Anatomy of the Gene

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Anatomy of the Gene

• MUPGRET Workshop
• June 19, 2006

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2003 50 Year Anniversary of the Discovery of
The DNA Double Helix
The famous DNA Double Helix paper was published
in Nature in 1953!
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What Is DNA?
DNA is a chemical contained in every cell of
your body.
Yes!
DNA is a Chemical!?
What other kinds of chemicals are in your body?

• We are made up of chemicals, formed from the
  elements carbon
• (C), hydrogen (H), oxygen (O), phosphate (P) and
  others
• DNA is made up of carbon (C), hydrogen (H),
  oxygen (O),
• phosphate (P)
• We breathe air which contains oxygen molecules
  (O2).
• We eat food which is composed of chemicals called
  proteins,
• sugars, and fats.
• Our bones are made up largely of calcium (Ca)
• Our bodies make energy by breaking down chemicals
  such as
• sugar!
• We store energy in our body in the form of
  carbohydrate
• chemicals.

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DNA

• Hereditary material.
• Contains all information to make proteins.
• Linear polymer of nucleotide.
• Each one has sugar, phosphate and a base.

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DNA

• Base connected to sugar by ß-glucosyl linkage.
• Nucleotides are connected to one another by a
  phosphodiester bond.
• Bases are perpendicular to helix.

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(No Transcript)
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The Double Helix

• Two strands of DNA run in opposite directions,
  complementing each other and pairing with
  hydrogen bonds.
• A and T pair together and C and G pair together.
• Helix is most often right-handed (B-form).

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3D DNA Strands Building Blocks are DNA Letters
Each DNA Strand Contains One Backbone and Many
Building Block DNA Letters (Bases)
Green Strand DNA Letters
Red Strand DNA Letters
Red DNA Strand
Green DNA Strand
DNA Letters A, G, C, T
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How Does DNA Carry Information?

• To answer this question we must take a closer
  look at DNA.
• DNA is a biopolymer
• Polymers are molecules made of repeating units or
  building blocks
• DNA has four chemical building blocks symbolized
  by the letters A,G,C, T
• The letters of your DNA are in a specific order
  that carries information about you!!
• So, a DNA polymer can be represented as a string
  of letters

A G C T T A G G G T A A A C C C A T A T A
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DNA Carries Information in the Sequence of DNA
Letters
. . .A G C T T A G G G T A A A C C C A T A G . . .
A gene

• A gene is a length of DNA letters that contain
• an instruction for a cell to follow.
• The cell uses specially designed protein
  machines
• to read the information in genes.

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The Order of DNA Letters Encodes the Genetic
Information
The order or sequence of the A, G, C and T
letters in the DNA polymer encodes the actual
genetic information

• Example of the DNA letters in a gene
• AGCTTAGGGTAAACCATATAGGGCCATACCCTATCGGTAAGCTT
• AGCTTAGGGAAAACCCATATAGGGCCATACCCTATCGGTAAG

• The specific order of the DNA letters carries
• the information.
• Changing the order of the DNA letters will
  change the information carried by the gene.
• We will talk about how this happens later!

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Secret of DNA Fingerprinting Lies in the Ability
to Detect Small Differences in DNA Letters Among
Individual Samples

• Look around the room and see how different we all
  look. Then compare any two human genomes
• The DNA letters are almost the identical order
  (sequence) between any two human genomes!
• A very small number (0.1) of the DNA letters
  differ between any two human genomes.
• Two plants that look very
• similar may be close or
• distantly related because
• humans select for desirable
• traits in new varieties.

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Genes Can Have Hundreds to Millions of DNA
Letters
. . .A G C T T A G G G T A A A C C C A T A G . . .
A gene
It can take hundreds, thousands or even a million
or more letters (bases) to spell out the
instructions in a single gene.
and what for?
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Controlling Gene Expression

• The specific order of DNA bases in a gene encode
• a protein product.
• Genes have START and STOP signals that specify
• the length of the protein chain.
• Control DNA region is in front of the coding
  region
• and controls expression of the gene.

