Molecular Biology 101: An Introduction to Cells, DNA, RNA, Proteins, and Sequencing, Essays (university) of Mathematics

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BASICS ON MOLECULAR BIOLOGYBASICS ON MOLECULAR BIOLOGY

Ŷ Cell – DNA – RNA – protein Ŷ Sequencing methods Ŷ arising questions for handling the data, making sense of it Ŷ next two week lectures: sequence alignment and genomeassembly

Cells

• Fundamental working units of every living system.
• Every organism is composed of one of two radically different types of cells:
  • prokaryotic cells
  • eukaryotic cells which have DNA inside a nucleus.
• Prokaryotes and Eukaryotes are descended from primitive cells and the results of 3.5 billion years of evolution.

All Cells have common Cycles

• Born, eat, replicate, and die

Common features of organisms

• Chemical energy is stored in ATP
• Genetic information is encoded by DNA
• Information is transcribed into RNA
• There is a common triplet genetic code
  • some variations are known, however
• Translation into proteins involves ribosomes
• Shared metabolic pathways
• Similar proteins among diverse groups of organisms

DNA structure

• DNA has a double helix structure

which is composed of

• sugar molecule
• phosphate group
• and a base (A,C,G,T)
• By convention, we read DNA

strings in direction of

transcription: from 5’ end to 3’

end

5’ ATTTAGGCC 3’

3’ TAAATCCGG 5’

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DNA is contained in chromosomes

http://en.wikipedia.org/wiki/Image:Chromatin_Structures.png

‡ In eukaryotes, DNA is packed into linear chromosomes

‡ In prokaryotes, DNA is usually contained in a single, circular chromosome

RNA

• RNA is similar to DNA chemically. It is usually only a single strand. T(hyamine) is replaced by U(racil)
• Several types of RNA exist for different functions in the cell.

tRNA linear and 3D view: http://www.cgl.ucsf.edu/home/glasfeld/tutorial/trna/trna.gif

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DNA, RNA, and the Flow of Information

Transcription Translation

Replication ”The central dogma”

Is this true?

http://velblod.videolectures.net/2007/pascal/eccs07_dresden/noble_denis/eccs07_noble_psb_01.ppt^ Denis Noble: The principles of Systems Biology illustrated using the virtual heart

Amino acids

http://upload.wikimedia.org/wikipedia/commons/c/c5/Amino_acids_2.png

How DNA/RNA codes for protein?

• DNA alphabet contains four

letters but must specify protein,

or polypeptide sequence of 20

letters.

• Trinucleotides (triplets) allow 4^3 =

64 possible trinucleotides

• Triplets are also called codons

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Genes

• “A gene is a union of genomic sequences encoding a coherent set of

potentially overlapping functional products”

• A DNA segment whose information is expressed either as an RNA

molecule or protein

… a t g a g t g g a … … t a c t c a c c t …

(transcription)

(translation) (^) MSG … (folding)

http://fold.it

Genes & alleles

• A gene can have different variants

• The variants of the same gene are called

alleles

… a t g a g t g g a … … t a c t c a c c t …

MS G …

… a t g a g t c g a … … t a c t c a g c t …

MS R …

Exons and introns & splicing

Introns are removed from RNA after transcription

Exons

Exons are joined: This process is called splicing

Alternative splicing

A 3’

B C

Different splice variants may be generated

A B C

B C

A C