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Chapter​ ​13:​ ​RNA​ ​and​ ​Protein​ ​Synthesis 
13
...
​ ​They​ ​figured​ ​out​ ​how​ ​replication​ ​separated​ ​two​ ​stands,​ ​created​ ​complementary
ones​ ​(yada​ ​yada​ ​yada)
...
​ ​So​ ​they​ ​discovered​ ​RNA​,
a​ ​nucleic​ ​acid​ ​like​ ​DNA,​ ​also​ ​made​ ​up​ ​of​ ​a​ ​long​ ​chain​ ​of​ ​nucleotides
...
’​ ​It​ ​copies​ ​a​ ​part​ ​of​ ​the​ ​base
sequence​ ​in​ ​DNA​ ​and​ ​uses​ ​the​ ​info​ ​to​ ​direct​ ​the​ ​productions​ ​of​ ​certain​ ​proteins​ ​that​ ​will​ ​affect
your​ ​genes
...

- Sugar​ ​in​ ​RNA​ ​is​ ​ribose,​ ​not​ ​deoxyribose​ ​(no​ ​oxygen)
- RNA​ ​is​ ​single​ ​stranded--​ ​not​ ​double
- Uracil​ ​is​ ​used​ ​in​ ​place​ ​of​ ​thymine
...
​ ​It​ ​is​ ​involved​ ​in​ ​protein​ ​synthesis
...

- Messenger​:​ ​carries​ ​instructions​ ​for​ ​assembling​ ​amino​ ​acids​ ​into​ ​proteins,​ ​takes​ ​it​ ​from
DNA​ ​to​ ​other​ ​parts​ ​of​ ​the​ ​cell
...
​ ​Ribosomes​ ​are​ ​made​ ​of​ ​two
subunits
...
​ ​(rRNA)
- Transfer​:​ ​When​ ​the​ ​protein​ ​is​ ​built,​ ​this​ ​RNA​ ​molecule​ ​transfers​ ​each​ ​amino​ ​acid​ ​to​ ​the
ribosomes
...
​ ​(tRNA)

RNA​ ​Synthesis:​​ ​The​ ​creation​ ​of​ ​RNA
...
​ ​Here,​ ​segments​ ​of​ ​DNA​ ​serve​ ​as​ ​templates​ ​to
produce​ ​complementary​ ​RNA​ ​molecules​ ​(transcribe​ ​anyone?)
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​ ​While​ ​eukaryotes
RNA​ ​is​ ​created​ ​in​ ​the​ ​nucleus​ ​then​ ​moved​ ​to​ ​the​ ​cytoplasm​ ​for​ ​protein​ ​synthesis
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​ ​Transcription​ ​requires​ ​an​ ​enzyme​ ​called​ ​RNA​ ​polymerase
...
​ ​It​ ​then​ ​uses
one​ ​strand​ ​of​ ​DNA​ ​as​ ​a​ ​template​ ​to​ ​assemble​ ​nucleotides​ ​and​ ​create​ ​a​ ​complementary​ ​RNA
strand​ ​parallel​ ​to​ ​the​ ​DNA​ ​strand
...
​ ​A​ ​region​ ​of​ ​the​ ​DNA​ ​that​ ​has​ ​a​ ​specific
base​ ​sequence
...
​ ​The​ ​same​ ​signal​ ​is​ ​used​ ​to​ ​stop​ ​the​ ​process​ ​of
transcription
...
​ ​Cephalopods!)
pre-mRNA​ ​molecules​ ​need​ ​editing​ ​before​ ​they​ ​are​ ​processed
...
​ ​The​ ​portions​ ​that​ ​are​ ​cut​ ​out​ ​and​ ​discarded​ ​are​ ​called​ ​introns​
...
​ ​The​ ​exons​,​ ​the​ ​remaining​ ​pieces,​ ​are​ ​spliced​ ​together
to​ ​form​ ​the​ ​final​ ​mRNA
...
​ ​splice​ ​out​ ​the​ ​unneeded​ ​genes)
...
2​ ​-​ ​Ribosomes​ ​and​ ​Protein​ ​Synthesis

