1. From Gene to Protein
How Genes Work
(Ch. 17)

2. What do genes code for? How does DNA code for cells & bodies? DNA
how are cells and bodies made from the instructions in DNA
DNA
proteins
cells
bodies

3. DNA gets all the glory, but proteins do all the work!
The “Central Dogma”
Flow of genetic information in a cell
How do we move information from DNA to proteins?
transcription
translation
DNA
RNA
protein
trait
To get from the chemical language of DNA to the chemical language of proteins requires 2 major stages:
transcription and translation
DNA gets all the glory, but proteins do all the work!
replication

4. Metabolism taught us about genes
Inheritance of metabolic diseases
suggested that genes coded for enzymes
each disease (phenotype) is caused by non-functional gene product
lack of an enzyme
Taysachs
PKU (phenylketonuria)
albinism
Am I just the sum of my proteins?
metabolic pathway
disease
disease
disease
disease A B C D E    
enzyme 1
enzyme 2
enzyme 3
enzyme 4

5. one gene : one enzyme hypothesis
Beadle & Tatum
1941 | 1958
one gene : one enzyme hypothesis
George Beadle
Edward Tatum
"for their discovery that genes act by regulating definite chemical events"

6. Beadle & Tatum Wild-type Neurospora Minimal medium Select one of
the spores
Grow on
complete medium
control
Nucleic
acid
Choline
Pyridoxine
Riboflavin
Arginine
Minimal media supplemented only with…
Thiamine
Folic
Niacin
Inositol
p-Amino
benzoic acid
Test on minimal
medium to confirm
presence of mutation
Growth on
complete
X rays or ultraviolet light
asexual
spores
create mutations
positive control
negative control
mutation identified
experimentals
amino acid supplements

7. From gene to protein DNA mRNA protein trait nucleus cytoplasmaa a
nucleus
cytoplasm
transcription
translation
DNA
mRNA
protein
ribosome
trait

8. From DNA nucleic acid language to RNA nucleic acid language
Transcription
From DNA nucleic acid language to RNA nucleic acid language

9. RNA DNA RNA ribose sugar N-bases single stranded lots of RNAs
uracil instead of thymine
U : A
C : G
single stranded
lots of RNAs
mRNA, tRNA, rRNA, siRNA…
transcription
DNA
RNA

10. Transcription Making mRNA transcribed DNA strand = template strand
untranscribed DNA strand = coding strand
same sequence as RNA
synthesis of complementary RNA strand
enzyme
RNA polymerase
coding strand 3 A G C A T C G T 5 A G A A A G T C T T C T C A T A C G
DNA T 3 C G T A A T 5 G G C A U C G U T 3 C
unwinding G T A G C A
rewinding
mRNA
RNA polymerase
template strand
build RNA 53 5

11. RNA polymerases 3 RNA polymerase enzymes RNA polymerase 1
only transcribes rRNA genes
makes ribosomes
RNA polymerase 2
transcribes genes into mRNA
RNA polymerase 3
only transcribes tRNA genes
each has a specific promoter sequence it recognizes

12. Which gene is read? Promoter region Enhancer region
binding site before beginning of gene
TATA box binding site
binding site for RNA polymerase & transcription factors
Enhancer region
binding site far upstream of gene
turns transcription on HIGH

13. Transcription Factors
Initiation complex
transcription factors bind to promoter region
suite of proteins which bind to DNA
hormones?
turn on or off transcription
trigger the binding of RNA polymerase to DNA

14. Matching bases of DNA & RNA
Match RNA bases to DNA bases on one of the DNA strands C U G A G U G U C U G C A A C U A A G C
RNA
polymerase U 5' A 3' G A C C T G G T A C A G C T A G T C A T C G T A C C G T

15. Eukaryotic genes have untranscribed regions!
Eukaryotic genes are not continuous
exons = the real gene
expressed / coding DNA
introns = the junk
inbetween sequence
introns come out!
intron = noncoding (inbetween) sequence
eukaryotic DNA
exon = coding (expressed) sequence

16. mRNA splicing Post-transcriptional processing
eukaryotic mRNA needs work after transcription
primary transcript = pre-mRNA
mRNA splicing
edit out introns
make mature mRNA transcript
eukaryotic RNA is about 10% of eukaryotic gene.
intron = noncoding (inbetween) sequence
~10,000 bases
eukaryotic DNA
exon = coding (expressed) sequence
pre-mRNA
primary mRNA
transcript
~1,000 bases
mature mRNA
transcript
spliced mRNA

