cmsc 828n introduction: molecular biology background

CMSC 828N Introduction: CMSC 828N Introduction: Molecular biology backgroundMolecular biology background

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Class web pageClass web page

http://cbcb.umd.edu/confcour/CMSC828N.shtml

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Course gradingCourse grading• 3 laboratory assignments

• 15% (Labs 1,2,3)• Lab 1 given out by Sept 9, due Sept 23 (see

syllabus)• Labs due by midnight on due date• Late penalty: 10%/day for 2 days maximum

• 1 class presentation of a research paper• 5%

• Lab 4 (mini-project)• 25%

• Final exam• 25%

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UMD Plagiarism policyUMD Plagiarism policy

Does this really happen?• Yes• Acknowledgement: many of the slides that follow are

from Michael Brent, a professor at Washington Univ.

What if I have a question?• You are required to ask if:

– you have any doubt about whether or not you can use any (text,code,data) as part of your work for this class

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LifeLife

Categories• Cellular organisms, viruses, prions• Cells are surrounded by a membrane

–By weight, inside is mostly water–Generally, outside is aqueous, also

• Major categories of cellular organisms are:–Prokaryotes–Eukaryotes

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ProkaryotesProkaryotes• Single-celled organisms• Only 1 membrane. I.e., single compartment• Typically about 1 micron diameter

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ProkaryotesProkaryotes

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EukaryotesEukaryotes• Single-celled organisms, plants & animals• Typical cell is 10 microns across (variable)• Membrane-bound nucleus contains DNA

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EukaryotesEukaryotes

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Some other cladesSome other clades

Tree of life: animals

Entrez: taxonomyEntrez: taxonomy

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Cell contents: small moleculesCell contents: small molecules

Examples:• Ions (Ca+, K+, Na+, Cl-)• Sugars• Fats• Vitamins

Can be obtained by• Import through membrane• Synthesis from imported precursors• Synthesis de novo

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Macromolecules (polymers)Macromolecules (polymers)

Synthesis• Made in cell by linking monomers from a

specified set

Examples• Polysaccharides (sugar chains)• Proteins (amino acid chains)• DNA & RNA (Nucleic acids; nucleotide

chains)

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Protein functionsProtein functionsStructural: e.g.,

• Cytoskeleton gives membrane strength & rigidity

Signaling (information transduction)• receptors on cell surface sense hormones• DNA binding to turn genes on and off

Enzymatic: speed up reactions to, e.g.,• Extract energy from nutrients• Interconvert small molecules• Immune response: bind and degrade invaders• Maintain circadian rhythm & other clocks

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Protein functionsProtein functionsEnzymatic functions (cont.)

• Programmed cell death (apoptosis)• Build macromolecular chains

–Copy cell’s DNA during replication–Build other proteins from DNA instructions

• Active transport through membrane–E.g. specific sugar transporters

• Etc., etc., etc.

Web resources• GO Browser, KEGG pathways, BioCarta

pathways

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ProteinsProteins• Built from 20 monomers called amino acids• Spontaneously fold into conformations

determined by their amino acid sequences–Folded shape is essential to function

• Often associate into complexes

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Nucleic acidsNucleic acids

Two major types of nucleic acid polymers• Deoxyribonucleic acid (DNA) • Ribonucleic acid (RNA).

Composition• Four monomers called nucleotides• DNA: deoxy

– Adenine (A), Guanine (G), Cytosine (C), Thymine (T)• RNA:

– Adenine (A), Guanine (G), Cytosine (C), Uracil (U)

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DNADNAFunction:

• Long term information storage & transmission

Structure: • Normally, double-helix

–Twisted ribbon

Base pairing• A:T and G:C

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2 strands of DNA2 strands of DNA

Orientation• Every (D/R)NA chain has a 5’ and a 3’ end

–Position of free attachment pt in sugar• Many biological processes go from 5’ to 3’

–Elongation: nucleotides added to 3’ end–Read-out: DNA->RNA->protein

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Orientation & the double helixOrientation & the double helix

Double helix is “anti-parallel”• 5’ end of each strand at 3’ end of the other• 5’ to 3’ motion in one strand is 3’ to 5’ in the other

