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From DNA to Protein
 DNA is just instructions
 Need to use the instructions
 2 processes
 Transcription—molecules of RNA formed from DNA
 Translation—RNA shipped from nucleus to cytoplasm to be used in polypeptide
DNA to RNA
 3 classes of DNA
 Messenger RNA: carries blueprint to ribosome
 Ribosomal RNA: combines with proteins to form ribosomes upon polypeptides are
assembled
 Transfer RNA: brings correct amino acids to ribosome and pairs up with mRNA
code for that amino acid
RNA
 Different sugar: ribose
 1 different base: uracil instead of thymine
 Cellular distribution: nucleus and cytoplasm
Transcription compared to Replication
 Only 1 region of DNA strand is used as a template
 RNA polymerase instead of DNA polymerase
 Result of transcription is single-stranded RNA
RNA
 Transcription begins when RNA polymerase binds to promoter region
 Moves along gene until the end of the gene
 Copies code
 Sustitutes uracil (U) for thymine base
RNA
 After copying info, RNA is modified
 Cap is attached to 5’end: start
 Tail is attached at end (poly A): finish
 RNA is edited
 Introns—no code—removed
 Exons—code—used to sequence amino acids
The Structure of Proteins
 Proteins are made from subunits called amino acids
 Hundreds of thousands of different proteins made by all living things are remarkably
similar in their construction
 All proteins in living things are assembled from only 20 different amino acids
The Structure of Proteins
 These 20 amino acids are strung together in different orders and to different lengths
to make different proteins
 The English alphabet contains a similar number of letters, but we can form an
infinite number of sentences with these letters
The Structure of Proteins
 A linear chain of amino acids forms a polypeptide
 A polypeptide chain can be more than 20 amino acids in length
 Only 20 different amino acids are used
 Some amino acids are used multiple times
The Structure of Proteins
 One or more polypeptide chains are folded into a single protein
 Each protein has a particular three-dimensional shape
 “Protein conformation”
 This shape is stabilized by chemical bonds
 Covalent, ionic, and hydrogen bonds
 The shape of a protein is critical to its function
4.3 A Closer Look at Transcription
DNA
 Polymer of deoxynucleotides
 Sugar
 Deoxyribose
 Bases
 G, A, C, and T
 Phosphates
RNA
 Polymer of nucleotides
 Sugar
 Ribose
 Bases
 G, A, C, and U
 Phosphates
A Closer Look at Transcription
 The enzyme RNA polymerase unwinds a region of the DNA double helix
 (RNA polymerase is actually an enzyme complex, consisting of a group of
enzymes)
 The two strands of the double helix are separated
 Single-stranded DNA is exposed
A Closer Look at Transcription
 RNA polymerase assembles complementary RNA nucleotides
 DNA:RNA base pairing similar to DNA:DNA
 Recall base pairing from Chapter 13
 G:C
 C:G
 A:U 
 T:A
A Closer Look at Transcription
 The completed portion of the RNA molecule separates from the DNA
 DNA double helix is rejoined in this region
 RNA polymerase moves along and unwinds more of the double helix
 New (untranscribed) regions of single-stranded DNA are exposed
A Closer Look at Transcription
 Upon completion of the RNA transcript
 The mRNA transcript is released from the DNA
 The DNA strands rejoin
 The DNA and enzyme are unchanged
 A new mRNA molecule has been produced
Transcription
 Transcription video
A Closer Look at Transcription
 Transcription takes place in the nucleus
 Translation takes place in the cytoplasm
 Following the production of an mRNA molecule, it must be transported to the
cytoplasm
 Transport is through a nuclear pore
14.4 A Closer Look at Translation
 Translation requires many players
 mRNA
 Ribosomes
 Transfer RNAs (tRNAs)
