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A. An overview of molecular biology. Read Human Molecular Genetic Ch. 1 A.1. Background A.2. Macromolecules A.3. DNA structure A.4. RNA transcription and Gene Expression A.5. RNA processing A.5.1. Splicing A.5.2. RNA Capping

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a an overview of molecular biology
A. An overview of molecular biology

Read Human Molecular Genetic Ch. 1

A.1. Background

A.2. Macromolecules

A.3. DNA structure

A.4. RNA transcription and Gene Expression

A.5. RNA processing

A.5.1. Splicing

A.5.2. RNA Capping

A.6. Translation, post-translation processing and protein structure

A.6.1. Translaion

A.6.2. Protein Folding

A.7. Summary

CS 6463: An overview of Molecular Biology

slide2
A.1 Background: Procaryotic and Eukaryotic Cells
  • Two types of cells:
  • Prokaryotic (bacteria: E. Coli)
  • Eukaryotic (multicellular organisms,
  • Ameba, Yeast)

CS 6463: An overview of Molecular Biology

a 1 1 3 domains in the living world

A.1.1 3 Domains in the Living World

CS 6463: An overview of Molecular Biology

a 1 2 bacteria archaea and eucaryotes

A.1.2 Bacteria, Archaea and Eucaryotes.

The bacterium: Vibrio Cholerae

A lithotrophic Bacterium (Archaea)

Eucaryotic Cell

CS 6463: An overview of Molecular Biology

slide5
A.1.3. Eukaryotic Cells

http://www-class.unl.edu/bios201a/spring97/group6/

CS 6463: An overview of Molecular Biology

a an overview of molecular biology6
A. An overview of molecular biology

Read Human Molecular Genetic Ch. 1

A.1. Background

A.2. Macromolecules

A.3. DNA structure

A.4. RNA transcription and Gene Expression

A.5. RNA processing

A.5.1. Splicing

A.5.2. RNA Capping

A.6. Translation, post-translation processing and protein structure

A.6.1. Translaion

A.6.2. Protein Folding

A.7. Summary

CS 6463: An overview of Molecular Biology

a 2 building blocks chemical composition of eukaryotic cell
A.2. Building Blocks: Chemical Composition of Eukaryotic Cell
  • Water [E. Coli: 70%, Mammalian Cell: 70%]
  • Macro-molecules:
    • DNA: Deoxyribonucleic Acid [E. Coli: 1%, Mammal: 0.25%]
    • RNA: Ribonucleic Acid [E. Coli: 6%, Mammal: 1.1%]
    • Proteins [E. Coli: 15%, Mammal: 18%]
  • Inorganic ions: Na+, K+, Mg+, Ca2+, Cl- [E. Coli: 1%, Mammal: 1%]
  • Lipids:
    • Phospholipids [E. Coli: 2%, Mammal: 3%]
    • Other lipids [E. Coli: -, Mammal: 0.2%]
  • Polysaccahrides [E. Coli: 1%, Mammal: 0.25%]
  • Volume: [E. Coli: 2 x 10-12cm, Mammal: 4 x 10-9cm]
  • Relative Volume: [E. Coli: Mammal = 1: 2000]

CS 6463: An overview of Molecular Biology

a 2 building blocks structure of bases nucleosides and nucleotides
A.2 Building Blocks: Structure of bases, nucleosides and nucleotides

Purines:

DNA: ‘polymer of A, G, T, C’

RNA: ‘polymer of A, G, U (replace T), C’

Pyrimidines:

base

sugar

CS 6463: An overview of Molecular Biology

a 2 building blocks common bases found in nucleic acids
A.2. Building Blocks: Common bases found in nucleic acids

CS 6463: An overview of Molecular Biology

a 2 building blocks 20 amino acids
A.2 Building Blocks: 20 amino acids

Polypeptides: chains of amino acids

Carboxyl group

Amino group

CS 6463: An overview of Molecular Biology

a 2 building blocks abbreviation of amino acids
A.2. Building Blocks: Abbreviation of Amino Acids

CS 6463: An overview of Molecular Biology

a 2 building blocks properties of amino acids i
A.2. Building blocks: Properties of Amino Acids I

http://www.russell.embl-heidelberg.de/aas/aas.html

CS 6463: An overview of Molecular Biology

a 2 building blocks some terms for describing properties of amino acids
A.2. Building blocks: Some Terms for describing Properties of Amino Acids
  • Hydrophobic amino acids are those with side-chains that do not like to reside in an aqueous (i.e. water) environment.
  • Polar amino acids are those with side-chains that prefer to reside in an aqueous (i.e. water) environment.
  • Strictly speaking, aliphatic implies that the protein side chain contains only carbon or hydrogen atoms.
  • A side chain is aromatic when it contains an aromatic ring system.

