 bp/turn), which is observed at high humidity, most closely corresponds to the average structure of DNA under physiological conditions

A form (11 bp/turn), which is observed under the condition of low humidity, presents in certain DNA/protein complexes. RNA double helix adopts a similar conformation.

6. The double helix exists in 6. The double helix exists in multiple conformations.multiple conformations.6. The double helix exists in 6. The double helix exists in multiple conformations.multiple conformations.

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DNA strands can DNA strands can separate and separate and reassociatereassociate

DN

A S

TR

UC

TU

RE (3

)

Key terms to understand1. Denaturation ( 立立 )2. Hybridization ( 立立 )

3. Annealing/renature ( 立立 )4. Absorbance ( 立立立 )

5. Hyperchromicity ( 立立立 )6. Tm (melting point) ( 立立 )

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DNA TOPOLOGY

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DN

A T

OP

OLO

GY

(1)

Structure (1): Linking number is Structure (1): Linking number is an invariant topological property an invariant topological property of covalently closed, circular DNA of covalently closed, circular DNA (cccDNA)(cccDNA)

Linking number is the number of times one strand have to be passed through the other strand in order for the two strands to be entirely separated from each other.

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Species of cccDNA1. Plasmid and circular bacterial

chromosomes 2. Linear DNA molecules of

eukaryotic chromosomes due to their extreme length, entrainment ( 立立 ) in chromatin and interaction with other cellular components (Ch 7)

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Structure (2): Linking Structure (2): Linking number is composed of number is composed of Twist and WritheTwist and WritheThe linking number is the sum of the twist and the writhe.

Twist is the number of times one strand completely wraps around the other strand.

Writhe is the number of times that the long axis of the double helical DNA crosses over itself in 3-D space.

DN

A T

OP

OLO

GY

(2)

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Local disruption of base pairs

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Function (1): DNA in cells is Function (1): DNA in cells is negatively supercoiled; negatively supercoiled; nucleosomes introduces negative nucleosomes introduces negative supercoiling in eukaryotessupercoiling in eukaryotes

Negative supercoils serve as a store of free energy that aids in processes requiring strand separation, such as DNA replication and transcription. Strand separation can be accomplished more easily in negatively supercoiled DNA than in relaxed DNA.

DN

A T

OP

OLO

GY

(3)

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Function (2): Function (2): Topoisomerases (P115-119) Topoisomerases (P115-119)

1. The biological importance of topoisomerase?

2. The functional difference of the two types of topoisomerases?

3. The working mechanism of topoisomerase (See the animation for detail)

DN

A T

OP

OLO

GY

(4)

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RNA STRUCTURE

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Biological roles of Biological roles of RNARNA

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1. RNA is the genetic material of some viruses2. RNA functions as the intermediate (mRNA)

between the gene and the protein-synthesizing machinery.

3. RNA functions as an adaptor (tRNA) between the codons in the mRNA and amino acids.

4. Through sequence complementarity, RNA serves as a regulatory molecule to bind to and interfere with the translation of certain mRNAs; or as a recognition molecule to guide many post-transcriptional processing steps.

5. Through the tertiary structures, some RNAs function as enzymes to catalyze essential reactions in the cell (RNase P ribozyme, large rRNA in ribosomes, self-splicing introns, etc).

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Structures of Structures of RNARNA

1.Primary structure

2.Sequence complementarity: base pairing as DNA

3.Secondary structure

4. Tertiary structure

1.Primary structure

2.Sequence complementarity: base pairing as DNA

3.Secondary structure

4. Tertiary structure23/4/18

RN

A S

TR

UC

TU

RE

RNA contains ribose and uracil and is usually single-stranded

1.Primary structure1.Primary structure

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RN

A S

TR

UC

TU

RE (1

)

Watson-Crick base pairing

U A-U

G-C

2.Sequence complementarity: inter- and intra-molecular base pairing

2.Sequence complementarity: inter- and intra-molecular base pairing

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3.Secondary structures and interactions

3.Secondary structures and interactions

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RNA chains fold back on RNA chains fold back on themselves to form local regions themselves to form local regions of double helix similar to A-form of double helix similar to A-form DNADNA

RN

A S

TR

UC

TU

RE (2

)

hairpin

bulge

loop

RNA helix are the base-paired segments between short stretches of complementary sequences, which adopt one of the various stem-loop structures

2nd structure elements

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Some tetraloop sequence can Some tetraloop sequence can enhance the stability of the RNA enhance the stability of the RNA helical structures helical structures For example, UUCG loop is unexpectedly

stable due to the special base-stacking in the loop

1

2

3

4

Special interactions

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Pseudoknots are complex secondary Pseudoknots are complex secondary structure resulted from base pairing structure resulted from base pairing of discontiguous RNA segmentsof discontiguous RNA segments

Figure 6-32 Pseudoknot.

Structurally special base-pairing

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Non-Watson-Crick G:U base pairs Non-Watson-Crick G:U base pairs represent additional regular base represent additional regular base pairing in RNA, which enriched the pairing in RNA, which enriched the capacity for self-complementarity.capacity for self-complementarity.

Figure 6-33 G:U base pair

Chemically special base-pairing

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The double helical structure of RNA resembles the A-form structure of DNA.

The minor groove is wide and shallow, but offers little sequence-specific information. The major groove is so narrow and deep that it is not very accessible to amino acid side chains from interacting proteins. Thus RNA structure is less well suited for sequence-specific interactions with proteins.

The minor groove is wide and shallow, but offers little sequence-specific information. The major groove is so narrow and deep that it is not very accessible to amino acid side chains from interacting proteins. Thus RNA structure is less well suited for sequence-specific interactions with proteins.

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RN

A S

TR

UC

TU

RE

RNA has enormous rotational freedom in the backbone of its non-base-paired regions.

Why?

4. RNA can fold up into complex tertiary structures

4. RNA can fold up into complex tertiary structures

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The structure of the hammerhead ribozyme 23/4/18

Interactions in the tertiary structure

Unconventional base pairing, such as base triples, base-backbone interactions

Proteins can assist the formation of tertiary structures by large RNA molecule

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The crystal structure of a 23S ribosme 23/4/18

Some RNAs with tertiary structures can catalyze

RN

A S

TR

UC

TU

RE (4

)

Ribozymes are RNA molecules that adopt complex tertiary structure and serve as biological catalysts.RNase P and self-splicing introns are ribozymes

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Structure & Function: The hammerhead ribozyme cleaves RNA by formation of a 2’,3’ cyclic phosphate

RN

A S

TR

UC

TU

RE (5

) See animation for detail

C1

7

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Key points for Chapter 61. DNA structure

• Building blocks and base pairing• Double helical structure • Application of the property of strand separation and

association in DNA techniquesCritical thinking: how DNA structure influence the

processes of genome maintenance and expression? [You are encouraged to take this question and find out the answers when we discuss the related contents]

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2. DNA topology• The biological relevance of cccDNA• Linking number, twist and writhe: how these

topological features are changed during DNA replication [answer the question after the related lecture].

• Topoisomerases 3. RNA structure

Composition, structure (2nd and tertiary) and functions (differences from DNA)

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