 Amino acids
A Closer Look at Translation
mRNA molecules
 Groups of three consecutive nucleotides are the functional units within mRNA
molecules
 “Codons”
 Each codon corresponds to a specific amino acid
 e.g., AUG  methionine
 e.g., UUU  phenylalanine
Cracking the Genetic Code
 The universal nature of the genetic code is useful in many ways
 Knowing a gene’s DNA sequence tells us the protein’s amino acid sequence
 Knowing a protein’s amino acid sequence tells us much about the gene’s DNA
sequence
 Genes from one organism can function in another organism: Makes
“biotechnology” possible
A Closer Look at Translation
tRNA molecules
 “Transfer RNA”
 Encoded by genes
 Functional as RNA molecules
 Not translated into proteins
 “Translates” information from mRNA to protein
A Closer Look at Translation
tRNA molecules
 One region binds to the mRNA molecule
 “Anticodon”
 Base pairs with mRNA codon
 Another region is linked to a specific amino acid
A Closer Look at Translation
Ribosomes
 Organelles
 Not surrounded by a membrane
 Two components
 Ribosomal RNA (rRNA)
 Encoded by a gene
 Not translated
 Forms the ribosome’s “skeleton”
 Proteins
 Attached to the rRNA scaffolding
A Closer Look at Translation
Ribosomes
 Two subunits
 Each is comprised of rRNA and protein
 When the subunits are joined, three binding sites exist
 E, P, and A
 tRNAs bind to these sites during translation
 Simultaneously bind to mRNA and tRNAs during translation
A Closer Look at Translation
Steps in translation
 mRNA binds to small ribosomal subunit
 First tRNA binds to an AUG codon
 “Start” codon
 tRNA anticodon is complementary to the mRNA codon
 tRNA already carries the amino acid methionine
 “Loaded”
A Closer Look at Translation
Steps in translation
 Large ribosomal subunit joins the ribosome
 First tRNA is in “P” site
 Second loaded tRNA arrives
 Attaches to “A” site
 Anticodon complementary to mRNA’s second codon
A Closer Look at Translation
Steps in translation
 Ribosome transfers met (aa1) to aa2
 Covalent linkage to aa2
 Met no longer attached to its tRNA
 Ribosome shifts one codon to the right
 First tRNA now in “E” site
 Second tRNA now in “P” site
 “A” site is open
A Closer Look at Translation
Steps in translation
 “Unloaded” tRNA leaves “E” (“exit”) site
 Can get “reloaded” and used again
 New loaded tRNA arrives
 Attaches to “A” site
 Anticodon complementary to mRNA’s third codon
A Closer Look at Translation
Steps in translation
 Ribosome transfers dipeptide to aa3
 Covalent linkage to aa3
 Tripeptide formed
 met-aa2-aa3-tRNA
 Ribosome shifts one codon to the right
 Repeat
A Closer Look at Translation
Steps in translation
 Ultimately, the codon in the ribosome’s “A” site will be a “stop” codon
 UAG, UGA, or UAA
A Closer Look at Translation
Steps in translation
 Ribosome transfers dipeptide to aa3
 Covalent linkage to aa3
 Tripeptide formed
 met-aa2-aa3-tRNA
 Ribosome shifts one codon to the right
 Repeat
A Closer Look at Translation
Steps in translation
 Ultimately, the codon in the ribosome’s “A” site will be a “stop” codon
 UAG, UGA, or UAA
A Closer Look at Translation
Steps in translation
 No tRNAs exist that can bind to stop codons
 Translation is terminated
 Polypeptide chain is severed from its tRNA
 Polypeptide is released
 Entire translation apparatus is disassembled
Translation
 Translation video
A Closer Look at Translation
 Translation proceeds very quickly
 E. coli can polymerize 40 amino acids per second
 A second ribosome can begin translation before the first ribosome is even done
 In fact, many ribosomes can simultaneously translate a single mRNA
A Closer Look at Translation
 Translation proceeds very quickly
 In prokaryotes, translation can even begin before transcription is complete
 Why is this not true of eukaryotes?
