Lecture 3 Molecular Biology Review

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Lecture 3Molecular Biology Review

• Chapter 3
• Jones Pevzner

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The cellular basis of life

• Discovered by Robert Hooke, 1665.
• Observedcells ofcork

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The Cell Theory

• Further observations in the 1800s by Schleiden
  and Schwann

http//members.tripod.com/blustein/Schwann_Cells/s
chwann_cells.htm
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What are cells?

• Fundamental, replicating units of living
  organisms.
• Machines with complex regulation and behaviors
  based on networks of chemical reactions called
  pathways.
• They carry the information needed to reproduce
  themselves.
• All cells based on molecules of a limited number
  of classes
• DNA
• RNA
• Proteins
• etcetera (Lipids, Carbohydrates, Metabolites)

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What is the genetic material?

• Chromosomes, threadlike structures, first
  observed by Nageli in 1842.
• Walter Flemming was the first to follow the
  process of mitosis and replication of
  chromosomes.
• Thomas Morgan, in his experiments with fruit
  flies, described genetic recombination, and
  demonstrated that traits were to inherited
  together to varying degrees.
• Alfred Sturtevant extended Morgans ideas, used
  observed recombination rates to produce the first
  genetic maps.

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The function of genes

• Beadle and Tatum produced strong evidence via
  mutation experiments with the mold Neurospora
  that genes direct the production of proteins
  (1941)
• Produced mutant strain using irradiation
• Some mutant strains would not grow on
  conventional media, but would grow on media with
  supplements (e.g. vitamin B6)
• The role of proteins as enzymes, and the part
  they play in metabolism, was already understood
  at this time the evidence suggested that some
  inherited mutations knocked out specific elements
  of metabolic machinery (i.e. proteins).

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What are genes made of?

• Miescher first isolated nuclein from the nuclei
  of white blood cells in 1869.
• By the early 1900s, nuclein was known to be a
  long polymer of nucleic acids, and by the 1920s
  DNA and RNA were separately isolated.
• Initially, biologists were not very interested in
  DNA - it was thought to have a simple sequence,
  like synthetic polymers

http//www.chemheritage.org/EducationalServices/ny
lon/chem/chem.html
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Genes are made of DNA

• Griffith showed that bacteria could be
  transformed
• pneumococcus colonies come in two varieties,
  rough (R) and smooth (S). S colonies are
  infectious, R are not.
• Kill S colony with heat, mix dead bacteria with
  R cells, inject into mouse. Mouse gets sick and
  dies can isolate S bacteria from carcass.
• Avery isolated the chemical components of S
  bacteria, demonstrated that the transforming
  factor was DNA.

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Structure of DNA

• Chargaff demonstrated that the ratio of A/T in
  genomic DNA was a constant, and likewise G/C.
• Wilkins and Franklin collected x-ray diffraction
  data for fibers of DNA, and determined that it
  had a helical structure.
• Watson Crick put these clues together with
  simple molecular modelling studies to deduce the
  structure of double-stranded DNA, and also to
  suggest the mechanism for copying DNAHeres the
  original paperhttp//www.nature.com/genomics/hum
  an/watson-crick/index.html

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dsDNA
www.csupomona.edu/shbryant/ansrs-p07.pdf
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http//faculty.clintoncc.suny.edu/faculty/Michael.
Gregory/files/Bio20101/Bio2010120Lectures/Bioch
emistry/biochemi.htm
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Genes code for proteins using symbolic information

• Gene sequences code for protein sequences via a
  symbolic code, the genetic code. This code is
  used nearly universally by living organisms it
  is one of the most ancient shared characteristics
  of living things.
• The words of the genetic code are nucleotide
  triplets called codons. Each codon codes for at
  most one amino acid.
• Codons that do not code for any amino acids,
  called nonsense or stop codons, terminate a
  coding region of the gene. They serve as
  punctuation marks

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ASCII TEXT CODON TABLE Third
Position A C G U
_____________________________ AA
Lys Asn Lys Asn F AC Thr
Thr Thr Thr i AG Arg Ser Arg
Ser r AU Ile Ile MET Ile s P
CA Gln His Gln His t o CC
Pro Pro Pro Pro s CG Arg Arg
Arg Arg i CU Leu Leu Leu
Leu t GA Glu Asp Glu Asp S i
GC Ala Ala Ala Ala e o GG
Gly Gly Gly Gly c n GU Val Val
Val Val o UA Z Tyr Z
Tyr n UC Ser Ser Ser Ser d
UG Z Cys Trp Cys UU
Leu Phe Leu Phe Z STOP CODON
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Lots of complexity

• In the preceding table, the nucleotide codes are
  A, C, G and U - what happened to T?
• The DNA sequence is first copied (transcribed)
  into an RNA sequence before it is translated into
  protein. The transcript is a molecule of
  messenger RNA (mRNA).
• In prokaryotes, the transcript is a faithful copy
  of the genomic sequence, but in eukaryotes the
  message is typically edited before translation.
  This is because the the regions of eukaryotic
  genes that code for protein (exons) are
  interrupted by introns.

