* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download READ: Protein Synthesis File
RNA interference wikipedia , lookup
List of types of proteins wikipedia , lookup
Molecular cloning wikipedia , lookup
Community fingerprinting wikipedia , lookup
Gene regulatory network wikipedia , lookup
Transcription factor wikipedia , lookup
Cre-Lox recombination wikipedia , lookup
Biochemistry wikipedia , lookup
RNA silencing wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Polyadenylation wikipedia , lookup
Messenger RNA wikipedia , lookup
Non-coding DNA wikipedia , lookup
Promoter (genetics) wikipedia , lookup
Molecular evolution wikipedia , lookup
RNA polymerase II holoenzyme wikipedia , lookup
Eukaryotic transcription wikipedia , lookup
Expanded genetic code wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Non-coding RNA wikipedia , lookup
Epitranscriptome wikipedia , lookup
Deoxyribozyme wikipedia , lookup
Silencer (genetics) wikipedia , lookup
Gene expression wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
TRANSCRIPTION AND TRANSLATON Gene Expression Transcription and translation are the two fundamental components of gene expression. These two processes are part of the transformation of genetic information into functional molecules. Transcription makes an RNA-based copy of a DNA sequence. Translation makes an amino-acid polymer based on an RNA sequence. Transcription and translation are usually coupled: transcription occurs first and translation follows. The information flow, from DNA to RNA via transcription, and then from RNA to protein via translation, is one-way. Cells do not make RNA sequences from amino-acid templates or DNA sequences from RNA templates. TRANSCRIPTION Transcription requires DNA: Prokaryotic DNA is located in the cytoplasm, so prokaryotic transcription occurs in the cytoplasm. In eukaryotes, the DNA is located in the nucleus, so eukaryotic transcription occurs in the nucleus. Mitochondria and chloroplasts have their own DNA, and transcription can also occur in each of these structures. Base Pairs: The nucleotides in RNA form base pairs with the nucleotides in DNA. RNA has four different nucleotides: adenine (A), cytosine (C), guanine (G), and uracil (U). DNA has the same nucleotides except for U, which is replaced by thymine (T) in DNA. Each nucleotide pairs exclusively with one of the others. G always pairs with C. T, which only occurs in DNA, pairs with A. In RNA, A pairs with U. RNA Polymerase: Transcription requires an enzyme called RNA polymerase. RNA polymerase links nucleotides together to make an RNA that is complementary to a pre-existing piece of DNA. The DNA must be uncoiled for the RNA polymerase to access its bases, and the hydrogen bonds between the base pairs of the DNA double helix must be broken. The template strand consists of the DNA strand that forms complementary base pairs with the nascent RNA. The coding strand is the DNA strand that is complementary to the template strand. The RNA polymerase always moves along the template strand in a 3’ to 5’ direction. The nucleotide sequence in the newly synthesized RNA is the same as the nucleotide sequence in the coding strand, except the Ts are replaced by Us in the RNA. Promoters: DNA sequences called promoters specify the location on the DNA strand where the RNA polymerase should start transcription. The promoters are upstream. This means that they are further toward the 3’ end of the template DNA than from the first nucleotide that is actually transcribed. In bacteria, the RNA polymerase binds to the promoters with the help of an accessory protein called sigma factor. In Archaea and eukaryotes, the RNA polymerase does not actually bind to the promoters. In these organisms, proteins called transcription factors are what bind to the promoters. After the transcription factors bind to the promoters, the RNA polymerase binds to the DNA and transcription begins. Once transcription initiates, the sigma factor (transcription factors) dissociate from the DNA, and the RNA polymerase moves along the template strand in a 3’ to 5’ direction, synthesizing a new RNA molecule. Transcription ends when the RNA polymerase reaches sequences in the DNA that cause the enzyme to dissociate from the DNA, either with or without the help of additional transcription-termination factors. The end result of transcription is a singlestranded RNA copy of a segment of the coding strand of the DNA. Types of RNA: Most of the RNAs synthesized via transcription are messenger RNAs (mRNAs). mRNAs serve as templates for protein synthesis. Not all RNAs are mRNAs. Ribosomal RNAs (rRNAs) function as components of ribosomes, or the RNA-protein complexes that synthesize proteins. Transfer RNAs (tRNAs) function as adapters to link specific amino acids with specific codons during translation. Other small RNAs function by binding through complementary base pairing to mRNAs, preventing their translation, or to sites within the DNA, enhancing or suppressing transcription. Small regulatory RNAs, rRNAs, and tRNAs do not encode proteins. These specific RNAs are non-coding, functional RNAs TRANSLATION Translation makes a polypeptide chain based in an mRNA. Translation occurs on ribosomes, which are located within the cytoplasm and on cytoplasmic membranes. Ribosomes match amino acids to nucleotide triplets, called codonsin the mRNA sequence. Each codon specifies a certain amino acid. The mapping of amino acids to their codons is called the genetic code. The genetic code is fairly consistent across all of the domains of life, with many slight variations. Mitochondria and some bacteria, for example, use slightly modified genetic codes. Condons and Anticodons: Ribosomes synthesize polypeptides through the successive formation of peptide bonds between amino acids. Ribosomes match amino acids to codons by bringing tRNAs together with mRNAs. tRNAs carry a specific amino acid at one end, and an anticodon at the other end. An anticodon is a nucleotide triplet that is complementary to a codon. For example, the anticodon for the GGG codon is CCC. The GGG codon specifies the amino acid glycine, so the corresponding tRNA has a glycine at one end and the CCC anticodon at the other end. When the ribosome reaches the GGG codon in the mRNA, it matches the codon to the CCC anticodon in a glycine tRNA, then adds the glycine at the other end of the tRNA to the growing polypeptide chain. The tRNA moves out of the ribosome after its amino acid joins the growing polypeptide, and the mRNA moves a distance of three nucleotides, or one codon, through the ribosome. Thus, during translation, the mRNA moves through the ribosome in threenucleotide