14.5 Genetic Regulation
 Not all genes are expressed in all cells at all times
 To do so would be wasteful
 e.g., The insulin gene is expressed only in cells of the pancreas, and not always at
the same level
 Gene expression is regulated
Genetic Regulation
 The DNA in one of your cells is about six feel long uncoiled
 Of this DNA, less than 1.2% encodes proteins
 Less than one inch of the six feet
 Most of our DNA is noncoding
 Some of it has regulatory functions
 This DNA exists both within and between genes
Genetic Regulation
 When a gene is transcribed, noncoding sequences within the coding sequences are
also transcribed
 Exons are coding sequences
 Introns are intervening “junk” sequences
 These sequences must be removed before the mRNA is functional
 Removal of introns is termed “splicing”
Genetic Regulation
Splicing
 The initial RNA transcript contains both exons and introns
 Enzymes cut the DNA at the exon/intron boundary
 The intron is discarded
 The exons are spliced back together
Genetic Regulation
 Certain genes control the development of their mid-body (“thoracic”) structures
 Hoxc8 is one of these genes
 This gene is nearly identical in reptiles, birds, and mammals
 Animal thoracic structures differ
 A chicken has 7 vertebrae
 A mouse has 13 vertebrae
Genetic Regulation
 How do nearly identical genes direct these different outcomes?
 The mouse Hoxc8 gene is transcribed more than the chicken Hoxc8 gene
 More transcription  more protein  broader distribution of the protein  more
vertebrae
 Why does this gene get transcribed more in the mouse than in the chicken?
Genetic Regulation
 Transcription begins at a DNA sequence termed a “promoter”
 RNA polymerase binds to the promoter
 The expression of a gene is largely determined by the ability of RNA polymerase to
bind to the gene’s promoter
Genetic Regulation
 Enhancer elements often exist upstream of the promoter
 Proteins bind to enhancer elements
 This binding can make it easier for RNA polymerase to bind
 Expression of the gene is increased
Genetic Regulation
 The Hoxc8 enhancer sequence differs between the mouse and the chicken
 The sets of proteins that bind to these enhancer elements differ between the
species
Genetic Regulation
 These enhancer-binding proteins have different effects in these two species
 Transcription greatly enhanced in mouse
 Transcription mildly enhanced in chicken
Genetic Regulation
 RNA regulates DNA
 Most RNA transcribed is mRNA
 mRNA is translated into protein
 Some RNA is not translated into protein
 tRNA
 rRNA
 microRNAs
Genetic Regulation
 All microRNAs identified to date reduce the production of specific proteins
 Interfere with mRNAs
 Target mRNAs for destruction
Genetic Regulation
 All organisms possess genes
 Eukaryotes possess thousands, though the numbers differ between species
 Humans possess ~ 20,000 – 25,000
Genetic Regulation
 The number of genes in different eukaryotes does not vary that extensively
 The regulation of these genes varies more extensively
 We likely contain more regulatory DNA than protein-encoding DNA
 Gene regulation accounts for much of the differences between species
The Magnitude of the Genetic Operation
 Humans possess
 20,000 – 25,000 genes
 3.2 billion base pairs
 100 trillion cells
Epigenetics
 Refers to all modifications to genes other than changes in the DNA sequence itself
 Epigenetic modifications include addition of molecules, like methyl groups, to the DNA
backbone
 Adding these groups changes the appearance and structure of DNA
 Alters how a gene can interact with important interpreting (transcribing) molecules in
the cell's nucleus.
Epigenetics
 Epigenetic modifications, or "marks," generally turn genes on or off
 Allowing or preventing the gene from being used to make a protein
 Mutations and bigger changes in the DNA sequence (insertions or deletions) change
the sequence of the DNA and RNA
 May affect the sequence of the protein as well
Imprinting
 Adding methyl groups to backbone of DNA: marking
 Marks both distinguish the gene copies and tell the cell which copy to use to make
proteins
 Maternal or paternal genes may be marked
 Non-Mendelian patterns of genetics