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Chapter 2 Genes and Chromosomes
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Transcript of Chapter 2 Genes and Chromosomes
Chapter 2
Genes and Chromosomes
2.1 DNA & DNA Structure
1. Nucleoside and Nucleotide
(1) Components : pentose, base, phosphate group
Base
Pentose
In DNA or RNA, a pentose is associated with only one phosphate group, but a cellular free nucleotide (such as ATP) may contain more than one phosphate group. If all phosphate groups are removed, a nucleotide becomes a nucleoside.
Adenine (A)
Cytosine (C)
Guanine (G)
Thymine (T)
Uracil (U).
(2) Bases in DNA or RNA
Albrecht Kossel
A, C, G and T exist in DNA;
A, C, G and U exist in RNA.
condensation reaction, phosphodiester bond, DNA polymerase
2. Nucleic Acid Chain
连接反应(ligation reaction)
Synthesis of a nucleic acid chain
always proceeds from 5’ to 3’.
(1) DNA Primary Structure The primary structure of DNA is the sequence itself - the order of nucleotides in the deoxyribonucleic acid polymer.
3. DNA Structure
Why is DNA sequence important?
Question 3
(2) DNA Secondary Structure
Right-handed or left-handed
Helix Diameter
Base Inclination
Bp / helical turn
Helix pitch
Major groove
Minor groove
10 bp/turn B-form
A B Z
Handedness
Pitch
Base Inclination
Animation
(3) DNA Supercoil
4. DNA denaturation and renaturation
Denaturation: dsDNA → ssDNA
Renaturation: ssDNA → dsDNA
2.2 Gene & Genome
1. Concepts of Gene
(1) Gene = In molecular terms, it is the entire D
NA sequence including exons, introns, and nonc
oding transcription-control regions necessary f
or production of a functional protein or RNA.
exons introns
noncoding transcription-control regions
(2) Regulatory Gene
A DNA sequence or a gene that functions
to control the expression of other genes.
(3) Structural Gene
A DNA sequence or a gene that codes the
production of RNA, a specific protein or peptide.
(4) Gene Cluster
It is a group of adjacent genes that are identical
or related.
(5) Gene Family A group of related genes having similar DNA
sequence evolved from a single ancestral. These
genes make similar products and may or may not
be located in the same region of a chromosome.
Question:
What is different between gene cluster or gene
family?
2. Genome
(1) Genome Complete collection of a cell or an organism’s genetic information as linked genes in a long strand of DNA.
(2) Genomics The branch of genetics that studies organisms in terms of their genomes (their full DNA sequences).
(3) Functional genomics
The branch of genomics that determines the
biological function of the genes and their resulting
proteins, and the role played by the proteins in the
organisms’ biochemical processes.
(4) Structural genomics
The branch of genomics that determines the three-
dimensional structures of proteins.
3. Size of genome
(1) Prokaryotic cell vs Eukaryotic cell
(2) Size ↔ Evolution ?
4. Model Organisms
Bacteria (E. coli, several others) Yeast (Saccharomyces cerevisiae) Plant (Arabidopsis thaliana) Caenorhabditis elegans Fruit fly Zebrafish Mouse Human………
Question
Why do we choose these organisms as models?
Animation
2.3 Features of Genomes
1. Features of Prokaryotic Genomes
(1) Relatively small -- size, content
(2) Simple structure
(3) Transcription unit
concept…..
(4) Overlapping gene
concept…..
Now, it is also found in eukaryotic genomes…..
2. Genomes of Prokaryotes
Most of them: double-helix , circular
Small number: single strand, DNA
Scaffold: loops, supercoiled
(1) E.coli Genome
4.6 million bp 90% of genome encodes protein 4288 genes. almost no repeated DNA
λ phage genome
Regulatory genes
Replication genes – 2 genes
Lysis genes – 3 genes
Recombination genes – 10 genes
Head – 10 genes
Tail – 12 genes
(2) Phage genome
3. Features of Eukaryotic Genomes
(1) Big size, big content
(2) Repeat sequence
(3) Single cistron
(4) Gene uncontinuous (intron and exon)
(5) Pseudogene
(6) mtDNA & ctDNA
4. Genome of Eukaryotes
(1) Human Genome
nuclear genome + mitochondrial genome
Information derived from the HGP
► less than 2% of the human genome codes for proteins
► almost all (99.9%) nucleotide bases are exactly the
same in all people
► ("junk DNA") make up at least 50%
► 24% important for translation
► Repetitive elements Satellites (regular, mini-, micro-)
Transposons
Retrotransposons
Parasites
Question
Is the junk DNA real junk?
HGP Goals Now
To identify the function of the human genome
To understand how and why genes can cause diseases
To speed up the use of genetic information in biomedical research and put it to work
(2) Other Genomes of Eukaryotes
Yeast genome
Drosophila genome
C. elegans genome
Mouse genome
Arabidopsis thaliana genome genome
2.4 Nucleosome and Chromosomes
2. Nucleosome
(1) concept
~200 bp of DNA Histone contains 5 kinds : H1, H2A, H2B, H3, H4
(2) packing
1. Histones and Non-histones
(1) Packing ratio
(2) Packing levels
solenoid
chromatin fiber
chromatid
chromosome
3. DNA Coiling into a chromosome
2.5 DNA Replication
1. Semiconservative Replication
(1) Models of DNA Replication
What is semiconservative replication?
Each strand acts as a template for a new double hel
ix. The established model of DNA replication in which
each double-stranded molecule is composed of one par
ental strand and one newly polymerized strand.
