1. The Blueprint of Life, From DNA to Protein
Chapter 7

2. The Blueprint of Life
Characteristics of each cell dictated by information contained on DNA
DNA holds master blueprint
All cell structures and processes directed by DNA

3. Overview Complete set of genetic information referred to as genome
Genome of all cells is composed of DNA
Some viruses have RNA genome
Functional unit of genome is the gene
Gene codes for gene product
Gene product is most commonly protein
Study of transfer of genes is genetics
Study of sequence of DNA is genomic

4. Overview Living cells must accomplish two general tasks to multiply
DNA replication
DNA expression (gene expression)
Expression involves two process
Transcription
Copies information in DNA to RNA
Translation
Interpret RNA to synthesize protein
Flow of information from DNA to RNA to protein
Central dogma of molecular biology

5. Overview Characteristics of DNA Made up of deoxy-ribonucleotides
Nucleotides include:
Phosphate group
5 carbon sugar
Deoxyribose
Nucleotides bond covalently between the 5’PO4 of one nucleotide and the 3’OH of another
Joining of nucleotides creates an alternating sugar-phosphate backbone

6. Overview Characteristics of DNA
Each sugar (deoxyribose) molecule is connected to a nitrogenous base
Nitrogenous bases
Adenine (A) - purine
Thymine (T) - pyrimidine
Guanine (G) - purine
Cytosine (C) – pyrimidine

7. Overview Characteristics of DNA
Chemical structure and joining of nucleotide subunits causes strands to differ at the ends
One strand has a phosphate attached at the number 5 carbon of the sugar.
Termed the five prime (5’) end
The other strand has a hydroxyl group attached to the number 3 carbon of the sugar.
Termed the three prime (3’) end

8. Overview Characteristics of DNA DNA occurs as double-stranded molecule
Strands are complementary to each other
Due to the specific base pairing of bases
A:T
C:G
Strands are held together with hydrogen bonds
Specific hydrogen bonding between bases
A is bound to T by two hydrogen bonds
G is bound to C by three hydrogen bond

9. Overview Characteristics of DNA DNA molecule is antiparallel
Strands are oriented in opposite directions
Strands differ at the ends
One strand oriented in the 5’ to 3’ direction.
The other strand is oriented in the 3’ to 5’ direction.

10. Overview Characteristics of RNA RNA is made up of nucleotides
Ribonucleotides
RNA contains nitrogenous bases
Adenine
Guanine
Cytosine
Uracil
Uracil replaces thymine in RNA
RNA usually exists as single stranded molecule

11. Overview Characteristics of RNA
Portion of DNA acts of template for RNA synthesis
RNA molecule called transcript
Numerous transcripts can be produced from one chromosome
Either strand of DNA can act as template
Three different functional groups of RNA
Messenger RNA (mRNA)
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)

12. Overview Regulating the expression of genes
Nucleotide sequence codes for regulation mechanism for gene expression
Mechanisms determine duration of synthesis of gene products
Products are only made when required
Key mechanism is regulation of mRNA synthesis from DNA
Regulation of transcription

13. DNA Replication DNA is replicated to create second copy of molecule
Molecule is identical to original
Replication is bidirectional
Replication begins at specific starting point
Proceeds in opposite directions
Allows replication to proceed more quickly
Bi-directional replication

14. DNA Replication DNA replication
The two strands are unwound and separated
Free, unbound nucleotides match up to the newly separated nitrogenous bases of the parent strand
The parent strand is also called the template strand

15. DNA Replication DNA replication
Base pairing is specific in DNA replication
Where adenine is present only thymine binds in the new strand and vice versa
Where guanine is present only cytosine binds in the new strand and vice versa
Bases that are improperly inserted are removed and replaced with the correct base
Newly added bases are added by the enzyme DNA polymerase

16. DNA Replication Specifics of DNA replication
As the strands of DNA unwind, it creates an area of replication called the replication fork
As nucleotides are added, the replication fork moves down the parental strand

17. DNA Replication Specifics of DNA replication
DNA polymerase adds new nucleotides as they become available.
DNA polymerase can only add nucleotides to the free hydroxyl at the 3’ end
DNA polymerase replicates in 5’ to 3’ direction
Enzymes READS DNA template in 3’ to 5’ direction
Because of the antiparallel nature of the strands of DNA, the two new strands will grow in opposite directions
One strand is the leading strand
One strand is the lagging strand

