Chapter 12: Molecular Biology of the Gene

Transcription

1 Biology Textbook Notes Chapter 12: Molecular Biology of the Gene p The Genetic Material (12.1) - Genetic Material must: 1. Be able to store information that pertains to the development, structure, and metabolic activities of the cell or organism 2. Be stable so that it can be replicated with high accuracy during cell division and be transmitted from generation to generation 3. Be able to undergo rare changes called mutations that provide genetic variability required for evolution to occur - Four types of nucleotides - Adenine (A) and Guanine (G) (purines) - double ring - Thymine (T) and Cytosine (C) (pyrimidines) - single ring Chargaff s rules 1. The amount of A, T, C, and G in DNA vary from species to species 2. In each species, the amount of A=T and the amount of C=G - DNA is a double helix with a sugar-phosphate backbone on the outside and paired bases on the inside - The strands of the double helix are antiparallel, meaning the phosphate groups that are chained together to make each strand are oriented in opposite directions - One strand runs from the 5 to 3 position, while the other runs from the 3 to 5 position - Complementary Base Pairing - means that a purine (A&G large, two ring base) is always bonded to a pyrimidine (C&T smaller, single ring base) 1

2 - Antiparallel strands ensures that the bases are oriented properly so they can interact p Replication of DNA (12.2) - DNA Replication: the process of copying a DNA molecule - following replication, there is usually an identical copy of the parent double helix - Template: most often a mols used to produce a shape complementary to itself - During DNA Replication, each DNA strand serves as a template for a new strand in a daughter molecule - Semiconservative Replication: DNA replication is termed this because each daughter DNA double helix contains an old strand from the parental DNA double helix and a new strand - Replication requires the following steps: 1. Unwinding- the old strands that make up the parental DNA are unzipped using an enzyme called helicase, where the helicase brakes the connective hydrogen bonds between the paired bases 2. Complementary Base Pairing- The new free nucleotides are paired with nucleotides on the parental strands. A with T, G with C 3. Joining- The complementary nucleotides paired with the parental strands are connected with each other to form a connected chain. Each daughter DNA contains an old strand and a synthesized strand - Steps 2 and 3 are carried out by DNA Polymerase, an enzyme complex - DNA replication occurs before mitosis or meiosis occur Prokaryotic DNA Replication - Process begins at the origin of replication, a specific site on the bacterial chromosome - Replication occurs in either one or two directions, always from 5 to 3 - The strands are separated, unwound, and DNA polymerase binds to to each side of the opening and begins the copying process - The two DNA polymerases meet at a termination region, and replication is halted, when the two copies of the loop chromosome separate 2

3 - Bacterial cells require only 40 minutes to replicate the DNA chromosome Eukaryotic DNA Replication - DNA Replication begins in numerous origins of replication - The replication bubbles spread bidirectionally until they meet - Replication Fork: the location where the two parental DNA strands separate, looks like a V - Eukaryotes replicate their DNA at a much slower rate compared to Prokaryotes, only 500-5,000 base pairs replicated per minute (there are over 6 billion base pairs in a human) - Due to the numerous occurrences of origins of replication, the process to completely replicate DNA only takes a few hours - The linear nature of chromosomes in eukaryotic cells, makes replicating the DNA difficult towards the end of the chromosome - Telomeres compose the ends of DNA chromosomes and are short DNA sequences that repeat - The replication of telomeres is made possible by an enzyme called telomerase Accuracy of Replication - A DNA polymerase makes a mistake about once every 100,000 base pairs at most - DNA Polymerase has the capability to proof-read the DNA sequence, and can reverse direction to fix a mix-matched base pair - Overall, the error rate for bacterial DNA polymerase is only one in 100 million base pairs p The Genetic Code of Life (12.3) RNA carries the information RNA: a polymer composed on nucleotides - a few differences from DNA; the sugar is ribose; instead of the nitrogenous base Thymine, it is replaced by Uracil; it is single stranded - Messenger RNA (mrna): takes a message from DNA in the nucleus to the ribosomes in the cytoplasm - Transfer RNA (trna): transfers amino acids to the ribosomes 3

4 - Ribosomal RNA (rrna): along with ribosomal proteins, makes up the ribosomes, where polypeptides are synthesized The GENETic code - Transcription: the first of two major steps converting DNA information into functioning proteins. This is the process by which a RNA molecule is produced based on a DNA template. DNA is either transcribed or copied base by base into mrna, trna, or rrna - Translation: the second major step where the mrna transcript is read by a ribosome and converted into the sequence of amino acids in a polypeptide - Central Dogma: processes that dictate the flow of information from the DNA to RNA to protein in a cell - Genetic Code: Universal code; existed for eons; allows for conversion of DNA and RNA s chemical codes to a sequence of amino acids in a protein finding the genetic code - Codon: coding unit - Triplet Code: each codon is made up of three nucleotides - Features of the code 1. The genetic code is degenerate. This terms means that most amino acids have more than one codon; leucine, serine, and arginine have six different codons, for example. The degeneracy of the code helps protect against potentially harmful mutations 2. The genetic code is unambiguous. Each triplet codon has only one meaning 3. The code has start and stop signals. There is only one start signal, but there are three stop signals p First Step: Transcription (12.4) Messenger RNA is produced - RNA Polymerase: joins the nucleotides together in the 5 > 3 direction - Similar to a DNA Polymerase, the RNA Polymerase only adds a nucleotide to the 3 end of the polymer under construction 4