To​ ​decode​ ​a​ ​genetic​ ​message,​ ​you​ ​have​ ​to​ ​transcribe​ ​a​ ​nucleotide​ ​base​ ​sequence​ ​from​ ​DNA​ ​to
RNA
...
​ ​Proteins​ ​are​ ​made​ ​by​ ​joining​ ​amino
acids​ ​together​ ​into​ ​long​ ​chains​ ​called​ ​polypeptides​
...
​ ​And​ ​these​ ​bases​ ​form​ ​a​ ​“language”​ ​with​ ​these​ ​4
letters
...
​ ​Genetic​ ​code​ ​is​ ​read​ ​three​ ​“letters”​ ​at​ ​a​ ​time
...
​ ​The​ ​“words”​ ​are
known​ ​as​ ​codons
...

Essentially,​ ​three​ ​bases​ ​correspond​ ​to​ ​the​ ​addition/creation​ ​of​ ​one​ ​amino​ ​acid​ ​to​ ​the​ ​protein’s
chain
...
​ ​Then​ ​one​ ​of​ ​the​ ​4​ ​subsetted​ ​letters,​ ​and​ ​finally
a​ ​letter​ ​that​ ​specifies​ ​the​ ​amino​ ​acid​ ​to​ ​be​ ​made​ ​into​ ​the​ ​chain
...
​ ​Tyrosine​ ​is​ ​both​ ​UAU​ ​and​ ​UAC)
...
​ ​After​ ​this​ ​start​ ​codon,​ ​the​ ​mRNA​ ​is​ ​read,​ ​three​ ​bases​ ​at​ ​a​ ​time,​ ​until​ ​it​ ​reaches​ ​a​ ​stop
codon​ ​(UAA,​ ​UAG,​ ​UGA)
...

Translation
When​ ​a​ ​polypeptide​ ​is​ ​complete,​ ​it​ ​joins​ ​with​ ​other​ ​polypeptides​ ​and​ ​becomes​ ​a​ ​functional
protein
...
​ ​The​ ​decoding​ ​of​ ​a​ ​mRNA​ ​message​ ​into​ ​a​ ​protein​ ​is​ ​called​ ​translation​
...


It​ ​starts​ ​when​ ​a​ ​ribosome​ ​attaches​ ​to​ ​a​ ​mRNA​ ​molecule​ ​in​ ​the​ ​cytoplasm
...
​ ​The​ ​ribosome​ ​takes​ ​it​ ​and
attaches​ ​them​ ​together​ ​in​ ​a​ ​chain
...

Also,​ ​each​ ​tRNA​ ​molecule​ ​has​ ​three​ ​unpaired​ ​bases,​ ​called​ ​the​ ​anticodon,​ ​they​ ​are
complementary​ ​to​ ​one​ ​mRNA​ ​codon
...

For​ ​example​ ​with​ ​the​ ​tRNA​ ​molecule​ ​for​ ​methionine,​ ​the​ ​anticodon​ ​is​ ​UAC,​ ​which​ ​will​ ​pair​ ​with
the​ ​methionine​ ​codon,​ ​AUG
...
​ ​The​ ​bond​ ​that
holds​ ​the​ ​molecule​ ​to​ ​the​ ​tRNA​ ​is​ ​broken​ ​(see,​ ​they​ ​are​ ​carrying​ ​it)​ ​and​ ​the​ ​tRNA​ ​exits​ ​the
ribosome
...
​ ​When​ ​it
reaches​ ​a​ ​stop,​ ​the​ ​ribosome​ ​lets​ ​go​ ​of​ ​the​ ​newly​ ​made​ ​polypeptide​ ​and​ ​the​ ​mRNA​ ​molecule
...


tRNA​ ​is​ ​an​ ​adaptor​ ​that​ ​allows​ ​the​ ​ribosome​ ​to​ ​“read”​ ​the​ ​mRNA
...
​ ​They​ ​hold​ ​ribosomal​ ​proteins​ ​in​ ​place​ ​and​ ​help​ ​to​ ​locate
the​ ​beginning​ ​of​ ​the​ ​mRNA​ ​message
...
​ ​The​ ​central​ ​dogma​ ​of
molecular​ ​biology​ ​is​ ​that​ ​information​ ​is​ ​transferred​ ​from​ ​DNA​ ​to​ ​RNA​ ​to​ ​proteins
...