18. DNA Replication Specifics of DNA replication Leading strand
Is synthesized CONTINUOUSLY as the DNA polymerase moves towards the replication fork
Lagging strand
Is synthesized DISCONTINUOUSLY in pieces as DNA polymerase moves away from the replication fork

19. DNA Replication Specifics of DNA replication
DNA polymerase must bind to an RNA primer to begin synthesis
A second DNA polymerase removes any RNA primers
An RNA primer is required at each newly synthesized section of the lagging strand
DNA ligase joins the fragments of the lagging strand

20. DNA Replication Specifics of DNA replication
Replication is completed when the replication fork reaches the end of the parent strands
The original parent strand and the newly synthesized daughter strand rewind
Each new strand of DNA consists of one parent strand and one daughter strand
DNA replication is referred to as semiconservative
DNA Replication

21. Gene Expression Involves two separate but interrelated process
Transcription
Process of synthesizing RNA from DNA template
Translation
RNA is deciphered to synthesize protein

22. Gene Expression Transcription
Transcription is the synthesis of a strand of mRNA from a DNA template
mRNA carries the coded information from DNA to the ribosome, which is the site of protein synthesis
mRNA also plays an important role in translation

23. Gene Expression Transcription
During transcription the enzyme, RNA polymerase, synthesizes a complementary strand of mRNA from a portion of unwound DNA

24. Gene Expression Specifics of Transcription
RNA polymerase binds to a region of the DNA called the promoter
Only one strand of DNA acts as a template
This is called the sense strand
The strand not transcribed is the nonsense strand

25. Genet Expression Specifics of transcription
Nucleotides in RNA are the same as those in DNA with one exception
Thymine is replaced with uracil
Binding in RNA is
A:U or U:A
C:G or G:C

26. Gene Expression Specifics of transcription
RNA polymerase continues down strand of DNA until it reaches a site on DNA called the terminator
At the terminator RNA polymerase and the new strand of mRNA are released from strand of DNA
Transcription

27. Gene Expression Translation
Translation is the decoding of information held in the mRNA to synthesize proteins
Two more RNA molecules become involved in translation
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)

28. Gene Expression
rRNA forms part of the ribosomal machinery used in protein synthesis
rRNA builds the ribosomes
tRNA recognizes specific sequences of mRNA and transports the required amino acids to form a polypeptide chain

29. Gene Expression Translation
The language of mRNA is in the form of codons
Codons are groups of three nucleotides situated next to each other on DNA
Codons are written in terms of their base sequence in mRNA
The sequence of codons determines the sequence of amino acids in the protein

30. Gene Expression Translation
There are 64 codons that make up the “alphabet” of proteins
Of the 64 codons, 61 are sense codons
Each coding a specific amino acid
The remaining 3 are nonsense codons
These code for termination of the message
Codons contained in mRNA are read into proteins through translation
The site of translation is the ribosome

31. Gene Expression
In response to each codon, tRNA brings the appropriate amino acid to the site of translation
Each codon has an anticodon
The anticodon is complementary sequence to the codon

32. Gene Expression Translation Ribosomes
The 30s and the 50s ribosomal subunits join together around the mRNA
The ribosomes direct the binding of tRNA to the correct codon on the mRNA
tRNA binds to the P site and the A site of the 50s ribosomal subunit
The ribosomes bind to the mRNA to be translated

33. Gene Expression Specifics of Translation
P site A site
Specifics of Translation
The first tRNA binds to a start codon in the P site of the ribosome
AUG is the start codon for EVERY protein
AUG codes for the amino acid methionine
When the second tRNA binds to the A site, the amino acid of the first tRNA forms a peptide bond with the amino acid of the second tRNA

34. Gene Expression Specifics of translation
After the peptide bond is formed between the two amino acids, the tRNA P site leaves the ribosome
The ribosome moves distance of one codon
Amino acid in the A site moves to the P site
A new tRNA fills the now empty A site