CS 6463: An overview of Molecular Biology

a 2 building blocks covalent and non covalent bonds
A.2 Building Blocks: Covalent and Non-covalent Bonds
  • Covalent bonds: stronger. Nucleic acid and protein polymers are from by covalent binds connecting nucleotides and amino acids (respectively) to form a linear backbone
  • Non-covalent bonds: weaker and revisible. 4 types:
    • Hydrogen bonds: N – H –O [double-stranded DNA, protein folding, …etc
    • Ionic bonds: Ionic interaction between charged group, sat Na+ and Cl-
    • Van der Waals: Optimum attraction between two atoms.
    • Hydrophobic forces: Water is polar molecules,

CS 6463: An overview of Molecular Biology

a an overview of molecular biology15
A. An overview of molecular biology

Read Human Molecular Genetic Ch. 1

A.1. Background

A.2. Macromolecules

A.3. DNA structure

A.4. RNA transcription and Gene Expression

A.5. RNA processing

A.5.1. Splicing

A.5.2. RNA Capping

A.6. Translation, post-translation processing and protein structure

A.6.1. Translaion

A.6.2. Protein Folding

A.7. Summary

CS 6463: An overview of Molecular Biology

a 3 dna structure the phosphodiester bond
A.3 DNA Structure: The Phosphodiester Bond

CS 6463: An overview of Molecular Biology

a 3 dna structure base pairing watson crick rule
A.3 DNA Structure: base pairing (Watson-Crick Rule).

CS 6463: An overview of Molecular Biology

a 3 dna structure dna is a double stranded anti parallel helix
A.3 DNA Structure: DNA is a double-stranded anti-parallel helix
  • %GC = 40%? How many % is G? C? A? T?

Complementary

DNA

(cDNA)

downstream

upstream

http://www.sumanasinc.com/webcontent/anisamples/molecularbiology/DNA_structure.html

CS 6463: An overview of Molecular Biology

a 3 dna structure dna is a double stranded anti parallel helix19
A.3 DNA Structure: DNA is a double-stranded anti-parallel helix

CS 6463: An overview of Molecular Biology

a 3 dna structure chromatin
A.3 DNA Structure:Chromatin

Histone

nucleosome

CS 6463: An overview of Molecular Biology

a 3 dna structure comparing human and mouse genome

A.3. DNA Structure: Comparing Human and Mouse Genome

mouse

Human

CS 6463: An overview of Molecular Biology

a 3 dna structure human chromosomes
A.3. DNA Structure: Human Chromosomes
  • 23 pairs of chromosomes.
  • Chromosome 1-22, both parent contribute one strand each.
  • Sex – XY (male) and female XX. Mother contribute X and father contribute either X or Y (determine sex).
  • Mitochondria DNA is inherited from the mother only.

CS 6463: An overview of Molecular Biology

a 3 dna structure rna structure
A.3 DNA Structure: RNA structure

palindrome

CS 6463: An overview of Molecular Biology

a 3 dna structure viral genomes
A.3 DNA Structure: Viral Genomes
  • Highly Variable:
    • DNA or RNA
    • Single stranded or double stranded
    • Linear or Circular
    • Segmented and Multipartite
  • Virus normally replicate in the cytosol. Unusal Retrovirus duplicate itself in the nucleus (using reverse transcriptase)

CS 6463: An overview of Molecular Biology

a 3 dna structure the central dogma
A.3 DNA Structure: The Central Dogma

Old 1-directional model

CS 6463: An overview of Molecular Biology

a 3 dna structure gene expression efficiency
A.3 DNA Structure: Gene Expression Efficiency

Microarray measurement of gene expression is limited.

