cmsc 828n introduction: molecular biology background
TRANSCRIPT
CMSC 828N Introduction: CMSC 828N Introduction: Molecular biology backgroundMolecular biology background
2
Class web pageClass web page
http://cbcb.umd.edu/confcour/CMSC828N.shtml
3
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%
4
5
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
6
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
7
ProkaryotesProkaryotes• Single-celled organisms• Only 1 membrane. I.e., single compartment• Typically about 1 micron diameter
8
ProkaryotesProkaryotes
9
EukaryotesEukaryotes• Single-celled organisms, plants & animals• Typical cell is 10 microns across (variable)• Membrane-bound nucleus contains DNA
10
EukaryotesEukaryotes
11
Some other cladesSome other clades
Tree of life: animals
Entrez: taxonomyEntrez: taxonomy
12
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
13
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)
14
15
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
16
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
17
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
18
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)
19
DNADNAFunction:
• Long term information storage & transmission
Structure: • Normally, double-helix
–Twisted ribbon
Base pairing• A:T and G:C
20
21
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
22
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’
23
RNARNA• Normally single-stranded• Much less stable than DNA. Shorter lifetime.• Can form complex structure by self-base-pairing
24
RNA self-base-pairingRNA self-base-pairing
25
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
26
3D shape of transfer RNA3D shape of transfer RNA
27
Quicktimeanimation
28
RNA ProcessingRNA Processing
29
RNA splicingRNA splicing
• Splice sites are encoded in the sequence.• Splice site recognition is complex and imperfect.
30
Splice sitesSplice sites
31
Gene structureGene structure
• Genes are highly structured regions of DNA• that ultimately yield a strand of amino acids
32
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
33
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
34
35
Fun animationsFun animations
Quicktime Animation: mRNA life cycle
Quicktime animation: Protein synthesis
36
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
37
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
38
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
39
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
40
-----------------------------------------------------------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