GENE
Control DNA region is called a promoter.
DNA region carrying protein information is
called the coding region.
1
PROTEIN CODING REGION
PROMOTER
mRNA
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Genes Contain Instructions for Building Proteins

• Genes contain instructions for making proteins,
  one of the major types of the molecules of life,
  or biomolecules
• Proteins, like DNA, are polymers
• Protein building blocks are called amino acids
• Amino acids are strung together into long, linear
  polymers by following the instructions in genes
• In general, a gene encodes the instructions for
  one protein
• When a gene is misspelled, the protein made
  from it
• may be made with an incorrect amino acid
• may not work properly

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Review of Gene Expression Pathway in Cells
GENE DNA mRNA copy of gene mRNA goes to
cytoplasm Ribosomes translate genetic
information encoded in the mRNA into protein
building blocks (chains of amino acids) Protein
folds into 3D active structure Protein
functions in cell
Focus on the Genetic Code!
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DNA Code Is Copied into a Portable Code mRNA
RNA POLYMERASE (RNAP COPIES DNA INTO mRNA)
DNA
DNA
U
A
C
A


A
T
T
G

Note DNA base-pairs between backbone strands are
not shown here

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mRNA

mRNA AUGGAGUACUAAUAUGUAAAAAAAAAAAAAAAAAAA-3 DNA
ATGGAGTACTAATATGT-3 TACCTCATGATTATACA-5

MFHMAF2001
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RNA Code has Different Alphabet Than DNA Code
(RNA has U instead of T)
DNA ATGGAGTACTAATATGT-3
TACCTCATGATTATACA-5 3-TACCTCATGATTATACA-5
DNA STRAND AUGGAGUACUAAUAUGU mRNA copied
from DNA
DNA Base-Pair
DNA strand has T
RNA has U instead of T
When DNA is copied into mRNA (transcription), U
is incorporated into mRNA in place of T
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DNA Strands Unzip so the DNA Letters Can be
Read
-ATGGAGTACTAATATGT- -TACCTCATGATTATACA-
-TACCTCATGATTATACA-
AUGGAGUACUAAUAUGU mRNA copied from
DNA -ATGGAGTACTAATATGT- AUGGAGUACUAAUAUGU
mRNA -TACCTCATGATTATACA-
DOUBLE-STRANDED DNA (Region from Chromosome)
DNA STRANDS SEPARATE
DNA STRANDS COME BACK TOGETHER BY BASE-PAIRING
mRNA GOES TO CYTOPLASM TO PROTEIN FACTORY
DNA HELIX STAYS IN NUCLEUS
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Genetic Code is Written in 3-Letter DNA Words
(Codons)
-TACCTCATGATTATACA- DNA(DNA strands separated)
-AUGGAGUACUAAUAUGU mRNA (copied from
DNA) 5-AUGGAGUACUAAUAUGU mRNA 5-AUG GAG UAC
UAA UAU mRNA
mRNA code read by ribosome in TANDEM triplets
called codons. Codon adaptors convert RNA
letters into the correct amino acid building
blocks in the protein chain.

• CODON MEANINGS
• A START PROTEIN SIGNAL AUG
• A STOP PROTEIN SIGNAL UAA, UGA, UAG
• An amino acid building block of a protein
• Codons identified in the Genetic Code Table

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The Universal Genetic Code Table
STOP Codons UAA UAG UGA
Name of Building Block Amino Acid
PhePhenylalanine LeuLeucine IleIsoleucine
AUG CODON Signal to start making the protein.
http//anx12.bio.uci.edu/hudel/bs99a/lecture20/le
cture1_6.html
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Genetic Code is Written in 3-Letter DNA Words
-TACCTCATGATTATACA- DNA STRAND
AUGGAGUACUAAUAUGU mRNA copied from
DNA 5-AUGGAGUACUAAUAUGU mRNA 5-AUG GAG UAC
UAA UAU mRNA Met-Glu-Tyr-STOP
mRNA code is read in TANDEM CODONS
A SHORT PROTEIN IS A PEPTIDE

• CODON MEANINGS
• START PROTEIN HERE AUG (START) Methionine
  (Met)
• STOP PROTEIN HERE UAA, UGA, UAG
• Amino acid building blocks N-Met-Glu-Tyr-C
• Codons are identified in the Genetic Code Table