17. Discovery of exons/introns
1977 | 1993
Richard Roberts
Philip Sharp
Beta thalassemia is an inherited blood disorder that reduces the production of hemoglobin. Symptoms of beta thalassemia occur when not enough oxygen gets to various parts of the body due to low levels of hemoglobin and a shortage of red blood cells (anemia).
Signs and symptoms of thalassemia major appear in the first 2 years of life. Infants have life-threatening anemia and become pale and listless. They also have a poor appetite, grow slowly, and may develop yellowing of the skin and whites of the eyes (jaundice). The spleen, liver, and heart may be enlarged, and bones may be deformed. Adolescents with thalassemia major may experience delayed puberty.
Thalassemia is a quantitative problem of too few globins synthesized, whereas sickle-cell anemia is a qualitative problem of synthesis of an incorrectly functioning globin.
adenovirus
CSHL
MIT
common cold
beta-thalassemia

18. Splicing must be accurate
No room for mistakes!
a single base added or lost throws off the reading frame
AUGCGGCTATGGGUCCGAUAAGGGCCAU
AUGCGGUCCGAUAAGGGCCAU
AUG|CGG|UCC|GAU|AAG|GGC|CAU
Met|Arg|Ser|Asp|Lys|Gly|His
AUGCGGCTATGGGUCCGAUAAGGGCCAU
AUGCGGGUCCGAUAAGGGCCAU
AUG|CGG|GUC|CGA|UAA|GGG|CCA|U
Met|Arg|Val|Arg|STOP|

19. we just broke a biological “rule”!
RNA splicing enzymes
Whoa! I think
we just broke a biological “rule”!
snRNPs
small nuclear RNA
proteins
Spliceosome
several snRNPs
recognize splice site sequence
cut & paste gene
snRNPs
exon
intron
snRNA 5' 3'
spliceosome
exon
excised
intron 5' 3'
lariat
mature mRNA
No, not smurfs!
“snurps”

20. Starting to get hard to define a gene!
Alternative splicing
Alternative mRNAs produced from same gene
when is an intron not an intron…
different segments treated as exons
Starting to get hard to define a gene!

21. More post-transcriptional processing
Need to protect mRNA on its trip from nucleus to cytoplasm
enzymes in cytoplasm attack mRNA
protect the ends of the molecule
add 5 GTP cap
add poly-A tail
longer tail, mRNA lasts longer: produces more protein
eukaryotic RNA is about 10% of eukaryotic gene. A
3' poly-A tail
mRNA 5'
5' cap 3' G P
A’s

22. From nucleic acid language to amino acid language
Translation
From nucleic acid language to amino acid language

23. How does mRNA code for proteins?
TACGCACATTTACGTACGCGG
DNA 4
ATCG
AUGCGUGUAAAUGCAUGCGCC
mRNA 4
AUCG ?
MetArgValAsnAlaCysAla
protein 20
How can you code for 20 amino acids with only 4 nucleotide bases (A,U,G,C)?

24. mRNA codes for proteins in triplets
TACGCACATTTACGTACGCGG
DNA
codon
AUGCGUGUAAAUGCAUGCGCC
mRNA
AUGCGUGUAAAUGCAUGCGCC
mRNA ?
MetArgValAsnAlaCysAla
protein

25. WHYDIDTHEREDBATEATTHEFATRAT WHYDIDTHEREDBATEATTHEFATRAT
Cracking the code
1960 | 1968
Nirenberg & Khorana
Crick
determined 3-letter (triplet) codon system
WHYDIDTHEREDBATEATTHEFATRAT
WHYDIDTHEREDBATEATTHEFATRAT
Nirenberg (47)& Khorana (17)
determined mRNA–amino acid match
added fabricated mRNA to test tube of ribosomes, tRNA & amino acids
created artificial UUUUU… mRNA
found that UUU coded for phenylalanine

26. Marshall Nirenberg
1960 | 1968
Har Khorana

27. The code Code for ALL life!
strongest support for a common origin for all life
Code is redundant
several codons for each amino acid
3rd base “wobble”
Why is the wobble good?
Strong evidence for a single origin in evolutionary theory.
Start codon
AUG
methionine
Stop codons
UGA, UAA, UAG

28. How are the codons matched to amino acids?3 5
DNA
TACGCACATTTACGTACGCGG 5 3
mRNA
AUGCGUGUAAAUGCAUGCGCC
codon 3 5
UAC
Met
GCA
Arg
tRNA
CAU
Val
anti-codon
amino acid

29. Transfer RNA structure
“Clover leaf” structure
anticodon on “clover leaf” end
amino acid attached on 3 end

30. tryptophan attached to tRNATrp tRNATrpbinds to UGG condon of mRNA
Loading tRNA
AminoacyltRNAsynthetase
enzyme which bonds amino acid to tRNA
bond requires energy
ATP AMP
bond is unstable
so it can release amino acid at ribosome easily
Trp
C=O
Trp
Trp
C=O OH
H2O
The tRNA-amino acid bond is unstable. This makes it easy for the tRNA to later give up the amino acid to a growing polypeptide chain in a ribosome. OH O
C=O O
activating
enzyme
tRNATrp A C C U G G
mRNA
anticodon
tryptophan attached to tRNATrp
tRNATrpbinds to UGG condon of mRNA