increments. Each time the mRNA moves ahead, a new tRNA enters the ribosome, adds its amino acid to the growing polypeptide, and then leaves the ribosome. Mapping the Genetic Code: As there are four different nucleotides, and three nucleotides make up one codon, there are 64 possible codons. Three of the 64 codons are stop codons. The stop codons do not code for an amino acid, but instead signal the point at which translation should stop. Each of the other 61 codons specifies an amino acid. There are only 20 standard amino acids, so most amino acids have more than one codon. Thus, the genetic code is redundant and also degenerate. Degeneracy refers to the fact that certain positions within certain codons can be changed without changing the amino acid. For example, the codons AAU and AAC both code for the amino acid asparagine. The third position in both of the asparagine codons is 2-fold degenerate, which means that two different nucleotides have the same meaning. The codons CUU, CUA, CUC, and CUG all code for the amino acid leucine, so the third position in these codons is 4-fold degenerate, as four different nucleotides have the same meaning. Polypeptides: The end result of translation is a polypeptide chain in which the sequence of amino acids matches the corresponding sequence of codons in an mRNA. The new polypeptide undergoes a complex folding process, often with the help of molecular chaperones and other posttranslational modifications, to finally become an active protein. A single mRNA can be used to synthesize multiple proteins with multiple ribosomes simultaneously translating the mRNA. Multiple RNA polymerases can also simultaneously transcribe mRNAs from a single gene by proceeding, one after another, along the DNA strand. REGULATORY NETWORK Transcription and translation are tightly regulated and controlled. No cell expresses all of its genes all of the time. For transcription, the region of DNA containing a gene must be accessible to transcription factors and RNA polymerases. Furthermore, the DNA cannot be bound by histones and must be mostly linear (not coiled). Enzymes called helicases unwind the DNA double helix. Regulatory proteins and small RNAs interact with non-coding sequences within the DNA to direct the conformational changes as well as the binding of helicases and transcription factors. Other non-coding DNA sequences called enhancers are not necessary for transcription, but their presence upstream or downstream from a gene can affect the rate of transcription. Protein expression is also regulated post-transcriptionally. Post-translational modifications and protein folding can be enhanced or suppressed, resulting in higher or lower levels of active proteins within the cell. Through intricate regulatory networks, cells turn genes on and off, depending on changing needs and conditions. The total number of genes is not very different between humans and single-celled organisms. Much of the difference between complex organisms and simpler ones is due to differences in the transcriptional regulatory networks rather than differences in the number of genes that they posses. The different proteins that are synthesized at different times determine the characteristics of cells and the organisms that they make up. GENETIC DISORDERS Genetic disorders arise from mutations in DNA sequences. For a genetic disorder to pass from one generation to the next in sexually reproducing organisms, the mutation must be carried by the gametes (sperm or eggs). Mutations in the somatic cells can cause problems for the individual in which they occur, but the offspring will not be affected as they inherit only the DNA carried by the gametes. Mutagens are physical or chemical agents that cause mutations. Mutations within protein-coding regions of DNA can cause problems if they are not repaired as they may result in dysfunctional proteins, especially if the mutation causes a frame-shift or a premature stop codon. Mutations outside of coding regions can also cause problems if they occur within promoters, enhancers, or other regulatory sites. A mutation that destroys a promoter can stop a protein from being transcribed, even though the coding region of the gene remains unchanged. Mutations are related to cancer, as they change gene expression and alter the properties of proteins. Point mutations are single-nucleotide changes. A point mutation within a coding region changes a codon, which may or may not result in a different amino acid in the corresponding polypeptide. A point mutation in a coding region that does not change the amino acid that is encoded is called a synonymous substitution, whereas one that changes the amino acid is called a non-synonymous substitution. Insertions and deletions: Insertions and deletions are the addition or removal of pieces of DNA within a chromosome. The size of insertions and deletions can range from a single nucleotide to entire chromosomes.These mutations can change the reading frame of a coding sequence. As the genetic code is read three nucleotides at a time, adding or removing a number of bases (other than by a factor of three) changes every codon after the mutation. For example, if the original nucleotide sequence is AAAGGGCCCAAA, then the codons are AAA, GGG, CCC, and AAA. If a single-base deletion changes the nucleotide sequence to AAGGGCCCAAA, then the codons become AAG, GGC, and CCA. Frame-Shift Mutation: A mutation that causes a change in the reading frame of a gene is called a frame-shift mutation. Frame-shift mutations are devastating as the resulting protein looks nothing like the un-mutated version, and is likely not to function at all. Mutations resulting in a premature stop codon are also highly disruptive. Any of the three stop codons will cause translation to terminate. For example, an mRNA with the sequence CACUGGUCU has the codons CAC, UGG, and UCU, which will make a polypeptide with histidine, tryptophan, and serine. If a mutation changes the sequence to CACUGAUCU, then the second codon becomes UGA, which stops translation after the histidine. A mutation resulting in a premature stop codon is usually referred to as a knockout (unless it is near the end of the gene) as it effectively removes the corresponding protein from production. Diploid organisms have two copies of each chromosome, so a knockout of one copy may not completely remove the protein from production. However, having only a single working copy of a gene may still have serious consequences. The cell may not be able to produce the protein at a high enough rate from only one chromosome, or the working copy of the gene may have some other mutation that causes it to function poorly.