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Proteins Have Two Ends The N- And C- Termini
5-AUGGAGUACUAAUAUGU mRNA 5-AUG GAG UAC
UAA mRNA Met-Glu-Tyr-STOP
A short protein (peptide) has only a few amino
acid (aa) building blocks. The first aa in the
chain (usually Met) (AUG) is at the N-terminus.
The final aa added to the chain is the
C-terminus.
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Ribosome Protein Factory Reads the RNA Codons
RNA is Copied From DNA (Gene)
NUCLEUS
GENE DNA UNZIPS
mRNA


Protein Synthesis
Protein Chain Folds
amino acid
N

AA
Transfer RNA (tRNA) Matches mRNA codon with
correct amino acid building block
mRNA
MFHMAF2001
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Proteins Fold into 3D Structures

• Proteins live in a watery environment (living
  organisms!).
• Chemical parts that hate water fold on inside of
  protein.
• Chemical parts that love water go to the outside
  surface of protein.
• Surface of the folded protein interacts with
  proteins, DNA, RNA, etc.

Polar Pocket
Small Folded Protein
C
N
Hydrophobic Pocket
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Different Protein Chains Fold to Make
Proteinswith Different 3D Shapes and Biological
Functions
Protein 1
Protein 2
Protein 3
Protein 2
Protein 1
Human proteins have 20 different amino acid
building blocks
Protein 3
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Molecular Structures Related to Protein Function
in the Cell
DNA Intersection Holliday Junction
EF Hand Binds Calcium
Basket
Syringe
Channel
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One Gene-One Protein

• Archibald Garrod (1902) described alkaptonuria, a
  hereditary disorder as an inborn error of
  metabolism.
• Proposed that mutations cause specific
  biochemical defects.
• Alkaptonuria defect is dark urine.

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A DNA Spelling Mistake Can Alter the Protein Chain
START
ADD
ADD
ADD
ADD
ADD
ADD
ADD
STOP
ATG TTC AGG CCA AAT TTT GTC GCG UAA GGA ATT
ATG TTT AGG CCA AAT TTT GTC GCG
TTC to TTT spelling change causes a different
protein building block to be inserted in the
second position. That is all it takes.
ADD Codon specifies the amino acid specified by
3-letter word ATG/AUG Codon specifies start
and methionine (met) UAA STOP adding amino
acids to protein chain
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A Mutation is a DNA Spelling Mistake

• Mutant Genes Encode Defective Proteins
• (1) WILDTYPE
  (2) MUTANT
• Example AAA GCT ACC TAT AAA
  GCT ATC TAT
• TTT CGA TGG
  ATA TTT CGA TAG ATA
• Phe Arg Trp
  Ile Phe Arg Stop
• 
  UAG
• PROTEIN WT FUNCTION
  NO FUNCTION
• (1) Normal DNA and amino acid sequence makes a
  wild-type protein.
• (2) Mutation in DNA changes Trp to Stop to make a
  short, mutant protein.
• Mutations in DNA can be Caused by
• Mistakes made when the DNA is replicated (wrong
  base inserted)
• Ultra violet (UV) light and ionizing radiation
  (X-rays) damage DNA
• Environmental chemical carcinogens can damage DNA
• Other factors

DNA Technology The Awesome Skill, I E Alcamo,
Harcourt Academic Press, 2001
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Misspelled Genes 3 Possible Outcomes
DNA
A misspelled gene
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DNA is Stored in the Nucleus (in Complex Cells)
Complex cells have compartments, bacterial cells
do not.
Minimalist Complex Cell
CELL MEMBRANE Controls entry and exit from
cell NUCLEUS Cell Control Center- contains DNA,
acivation of gene send RNA copies out into the
cytoplasm. This is called gene expression.
CYTOPLASM The area and material inside the
cell, but outside the nucleus and other
comparments
RIBOSOMESMake proteins from RNA instructions
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Gene Structure
Exon 1
Intron
Exon2
Introns are removed during translation
Exon 1
Exon2
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Intron

• A noncoding DNA sequence in a gene that is
  transcribed but is then excised from the primary
  transcript in formation a mature mRNA molecule.

