Bacterial Genome Replication and Expression

• Chapter 13 discusses bacterial genome replication and expression
• The chapter explains that genetic information is stored in DNA and details the research which led to this discovery.
• It describes the structure of DNA, RNA, and proteins, including their components and how they fold to gain function.

Genetic Information Storage

• Initially, it was unknown that DNA stored genetic information
• Researchers figured out what was going on, Griffith, Hersey and Chase, as well as Avery, Macleod and McCarthy, shed light on how genetic information is carried.

DNA vs Protein

• DNA is a smaller, less complex molecule with only 4 nucleotides
• Proteins are larger, more complex molecules comprised of at least 20 different amino acids

Fred Griffith's Experiment (1928)

• Griffith's experiments showed the transfer of virulence in Streptococcus pneumoniae
• Mice injected with smooth S. pneumoniae died because the capsule stops the mice's defense systems.
• Bacteria with the slimy capsule appear as smooth colonies
• Non-virulent rough S. pneumoniae (lacking a capsule) injected into mice did not cause death.
• Capsule importance for S. pneumoniae survival was confirmed
• Heat-killed smooth virulent S. pneumoniae did not kill mice
• Mice died when injected with a mixture of heat-killed smooth virulent and live rough S. pneumoniae
• Heat-killed smooth organisms could not kill the mice on their own
• Live rough organisms could not kill the mice alone
• The heat-killed cells gave the non-virulent rough cells information to produce capsules

Griffith's Experiment Conclusion

• Information was transferred from one organism to another, changing a non-virulent cell into a virulent one.
• The Griffith transformation is the transformation of a harmless organism into a virulent one
• The which molecule carried the information was unknown

Avery, Macleod, and McCarthy Experiment (1944)

• Researchers used smooth cells to make cell extracts for their experiments
• These cell extracts contained DNA, RNA, and protein
• These researchers converted virulent S. pneumoniae cells into non-virulent S. pneumoniae
• Mixing rough non-virulent R cells with the extract resulted in a change to smooth virulent cells.
• This extract was then divided into 3 tubes:
• Tube 1: Extract + DNase, which destroys DNA
• Tube 2: Extract + RNase, which destroys RNA
• Tube 3: Extract + proteinase, which destroys proteins
• When these were mixed with R cells, only the DNase tube prevented transformation
• No genetic information is transferred, and transformation does not occur when DNA is destroyed

Hershey and Chase Experiment (1952)

• Alfred D. Hershey and Martha Chase aimed to identify the viral component carrying genetic information into E. coli
• T2 bacteriophages, which infect E. coli, were used in the study to determine if hereditary information happens in viruses.
• They made T2 DNA and proteins radioactive with 32P and 35S
• They waited for test tube viruses to infect E. coli
• E. coli cells were centrifuged to create a pellet, leading to the removal of any free viruses in the supernatant
• The scientists infected E. coli cells in a buffer, then blended the cells to remove surface-attached virus particles
• Centrifuging separated E. coli from the buffer was done
• 32P radioactivity (DNA) was detected in the supernatant, while 35S radioactivity (protein) was found outside of the cells
• T2 bacteriophages inject DNA to cause new viruses, showing DNA is genetic
• The injected buffer caused viruses to form

DNA and RNA Structure

• Nucleic acids, DNA, and RNA are polymers of nucleotides
• Nucleotides are composed of a nitrogenous base, sugar, and phosphate group

Nucleosides vs. Deoxynucleosides

• Ribose or deoxyribose is used as a sugar
• Nucleosides have ribose sugars
• Deoxynucleosides attach deoxyribose as the sugar instead

Nitrogenous Bases vs. Sugars

• Purine and pyrimidine are types of nitrogenous bases.
• Ribose and deoxyribose are two types of sugars.

DNA & RNA

• DNA and RNA both contain nucleic acids made of polymers of nucleotides
• Nucleotides are linked by a phosphodiester bond
• The difference between DNA and RNA is the nitrogenous bases and sugar they contain, along with whether they are single or double stranded

DNA Nucleotides

• DNA's sugars are deoxyribose
• DNA's bases are adenine, guanine, cytosine, and thymine
• A phosphate is esterified to a sugar carbon to form a sugar phosphate backbone

DNA Bases

• Adenine, guanine, cytosine, and thymine are nitrogenous bases found in DNA
• Adenine and guanine (A and G) are purines.
• Thymine and cytosine (T and C) are pyrimidine.

Phosphate in DNA

• Phosphate creates a bond between two sugars to form a phosphoryl-based backbone
• Hydroxyls bond
• Phosphate attaches to the 3'-hydroxyl of one sugar and the 5'-phosphate of an adjacent sugar
• A diester bond forms and links a C and an O together

DNA Strands

• The DNA double helix is double-stranded and kept together by phosphodiester bonds
• The nitrogenous bases on the inside and the sugars make the strands
• Hydrogen bonds bind these strands
• A specific base on one strand can only bind to a specific opposite base
• Adenine (a purine) always pairs with thymine (a pyrimidine) by 2 hydrogen bonds.
• Guanine (a purine) always pairs with cytosine (a pyrimidine) by 3 hydrogen bonds.

DNA Double Helix

• The sugars run opposite to each other in the DNA double helix
• DNA with phosphodiester bonds has an antiparallel backbone because sugars face opposite directions
• Complementary bases are: A-T and G-C
• Major and minor grooves exist on DNA due to the sugar not directly crossing from each other
• 10.5 base pairs per turn exist in DNA’s helix
• DNA spins counter-clockwise when viewed down the helix

RNA Structure

• RNA is a polymer of nucleotides which consists of ribose for its sugar, adenine, guanine, cytosine, and uracil for its bases
• RNA has a sugar-phosphate backbone, single-stranded, and is able to coil to for hair pins structure

Protein Composition

Components:

• Central carbon
• Carboxyl group (C-terminal)
• Amino group (N-terminal)
• Variable side chain, either polar, charged, or nonpolar
• Amino acids link by peptide bonds and form C-N bonds
• Polypeptides (amino acid chains) are polar – one end has an amino group (N- terminus) and the other end has a carboxyl group (C-terminus)
• Fold into 3D structures (primary, secondary and tertiary structures)
• The amino acid chain is a straight chain of bound amino acids (peptide bonds), aka the “primary structure”
• This straight chain then twists in to spirals or weaves, known as the “secondary structure” These secondary structures then fold into more complex shapes, known as “tertiary structures.” After this folding two or more tertiary polypeptides can bind together, known as the complete/functional protein
• These bonds are kept together by inter- and intra-chain bonds

Chapter 13 focuses on bacterial genome replication and expression. It explains how genetic information is stored in DNA, highlighting key research. The chapter also describes the structure of DNA, RNA, and proteins, along with their components and folding processes.