35. Gene Expression Specifics of translation
The ribosome continues down the strand of mRNA
Amino acids form peptide bonds along the way
Translation is terminated when the ribosomes come to a stop or nonsense codon
At this point the ribosomes separate
The new polypeptide chain is released
The ribosome and the mRNA are free to begin translation again

36. Gene Expression Specifics of translation
As the ribosome moves down the strand of mRNA, the start codon is exposed
Once exposed, a new ribosome will attach and begin another polypeptide chain
Translation

37. Regulation of Gene Expression
Microorganisms posses mechanism to synthesize maximum amount of cell material from limited energy
Controls directed at metabolic pathways
Two general mechanism
Allosteric inhibition of enzymes
Controlling synthesis of enzymes
Directed at making only what is required

38. Regulation of Gene Expression
Principles of regulation
Not all genes subjected to regulation
Enzymes can be classified according to characteristics of regulation
Constitutive enzymes
Constantly synthesized
Enzymes of glycolysis
Inducible enzymes
Not regularly produced
turned on in certain conditions
Β-galactosidase
Repressible enzymes
Routinely synthesized
Generally involved in biosynthesis

39. Regulation of Gene Expression
Mechanisms controlling transcription
Often controlled by regulatory region near promoter
Protein binds to region and acts as “on/off” switch
Binding protein can act as repressor or activator
Repressor blocks transcription
Activator facilitates transcription
Set of genes controlled by protein is called an operon

40. Regulation of Gene Expression
Repressors
Control mechanism that inhibits gene expression and decreases the synthesis of enzymes
Repression is usually in response to the overabundance of an end product
Repression decreases the rate synthesis of enzymes leading to the formation of the particular end product
Regulatory proteins called repressors mediate repression
Repressors block the ability of RNA polymerase to bind and initiate protein synthesis

41. Regulation of Gene Expression
Activators
Control mechanism that turns on the transcription of a gene or set of genes
Inducers are substances that act to induce transcription
Enzymes synthesized in the presence of inducers are called inducible enzymes

42. Regulation of Gene Expression
Operon model of gene expression
An operon is a set of genes that includes an operator, promoter and structural genes
An operon is divided into two regions, the control region and the structural region
The control region include the operator and the promoter
This region controls transcription
The operator acts as the “on-off” switch
The structural region includes the structural genes
This region contains the genes being transcribed

43. Operon structure Promoter – Binding site for RNA polymerase
Operator
Gene 1
Gene 3
Gene 2
Promoter
Promoter – Binding site for RNA polymerase
Operator – binding site for the repressor protein for the regulation of gene expression
Structural Genes – DNA sequence for specific proteins

44. Regulation of Gene Expression
Lac operon
Example of induction of gene expression
Near the operon on the DNA is a regulatory gene called the “I” gene
This codes for the repressor protein
When lactose is absent, the repressor protein binds to the operator gene
Binding of the repressor gene prevents RNA polymerase from transcribing the structural genes
No mRNA is made and no enzymes are synthesized

45. Regulation of Gene Expression
Lac operon
When lactose is present the repressor binds to lactose instead of the operator
With the repressor bound to lactose, RNA polymerase is able to bind to the promoter and transcribes the structural genes
Lactose acts as an inducer by keeping the repressor from binding to the operator
It induces the transcription of the structural genes

46. Lac Operon 1. 2. 3. Lac Operon Operator Gene 1 Gene 3 Gene 2 Promoter
RNA polymerase
Repressor 2. 3.
Lac Operon
Lactose

47. Gene Expression and Environmental Fluctuations
Many organisms adapt to changing environments by altering level of gene expression
Mechanisms include
Signal transduction
Natural selection

48. Gene Expression and Environmental Fluctuations
Signal transduction
Process that transmits information from external environment to inside cell
Allows cell to respond to changes
Two-component regulatory systems
Relies on sensor and response regulator proteins
Sensors recognize change in environment
Response regulators activate or repress gene expression
Quorum sensing
Organisms sense density of population
Enables activation of genes beneficial to the mass

49. Gene Expression and Environmental Fluctuations
Natural selection
Mechanisms to enhance survivability
Antigenic variation
Alteration in characteristics of certain surface proteins
Example: Neisseria gonorrhoeae hides from host immunity by changing numerous surface proteins
Phase variation
Routine switching on and off of certain genes
Altering expression allows portions of population to survive and multiply