Hartl and Jones. Genetics Analysis of Genes and
Genomes
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Exon

• The sequences in a gene that are retained in the
  messenger RNA after the introns are removed from
  the primary transcript.

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• What effect does the presence of introns have on
  the number of deleterious mutations?

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Heterochromatin characteristics

• Condensed throughout interphase
• Late replicating, ie. out of phase with
  euchromatin
• Transcriptionally inactive in the condensed
  state.
• Under-replicated in polytene chromosomes.

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Constitutive heterochromatin

• Present in all cells at identical positions on
  both homologous chromosome and forms a permanent
  structural characteristic of a given chromosome
  pair.

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Facultative heterochromatin

• Varies in state between cell types, developmental
  stages or homologous chromosome.
• Ex. differential state in homologous chromosomes
  seen in Barr bodies.

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Some proposed functions

• Chromosome level
• Stabilize centromeres and telomeres
• Facilitate chromosome pairing
• Cause variegation or sticky effects
• Gene level
• Modify gene action, penetrance, or specificity
• Control mutation

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More proposed functions

• Across chromosomes
• Control of chromosome dimensions
• Regulation of crossing-over, pairing, and
  disjunction
• Control of variegation from genes on other
  chromosomes
• Control of cell size
• Regulation of growth and differentiation rates

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What is heterochromatin?

• Composed primarily of repetitive DNA.
• Methylated
• Composed primarily of highly repetitive and
  middle repetitive DNA.
• An example from maize

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Mobile element

• About 50 of genome in mammals.
• Up to 90 of genome in plants.
• If the origin of life was in the RNA world,
  then they could be early participants in
  formation of genomes as we know them today.

Kazazian. 2004. Science 303 1626-1632.
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Retrotransposon

• Special transposon whose sequence is transcribe
  to RNA in the cell. After generation of the RNA
  strand a reverse transcriptase produced by the
  retrotransposon reconverts the RNA to DNA. This
  sequence is integrated into the original DNA
  strand at any position.

http//dvsinfo.weihenstephan.de/genglos/asp/genreq
.asp?nr620
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Retrotransposons

• Specific type of transposable element.
• Ancient
• Ubiquitous
• Mobility occurs at different rates depending on
  class of retrotransposon.
• Can effect gene function

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Retrotransposons

• Not all retrotransposons have a preference for
  heterochromatin.
• Ex. MITES preferentially insert into genes.
• Important in genome organization.
• Important evolutionary force.

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Genome Evolution

• Average human diploid genome has 80-100 active
  L-1s.
• L1 insertions account for 1 in 1200 human
  mutations some of which result in disease.
• 1 in 50 humans has a NEW genomics L1 insertion
  occurring in germ cell.

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Retroelements stabilize telomeres

• No telomerase in Drosophila.
• Drosophila telomeres are long tandem arrays of
  two non-LTR retrotransposons HeT-A and TART.
• First elements found to have a confirmed role in
  cell structure by assisting in maintenance of
  chromosome ends.

Pardue and deBaryshe. 2003. Ann Rev Genet 37
485-511.
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Genome Duplication

• Evidence is accumulating to support the idea of
  both complete or partial duplication within the
  genome of a number of organisms.

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Primates

• Originally thought chromosome evolution occurred
  by random breakage but comparison of mouse and
  human sequence says
• Segmental duplication happened with syntenic
  blocks of the genome.
• 25 of all breakpoints contain gt 10 Kb of
  duplicated sequence so not random.
• Duplication is not necessarily causal.

Bailey et al. 2004 Genome Biology 5 R23
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Every Cell Has a Complete Copy of Genome DNA

• Virtually every cell in your body contains its
  own complete copy of all your DNA

• A single, complete copy of an organisms DNA is
  called its genome

• The genome is a set of instructions, like a
  master plan, written in a molecular language,
  using DNA instead of paper and ink

• Therefore, each cell in your body has a copy of
  your genome, which is, in essence, a master plan
  for making you.

