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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 l.jpg
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


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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


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A.1.1 3 Domains in the Living World

CS 6463: An overview of Molecular Biology


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A.1.2 Bacteria, Archaea and Eucaryotes.

The bacterium: Vibrio Cholerae

A lithotrophic Bacterium (Archaea)

Eucaryotic Cell

CS 6463: An overview of Molecular Biology


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A.1.3. Eukaryotic Cells

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

CS 6463: An overview of Molecular Biology


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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

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


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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


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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


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A.2. Building Blocks: Common bases found in nucleic acids nucleotides

CS 6463: An overview of Molecular Biology


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A.2 Building Blocks nucleotides: 20 amino acids

Polypeptides: chains of amino acids

Carboxyl group

Amino group

CS 6463: An overview of Molecular Biology


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A.2. Building Blocks: Abbreviation of Amino Acids nucleotides

CS 6463: An overview of Molecular Biology


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A.2. Building blocks: Properties of Amino Acids I nucleotides

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

CS 6463: An overview of Molecular Biology


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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


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A.2 Building Blocks: Covalent and Non-covalent Bonds of Amino Acids

  • 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


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A. An overview of molecular biology of Amino Acids

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


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A.3 DNA Structure: The Phosphodiester Bond of Amino Acids

CS 6463: An overview of Molecular Biology


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A.3 DNA Structure: base pairing (Watson-Crick Rule). of Amino Acids

CS 6463: An overview of Molecular Biology


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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


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

CS 6463: An overview of Molecular Biology


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A.3 DNA Structure:Chromatin helix

Histone

nucleosome

CS 6463: An overview of Molecular Biology


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

mouse

Human

CS 6463: An overview of Molecular Biology


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A.3. DNA Structure: Human Chromosomes helix

  • 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


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A.3 DNA Structure: RNA structure helix

palindrome

CS 6463: An overview of Molecular Biology


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A.3 DNA Structure: Viral Genomes helix

  • 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


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A.3 DNA Structure: The Central Dogma helix

Old 1-directional model

CS 6463: An overview of Molecular Biology


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A.3 DNA Structure: helixGene Expression Efficiency

Microarray measurement of gene expression is limited.

CS 6463: An overview of Molecular Biology


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A. An overview of molecular biology helix

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


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A.4. Transcription and Gene Expression: Tanscription helix

CS 6463: An overview of Molecular Biology


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A.4 Transcription and Gene Expression:Gene Regulation helix

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


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A.4 Transcription and Gene Expression:RNA Polymerase helix

  • 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


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A.4 Transcription and Gene Expression: DNA-Protein Binding helix

CS 6463: An overview of Molecular Biology


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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


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A.4 Transcription and Gene Expression: Promoters cis-elements

Start from 1 not 0

CS 6463: An overview of Molecular Biology


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A.4 Transcription and Gene Expression: Polymerase II & Promoter

CS 6463: An overview of Molecular Biology


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A.4 Transcription and Gene Expression: : Transcription under the Electron Microscope

CS 6463: An overview of Molecular Biology


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A.4 Transcription and Gene Expression: Transcription in Bacterial

CS 6463: An overview of Molecular Biology


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A.4 Transcription and Gene Expression: Enhancers and Silencers (Transcription Factors)

Many basepairs

away

CS 6463: An overview of Molecular Biology


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A.4 Transcription and Gene Expression: Tissue Specific Genes Silencers (Transcription Factors)

  • 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


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A. An overview of molecular biology Silencers (Transcription Factors)

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


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A.5 RNA Processing: RNA Splicing Silencers (Transcription Factors)

acceptor

donor

GT-AG spliceosome

AT-AC spliceosome (rare)

CS 6463: An overview of Molecular Biology


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A.5.1 Splicing Silencers (Transcription Factors)

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


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A.5.1 Splicing: Consensus Sequences at splice donor, acceptor and branch sites

CS 6463: An overview of Molecular Biology


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A.5.1 Splicing acceptor and branch sites : RNA Splicing