Double helix has no orientation• Biology has no “forward” and “reverse” strand• Both strands are equal• Relative to any single strand, there is a “reverse

complement” or “reverse strand”5’TTTTACAGGACCATG 3’3’AAAATGTCCTGGTAC 5’ 5’CATGGTCCTGTAAAA 3’

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RNARNA• Normally single-stranded• Much less stable than DNA. Shorter lifetime.• Can form complex structure by self-base-pairing

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RNA self-base-pairingRNA self-base-pairing

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DNA DNA mRNA mRNA Protein Protein

• RNA polymerase transcribes a segment of DNA to a complementary messenger RNA

• In eukaryotic cells:– Primary messenger RNA is processed to create mature

mRNA– this processing involves splicing out certain segments of

the RNA called introns– mature mRNA then transported out of the nucleus

• Mature mRNA is translated into protein – by a ribosome

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3D shape of transfer RNA3D shape of transfer RNA

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Quicktimeanimation

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RNA ProcessingRNA Processing

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RNA splicingRNA splicing

• Splice sites are encoded in the sequence.• Splice site recognition is complex and imperfect.

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Splice sitesSplice sites

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Gene structureGene structure

• Genes are highly structured regions of DNA• that ultimately yield a strand of amino acids

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Translation of mRNA to ProteinTranslation of mRNA to Protein• DNA & mRNA represent protein sequences

via a 3-letter code• there are 3 possible reading frames

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Translation of mRNA to ProteinTranslation of mRNA to Protein

• Each triplet is called a codon• The code is degenerate

–61 codons map to 20 amino acids–Between 1 and 6 codons per amino acid–3 codons stop translation (TAA, TGA, TAG)–Codons for the same amino acid are called

synonymous–DNA mutations that do not change the amino

acid are called silent

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Fun animationsFun animations

Quicktime Animation: mRNA life cycle

Quicktime animation: Protein synthesis

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Non-coding RNANon-coding RNAFunctions

• Transfer RNAs: codon-to-amino-acid adapters• Ribosomes catalyze amino acid linkage

–Protein-RNA complex. RNA is catalytic!• Small RNAs editing specific mRNAs, or• Prevent translation of specific mRNAs• All transcribed from DNA but not translated

Structure• Shape, determined by self-pairing, is essential• External base-pairing is usually essential, too

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GenesGenes

Molecular definition• Regions of DNA that are transcribed into a

single RNA strand, with nearby DNA regions controlling time and quantity of transcription

• Protein-coding genes and ncRNA genes

Classical definition• Whatever it is that gives rise to a heritable trait

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DNA PackagingDNA Packaging• DNA is packed hierarchically• The chromosome is the largest package

–Width: ~50 times that of smallest transistor–Humans have 22 chrs + 2 sex chrs

• Human genome 1-2m long: 0.34nm/base• DNA is ~1 picogram (10-12g) per gigabase

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Genome sizesGenome sizes

• Widely varied• Not well correlated with organism

complexity/sophistication–Typical bacterium: 1-10 megabases (mb)–Typical single-celled eukaryote: 10-30 mb–Smallest plants and animals: 100 mb (fruit

fly, worm, mustard weed)–Human: 3 gb; some rats & gophers: 5-6 gb–Pine tree 60 g; Fern is 160 gb

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-----------------------------------------------------------Organism Genome size-----------------------------------------------------------Amoeba dubia 670,000,000,000Amoeba proteus 290,000,000,000Ophioglossum petiolatum 160,000,000,000Protopterus aethiopicus 139,000,000,000Lilium longiflorum 90,000,000,000Pinus resinosa 68,000,000,000Lilium formosanum 36,000,000,000Paramecium caudatum 8,600,000,000Tarsius syrichta 5,151,600,000Cercopithecus cephus 5,141,700,000Zea mays 5,000,000,000Hordeum vulgare 5,000,000,000Macropus robustus 4,396,600,000Parameles gunni 4,357,200,000Monodelphis dimidiata 4,115,400,000Pongo pygmaeus 4,046,300,000Gerbillus pyramidum 3,913,100,000Cercopithecus aethiops tantalus 3,898,300,000Galago alleni 3,878,500,000Didelphis marsupialis aurita 3,848,900,000Ctenomys conoveri 3,848,900,000Cebus capucinus 3,829,200,000Ctenomys leucodon 3,824,200,000Nicotiana tabaccum 3,800,000,000Pan troglodytes 3,799,600,000