CS 6463: An overview of Molecular Biology

a an overview of molecular biology27
A. An overview of molecular biology

Read Human Molecular Genetic Ch. 1

A.1. Background

A.2. Macromolecules

A.3. DNA structure

A.4. RNA transcription and Gene Expression

A.5. RNA processing

A.5.1. Splicing

A.5.2. RNA Capping

A.6. Translation, post-translation processing and protein structure

A.6.1. Translaion

A.6.2. Protein Folding

A.7. Summary

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression tanscription
A.4. Transcription and Gene Expression: Tanscription

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression gene regulation
A.4 Transcription and Gene Expression:Gene Regulation

G

C

G

A G T C

U C A G

http://henge.bio.miami.edu/mallery/movies/transcription.mov

http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression rna polymerase
A.4 Transcription and Gene Expression:RNA Polymerase
  • There are three classes of RNA Polymerases:
    • Polymerase I: Localized in the nucleolus. Transcribe rRNA (ribosome RNA) 28S, 18S 5.8S rRNA.
    • Polymerase II: All protein-coding genes most smRNAs. Unique in capping and polyadenylation.
    • Polymerase III: tRNA, other rRNAs, snRNAs. [The promoter can be downstream]
  • Pusedo-genes (gene fragments): Previously were genes
  • Only 2% of the human genome encode proteins.

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression dna protein binding
A.4 Transcription and Gene Expression: DNA-Protein Binding

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression trans and cis elements
A.4 Transcription and Gene Expression: Trans- and cis-elements

Important: If pattern is there, does not necessary mean it is a cis-element.

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression promoters
A.4 Transcription and Gene Expression: Promoters

Start from 1 not 0

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression polymerase ii promoter
A.4 Transcription and Gene Expression: Polymerase II & Promoter

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression transcription under the electron microscope
A.4 Transcription and Gene Expression: : Transcription under the Electron Microscope

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression transcription in bacterial
A.4 Transcription and Gene Expression: Transcription in Bacterial

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression enhancers and silencers transcription factors
A.4 Transcription and Gene Expression: Enhancers and Silencers (Transcription Factors)

Many basepairs

away

CS 6463: An overview of Molecular Biology

a 4 transcription and gene expression tissue specific genes
A.4 Transcription and Gene Expression: Tissue Specific Genes
  • House keeping genes: Genes encoding histone protein, ribosome protein. Always on.
  • Tissue or development-specific (non-housekeeping) genes:
    • Transcriptional inactive chromatin
    • Methylation of Cytosine, replacing a hydrogen (H) with methyl (CH3)
    • Transcription factors’ expression levels are low.
  • Microarrays measure the expression levels of genes

CS 6463: An overview of Molecular Biology

a an overview of molecular biology39
A. An overview of molecular biology

Read Human Molecular Genetic Ch. 1

A.1. Background

A.2. Macromolecules

A.3. DNA structure

A.4. RNA transcription and Gene Expression

A.5. RNA processing

A.5.1. Splicing

A.5.2. RNA Capping

A.6. Translation, post-translation processing and protein structure

A.6.1. Translaion

A.6.2. Protein Folding

A.7. Summary

CS 6463: An overview of Molecular Biology

a 5 rna processing rna splicing
A.5 RNA Processing: RNA Splicing

acceptor

donor

GT-AG spliceosome

AT-AC spliceosome (rare)

CS 6463: An overview of Molecular Biology

a 5 1 splicing
A.5.1 Splicing

intron

intron

exon

exon

exon

Pre-mRNA

5’ UTR

start

stop

3’ UTR

poly A

(complementary nucleotides)

(2nd key, May not be there)

(1st key)

intron

intron

exon

exon

exon

promoter

5’ UTR

start

stop

3’ UTR

TFBS

TFBS

5’

3’

(almost always there)

(mostly for non-housing gene)

cap

exon

exon

exon

5’ UTR

start

stop

3’ UTR

poly A

Massager RNA (mRNA)

pore

Nuclear membrane

Splicing the introns: http://www.sumanasinc.com/webcontent/anisamples/molecularbiology/mRNAsplicing.html

CS 6463: An overview of Molecular Biology

a 5 1 splicing consensus sequences at splice donor acceptor and branch sites
A.5.1 Splicing: Consensus Sequences at splice donor, acceptor and branch sites