13
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Gene​ ​mutations​ ​that​ ​involve​ ​changes​ ​in​ ​one​ ​or​ ​a​ ​few​ ​nucleotides​ ​are​ ​called​ ​point​ ​mutations
...
​ ​Characterized​ ​by​ ​substitution,​ ​insertion,​ ​or
deletion
...


Substitution:​ ​One​ ​base​ ​is​ ​changed​ ​to​ ​a​ ​different​ ​base
...
​ ​For​ ​example,​ ​if
the​ ​codon​ ​is​ ​accidentally​ ​changed​ ​from​ ​CCC​ ​to​ ​CCA,​ ​it's​ ​allright​ ​because​ ​the​ ​the​ ​same​ ​amino
acid​ ​(proline)​ ​would​ ​be​ ​specified
...

Insertions​ ​and​ ​Deletions:​ ​When​ ​one​ ​base​ ​is​ ​inserted​ ​or​ ​deleted​ ​from​ ​the​ ​DNA​ ​sequence
...
​ ​Basically,​ ​the​ ​entire​ ​order​ ​of​ ​the​ ​codons​ ​is​ ​compromised
...
​ ​Because​ ​they​ ​shift​ ​the​ ​“reading​ ​frame”​ ​of​ ​the​ ​message
...
​ ​They​ ​can
change​ ​the​ ​location​ ​of​ ​genes​ ​and​ ​can​ ​change​ ​the​ ​number​ ​of​ ​copies​ ​of​ ​each​ ​gene
...

- Duplication:​ ​Extra​ ​copy​ ​of​ ​all​ ​or​ ​part​ ​of​ ​a​ ​chromosome
...

- Translocation:​ ​when​ ​one​ ​part​ ​of​ ​a​ ​chromosome​ ​breaks​ ​off​ ​and​ ​attaches​ ​to​ ​another
...
​ ​Like​ ​pesticides,​ ​plant​ ​alkaloids,
tobacco,​ ​and​ ​environmental​ ​pollutants
...
​ ​These
agents​ ​can​ ​produce​ ​mutations​ ​at​ ​high​ ​rates
...


Negatives:​ ​Defective​ ​proteins,​ ​which​ ​can​ ​disrupt​ ​normal​ ​biological​ ​activities​ ​and​ ​result​ ​in
genetic​ ​disorders
...

Positives:​ ​Sometimes​ ​mutations​ ​produce​ ​proteins​ ​with​ ​new​ ​or​ ​altered​ ​functions​ ​that​ ​can​ ​be
useful​ ​to​ ​organisms​ ​in​ ​different​ ​or​ ​changing​ ​environments
...

The​ ​condition​ ​where​ ​organisms​ ​have​ ​extra​ ​sets​ ​of​ ​chromosomes​ ​is​ ​called​ ​polyploidy​
...


13
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​ ​To
conserve​ ​energy​ ​and​ ​resources,​ ​they​ ​regulate​ ​and​ ​only​ ​use​ ​genes​ ​needed​ ​to​ ​function
...
​ ​DNA-binding​ ​proteins​ ​in​ ​prokaryotes​ ​regulate​ ​genes​ ​by​ ​controlling​ ​(hijacking)
transcription
...
​ ​Usually​ ​having​ ​related
functions
...
​ ​E
...
​ ​These​ ​3​ ​are​ ​called​ ​the​ ​lac​ ​operon
...
​ ​Coli​ ​need​ ​to​ ​turn​ ​these​ ​genes​ ​off​ ​and​ ​on?​ ​Lactose​ ​is​ ​made​ ​of​ ​two​ ​simple​ ​sugars
...
​ ​The​ ​task​ ​is​ ​done​ ​by​ ​proteins​ ​coded
by​ ​genes​ ​of​ ​the​ ​lac​ ​operon
...
​ ​When​ ​lactose​ ​isn’t​ ​present,​ ​lac​ ​genes​ ​are​ ​turned​ ​off​ ​by
proteins​ ​that​ ​bind​ ​to​ ​DNA​ ​and​ ​block​ ​transcription
...
​ ​Promoter​,​ ​where
RNA-polymerase​ ​binds​ ​to​ ​start​ ​transcription,​ ​and​ ​the​ ​operator​
...

