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Nucleic Acids

Large molecules composed of a chain of smaller nucleotide molecules



Composed of one phosphate group (PO3), one 5-carbon, ringed sugar, and one of five nitrogenous base molecules



- Ribose Sugar
- Adenine, Uracil, Cytosine, and Guanine base molecules
- 100-50000 nucleotides in nucleic acid strand
- single stranded; linear
- variety of functions related to protein synthesis



- Deoxyribose sugar
- Adenine, Thymine, Cytosine, and Guanine base molecules
- Chromosomes have about 45 million nucleotides in nucleic acid strand
- Double stranded helix; bases bonded by weak hydrogen bonds
- Stores genetic information (genes) that direct RNA to perform protein synthesis


Complementary Base Pairs

Certain bases will form weak hydrogen bonds between them; no exchange of electrons; allow two long strands of DNA to stick together; the second strand is complementary to the first


Central Dogma

DNA replication
Protein Synthesis
- DNA --transcription--> mRNA --translation--> protein


DNA Replication

A process that allows two identical copies of DNA for the bacterial chromosome occurring prior to cell division:
- Helicase unwinds and "unzips" the double stranded helix at the origin of replication (begins process)
- Bacteria have one origin of replication; eukaryotic cells have many (several thousand)
- Unwinds and unzips in both directions (5' to 3')
- Complementary base pairing of new nucleotides to the original strands (adenine --- thymine; cytosine -- guanine)



Short, thick strand of DNA and protein; regulate cellular activity by controlling which genes are expressed to produce proteins


DNA Polymerase

- Proof reads the new complementary nucleotide base pairs
- Joins the new complementary base pairs together
- This proceeds until two identical strands are made; strands will eventually separate
- 500-1000 base pairs in a second
- E. coli has 4,639,221 base pairs


Lead Strand

DNA replication occurs towards the replication fork; nucleotides are added continuously in the 3' direction


Lagging Strand

DNA replication occurs away from the replicating fork; nucleotides are added in segments in the 5' direction (Okazaki fragments)


Semiconservative Replication

Type of DNA replication in which half of the original strand of the DNA molecule is conserved in each new DNA molecule produced


Organization of the Chromosome

Circular; made of DNA and protein; divided into genes, each of which is a sequence of DNA nucleotides; Bacterial cells will:
- code for the production of a single protein (coding region
- regulate the expression of genes (regulatory region)



An area where RNA polymerase will bind to a chromosome (always unzipped)



A gene can be turned off by placing a protein here



How genes are divided; composed of a sequence of three nucleotides found within the same gene; if the gene codes for a protein, this will code for one specific amino acid found within the protein that will be produced; 64 possible combinations but only 20 different amino acids (more than one for each amino acid)


Stop Triplets

Found at the end of the coding region, they stop the reading of a gene


Protein Synthesis

The joining of amino acids to produce proteins; occurs in two distinct phases: transcription and translation



Steps used to convert a segment of DNA (template) into mRNA


mRNA (messenger)

A sequence of codons that is a complementary copy of a single gene; carries the information from the DNA to the ribosome; must be present for translation to occur


Phases of Transcription

- Initiation: The enzyme RNA polymerase attaches to the promotor region of a gene
- Elongation: The enzyme unzips the DNA molecule and moves along the template of DNA, synthesizing a single stranded mRNA strand one nucleotide at a time
- Termination: The enzyme encounters a "stop signal" and terminates the construction of mRNA

- A typical gene is composed of 1000 nucleotides and it takes about 30 seconds to make a copy



The synthesis of an amino acid strand (protein) from codons found on mRNA



Made of rRNA and protein; mRNA binds here; must be present for translation to occur


tRNA (transfer)

Brings a specific amino acid to the mRNA and ribosome; must be present for translation to occur:
- three nucleotides (anti-codon) which is complementary to the codon found on the mRNA
- charged when a specific amino acid is attached to it
- uncharged, it will not have specific amino acid attached, but will eventually find and attach to become charged


Phases of Translation

- Initiation: mRNA binds to the 30S portion of the ribosome
- Elongation: A protein is constructed, one amino acid at a time
- Termination: The ribosome reaches a "stop codon" which will terminate production of the protein, and the protein is released


Stop Codons

Found at the end of a mRNA strand that signal the termination of protein synthesis; UAA, UAG, and UGA



An antibiotic that binds to the 50S subunit, inhibiting protein synthesis


The Elongation Phase of Translation

- P site: first tRNA will bind here, it is complementary to the first mRNA codon
- A site: second tRNA will bind here, it is complementary to the second mRNA codon
- the two charged tRNA will release their amino acid which form peptide bonds between them, forming a short polypeptide
- the mRNA shifts over one codon and the process continues one amino acid at a time, until a stop codon is reached


Environmental Effects on Anabolic Chemical Reactions

Bacteria live in environments that are changing rapidly; their energy supply or supply of essential nutrients may "dry up"; they must be able to control their biochemical pathways in order to conserve energy (90% of energy used goes to protein synthesis) and spare materials


How Bacteria Conserve Energy and Spare Materials

- Will utilize any and all molecules found within the environment instead of producing them themselves; genes that control the production of certain molecules will be turned off during periods of plenty: energy is conserved and can be used in cell division
- When molecules dry up, the macromolecule must be produced by the machinery of the cell; genes must be able to turn on when needed: energy reserves are used up inside the cell and cell division occurs slowly


End Product Repression

The end product of a series of chemical reactions will inhibit the expression of a gene and prevent further synthesis of all those enzymes necessary to produce the end product (turns genes on or off); e.g., production of the five enzymes responsible for the production of tryptophan


Production of Tyrptophan

- Five genes (one of each enzyme) are located side by side and controlled by the same promotor and operator region (operons); if RNA polymerase attaches to the promotor and no inhibitor exists, then all five genes will be expressed
- Another gene is responsible for the production of an inactive inhibitor protein; it will not bind to the operator region unless this end product is very abundant
- If so, then it will bind to the inhibitor protein, changing its shape, and allowing it to bind to the operator region; the synthesis of all the enzymes are inhibited; once the enzymes within the cell are used up, synthesis of this product will cease


Feedback Inhibition

The end product will inhibit the function of one enzyme (of a series of enzymes) responsible for the synthesis of the end product


Non-Competitive Inhibition

An inhibitor molecule binds to the allosteric site of an enzyme and permanently changes the shape of the enzyme, preventing the substrate from binding to the enzyme


Competitive Inhibition

An inhibitor molecule binds to the active site of an enzyme and prevents the substrate from binding to the enzyme