5 - Promoter: defines the start of transcription, the direction of transcription, and the strand to be transcribed. A region of DNA - Transcription begins when RNA polymerase attaches to the promoter. The binding is called initiation of transcription - Elongation of the mrna molecule occurs as the RNA polymerase reads down the DNA template strand in a 5 to 3 direction - It continues until the RNA polymerase comes to a DNA stop sequence, where termination occurs - The stop sequence causes RNA polymerase to stop transcribing the DNA, and releases the mrna molecule, now called an mrna transcript - RNA polymerase can produce many copies of the mrna transcript at the same time, as long as it has access to the gene s promoter RNA Molecules undergo processing - A newly formed RNA transcript, called a pre-mrna is modified before leaving the eukaryote nucleus - The molecule receives a cap (modified guanine nucleotide) at the 5 end and a tail at the 3 end - The cap helps tells ribosomes where to attach when translation begins - The tail consists of a chain of adenine nucleotides; the poly- A tail facilitates the transport of mrna out of the nucleus, helps start the loading of ribosomes (and the start of translation), and also delays the degradation of mrna by hydrolytic enzymes - the pre-mrna contains a mix of protein coding regions called exons and non-protein coding regions called introns - Only the exons of the pre-mrna will be contained in the mature mrna, the introns have to be spliced out of the rough-form of mrna, just made by the RNA polymerase - In lower eukaryotes, introns have the capability of enzymatically splicing itself out of the pre-mrna and are self-splicing - In higher eukaryotes, spliceosomes containing small nuclear RNA (snrna) do the splicing of the introns - snrnas are capable of identifying the introns to be removed by means of complementary base pairing 5

6 - Ribozyme: an enzyme made of RNA rather than just protein - the spliceosome utilizes a ribozyme to cut and remove the introns - After the cap and poly-a tail are placed on the mrna, and the introns have been removed, the mrna is ready to leave the nucleus Function of introns - the presence of introns allows the cell to pick and choose which exons will go into a particular mrna from the pre-mrna - based on environmental conditions, a gene may produce different exons based on needs - if a cell has three exons, it may choose to produce only exons 1 and 3 or exons 2 and three, due to the conditions listed directly above - this is called alternative mrna splicing - It is also possible that the presence of introns encourages crossing-over during meiosis and permits a phenomenon called exon shuffling which can play a role in the evolution of new genes p Second Step: Translation (12.5) - Translation takes place in the cytoplasm of the eukaryote - Second step to express a gene into a protein - Requires the conversion of information from DNA and RNA (nucleic acid) into a protein (amino acid) The role of transfer rna - trna: a single-stranded nucleic acid that double backs on itself to create regions where complementary bases are hydrogen bonded to each-other - at least one trna molecule for each of the 20 amino acids found in proteins - the amino acid binds to the 3 end of the trna - opposite to the amino acid is an anticodon group - Anticodon: a group of three bases complementary and antiparallel to a specific mrna codon - In the genetic code, there are 61 codons that specify certain amino acids; the other 6

7 three are stop sequences - Wobble Hypothesis: states that the first two positions in a trna anticodon pair observe the A-U and G-C configuration rule. The third position can be variable, but still produce a correct protein. This is called the wobble effect - Despite changes in the DNA base sequences, the resulting sequence of amino acids will produce a correct protein - Amino acid-charging enzymes (generically called aminoacyl-trna synthetases) have a recognition site for a particular amino-acid to be joined to a specific trna - This process requires ATP - A trna with its amino acid is called a charged trna - After the amino acid-trna complex is formed, it is added to a large pool of charged trnas that exist in the cytoplasm, accessible by a ribosome during protein synthesis the role of ribosomal rna - Ribosomal RNA (rrna) is produced from a DNA template in the nucleolus of a nucleus - The rrna is packaged with a variety of proteins into two ribosomal subunits - There is a large and small subunit in the rrna - The subunits move separately through the nuclear envelope pores into the cytoplasm, where they join together again at the start of translation - Once translation begins, the ribosomes can remain in the cytoplasm or become attached to the endoplasmic reticulum - Ribosomes have a binding site for mrna and three binding sites for trna - The three binding sites for trna are E (for exit), P (for peptide), and A (for amino acid) - The trna binding sites facilitate complementary base pairing for mrna codons and trna anticodons - The large ribosomal subunit has enzyme activity from rrna (a ribozyme) that creates the peptide bonds between adjacent amino acids - The peptide bonds are created many times to form a polypeptide, which in turn folds into its three dimensional shape, and becomes a protein - As the ribosome moves down the mrna molecule, the polypeptide increases by one 7

8 amino acid at a time - Translation stops at a stop codon - After translation stops, the polypeptide is completed and dissociates from the ribosome - Once it emerges from the ribosome, it folds into its normal shape - Chaperone molecules present in the cytoplasm and ER ensure that the polypeptide is folded correctly - For proteins with multiple polypeptide chains, each polypeptide is folded and then the subunits join together into a final, functional protein - Similar to RNA primes in Transcription, many ribosomes can attach and translate the mrna into proteins at one time - As soon as the initial portion of mrna has been translated by one ribosome, another ribosome can attach to the mrna. This greatly increases the efficiency of translation - The entire complex of mrna and multiple ribosomes is called a polyribosome Translation Requires Three steps - The codons of mrna and the anticodons of trna must be extremely orderly to ensure that the amino acids of a polypeptide are sequenced correctly - A single amino acid change has the potential to dramatically affect a protein s function - Enzymes are required for each of the three steps to function properly Initiation - The step that brings all the translation components together - Proteins called initiation factors are required to assemble the small ribosomal subunit, mrna, initiator trna, and the large ribosomal subunit for the start of protein synthesis - In prokaryotes, a small ribosomal subunit attaches to the mrna in the vicinity of the start codon (AUG) - The first or initiator trna pairs with this codon - Then a large ribosomal subunit joins to the small subunit 8