1. Chapter 9 From DNA to Protein

2. 9.1 Ricin, RIP
A tiny amount of ricin, a natural protein found in castor-oil seeds, can kill an adult human – there is no antidote
Ricin is a ribosome-inactivating protein (RIP)
Inactivates the organelles which assemble amino acids into proteins
Other RIPs include Shiga toxin, made by Shigella dysenteriae bacteria, and Shiga-like toxin made by E. coli bacteria

3. RIPs and Their Sources
Castor-oil seeds
Jequirity beans
Camphor tree seeds
Ricin
Abrin
Cinnamomin
Figure 9.1 Lethal lineup: a few toxic ribosome-inactivating proteins (RIPs) and their sources. One of the two chains of a toxic RIP (brown) helps the molecule cross a cell’s plasma membrane; the other (gold) is an enzyme that inactivates ribosomes.
Shigella dysenteriae
Escherichia coli O157:H7
Shiga toxin
Shiga-like toxin

4. 9.2 DNA, RNA, and Gene Expression
Transcription converts information in a gene to RNA
DNA → transcription → mRNA
Translation converts information in an mRNA to protein
mRNA → translation → protein

5. DNA to RNA
Each DNA strand consists of a chain of the four nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C)
The sequence of the bases in the strand is the genetic code
All of a cell’s RNA and protein products are encoded by DNA sequences called genes

6. DNA to RNA DNA is transcribed to RNA
Enzymes synthesize a complementary strand of RNA from the DNA template
DNA versus RNA
Most RNA is single-stranded
RNA uses ribose instead of deoxyribose as its sugar
RNA uses uracil instead of thymine

7. A DNA Nucleotide: Guanine
base (guanine)
3 phosphate groups
Figure 9.2 Comparing nucleotides of DNA and RNA.
A The DNA nucleotide guanine (G), or deoxyguanosine triphosphate, one of the four nucleotides in DNA. The other nucleotides—adenine, uracil, and cytosine—differ only in their component bases (blue). Three of the four bases in RNA nucleotides are identical to the bases in DNA nucleotides.
sugar (deoxyribose)

8. An RNA Nucleotide: Guanine
base (guanine)
3 phosphate groups
Figure 9.2 Comparing nucleotides of DNA and RNA.
B The RNA nucleotide guanine (G), or guanosine triphosphate. The only difference between the DNA and RNA versions of guanine (or adenine, or cytosine) is that RNA has a hydroxyl group (shown in red) at the 2′carbon of the sugar.
sugar (ribose)

9. deoxyribonucleic acid RNA ribonucleic acid adenine A adenine A
DNA
deoxyribonucleic acid
RNA
ribonucleic acid
adenine A
adenine A
sugar– phosphate backbone
guanine G
guanine G
cytosine C
cytosine C
nucleotide base
Figure 9.3 Comparing the structure and function of DNA and RNA.
base pair
thymine T
uracil U
DNA has one function: It permanently stores a cell’s genetic information, which is passed to offspring.
RNAs have various functions. Some serve as disposable copies of DNA’s genetic message; others are catalytic. Still others have roles in gene control.
Nucleotide bases of DNA
Nucleotide bases of DNA

10. 3 Types and Functions of RNA
Messenger RNA (mRNA)
Contains the information transcribed from DNA
Ribosomal RNA (rRNA)
Main component of ribosomes, which build polypeptide chains
Transfer RNA (tRNA)
Delivers amino acids to ribosomes

11. RNAProtein mRNA is translated to protein
rRNA and tRNA translate the sequence of base triplets in mRNA into a sequence of amino acids
Translation
Information carried by mRNA is decoded into a sequence of amino acids
Results in a polypeptide chain that folds into a protein

12. Gene Expression
The DNA sequence (genes) contains all the information needed to make the molecules of life
Gene expression is a multistep process
Includes transcription and then translation
Genetic information from the genes is converted into a structural or functional part of a cell or organism

13. 9.3 Transcription: DNA to RNA
RNA polymerase assembles RNA by linking RNA nucleotides into a chain, in the order dictated by the base sequence of a gene
A new RNA strand is complementary in sequence to the DNA strand from which it was transcribed
{DNA replication and transcription both synthesize new molecules by base-pairing}
*Uracil (U) pairs with adenine (A)
*RNA polymerase adds nucleotides to transcript, no need for a primer

14. Transcription – Base-Pairing

15. The Process of Transcription
RNA polymerase and regulatory proteins attach to a promoter (a specific binding site in DNA close to the start of a gene)
RNA polymerase
Moves over the gene in a 5' to 3' direction
Unwinds the DNA helix
Reads the base sequence
Joins free RNA nucleotides into a complementary strand of mRNA

