1. Chapter 14.
From Gene to Protein
Biology 114

2. Metabolism teaches us about genes
Metabolic defects
studying metabolic diseases suggested that genes specified proteins
alkaptonuria (black urine from alkapton)
PKU (phenylketonuria)
each disease is caused by non-functional enzyme
Genes create phenotype A B C D E

4. 1 gene – 1 enzyme hypothesis
Beadle & Tatum
Compared mutants of bread mold, Neurospora fungus
created mutations by X-ray treatments
X-rays break DNA
inactivate a gene
wild type grows on “minimal” media
sugars + required precursor nutrient to synthesize essential amino acids
mutants require added amino acids
each type of mutant lacks a certain enzyme needed to produce a certain amino acid
non-functional enzyme = broken gene

5. 1941 | 1958
Beadle & Tatum
George Beadle
Edward Tatum

6. Beadle & Tatum’s Neurospora experiment

7. Where does that leave us?!
So… What is a gene?
One gene – one enzyme
but not all proteins are enzymes
but all proteins are coded by genes
One gene – one protein
but many proteins are composed of several polypeptides
but each polypeptide has its own gene
One gene – one polypeptide
but many genes only code for RNA
One gene – one product
but many genes code for more than one product …
Where does that leave us?!

8. if you don’t know what a wabbit looks like.
Defining a gene…
“Defining a gene is problematic because… one gene can code for several protein products, some genes code only for RNA, two genes can overlap, and there are many other complications.”
– Elizabeth Pennisi, Science 2003
gene
RNA
It’s hard to
hunt for wabbits,
if you don’t know what a wabbit looks like.
1990s -- thought humans had 100,000 genes
,000 was considered a good estimate
,000
,000 is our best estimate
polypeptide 1
polypeptide 2
polypeptide 3
gene

9. let’s go back to genes that code for proteins…
The “Central Dogma”
How do we move information from DNA to proteins?
transcription
translation
DNA
RNA
protein
For
simplicity sake,
let’s go back to genes that code for proteins…
replication

10. From nucleus to cytoplasm…
Where are the genes?
genes are on chromosomes in nucleus
Where are proteins synthesized?
proteins made in cytoplasm by ribosomes
How does the information get from nucleus to cytoplasm?
messenger RNA
nucleus

11. transcription and translation
RNA
ribose sugar
N-bases
uracil instead of thymine
U : A
C : G
single stranded
mRNA, rRNA, tRNA, siRNA….
To get from the chemical language of DNA to the chemical language of proteins requires 2 major stages:
transcription and translation
transcription
DNA
RNA

12. Transcription Transcribed DNA strand = template strand
untranscribed DNA strand = coding strand
Synthesis of complementary RNA strand
transcription bubble
Enzyme
RNA polymerase

13. Transcription in Prokaryotes
Initiation
RNA polymerase binds to promoter sequence on DNA
Role of promoter
1. Where to start reading
= starting point
2. Which strand to read
= template strand
3. Direction on DNA
= always reads DNA 3'5'

14. Transcription in Prokaryotes
Promoter sequences
RNA polymerase molecules bound to bacterial DNA

15. Transcription in Prokaryotes
Elongation
RNA polymerase unwinds DNA ~20 base pairs at a time
reads DNA 3’5’
builds RNA 5’3’ (the energy governs the synthesis!)
No proofreading
1 error/105 bases
many copies
short life
not worth it!

16. Transcription
RNA

17. Transcription in Prokaryotes
Termination
RNA polymerase stops at termination sequence
mRNA leaves nucleus through pores
RNA GC hairpin turn

18. Transcription in Eukaryotes
Biology 114

19. 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
Exon: Segmnent of DNA that is both transcribed into RNA and translated into protein
Intron: Portion of mRNA as transcribed from Eukaryotic DNA that is removed by enzymes before mRNA is translated into proteins
intron = noncoding (inbetween) sequence
eukaryotic
DNA
exon = coding (expressed) sequence

20. Transcription in Eukaryotes
3 RNA polymerase enzymes
RNA polymerase I
only transcribes rRNA genes
RNA polymerase I I
transcribes genes into mRNA
RNA polymerase I I I
only transcribes tRNA genes
each has a specific promoter sequence it recognizes