CS 6463: An overview of Molecular Biology


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A.5.1 Splicing acceptor and branch sites : 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


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A.5.1 Splicing acceptor and branch sites : 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


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A.5.1 Splicing acceptor and branch sites : Alternative Splicing

CS 6463: An overview of Molecular Biology


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A.5.1 Splicing acceptor and branch sites : Isoforms

CS 6463: An overview of Molecular Biology


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A. An overview of molecular biology acceptor and branch sites

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


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A.5.2 RNA Capping: 5’ End Capping acceptor and branch sites

CS 6463: An overview of Molecular Biology


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A.5.2 RNA Capping: acceptor and branch sitesEucaryotic and Procaryotic mRNAs

CS 6463: An overview of Molecular Biology


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A.5.2 RNA Capping: acceptor and branch sites3’ end polyadenylated.

CS 6463: An overview of Molecular Biology


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A.5.2 RNA Capping: acceptor and branch sitesFunctions 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


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A.5.2 RNA Capping: acceptor and branch sitesExample of the human b-globin gene

CS 6463: An overview of Molecular Biology


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A.5.2 RNA Capping: acceptor and branch sitesExport out of the nuclear

CS 6463: An overview of Molecular Biology


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A. An overview of molecular biology acceptor and branch sites

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


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A.6.1 Translation: The Codon-anticodon Recognition acceptor and branch sites

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 l.jpg
A.6.1 Translation: Wobbing Effect acceptor and branch sites

CS 6463: An overview of Molecular Biology


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A.6.1 Translation: Translating a mRNA molecule acceptor and branch sites

CS 6463: An overview of Molecular Biology


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A.6.1 Translation: Peptide Bond Formation acceptor and branch sites

CS 6463: An overview of Molecular Biology


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A.6.1 Translation: The Genetic Codes acceptor and branch sites

C-terminal

N-terminal

CS 6463: An overview of Molecular Biology


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A.6.1 Translation: acceptor and branch sitest-RNA

CS 6463: An overview of Molecular Biology


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A.6.1 Translation: The Genetic Codes acceptor and branch sites

- 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


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A.6.1 Translation: acceptor and branch sitesPost-Translational Processing: Translating a mRNA molecule

CS 6463: An overview of Molecular Biology


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A.6.1 Translation: acceptor and branch sitesPolyribosome

CS 6463: An overview of Molecular Biology


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A. An overview of molecular biology acceptor and branch sites

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


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A.6.2 Protein Folding: Protein Secondary Structure acceptor and branch sites

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: acceptor and branch sitesQuaternary

Amino acid sequence  secondary structure  tertiary structure

Amino acid sequence

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: acceptor and branch sitesQuaternary Structure

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: acceptor and branch sitesDisulfide Bridges

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: Multiple Post-Translational Cleavages of Polypeptide Precursors

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: Types of of Polypeptide PrecursorsPost-translational Modification

  • http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=hmg.table.103

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: The Big Picture of Polypeptide Precursors

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: of Polypeptide Precursorsco-tranlsational folding of a protein

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: of Polypeptide Precursors‘Current view’ of folding

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: of Polypeptide Precursorshsp70

There are two mainfamilies of molecular chaperones – hsp70, hsp60

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: Protein Sorting (Localization) of Polypeptide Precursors

1. Signal Peptide

2. Post-translational modification

CS 6463: An overview of Molecular Biology


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A.6.2 Protein Folding: Quality Control of Protein Folding of Polypeptide Precursors

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


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A. An overview of molecular biology of Polypeptide Precursors

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


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A.7 Summary: Central Dogma Simplify of Polypeptide Precursors

Enzymes, Receptors,

... etc

CS 6463: An overview of Molecular Biology


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A.7 Summary: Don’t forget about mitochondria! of Polypeptide Precursors

CS 6463: An overview of Molecular Biology


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A.7 Summary: Life is more complex of Polypeptide Precursors

CS 6463: An overview of Molecular Biology


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