16. RNA polymerase binds to a promoter in the DNA
RNA polymerase binds to a promoter in the DNA. The binding positions the polymerase near a gene. In most cases, the base sequence of the gene occurs on only one of the two DNA strands. Only the DNA strand complementary to the gene sequence will be translated into RNA.
promoter sequence in DNA
gene region
RNA polymerase 1 2
The polymerase begins to move along the DNA and unwind it. As it does, it links RNA nucleotides into a strand of RNA in the order specified by the base sequence of the DNA. The DNA winds up again after the polymerase passes. The structure of the “opened” DNA at the transcription site is called a transcription bubble, after its appearance.
DNA unwinding
DNA winding up
RNA 3
Zooming in on the gene region, we can see that RNA polymerase covalently bonds successive nucleotides into an RNA strand. The base sequence of the new RNA strand is complementary to the base sequence of its DNA template strand, so it is an RNA copy of the gene.
direction of transcription
Figure 9.4 Animated Transcription. By this process, a strand of RNA is assembled from nucleotides according to a template: a gene region in DNA. Figure It Out: After the guanine, what is the next nucleotide that will be added to this growing strand of RNA?
Stepped Art

17. Transcription – A New Strand of RNA
gene region
RNA
polymerase
RNA
promoter sequence in DNA
DNA winding up
DNA unwinding
1 The enzyme RNA polymerase binds to a promoter in the DNA. The binding positions the polymerase near a gene. Only the DNA strand complementary to the gene sequence will be translated into RNA.
2 RNA polymerase begins to move along the gene and unwind the DNA. As it does, it links RNA nucleotides in the order specified by the sequence of the complementary (noncoding) DNA strand. The DNA winds up again after the polymerase passes.
3 Zooming in on the site of transcription, we see that RNA polymerase covalently bonds successive nucleotides into a new strand of RNA. The new RNA is complementary in sequence to the template DNA strand, so it is an RNA copy of the gene. 5' U
T A
Figure 9.4 Animated Transcription. By this process, a strand of RNA is assembled from nucleotides according to a template: a gene region in DNA. Figure It Out: After the guanine, what is the next nucleotide that will be added to this growing strand of RNA? G C A
T A C A C
direction of transcription C C G T G
A U A
A G T C U A U U C
U A A G C G G G T

18. Post-Transcriptional Modifications
RNA is modified before it leaves the nucleus as mature mRNA
Introns
Nucleotide sequences that are removed from new RNA strands
Exons
Sequences that stay in RNA

19. Alternative Splicing Allows one gene to encode multiple proteins
Some introns removed from RNA
Other exons spliced together in various combination
After splicing, final transcripts are finished
Modified guanine ‘cap’ at the 5' end
Poly-A tail at the 3' end

20. Post-Transcriptional Modifications
promoter
exon
intron
gene
DNA
transcription
new transcript
RNA processing
finished RNA
cap
poly-A tail 5′ 3′
Figure 9.6 Post-transcriptional modification of RNA. introns are removed and exons spliced together. Messenger RNAs also get a poly-A tail and modified guanine “cap.”

21. 9.4 RNA and the Genetic Code
mRNA carries the information for building proteins to ribosomes and tRNA for translation
Protein building information is carried in codons
Sequence of three mRNA nucleotides
Codes for a specific amino acid
Order of codons in mRNA dictates the order of amino acids in the polypeptide chain

22. The Genetic Code
There are 64 codons possible in making up the genetic code
20 kinds of amino acids found in proteins
Some amino acids coded by more than one codon
Some codons signal the start or end of genes
AUG (methionine) is the start codon
UAA, UAG, and UGA are stop codons

23. Codon Chart-mRNA

24. The 20 Amino Acids Specified by the Genetic Code
ala
arg
asn
asp
cys
glu
gln
alanine (A)
arginine (R)
asparagine (N)
aspartic acid (D)
cysteine (C)
glutamic acid (E)
glutamine (Q)
gly
his
ile
leu
lys
met
phe
glycine (G)
histidine (H)
isoleucine (I)
leucine (L)
lysine ( K)
methionine (M)
phenylalanine ( F)
pro
ser
thr
trp
tyr
val
proline (P)
serine (S)
threonine (T)
tryptophan (W)
tyrosine (Y)
valine (V)
Figure 9.7 The genetic code
B Names and abbreviations of the 20 naturally occurring amino acids specified by the genetic code (A).

25. Where do amino acids come from?
Humans can produce 10 of the 20 amino acids. The others must be supplied in the food.
The 9 essential amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine
Failure to obtain enough of even 1 of the 10 essential amino acids, those that we cannot make, results in degradation of the body's proteins—muscle and so forth—to obtain the one amino acid that is needed.

