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9 week:: Molecular Biology of Bacteria (의 분자생물학)

The document summarizes key concepts about molecular biology of bacteria from Chapter 6 and 7 of the 12th edition textbook. It discusses the central dogma of DNA to RNA to protein, DNA and RNA structure, DNA replication, transcription, and translation. The functional unit of genetic information is the gene. Genetic information flows from DNA replication to transcription of DNA into RNA to translation of RNA into proteins.

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0% found this document useful (0 votes)
77 views27 pages

9 week:: Molecular Biology of Bacteria (의 분자생물학)

The document summarizes key concepts about molecular biology of bacteria from Chapter 6 and 7 of the 12th edition textbook. It discusses the central dogma of DNA to RNA to protein, DNA and RNA structure, DNA replication, transcription, and translation. The functional unit of genetic information is the gene. Genetic information flows from DNA replication to transcription of DNA into RNA to translation of RNA into proteins.

Uploaded by

MoonHoLee
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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9th week:

Chapter 6.
Molecular Biology of Bacteria
(Bacteria의 분자생물학)
Chapter 6

Chapter 7
(12th Edition)
Molecular Biology of Bacteria
(Bacteria 의 분자생물학)
Genes and Gene Expression
(유전자와 유전자 발현)
• Functional unit of genetic information is the gene 유전자, 유전정보의 기능적
단위
• Genes in cells, composed of DNA
• Three informational macromolecules in cell
– DNA, RNA, Protein
• Genetic information flow can be divided into three stages
– Replication 복제: DNA is duplicated
– Transcription: information from DNA is transferred to RNA
• mRNA (messenger RNA): encodes polypeptides
• tRNA (transfer RNA): plays role in protein synthesis
• rRNA (ribosomal RNA): plays role in protein synthesis
– Translation: information in RNA is used to build polypeptides
• Central dogma of molecular biology
– DNA to RNA to protein
Genes and Gene Expression
(유전자와 유전자 발현)
• Eukaryotes 진핵생물: each gene is transcribed individually
• Prokaryotes 원핵생물: multiple genes may be transcribed together

 Synthesis of the
Informational Macromolecules

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.1
DNA Structure (DNA 구조)
• Four nucelotides found in DNA
– Adenine (A), Guanine (G), Cytosine (C), Thymine (T)
• Backbone of DNA chain is alternating phosphates and the pentose
sugar deoxyribose
• Phosphates connect 3′- carbon of one sugar to 5 of the adjacent sugar
• All cells and some viruses have DNA in double- stranded molecule
• Two strands are antiparallel
• Two strands have complementary base sequences
– Adenine always pairs with Thymine
– Guanine always pairs with Cytosine
• Two strands form a double helix 이중나선
DNA Structure (DNA 구조)

 DNA Structure

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.4
DNA Structure (DNA 구조)
• Size of DNA molecule is expressed in base pairs
• 1,000 base pairs = 1 kilobase pairs = 1 kbp
• 1,000,000 base pairs = 1 megabase pairs = 1Mbp
• E. coli genome 유전체 = 4.64 Mbp
• Each base pair takes up 0.34 nm of length along the helix
• 10 base pairs make up 1 turn of the helix

• Inverted Repeats
– Repeated sequence that is arranged in an inverse orientation
• Stem Loops
– Short double-helical regions caused by nearby inverted repeats
– Common in RNA, but not DNA
DNA Structure (DNA 구조)
• Hydrogen bonds between DNA strands hold two strands together
• Adenine–Thymine pair has two hydrogen bonds and Guanine–
Cytosine pair has three hydrogen bonds
– GC pairs are stronger than AT pairs
• High heat breaks hydrogen bonds causing denaturation (melting)
• GC-rich DNA melts at higher temperatures than AT-rich DNA

 Thermal Denaturation of DNA

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.7
DNA Structure (DNA 구조)
• Supercoiled DNA: DNA is further twisted to save space
– Negative supercoiling: double helix is underwound
– Positive supercoiling: double helix is overwound
• Relaxed DNA: DNA has number of turns predicted by number of base
pairs
• Negative supercoiling is predominantly found in nature
• DNA Gyrase: introduces supercoils into DNA

• Genome 유전체: entire complement of genes in cell or virus


• Chromosome 염색체: main genetic element in prokaryotes
• Other genetic elements include virus genomes, plasmids, organelle
genomes, and transposable elements
DNA Structure (DNA 구조)
• Viruses contain either RNA or DNA genomes
– Can be linear or circular
– Can be single or double stranded
• Plasmids: replicate separately from chromosome
– Great majority are double stranded
– Most are circular
– Generally beneficial for the cell (i.e., antibiotic resistance)

• Chromosome is a genetic element with “housekeeping” genes


• Plasmid is a genetic element that is expendable and rarely contains
genes for growth under all conditions
• Presence of essential genes is necessary for a genetic element to be
called a chromosome
DNA Structure (DNA 구조)
• Transposable Elements
– Segment of DNA that can move from one site to another site on the same or
different DNA molecule
– Inserted into other DNA molecules
• Three main types
– Insertion sequences
– Transposons
– Special viruses
DNA Replication (DNA 복제)
• DNA replication is semiconservative 반보전적 복제
– Each of the two progeny double helices have one parental and one new
strand
• Precursor of each nucleotide is a deoxynucleoside 5′ triphosphate
(dNTP)
• Replication ALWAYS proceeds from the 5′ end to the 3′ end
• DNA polymerases catalyze the addition of dNTPs
• Five different DNA polymerases in E. coli
– DNA polymerase III is primary enzyme replicating chromosomal DNA
• DNA polymerases require a primer
– Primer made from RNA
DNA Replication (DNA 복제)
Overview of DNA Replication