21. Transcription in Eukaryotes
Initiation complex
transcription factors prokarytoes have 1 the holoenzyme, bind to promoter region upstream of gene
proteins which bind to DNA & turn on or off transcription
TATA box binding site like a prokaryote, too simple, additional control for time and tissue specific.
only then does RNA polymerase bind to DNA

22. Post-transcriptional processing
Primary difference between Pro&Euk
Primary transcript
eukaryotic mRNA needs work after transcription
Protect mRNA
from RNase enzymes in cytoplasm
add 5' cap
add polyA tail
Edit out introns A
3' poly-A tail
CH3
mRNA 5'
5' cap 3' G P
A’s
intron = noncoding (inbetween) sequence
eukaryotic
DNA
exon = coding (expressed) sequence
pre-mRNA
primary mRNA
transcript
mature mRNA
transcript
spliced mRNA

23. 5’ CAP 3’ Poly Tail “PROTECTION”
Eukaryotes ; The first base in transcript is usually A or G and modified by GTP to the 5’ PO4 group forming a 5’ Cap. The G nucleotide in the cap is joined to the transcript by its 5’ end making the only 5’ to 5’ bond. This protects the mRNA cap from degradation.
The Euk transcript is cleaved downstream from (AAUAAA) A series of residues called the 3’ poly a tail are added by poly-A-polymerase. Adds protection.

24. Transcription to translation
Differences between prokaryotes & eukaryotes
time & physical separation between processes
RNA processing

25. Translation in Prokaryotes
Transcription & translation are simultaneous in bacteria
DNA is in cytoplasm
no mRNA editing needed

26. DNA mRNA protein From gene to protein transcription translationaa
transcription
translation
DNA
mRNA
protein
ribosome
mRNA leaves nucleus through nuclear pores
proteins synthesized by ribosomes using instructions on mRNA
nucleus
cytoplasm

27. Removing Introns Intron: Non-coding sequence 24% out of human genome
Exon: expressed 1% encode for proteins
Pre-mRNA splicing in the nucleus
snRNP cluster to make splicesosome which recognize and cut out introns.

28. How does mRNA code for proteins?
TACGCACATTTACGTACGCGG
DNA
AUGCGUGUAAAUGCAUGCGCC
mRNA ?
Met Arg Val Asn Ala Cys Ala
protein
How can you code for 20 amino acids with only 4 nucleotide bases (A,U,G,C)?

29. Cracking the code 1960 | 1968 Nirenberg & Matthaei
determined 1st codon–amino acid match
UUU coded for phenylalanine
created artificial poly(U) mRNA
added mRNA to test tube of ribosomes, tRNA & amino acids
mRNA synthesized single amino acid polypeptide chain
phe–phe–phe–phe–phe–phe

30. Heinrich Matthaei
Marshall Nirenberg

31. Translation
Codons
blocks of 3 nucleotides decoded into the sequence of amino acids

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

33. The code For ALL life! Code is redundant Why is this a good thing?
strongest support for a common origin for all life
Code is redundant
several codons for each amino acid
Why is this a good thing?
Strong evidence for a single origin in evolutionary theory.
Start codon
AUG
methionine
Stop codons
UGA, UAA, UAG

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

35. cytoplasm
transcription
translation
protein
nucleus

36. tRNA structure “Clover leaf” structure anticodon on “clover leaf” end
amino acid attached on 3' end

37. Loading tRNA Aminoacyl tRNA synthetase
enzyme which bonds amino acid to tRNA
endergonic reaction
ATP  AMP
energy stored in tRNA-amino acid bond
unstable
so it can release amino acid at ribosome
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.

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

39. Ribosomes P site (peptidyl-tRNA site) A site (aminoacyl-tRNA site)
holds tRNA carrying growing polypeptide chain
A site (aminoacyl-tRNA site)
holds tRNA carrying next amino acid to be added to chain
E site (exit site)
empty tRNA leaves ribosome from exit site

40. Building a polypeptide
Initiation
brings together mRNA, ribosome subunits, proteins & initiator tRNA
Elongation
Termination

41. Elongation: growing a polypeptide

42. Termination: release polypeptide
Release factor
“release protein” bonds to A site
bonds water molecule to polypeptide chain
Now what happens to the polypeptide?

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

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

45. Put it all together…

46. Any Questions??
Biology 114