31. Ribosomes Facilitate coupling of tRNAanticodon to mRNA codon Structure
organelle or enzyme?
Structure
ribosomal RNA (rRNA) & proteins
2 subunits
large
small E P A

32. Ribosomes A site (aminoacyl-tRNA site) P site (peptidyl-tRNA site)
holds tRNA carrying next amino acid to be added to chain
P site (peptidyl-tRNA site)
holds tRNA carrying growing polypeptide chain
E site (exit site)
emptytRNA leaves ribosome from exit site
Met U A C 5' U G A 3' E P A

33. Building a polypeptide1 2 3
Initiation
mRNA, ribosome subunits, initiator tRNA come together
Elongation
adding amino acids based on codons
Termination
STOP codon = Release factor
Leu
Val
release
factor
Ser
Met
Met
Met
Met
Leu
Leu
Leu
Ala
Trp
tRNA C A G U A C U A C G A C A C G A C A 5' U 5' U A C G A C 5' A A A U G C U G U A U G C U G A U A U G C U G A A U 5' A A U
mRNA A U G C U G 3' 3' 3' 3' A C C U G G U A A E P A 3'

34. start of a secretory pathway
Protein targeting
Destinations:
secretion
nucleus
mitochondria
chloroplasts
cell membrane
cytoplasm
etc…
Signal peptide
address label
start of a secretory pathway

35. Can you tell the story? exon intron 5' GTP cap
RNA polymerase
DNA
Can you tell the story?
amino acids
exon
intron
tRNA
pre-mRNA
5' GTP cap
mature mRNA
aminoacyltRNA synthetase
poly-A tail
large ribosomal subunit 3'
polypeptide 5'
tRNA
small ribosomal subunit E P A
ribosome

36. The Transcriptional unit (gene?)
enhancer
1000+b
translation
start
translation
stop
exons
20-30b
transcriptional unit (gene)
RNA
polymerase 3'
TAC
ACT 5'
TATA
DNA
transcription
start
UTR
introns
transcription
stop
UTR
promoter
DNA
pre-mRNA 5' 3'
mature mRNA 5' 3'
GTP
AAAAAAAA

37. Protein Synthesis in Prokaryotes (Ch. 18)
Bacterial chromosome
Protein Synthesis in Prokaryotes (Ch. 18)
Transcription
mRNA
Psssst… no nucleus!
Cell
membrane
Cell wall

38. Prokaryote vs. Eukaryote genes
Prokaryotes
DNA in cytoplasm
circular chromosome
naked DNA
no introns
Eukaryotes
DNA in nucleus
linear chromosomes
DNA wound on histone proteins
introns vs. exons
Walter Gilbert hypothesis:
Maybe exons are functional units and introns make it easier for them to recombine, so as to produce new proteins with new properties through new combinations of domains.
Introns give a large area for cutting genes and joining together the pieces without damaging the coding region of the gene…. patching genes together does not have to be so precise.
intron = noncoding (inbetween) sequence
eukaryotic
DNA
introns come out!
exon = coding (expressed) sequence

39. Translation in Prokaryotes
Transcription & translation are simultaneous in bacteria
DNA is in cytoplasm
no mRNA editing
ribosomes read mRNA as it is being transcribed

40. Translation: prokaryotes vs. eukaryotes
Differences between prokaryotes & eukaryotes
time & physical separation between processes
takes eukaryote ~1 hour from DNA to protein
no RNA processing

41. Mutations
(Ch. 17)

42. When do mutations affect the next generation?
Point mutations
single base change
silent mutation
no amino acid change
redundancy in code
missense
change amino acid
nonsense
change to stop codon
When do mutations affect the next generation?

43. Point mutation lead to Sickle cell anemia
What kind of mutation?
Missense!

44. Mutations Frameshift shift in the reading frame
changes everything “downstream”
insertions
adding base(s)
deletions
losing base(s)
Where would this mutation cause the most change: beginning or end of gene?