When​ ​lac​ ​repressor​ ​binds​ ​to​ ​the​ ​operator​ ​region,​ ​RNA-polymerase​ ​can​ ​no​ ​longer​ ​transcribe
...

So​ ​how​ ​does​ ​it​ ​turn​ ​on​ ​then?​ ​The​ ​lac​ ​repressor​ ​has​ ​a​ ​binding​ ​site​ ​(it​ ​is​ ​a​ ​binder​ ​and​ ​a​ ​bindee-cool)​ ​for​ ​lactose
...
​ ​Now​ ​RNA-polymerase​ ​can​ ​do​ ​its​ ​job​ ​and​ ​transcribe,​ ​so​ ​it​ ​is​ ​turned​ ​on
...
​ ​TATA,​ ​TATA,​ ​TATA,​ ​TATA--​ ​I'll​ ​stop​ ​now
...
​ ​It​ ​basically​ ​binds​ ​a​ ​protein​ ​that​ ​positions​ ​RNA​ ​polymerase​ ​by
marking​ ​a​ ​point​ ​before​ ​the​ ​beginning​ ​of​ ​a​ ​gene
...
​ ​ ​Some​ ​factors​ ​enhance​ ​transcription,​ ​some​ ​attract​ ​RNA

polymerase,​ ​some​ ​black​ ​access​ ​to​ ​certain​ ​genes
...

Cell​ ​specialization:​ ​So​ ​why​ ​is​ ​eukaryotic​ ​gene​ ​regulation​ ​so​ ​weird​ ​and​ ​convoluted?​ ​Well,​ ​each
major​ ​organ​ ​uses​ ​different​ ​types​ ​of​ ​cells
...
​ ​keratin​ ​in​ ​skin​ ​cells,​ ​nerve​ ​cells​ ​etc
...
​ ​It​ ​was
only​ ​seen​ ​recently​ ​(sigh)​ ​that​ ​they​ ​are​ ​used​ ​in​ ​regulation
...
​ ​After
formation,​ ​the​ ​small​ ​strands​ ​fold​ ​into​ ​double​ ​stranded​ ​“hairpin​ ​loops”​ ​and​ ​an​ ​enzyme​ ​called​ ​the
“dicer”​ ​dices​ ​them​ ​into​ ​miRNA​
...

The​ ​strand​ ​then​ ​attaches​ ​to​ ​a​ ​cluster​ ​of​ ​proteins​ ​to​ ​create​ ​the​​ ​silencing​ ​complex​
...
​ ​It​ ​stops​ ​some​ ​of​ ​the
mRNA​ ​from​ ​working
...
​ ​This​ ​is
called​ ​RNA​ ​interference​ ​(RNAi)​,​ ​where​ ​gene​ ​expression​ ​is​ ​blocked​ ​by​ ​a​ ​silencing​ ​complex
...
​ ​This​ ​gives​ ​the​ ​possibility
of​ ​turning​ ​off​ ​the​ ​expression​ ​of​ ​genes​ ​from​ ​viruses​ ​and​ ​cancer​ ​cells,​ ​which​ ​can​ ​maybe​ ​treat​ ​and
cure​ ​disease
...
​ ​Homeotic​ ​genes​​ ​regulate​ ​organs
that​ ​develop​ ​in​ ​specific​ ​parts​ ​of​ ​the​ ​body
...
​ ​Hox​ ​genes​​ ​tell​ ​the​ ​cells
of​ ​the​ ​body​ ​how​ ​to​ ​differentiate​ ​during​ ​growth

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