CS 6463: An overview of Molecular Biology

a 5 1 splicing rna splicing
A.5.1 Splicing : RNA Splicing

CS 6463: An overview of Molecular Biology

a 5 1 splicing mechanism of rna splicing gu ag introns
A.5.1 Splicing : Mechanism of RNA Splicing (GU-AG introns)

Splicesome

(5 snRNA)

http://www.nature.com/nrn/journal/v2/n1/animation/nrn0101_043a_swf_MEDIA1.html

CS 6463: An overview of Molecular Biology

a 5 1 splicing short exons
A.5.1 Splicing : Short Exons

Exon length does not vary as much as intron length, therefore splicing control is probably done on the exon.

CS 6463: An overview of Molecular Biology

a 5 1 splicing alternative splicing
A.5.1 Splicing : Alternative Splicing

CS 6463: An overview of Molecular Biology

a 5 1 splicing isoforms
A.5.1 Splicing : Isoforms

CS 6463: An overview of Molecular Biology

a an overview of molecular biology48
A. An overview of molecular biology

Read Human Molecular Genetic Ch. 1

A.1. Background

A.2. Macromolecules

A.3. DNA structure

A.4. RNA transcription and Gene Expression

A.5. RNA processing

A.5.1. Splicing

A.5.2. RNA Capping

A.6. Translation, post-translation processing and protein structure

A.6.1. Translation

A.6.2. Protein Folding

A.7. Summary

CS 6463: An overview of Molecular Biology

a 5 2 rna capping 5 end capping
A.5.2 RNA Capping: 5’ End Capping

CS 6463: An overview of Molecular Biology

a 5 2 rna capping eucaryotic and procaryotic mrnas
A.5.2 RNA Capping: Eucaryotic and Procaryotic mRNAs

CS 6463: An overview of Molecular Biology

a 5 2 rna capping 3 end polyadenylated
A.5.2 RNA Capping: 3’ end polyadenylated.

CS 6463: An overview of Molecular Biology

a 5 2 rna capping functions of 5 end cap and poly a tail
A.5.2 RNA Capping: Functions of 5’ End Cap and Poly A tail
  • Functions of 5’ end cap
  • Prevent mRNA molecules degradation.
  • Facilitate transport to cytoplasm
  • RNA splicing
  • Facilitate translation
  • Function of 3’ end poly(A) tail
  • 1. Facilitate transport to cytoplasm
  • 2. Stabilize the mRNA in the cytoplasm
  • 3. Facilitate translation

CS 6463: An overview of Molecular Biology

a 5 2 rna capping example of the human b globin gene
A.5.2 RNA Capping: Example of the human b-globin gene

CS 6463: An overview of Molecular Biology

a 5 2 rna capping export out of the nuclear
A.5.2 RNA Capping: Export out of the nuclear

CS 6463: An overview of Molecular Biology

a an overview of molecular biology55
A. An overview of molecular biology

Read Human Molecular Genetic Ch. 1

A.1. Background

A.2. Macromolecules

A.3. DNA structure

A.4. RNA transcription and Gene Expression

A.5. RNA processing

A.5.1. Splicing

A.5.2. RNA Capping

A.6. Translation, post-translation processing and protein structure

A.6.1. Translaion

A.6.2. Protein Folding

A.7. Summary

CS 6463: An overview of Molecular Biology

a 6 1 translation the codon anticodon recognition
A.6.1 Translation: The Codon-anticodon Recognition

tRNA

(almost always)

http://henge.bio.miami.edu/mallery/movies/translation.mov

CS 6463: An overview of Molecular Biology

a 6 1 translation wobbing effect
A.6.1 Translation: Wobbing Effect

CS 6463: An overview of Molecular Biology

a 6 1 translation translating a mrna molecule
A.6.1 Translation: Translating a mRNA molecule

CS 6463: An overview of Molecular Biology

a 6 1 translation peptide bond formation
A.6.1 Translation: Peptide Bond Formation

CS 6463: An overview of Molecular Biology

a 6 1 translation the genetic codes
A.6.1 Translation: The Genetic Codes

C-terminal

N-terminal

CS 6463: An overview of Molecular Biology

a 6 1 translation t rna
A.6.1 Translation:t-RNA

CS 6463: An overview of Molecular Biology

a 6 1 translation the genetic codes62
A.6.1 Translation: The Genetic Codes

- mitochondrial

wobble

64 possible codons: 1 Start codon AUG. 3 stop codons, 20 amino acids

Signal in mRNAs can lead to alternative interpretation of stop codons:

UGA  21st AA selencocysteine, UAG 22nd AA pyrrolysine.