46. What’s the value of mutations?

47. Review Questions

48. 1. If proteins were composed of only 12 different kinds of amino acids, what would be the small-est possible codon size in a genetic system with four different nucleotides? 1 2 3 4 12
Answer: b
Source: Barstow - Test Bank for Biology, Seventh Edition, Question #9

49. 2. A portion of the genetic code is UUU = phenylalanine, GCC = alanine, AAA = lysine, and CCC = proline. Assume the correct code places the amino acids phenylalanine, alanine, and lysine in a protein (in that order). Which of the following DNA sequences would substitute proline for alanine?
AAA-CGG-TTA
AAT-CGG-TTT
AAA-CCG-TTT
AAA-GGG-TTT
AAA-CCC-TTT
Answer: d
Source: Barstow - Test Bank for Biology, Seventh Edition, Question #20

50. 3. What is the relationship among DNA, a gene, and a chromosome?
A chromosome contains hundreds of genes, which are composed of protein.
A chromosome contains hundreds of genes, which are composed of DNA.
A gene contains hundreds of chromosomes, which are composed of protein.
A gene is composed of DNA, but there is no relationship to a chromosome.
A gene contains hundreds of chromosomes, which are composed of DNA.
Answer: b
Source: Barstow - Test Bank for Biology, Seventh Edition, Question #75

51. 4. A particular triplet of bases in the coding sequence of DNA is AAA
4. A particular triplet of bases in the coding sequence of DNA is AAA. The anticodon on the tRNA that binds the mRNA codon is
TTT.
UUA.
UUU.
AAA.
either UAA or TAA, depending on wobble in the first base.
Answer: d
Source: Barstow - Test Bank for Biology, Seventh Edition, Question #39

52. The dipeptide that will form will be
5. A part of an mRNA molecule with the following sequence is being read by a ribosome: 5' CCG-ACG 3' (mRNA). The following activated transfer RNA molecules are available. Two of them can correctly match the mRNA so that a dipeptide can form.
tRNA Anticodon
Amino Acid
GGC
Proline
CGU
Alanine
UGC
Threonine
CCG
Glycine
ACG
Cysteine
CGG
The dipeptide that will form will be
cysteine-alanine.
proline-threonine.
glycine-cysteine.
alanine-alanine.
threonine-glycine.
Answer: b
Source: Barstow - Test Bank for Biology, Seventh Edition, Question #42

53. 6. This figure represents tRNA that recognizes and binds a particular amino acid (in this instance, phenylalanine). Which of the following triplets of bases on the mRNA strand codes for this amino acid?
UGG
GUG
GUA
UUC
CAU
Answer: d
Source: Barstow - Test Bank for Biology, Seventh Edition, Question #44

54. 7. How is the template strand for a particular gene determined?
It is the DNA strand that runs from the 5' → 3' direction.
It is the DNA strand that runs from the 3' → 5' direction.
It depends on the orientation of RNA polymerase, whose position is determined by particular sequences of nucleotides within the promoter.
It doesn’t matter which strand is the template because they are complementary and will produce the same mRNA.
The template strand always contains the TATA box.
Answer: c
Source: Taylor - Student Study Guide for Biology, Seventh Edition, Test Your Knowledge Question #5

55. 8. A biologist inserts a gene from a human liver cell into the chromosome of a bacterium. The bacterium then transcribes this gene into mRNA and translates the mRNA into protein. The protein produced is useless. The biologist extracts the protein and mature mRNA that codes for it. When analyzed you would expect which of the following results?*
the protein and the mature mRNA are longer than in human cells
the protein and mature mRNA are shorter than expected
the protein is longer and the mRNA is shorter than expected
the protein is shorter and the mRNA is longer than expected
Answer: a
Source: Campbell/Reece - Biology, Seventh Edition, EOC Process of Science Question
Discussion Notes for the Instructor
There are several questions which can be asked to guide the discussion of this question, including:
What are the differences between the way the genetic information in prokaryotes and eukaryotes is packaged?
How do transcription and translation differ in prokaryotes and eukaryotes?
Using these questions as an outline, discussion of the choices might look like this:
Choice A, correct
Choice B, eukaryotes contain introns that are normally removed after transcription. In bacteria these introns would not be removed and then subsequently would be translated
Choice C, the protein would not be expected to be longer if the mRNA is shorter
Choice D, while it is possible for the protein to be shorter, owing to a termination sequence being found in what was an intron, this is unlikely.

56. 9. If the structure of a TV show is analogous to the structure of a gene, then the introns of a gene would be analogous to
the opening theme music.
the segments of the show.
the commercials between segments of the show.
the commercials between shows.
the closing credits. *
Answer: c
Source: Barstow - Test Bank for Biology, Seventh Edition, Question #41

57. 10. Each of the following is a modification of the sentence THECATATETHERAT. A. THERATATETHECAT B. THETACATETHERAT C. THECATARETHERAT D. THECATATTHERAT E. CATATETHERAT Which of the above is analogous to a frameshift mutation? A B C D E
Answer: d
Source: Barstow - Test Bank for Biology, Seventh Edition, Question #68

58. 11. Each of the following is a modification of the sentence THECATATETHERAT. A. THERATATETHECAT B. THETACATETHERAT C. THECATARETHERAT D. THECATATTHERAT E. CATATETHERAT Which of the above is analogous to a single substitution mutation? A B C D E
Answer: c
Source: Barstow - Test Bank for Biology, Seventh Edition, Question #69