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(No Transcript)
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www.idmb.tamu.edu/botany101/ 04/week-09-nucleic-ac
ids.pdf
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More complexity via Alternative Splicing
Role of Alternative Splicing in Generating
Isoform Diversity Among Plasma Membrane Calcium
Pumps, EMANUEL E. STREHLER AND DAVID A.
ZACHARIAS, PHYSIOLOGICAL REVIEWS Vol. 81, No. 1,
January 2001
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Translation into protein

• Requires an adaptor molecule which can translate
  3-letter codons into amino acids. This function
  is provided by transfer RNA (tRNA) molecules,
  which have an RNA region complementary to a
  target codon, and which are specifically
  charged with the corresponding amino acid.
• The complex process of assembling a polymer of
  amino acids under the direction of an mRNA
  molecule is carried out by the ribosome.

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http//wsrv.clas.virginia.edu/rjh9u/trtrpict.html
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The central dogma
transcription
translation
DNA
RNA
PROTEIN
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Copying DNA
http//www.accessexcellence.org/RC/VL/GG/polymeras
e.html
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Cloning (another way to copy)
http//www.ornl.gov/sci/techresources/Human_Genome
/publicat/primer/fig11a.html
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Restriction enzymes (molecular scissors)
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Genetic Diversity

• Many genes are highly conserved across species
  this is most true for genes involved in basic
  metabolism, DNA organization (e.g. histones),
  etc.
• The genome for a species refers to a
  hypothetical consensus. In the case of the HGP, a
  small number of individuals were selected for
  sequencing. A Human Diversity Project is now
  underway to analyze the small, but crucial
  differences that distinguish individuals (and
  which may be responsible for inherited diseases).

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Data Types

• Kernighan Ritchie
• Chapter 2

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Some primitive data types

• int - integer (usually four bytes by default,
  including a sign bit)
• float - floating point number (usually four
  bytes, precision of 7-8 decimal digits)
• double - double precision floating point number
  (14-16 decimal digits precision). Usually eight
  bytes.
• char - single ASCII character (one byte)

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Constants

• You can declare a variable a constant by adding
  the const modifier in front of its definition
• const int 246
• Constants of various kinds can be declared in
  your code
• 0xEF - Hex constant
• 0777 - Octal constant
• 1.34e12 - Floating point constant
• \n - escape sequence (here a new line)
• 382719230003982L - long integer
• \xF - bit string

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Modifiers

• short and long can be used to specify the short
  and long forms of variables short int
• unsigned can be used to specify a special form of
  some types where sign is not considered
  unsigned int

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Enumerated types

• Enumerated types can take on only a finite list
  of values, which are given symbolic names (they
  are really integers in disguise) enum JAN,
  FEB, MAR, APR, MAY, JUN, JUL, AUG, SEP, OCT, NOV,
  DEC lastMonth The preceding declares a
  variable lastMonth which may only take on one of
  12 distinct values lastMonth JAN

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Strings

• Strings in C are arrays of characterschar
  myString1000 // Declare a string to //
  hold up to 1000 chars
• myString0 is the first (0th) character in
  the string.Strings must be terminated with a
  byte of value 0, symbolized \0.

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Modulus operator ()

• Provides the remainder of an integer
  division 40 3would produce the result 1
  (40 divided by 3 equals 13 with one left over).

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Type conversions

• The compiler will generally attempt to do type
  conversions where possible. For example, int
  myInt double myFloat myInt 4 myFloat
  myInt
• will assign the floating point number 4.0 the
  variable myFloat

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Type coercion

• This feature is often used in function calls. For
  example, the sqrt() function expects a double as
  argument how do we pass a float? float myFloat
  result sqrt((double)myFloat)

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Bit operations (,,,gtgt,ltlt,)

• Can be applied to integer operands. These allow
  us to operate on individual bits. unsigned
  short x, y // Set the lowest eight bits of x
  to 1 x 0 x x 0x00FF // Test if the
  lowest four bits of y are // set if( (y
  0xFFF0) 0xFFFF )