But Most of My Cells Dont Make Melanin-- Right?
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How BIG is 3.2 Billion DNA Letters?
Human Genome

• Human Genome Has 3.2 Billion
• DNA Letters 3,200,000,000 bp
• 3.2 billion (3.2 x 109) is the same as
• 200 (1000 pages each) New York
• City telephone books
• 3 Gigabyte computer hard drive
• a person typing 60 words/minute
• for 8 hours/day, would take more than 50 years to
  type the entire human genome sequence
• placed end-to-end the DNA in one
• human cell extends almost 6 feet

One DNA base-pair
Genome Facts NOVA Online Access Excellence Cell
to Chromosome to DNA
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How Big are Plant Genomes?
Plant Genome

Human Genome Has 3.2 Billion DNA Letters 3200
million bp Maize (Corn) Genome has 2.5 Billion
DNA Letters 2500 million bp Arabidopsis Genome
has 125 million bp Rice Genome has 430
million bp Wheat Genome has 16,000 million bp

One DNA base-pair
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Nucleus Executes The Genome Master Plan
PLANT CELL

• Genome Master Plan is Executed
• DNA is copied into RNA code (mRNA)
• (2) mRNA is transported to the cytoplasm
• (3) Translate mRNA code into chain of protein
  building blocks at the ribosome.

NUCLEUS

CHLOROPLAST
CELL WALL
DNA
(2)
(1)
mRNA
(3)
mRNA



PROTEIN

mRNA

NUCLEAR PORE



RIBOSOME
CYTOPLASM
CYTOPLASM
CELL MEMBRANE
Danny Schnell, BMB
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DNA is Packaged Into Chromosomes
DNA double helix
GENE (blue)
Several GENES along a length of DNA
DNA is coiled around proteins (more on this
later)
Small region of unwrapped chromosome
Loosely wrapped DNA in chromosome
Tightly wrapped chromosome
Adapted from Alberts et al. Molecular Cell
Biology
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How Many Chromosomes Are There?

• Bacteria usually have one circular
• chromosome and no nucleus
• Organisms with nuclei have variable numbers of
  chromosomes
• depending on the species
• Mosquito 6
• Chimpanzees 48
• Goldfish 94

 
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How Many Chromosomes Are There?
Some plants have few chromosomes like
Arabidopsis. Others, like sugarcane, have many.
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Wheat
24
Rice
 
10
Arabidopsis
Sugarcane
100
20
Maize
Potato
48
Tomato
24
Cabbage
20
Carrot
18
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Chromosomes are Dynamic Structures
Human Chromosomes
Metaphase Chromosome
CONDENSED EXTENDED
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DNA Discovery

• Discover DNA It is Changing OUR Lives
• Human Cloning
• (imagine dozens of identical siblings!!)
• Designer Babies
• (and all of them perfect!?!)
• Stem Cells
• (can we help paralyzed people to walk?)
• Gene Therapy
• (can we fix broken genes?)
• DNA Fingerprinting
• (nowhere to hide??!!)

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Some Questions Students May Have?
Most of us know we have DNA and genes
What are genes and how much do they influence us?
What do genes and DNA actually do?
What is a genome?
What is the Human Genome Project?
Will the Human Genome Project affect me?
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Our DNA Story
Variations on the Human Theme! People look very
different from each other. Yet we all have
features in common, 2 arms, 2 legs, one head, one
nose, etc.
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Traits are Inherited

• Traits are characteristics that vary among
  individuals.
• Simple trait
• Eye color Blue, brown, green
• Seed coat color
• Complex traits
• Blood types A, B, AB, O
• Plant height.
• Plant disease resistance.
• Connection between traits and genes TRAITS are
  inherited from parents through GENES!

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Genes are Responsible for the Traits You Inherit

• Genes determine
• physical traits and influence personality
• biological characteristics such as blood type
• level of health risk (heart disease, stroke,
  alcoholism, Alzheimers)
• specific genetic diseases (sickle cell,
  hemophilia, cancer, etc.)
• inherited traits that are passed on to your
  biological children
• However the environment always affects the
  result of genetic inheritance.
• Example genes for growth are influenced by
  nutrition
• available during child development