CS 6463: An overview of Molecular Biology

a 6 1 translation post translational processing translating a mrna molecule
A.6.1 Translation: Post-Translational Processing: Translating a mRNA molecule

CS 6463: An overview of Molecular Biology

a 6 1 translation polyribosome
A.6.1 Translation:Polyribosome

CS 6463: An overview of Molecular Biology

a an overview of molecular biology65
A. An overview of molecular biology

Read Human Molecular Genetic Ch. 1

A.1. Background

A.2. Macromolecules

A.3. DNA structure

A.4. RNA transcription and Gene Expression

A.5. RNA processing

A.5.1. Splicing

A.5.2. RNA Capping

A.6. Translation, post-translation processing and protein structure

A.6.1. Translaion

A.6.2. Protein Folding

A.7. Summary

CS 6463: An overview of Molecular Biology

a 6 2 protein folding protein secondary structure
A.6.2 Protein Folding: Protein Secondary Structure

CS 6463: An overview of Molecular Biology

a 6 2 protein folding quaternary
A.6.2 Protein Folding: Quaternary

Amino acid sequence  secondary structure  tertiary structure

Amino acid sequence

CS 6463: An overview of Molecular Biology

a 6 2 protein folding quaternary structure
A.6.2 Protein Folding: Quaternary Structure

CS 6463: An overview of Molecular Biology

a 6 2 protein folding disulfide bridges
A.6.2 Protein Folding: Disulfide Bridges

CS 6463: An overview of Molecular Biology

a 6 2 protein folding multiple post translational cleavages of polypeptide precursors
A.6.2 Protein Folding: Multiple Post-Translational Cleavages of Polypeptide Precursors

CS 6463: An overview of Molecular Biology

a 6 2 protein folding types of post translational modification
A.6.2 Protein Folding: Types ofPost-translational Modification
  • http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=hmg.table.103

CS 6463: An overview of Molecular Biology

a 6 2 protein folding the big picture
A.6.2 Protein Folding: The Big Picture

CS 6463: An overview of Molecular Biology

a 6 2 protein folding co tranlsational folding of a protein
A.6.2 Protein Folding: co-tranlsational folding of a protein

CS 6463: An overview of Molecular Biology

a 6 2 protein folding current view of folding
A.6.2 Protein Folding: ‘Current view’ of folding

CS 6463: An overview of Molecular Biology

a 6 2 protein folding hsp70
A.6.2 Protein Folding: hsp70

There are two mainfamilies of molecular chaperones – hsp70, hsp60

CS 6463: An overview of Molecular Biology

a 6 2 protein folding protein sorting localization
A.6.2 Protein Folding: Protein Sorting (Localization)

1. Signal Peptide

2. Post-translational modification

CS 6463: An overview of Molecular Biology

a 6 2 protein folding quality control of protein folding
A.6.2 Protein Folding: Quality Control of Protein Folding

Incorrectly fold proteins cause disease (Huntington’s and Alzheimer’s diseases ). Particularly, protein with large exterior hydrophobic region, tend to stick together. The enzyme proteasome and others detect such incorrectly folded proteins and destroy them [359-363, FYI].

CS 6463: An overview of Molecular Biology

a an overview of molecular biology78
A. An overview of molecular biology

A.1. Background

A.2. Building Blocks of Macromolecules

A.3. DNA structure

A.4. RNA transcription and Gene Expression

A.5. RNA processing

A.6. Translation, post-translation processing and protein structure

A.7. Summary

CS 6463: An overview of Molecular Biology

a 7 summary central dogma simplify
A.7 Summary: Central Dogma Simplify

Enzymes, Receptors,

... etc

CS 6463: An overview of Molecular Biology

a 7 summary don t forget about mitochondria
A.7 Summary: Don’t forget about mitochondria!

CS 6463: An overview of Molecular Biology

a 7 summary life is more complex
A.7 Summary: Life is more complex

CS 6463: An overview of Molecular Biology

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