Two requirements:
● DNA template
● Free 3' -OH group
(2) Replication elements
Origin, Ori
Replicon
Replication fork
Bidirection
2. The Enzymology of DNA Replication
substrate,
polymerase,
DNA template,
primer,
enzymes,
proteins
……
(1) Topoisomerase
(2) Helicase
(4) Primase
(5) DNA Polymerase III
(6) DNA polymerase I
(7) DNA ligase
3. Features of DNA Replication in Prokaryores
(1) Replication Ori in E.coli
(2) Initiation of DNA replication in E.coli
SynthesisDNA repairDNA repair
1011subunit
--+5 exdonuclease
+++ 5 exdonuclease
+++5 polymerase
pol IIIpol IIpol I
(3) DNA polymerase in E.coli
Question
What is Klenow fragment?
Animation
General Model for DNA Replication Process
(4) Semicontinuous replication
(5) Termination of Replication
Forks meet opposite originForks meet opposite origin Two termination regions Two termination regions Regions act as “traps” Regions act as “traps”
(6) Rolling Circle
Replication
(1) Multiple replicons
(2) DNA Polymerase
(3) Replication of telomere
4. Features of DNA Replication in Eukaryores
(4) Replication of mtDNA
Replicating DNA of Drosophila melanogaster
(1) Multiple replicons
(2) DNA Polymerase in Eukaryotes
Pol α: acts as a primase
Pol β: repairing DNA
Pol γ: replicates mt DNA
Pol δ: proofreading
Pol ε: proofreading
Others: η, ι, κ, θ, λ, φ, σ, μ, Rev1
Telomerase
It is an enzyme made of protein and RNA
subunits. Its role is to elongate chromosomes
by adding telomeric sequences to the end of e
xisting chromosomes.
(3) Replication of telomere
Replication of telomere
(4) mtDNA Replication
D-loop replication
mtDNA & ctDNA
Progress
Discovery of a Major D-Loop Replication Origin
Reveals Two Modes of Human mtDNA Synthesis.
Science , 2004, 306: 2098 - 2101
Schematic representation of H-strand replication initiation in human mtDNA D-loop region.
Proofreading
4. Proofreading
2.6 DNA Mutagenesis
1. Mutation types
(1) Base Substitution
(2) Frameshift
Deletion
Insertion
(3) Exon skipping
2. Mutagens
(1) Base analog
(2) Base modifier
(3) Intercalation dye
(4) Ultraviolet, ionizing radiation
3. Meanings of Mutation
2.7 DNA Repair
Errors in DNA replication
Endogenous DNA damage and mutated
Environmental insults to DNA
Why repair DNA?
Un-repaired damage leads to:
Mistakes in RNA/protein synthesis
Inherited as genetic alteration
Mutation
Death
1. Excision Repair - Dar Repair
(1) Mismatch Repair
(2) Base Excision Repair – AP Repair
(3) Nucleotide Excision Repair
3. Recombinational Repair
2. Direct Repair – Light Repair
(1) Concept (2) Involved Genes and Proteins Repressor: LexA Inducer: RecA Repair proteins: UvrABC SOS genes SOS box
4. SOS response—Error prone repair4. SOS response—Error prone repair
(3) Mechanism
ProgressPrecise temporal modulation in the response of the SO
S DNA repair network in individual bacteria.
PLoS Biol. 2005. 3:e238.
(A) 8 min and (B) 70 min after irradiation with a UV
filamentation
2.8 DNA Recombination
1. Overview
(1) Important Contributions
(2) Types of Recombination
homologous recombination
site-specific recombination
transpositional recombinatio
n
2. Homologous recombination
(1) Concept
(2) Holiday model
Nicking of two strandsNicking of two strands
Crossing over: Holliday junctionCrossing over: Holliday junction
Branch migrationBranch migration
ResolvingResolving
Isomerization and resolution of Holliday junctions
3. Site-specific
Recombination
4. Transposition and Retrotransposition
(1) Concepts
Transposition is a unique form of recombination wh
ere mobile genetic elements can virtually move from one
region to another within one chromosome or to another c
hromosome entirely.
Retrotransposon is genetic elements and mobilizes vi
a an RNA form. It is transcribed into RNA, and then rev
erse-transcribed into DNA, which is inserted at a new sit
e in the genome.
(2) Types and Features
Insertion Sequences (IS elements)
Transposon
Composite Transposons
Retrotransposon
long terminal repeat (LTR)
non-LTR retrotransposons
(3) Transposition mechanism (3) Transposition mechanism
conservative transposition
replicative transposition
retrotransposition
(4) The difference between Transposition and Retrotransposon
Summary
Concepts
Genomes of prokaryotes and eukaryotes
Genomic structure of prokaryotes and eukaryotes
DNA polymerase of prokaryotes and eukaryotes
Mechanism of DNA replication in prokaryotes and eukaryotes
Mechanism of DNA mutation, repair and recombination
Mechanism of DNA transposition and retrotransposition
Gene Genomics Excision Repair
Regulatory
Gene
Functional Genomics Directed Repair
Structural Gene Structural Genomics Recombination Repair
Gene Cluster DNA Primary Structure Error-prone Repair (SOS
response)
Gene Family DNA Secondary Structure Homologous Recombination
Genome DNA Supercoiling Site-specific Recombination
Exon & Intron Semi-conservative
Replication
Transposition
Pseudogene Semi-discontinous Replicatio
n
Transposon
C value Substitution Retrotransposon
C value paradox Mismatch Repair
Concepts