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.10
DNA Replication (DNA 복제)
• DNA synthesis begins at the origin of replication in prokaryotes
• Replication fork: zone of unwound DNA where replication occurs
• DNA helicase unwinds the DNA
• Extension of DNA
– Occurs continuously on the leading strand
– Discontinuously on the lagging strand
• Okazaki fragments are on lagging strand
DNA Replication (DNA 복제)
Events at the DNA Replication Fork

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.13
DNA Replication (DNA 복제)
Sealing Two Fragments on the Lagging Strand

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.15
DNA Replication (DNA 복제)
• DNA synthesis is bidirectional in prokaryotes
– Two replication forks moving in opposite directions
• DNA Pol III adds 1,000 nucleotides per second
• Replisome complex of multiple proteins involved in replication
– DNA pulled through the replisome
DNA Replication (DNA 복제)
Replication of Circular DNA: The Theta Structure

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.16
DNA Replication (DNA 복제)
The Replisome

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.19
DNA Replication (DNA 복제)
• DNA replication is extremely accurate
– Proofreading helps to ensure high fidelity
• Mutation rates in cells are 10-8–10-11 errors per base inserted
• Polymerase can detect mismatch through incorrect hydrogen
bonding
• Proofreading occurs in prokaryotes, eukaryotes and viral DNA
replication systems
RNA Synthesis: Transcription (전사)
• Transcription (DNA to RNA) is carried out by RNA polymerase
• RNA polymerase uses DNA as template
• RNA precursors are ATP, GTP, CTP, and UTP
• Chain growth is 5′ to 3′ just like DNA replication
• Only one of the two strands of DNA are transcribed by RNA
polymerase for any gene
• Genes are present on both strands of DNA, but at different locations
• RNA polymerase has five different subunits
• RNA polymerase recognizes DNA sites called promoters
• Promoters: site of initiation of transcription
• Promoters are recognized by sigma factor of RNA polymerase
• Transcription stops at specific sites called transcription terminators
• Unlike DNA replication, transcription involves smaller units of DNA
RNA Synthesis: Transcription (전사)
• Sigma factors recognize two highly conserved regions of promoter
• Two regions within promoters are highly conserved
– Pribnow box: located 10 bases before the start of transcription (-10 region)
– -35 region: located ~35 bases upstream of transcription
• Termination of RNA synthesis is governed by a specific DNA
sequence
– Intrinsic terminators: transcription is terminated without any additional factors
– Rho-dependant termination: Rho protein recognizes specific DNA sequences
and causes a pause in the RNA polymerase
• Unit of transcription: unit of chromosome bounded by sites where
transcription of DNA to RNA is initiated and terminated
• Most genes encode proteins, but some RNAs are not translated (i.e.,
rRNA, tRNA)
RNA Synthesis: Transcription (전사)

Transcription: Steps in RNA


Synthesis

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.21
RNA Synthesis: Transcription (전사)
The Interaction of RNA Polymerase with the Promoter

Source: Brock Biology of Microorganisms 12th edition.


Figure 7.22
Protein Synthesis: Translation (번역)
• Translation: the synthesis of proteins from RNA
• Genetic code: a triplet of nucleic acid bases (codon) encodes a single
amino acid
– Specific codons for starting and stopping translation
– Degenerate code: multiple codons encode a single amino acid
– Anti-codon on tRNA recognizes codon
– Wobble: irregular base pairing allowed at third position of tRNA
• Stop codons: signal the termination of translation (UAA, UAG, and
UGA)
• Start Codon: translation begins with AUG
• Reading frame: triplet code requires translation to begin at the correct
nucleotide
• Shine-Dalgarno sequence: ensures proper reading frame
• Open Reading Frame (ORF): AUG followed by a number of codons
and a stop codon in the same reading frame
Protein Synthesis: Translation (번역)
• Codon bias: multiple codons for the same amino acid are not used
equally
– Varies with organism
– Correlated with tRNA availability
– Cloned genes from one organism may not be translated by recipient organism
because of codon bias
• Some organelles and a few cells have slight variations of the genetic
code (i.e., mitochondria of animals)
• Transfer RNA: at least one tRNA per amino acid
– Bacterial cells have 60 different tRNAs
– Mammalian cells have 100–110 different tRNAs
• Specific for both a codon and its cognate amino acid
• tRNA and amino acid brought together by aminoacyl-tRNA
synthetases
– ATP is required to attach amino acid to tRNA
• tRNA is cloverleaf in shape
Protein Synthesis: Translation (번역)
• Anti-codon: three bases of tRNA that recognize three complementary
bases on mRNA
• Fidelity of recognition process between tRNA and aminoacyl-tRNA
synthetase is critical
– Incorrect amino acid could result in a faulty/non-functioning protein
• Ribosomes: sites of protein synthesis
– Thousands of ribosomes per cell
– Composed of two subunits (30S and 50S in prokaryotes)
– S = Svedberg units
– Combination of rRNA and protein
• E. coli has 52 distinct ribosomal proteins

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