Lecture 7-1 Principles of Microbial Molecular Biologymicro.sjtu.edu.cn/PDF-Microbiology/08-2 Lecture 7-1... · No. 12 Chen Feng, Shanghai Jiao Tong University How does the base sequence

1896 1920 1987 2006

Lecture 7-1

Principles of Microbial

Molecular Biology

Zhao Liping and Chen Feng

School of Life Science and Technology

Shanghai Jiao Tong University

http://micro.sjtu.edu.cn

Chapter 6 inBROCK BIOLOGY OF MICROORGANISMS

The oldest questions:

why and how can

parents transfer the

basic traits

to their children?

If babies develop from

the combination

(fertilization) of egg and

sperm cells, what are

really inside these cells

to make them become

the baby?

A tiny man in the sperm cell?

Fertilization

Chen Feng, Shanghai Jiao Tong UniversityNo. 3

Questionnaire before the class

1. Did you learn “Exon” and “Intron” before?

1) Yes; 2) Not sure; 3)No

2. Did you learn “Inverted repeat” and “Hairpin” before?


3. Did you learn “supercoiling” before?




4. Did you learn “replication fork” before?


5. Did you learn “Bidirectional Replication” and

“Replisome” before?


6. Did you learn “Sanger sequencing” before?




7. Did you learn “PCR” before?


8. Did you learn “Transcription process” before?


9. Did you learn “Translation process” before?


10) Did you learn “molecular chaperones” before?


1896 1920 1987 2006

I. Genes and Gene Experession

7.1 Macromolecules and

Genetic Information


Genes and proteins synthesis

A gene is a DNA segment specifying the sequence

of a protein (or a rRNA, tRNA)

Protein synthesis : information within DNA

molecule is used to direct the linking of different

amino acids in a specific order/ sequence.

Steps in Information Flow

Three stages:

1. Replication复制

2. Transcription转录

3. Translation翻译

Central dogma

中心法则


Prokaryotic and Eukaryotic

Genetics

Replication, transcription, and translation occur

in all organisms.

There are some differences in prokaryotes and

in eukaryotes.

Information transfer in prokaryotes 原核生物的信息传递

A single mRNA often contains more than one

coding region (polycistronic)多顺反子的

information transfer in eukaryotes. 真核生物的信息传递

Noncoding regions

(introns) are removed

from the primary mRNA

before translation. The

mRNAs of eukaryotes are

almost always

monocistronic单顺反子


How does the base sequence in DNA

determine amino acid sequence in protein?

Rosetta stone: The same message

was inscribed in three different

languages, Hieroglyphs, demotic

and Greek罗塞塔石:一段文字三种

语言

The same genetic information was

encoded in three forms

• DNA base sequence

• mRNA base sequence

• Amino acid sequence

Rosetta stone and decoding of genetic code

1896 1920 1987 2006

II. DNA STRUCTURE

7.2 DNA Structure: The

Double Helix

双螺旋


Double helix model of DNA and the two

young discovers

Watson, 25

year

old post doc

Crick, 35 year

old PhD student

The basic unit of DNA molecule: Nucleotides

Ribonucleotide in RNA.

(Deoxyribonucleotides in

DNA)

REVIEW

AGTCGTCATTAGCT

DNA strand has directions

5’ p-AGTCGTCATTAGCT-OH 3’

Structural features of

DNA molecules

one chain ends in a 5’-phosphate

group, whereas the other ends in a

3’-hydroxyl.


DNA as a double helix

Two complementary strands

• A-T, G-C coupling via hydrogen bonds

In anti-parallel directions-head to toe

• One strand is in direction of 5’P-3’OH

• The other strand is in direction of 3’OH-5’P


Double helix model of DNA

Major grooves are

sites for

interaction with

proteins


Hydrogen bonding between strands

GC pair:3 hydrogen bonds

AT pair:2 hydrogen bonds


Important numbers

One nucleotide molecular weight: 330

1 kb=kilobase pairs (one thousand basepairs)

1Mb=magabase pairs (one million basepairs)

Each base pair takes 0.34nm along the helix

Each turn takes 10 base pairs, 3.4nm long

1 kb =100 turns=0.34 mm

E. coli genome=4.6 Mb=4600kb=1564 mm=1.56mm

Sequence-specific Feature of DNA

1. Inverted repeat:

sequences that repeat in

inverse orientation.

Nearby inverted repeats

could theoretically lead

to the formation of stem-

loop (cruciform)

structures in DNA.反向

重复序列导致茎-环结

构

2. Hairpin: like a stem-loop but with almost no loop. 发夹结构

Hairpins is usually formed from a single-stranded region at the end of

a molecule that contains an inverted repeat.

1896 1920 1987 2006

5.3 DNA Structure:

Supercoiling

超螺旋结构


DNA molecules are very long

Lamda Phage

• 48.6 kb, 17 micrometer

E. coli

• 4,000 kb, 1.56 mm

Yeast

• 13,500 kb, 4.6 mm

Drosophila

• 165,000 kb, 56 mm

Human

• 2,900,000 kb, 990 mmLamda Phage





Genome sizes vary greatly ranging from viruses with the smallest

to algae and vertebrates possessing the greatest amount.

1896 1920 1987 2006

How can a very long DNA

molecule be packaged in a cell?


DNA supercoiling is the

solution超螺旋

Supercoiling is the further twisting of DNA double

helix----coiling of coils

Directions of supercoiling

• Negative-DNA is twisted about its axis in the opposite

direction from that of the right-handed double helix.

(predominantly found in nature)

• Positive-


Nucleosome introduce negative supercoils

in eukaryotes 核小体

The linear DNA is wound around

proteins called histones to form

nucleasomes. DNA围绕组蛋白而形

成核小体

Nucleosome introduces negative

supercoils. 核小体形成负超螺旋

FLASH

Animations/Lecture7_supercoiling.MOV


Supercoiling is introduced by DNA gyrase

in Bacteria and most Archaea

Topoisomerase II (DNA gyrase)-break and reseal of

double strands拓扑异构酶II (DNA促旋酶)

Topoisomerase I-break single strand, remove

supercoiling in DNA 拓扑异构酶I (DNA解旋酶)

interconversions of supercoiled circular DNA and relaxed,

nicked circular DNA.

DNA in the bacterial chromosome is arranged not in one supercoil but in several

supercoiled domains.细菌DNA可形成多个超螺旋域

E. coli chromosome contains over 50 supercoiled domains, each of which is

stabilized by specific proteins.

DNA gyrase

Introduction of supercoiling into a circular DNA by activity of

topoisomerase II, which makes double-strand breaks.


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Lecture 7-1 Principles of Microbial Molecular Biologymicro.sjtu.edu.cn/PDF-Microbiology/08-2 Lecture 7-1... · No. 12 Chen Feng, Shanghai Jiao Tong University How does the base sequence