Microbiology Chapter 10 & 11 PDF

9/29/2020 MICROBIOLOGY CHAPTER 10 BIOCHEMISTRY OF THE GENOME 1 DNA (a) Each deoxyribonucleotide is made up of a sugar called deoxyribose, a phosphate group, and a nitrogenous base—in this case, adenine. (b) The five carbons within...

9/29/2020 MICROBIOLOGY CHAPTER 10 BIOCHEMISTRY OF THE GENOME 1 DNA (a) Each deoxyribonucleotide is made up of a sugar called deoxyribose, a phosphate group, and a nitrogenous base—in this case, adenine. (b) The five carbons within deoxyribose are designated as 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ. 2 1  9/29/2020 PURINES AND PYRIMIDINES Nitrogenous bases within DNA are categorized into the two-ringed purines adenine and guanine and the single-ringed pyrimidines cytosine and thymine. Thymine is unique to DNA. 3 SUGAR-PHOSPHATE BACKBONE Phosphodiester bonds form between the phosphate group attached to the 5ʹ carbon of one nucleotide and the hydroxyl group of the 3ʹ carbon in the next nucleotide, bringing about polymerization of nucleotides in to nucleic acid strands. Note the 5ʹ and 3ʹ ends of this nucleic acid strand. 4 2  9/29/2020 THE DOUBLE HELIX Watson and Crick proposed the double helix model for DNA. (a) The sugar-phosphate backbones are on the outside of the double helix and purines and pyrimidines form the “rungs” of the DNA helix ladder. (b) The two DNA strands are antiparallel to each other. (c) The direction of each strand is identified by numbering the carbons (1 through 5) in each sugar molecule. The 5ʹ end is the one where carbon #5 is not bound to another nucleotide; the 3ʹ end is the one where carbon #3 is not bound to another nucleotide. 5 COMPLEMENT BASE-PAIRING Hydrogen bonds form between complementary nitrogenous bases on the interior of DNA. 6 3  9/29/2020 RNA (a) Ribonucleotides contain the pentose sugar ribose instead of the deoxyribose found in deoxyribonucleotides. (b) RNA contains the pyrimidine uracil in place of thymine found in DNA. 7 RNA IS SINGLE-STRANDED (a) DNA is typically double stranded, whereas RNA is typically single stranded. (b) Although it is single stranded, RNA can fold upon itself, with the folds stabilized by short areas of complementary base pairing within the molecule, forming a three- dimensional structure. 8 4  9/29/2020 THE CENTRAL DOGMA The central dogma states that DNA encodes messenger RNA, which, in turn, encodes protein. 9 GENE EXPRESSION Phenotype is determined by the specific genes within a genotype that are expressed under specific conditions. Although multiple cells may have the same genotype, they may exhibit a wide range of phenotypes resulting from differences in patterns of gene expression in response to different environmental conditions. 10 5  9/29/2020 DNA REPLICATION Enzymes involved: DNA Helicase - unzips double-stranded DNA DNA Primase - synthesizes RNA primer DNA Polymerase - adds nucleotides to 3’ end DNA Ligase - joins fragments 11 HOW DOES DNA ELONGATE? New subunits are added at the existing 3’ end – ONLY The new strand undergoes base pairing with the mother strand. 12 6  9/29/2020 HOW DOES REPLICATION START? The replication complex binds at the origin of replication, which is identified by a particular base sequence Helicase unwinds the DNA, which is held open with helix- destabilizing proteins. Replication starts in the replication fork. 13 REPLICATION PROCEEDS ON 2 STRANDS Subunits always add at 3’ end, but new strands elongate in opposite directions Leading strand elongates into fork Lagging strand elongates away from fork RNA primers are first laid down (red) Elongation proceeds smoothly on leading strand 14 7  9/29/2020 TRANSCRIPTION ❖ RNA polymerase binds to a promotor sequence ❖ During elongation, the bacterial RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5ʹ to 3ʹ direction, and unwinds and rewinds the DNA as it is read. 15 THE GENETIC CODE A codon is a unit of 3 consecutive bases of mRNA a) each codon codes for 1 amino acid, start, or stop b) Universal c) Redundant a) 4 bases can combine in 43 combinations: b) Enough to code for ~64 amino acids a) Only 20 amino acids 16 8  9/29/2020 TRNA (a) After folding caused by intramolecular base pairing, a tRNA molecule has one end that contains the anticodon, which interacts with the mRNA codon, and the CCA amino acid binding end. (b) A space-filling model is helpful for visualizing the three-dimensional shape of tRNA. (c) Simplified models are useful when drawing complex processes such as protein synthesis. 17 TRANSLATION ❖ Translation in bacteria begins with the formation of the initiation complex, which includes the small ribosomal subunit, the mRNA, the initiator tRNA carrying N-formyl-methionine, and initiation factors. Then the 50S subunit binds, forming an intact ribosome. ❖ Elongation occurs as the ribosome reads the mRNA in the 5’ → 3’ direction ❖ Termination occurs when the ribosome encounters a stop codon 18 9  9/29/2020 PROKARYOTES VS EUKARYOTES (a) In prokaryotes, the processes of transcription and translation occur simultaneously in the cytoplasm, allowing for a rapid cellular response to an environmental cue. (b) In eukaryotes, transcription is localized to the nucleus and translation is localized to the cytoplasm, separating these processes and necessitating RNA processing for stability. 19 MUTATIONS Mutations can lead to changes in the protein sequence encoded by the DNA. 20 10  9/29/2020 HORIZONTAL GENE TRANSFER IN BACTERIA There are three prokaryote-specific mechanisms leading to horizontal gene transfer in prokaryotes. (a) In transformation, the cell takes up DNA directly from the environment. The DNA may remain separate as a plasmid or be incorporated into the host genome. (b) In transduction, a bacteriophage injects DNA that is a hybrid of viral DNA and DNA from a previously infected bacterial cell. (c) In conjugation, DNA is transferred between cells through a cytoplasmic bridge after a conjugation pilus draws the two cells close enough to form the bridge. 21 11