1. D.N.A 1. The information carried by a DNA molecule is in
A. Its amino acid sequence
B. The sugars and phosphates forming its backbone
C. The order of the bases in the molecule
D. The total number of nucleotides it contains
E. The RNA units that make up a molecule
DNA replication occurs
A. Whenever a cell makes protein
B. To repair gene damage caused by mutation
C. Before a cell divides
D. Whenever a cell needs RNA
E. In the cytoplasm of a eukaryotic cell
3. The complementary strand of DNA to the DNA fragment 5’- GGC ATA CAT – 3” is
A . 3’ – CCG UAU GUA – 5’
B. 3’ – GTA TAT CCG -5’
C. 3’ – ATG TAT GCC – 5’
D. 3’ – CCG TAT GTA – 5’
E. 3’ – CCG AUA GUA – 5’

2. From Gene to Protein
How Genes Work

3. 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

4. transcription and translation
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

5. 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
Tay sachs
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

6. from DNA nucleic acid language to RNA nucleic acid language
Transcription
from DNA nucleic acid language to RNA nucleic acid language

7. Transcription
Transcription is the synthesis of messenger RNA (mRNA) from DNA
Occurs in the nucleus
DNA does not leave the nucleus
Analogy: blueprints do not get used at the job site when constructing a house

8. DNA vs. RNA DNA RNA Contains: Adenine, guanine, cytosine, thymine
Adenine, guanine, cytosine, uracil
5-carbon sugar is deoxyribose
5-carbon sugar is ribose
Double-stranded
Single-stranded

9. Transcription Making mRNA transcribed DNA strand = template 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

10. Transcription: Initiation
Promoter = a specific sequence of DNA (starting point)
RNA polymerase binds to the promoter on the DNA molecule
Transcription factors (proteins) bind to promoter region to help RNA polymerase find the starting point.
RNA polymerase then separates the 2 DNA strands

11. Transcription: Elongation
As RNA polymerase moves along the DNA, it untwists the double helix and separates the strands
RNA polymerase adds nucleotides to the 3’ end of the mRNA molecule
Follows the base-pairing rules
G = C
A = U

12. Matching bases of DNA & RNAU
Match RNA bases to DNA bases on one of the DNA strands 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

13. Transcription: Termination
Termination signal = sequence of bases in DNA molecule that tell RNA polymerase to stop transcription
“finish line” in a race
mRNA is released from the DNA

15. RNA Modifications
In eukaryotes, mRNA is edited before it’s sent out of the nucleus
2 major types of modifications:
Alteration of mRNA ends
RNA splicing

16. RNA Splicing
Genes have stretches of nucleotides that don’t code for anything
“junk DNA”
Noncoding sequence = introns
“intervening sequences”
Coding regions = exons
During RNA splicing, the introns are removed by enzymes and the exons are joined together

17. Alteration of mRNA Ends
Need to protect mRNA on its trip from nucleus to cytoplasm
enzymes in cytoplasm attack mRNA
protect the ends of the molecule
add 5 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

18. from nucleic acid language to amino acid language
Translation
from nucleic acid language to amino acid language

19. How does mRNA code for proteins?
TACGCACATTTACGTACGCGG
DNA
ATCG
AUGCGUGUAAAUGCAUGCGCC
mRNA
AUCG ?
Met Arg Val Asn Ala Cys Ala
protein

20. mRNA codes for proteins in triplets
TACGCACATTTACGTACGCGG
DNA
codon
AUGCGUGUAAAUGCAUGCGCC
mRNA
AUGCGUGUAAAUGCAUGCGCC
mRNA ?
Met Arg Val Asn Ala Cys Ala
protein

21. Cracking the code WHYDIDTHEREDBATEATTHEFATRAT
1960 | 1968
Cracking the code
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

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

23. 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

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

25. DNA strand
mRNA strand – codon
Amino acid
CGC
AGT
GAC
GCG
Alanine
UCA
Serine
CUG
Leucine

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

27. 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

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

29. Loading tRNA Aminoacyl tRNA synthetase
enzyme which bonds amino acid to tRNA
bond requires energy
ATP  AMP
bond is unstable
so it can release amino acid at ribosome easily
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.
Trp
C=O
Trp
Trp
C=O OH
H2O OH O
C=O O
activating
enzyme
tRNATrp A C C U G G
mRNA
anticodon
tryptophan attached to tRNATrp
tRNATrp binds to UGG codon (mRNA)

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

31. 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)
empty tRNA leaves ribosome from exit site
Met U A C 5' U G A 3' E P A

32. Building a polypeptide1 2 3
Initiation
brings together mRNA, ribosome subunits, initiator tRNA
Elongation
adding amino acids based on codon sequence
Termination
end codon
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'

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

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

35. Prokaryote vs. Eukaryote genes
Eukaryotes
DNA in nucleus
linear chromosomes
DNA wound on histone proteins
introns vs. exons
Prokaryotes
DNA in cytoplasm
circular chromosome
naked DNA
no introns
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.
introns come out!
intron = noncoding (inbetween) sequence
eukaryotic
DNA
exon = coding (expressed) sequence

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

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