26. From DNA through RNA to Protein
A T G T A C T C A G
a gene region in DNA
T A C A T G A G T C
transcription
mRNA
A U G U A C U C A G
codon codon codon
translation
Figure 9.8 Example of the correspondence between DNA, RNA, and protein. A gene region in a strand of chromosomal DNA is transcribed into an mRNA, and the codons of the mRNA specify a chain of amino acids—a protein.
met
tyr
ser
protein

27. All Types of RNA Work Together
tRNAs deliver amino acids to ribosomes
Contains an anticodon complementary to an mRNA codon
Contains a binding site for the amino acid coded by the codon
rRNA and proteins make up ribosomes
Link amino acids into polypeptide chains
Two rRNA subunits and 50+ proteins make up each ribosome

28. rRNA – Ribosome Structure
Figure 9.19 Ribosome structure. Each intact ribosome consists of a large and a small subunit. The structural protein components of the two subunits are shown in green; the catalytic rRNA components, in brown.
large subunit
small subunit
intact ribosome

31. 9.5 Translation: RNA to Protein
Translation converts genetic information from mRNA into a new polypeptide chain
Amino acid order is determined by codon order
Occurs in the cytoplasm
Occurs in three stages
Initiation
Elongation
Termination

32. Overview of Translation in a Eukaryotic Cell
1 Transcription
r bosome subunits ri
2 RNA transport
tRNA
3 Convergence of RNAs
Figure 9.11 Overview of translation in a eukaryotic cell. RNAs are transcribed in the nucleus, then transported into the cytoplasm through nuclear pores. Translation begins when ribosomal subunits and tRNA converge on an mRNA in cytoplasm.
mRNNA
4 Translation
polypeptide

34. Initiation Initiation complex forms
A small ribosomal subunit binds to mRNA
The anticodon of initiator tRNA base pairs with the start (AUG) codon of mRNA
A large ribosomal subunit joins the small ribosomal subunit

35. Elongation
The ribosome assembles a polypeptide chain as it moves along the mRNA (using energy)
Initiator tRNA carries methionine, the first amino acid of the chain
The ribosome joins each amino acid to the polypeptide chain with a peptide bond

36. Termination
When the ribosome encounters a stop codon, polypeptide synthesis ends
Release factors bind to the ribosome
Enzymes detach the mRNA and polypeptide chain from the ribosome

37. Infer what the E, P, A sites stand for/function?

39. 9.6 Mutated Genes and Their Protein Products
If the nucleotide sequence of a gene changes, it may result in an altered gene product, with harmful effects
Mutations
Small-scale changes in the nucleotide sequence of a cell’s DNA that alter the genetic code
Relative uncommon events in normal cells

40. Mutations and Proteins
A mutation that changes a UCU codon to UCC is “silent”
It has no effect on the gene’s product because both codons specify the same amino acid
Other mutations can have severe consequences for the organism
May change an amino acid in a protein
Can result in a premature stop codon that shortens a protein

41. Common Mutations Base-pair-substitution
May result in a premature stop codon or a different amino acid in a protein product
Example: sickle-cell anemia

43. Common mutations Deletion or insertion
Can cause the reading frame of mRNA codons to shift, changing the genetic message
Example: thalassemia

44. Hemoglobin mutations Abnormal cell shape Pale, small red blood cells
Sickle cell anemia
Thalassemia
Abnormal cell shape
Pale, small red blood cells
In thalassemia, both α and β globin chains can be affected but in sickle cell anemia only the β globin chains are affected.

45. Examples of Mutations
pro
glu
glu
lys
ser
pro
gly
arg
ser
leu
B Part of the DNA (blue), mRNA (brown), and amino acid sequence of human beta globin. Numbers indicate nucleotide position in the mRNA.
D A base-pair deletion shifts the reading frame for the rest of the mRNA, so a completely different protein product forms. The mutation shown results in a defective beta globin. The outcome is beta thalassemia, a genetic disorder in which a person has an abnormally low amount of hemoglobin.
Figure 9.13 Examples of mutations
pro
val
glu
lys
ser
pro
glu
glu
glu
glu
C A base-pair substitution replaces a thymine with an adenine. When the altered mRNA is translated, valine replaces glutamic acid as the sixth amino acid. Hemoglobin with this form of beta globin is called HbS, or sickle hemoglobin.
E An insertion of one nucleotide causes the reading frame for the rest of the mRNA to shift. The protein translated from this mRNA is too short and does not assemble correctly into hemoglobin molecules. As in D, the outcome is beta thalassemia.
A Hemoglobin, an oxygen-binding protein in red blood cells. This protein consists of four polypeptides: two alpha globins (blue) and two beta globins (green). Each globin has a pocket that cradles a heme (red). Oxygen molecules bind to the iron atom at the center of each heme.

46. Points to Ponder Why are ribosomes essential to protein synthesis?
Why is transcription necessary? Why don’t cells use their DNA as a direct model for protein synthesis?
In what ways does RNA differ from DNA?