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BIOLOGY CHAPTER 3
| Question | Answer |
|---|---|
| The nature of the proteome | complete set of proteins expressed by the genome. The proteome varies between cell type, developmental stage and environmental conditions. Although a cell may contain the entire genome, only specific genes will be expressed, or ‘switched on’ |
| Synthesis of proteins | All proteins are made up amino acids. These smaller subunits are joined together in a particular order to form polypeptide chains, are then folded and coiled into proteins. |
| Condensation polymerisation of amino acids | Joins amino acids • A hydrogen and oxygen from the carboxyl group of one amino acid join with a hydrogen atom from the amine group of another amino acid to produce water. • The water is released • A peptide bond holds the two amino acids together |
| Protein Structure | Proteins are large biomolecules that can contain thousands of amino acids and may be synthesised as one or several polypeptide chains. These polypeptide chains are folded and organised into specific shapes, vital to the correct functioning of the protein |
| primary structure - linear sequence of amino acids in the polypeptide chain | The linear sequence provides information on how proteins will fold (functional and non-functional proteins), they can be compared in order to identify what changes to the sequence render the protein non-functional |
| secondary structure - the coiled or pleated structure | Folding or coiling occurs due to the formation of hydrogen bonds between the amine and carboxyl groups of amino acids within a polypeptide chain that have come in close proximity to each other |
| Alpha helix | Hydrogen bonds cause formation of a helical shape |
| Beta-pleated sheets | Hydrogen bonds cause the chains to fold back on each other |
| Random coil | Although parts of the polypeptide chain appear to have a random structure, the folding is not in fact random and the same folding occurs in all molecules of the same protein |
| tertiary structure - A 3D structure composed of secondary structures | Polypeptides also fold further, forming more stable globular or fibrous three- dimensional shapes, result of a combination of alpha helices and beta-pleated sheets along with other folded areas |
| quaternary structure- Two or more polypeptide chains joined together | formed when two or more polypeptide chains or prosthetic groups (an inorganic compound that is involved in protein structure or function) join together to create a single functional protein. The polypeptides may be identical or different |
| Nucleic acids | Are polymers, made up of repeated subunit monomers called nucleotides. Nucleic acids are organic biomolecules that store and transmit inherited characteristics of organisms- specifically, nucleic acids encode instructions for the synthesis of proteins |
| DNA and RNA | DNA carries the instructions that code for the production of RNA, which may be functional tRNA or have info for protein synthesis mRNA. DNA is able to self-replicate. RNA plays a major role in the process of protein synthesis |
| Nucleotides | A single nucleotide consists of three basic units: • a phosphate group—the same in all nucleotides • a five-carbon (pentose) sugar (deoxyribose in DNA nucleotides, ribose in RNA nucleotides) • a nitrogenous (nitrogen-containing) base |
| The nitrogenous bases | There are five different nitrogenous bases: • adenine (A) • guanine (G) • cytosine (C) • thymine (T)—in DNA only • uracil (U)—in RNA only |
| Purines | A and G have two rings in their structure |
| Pyrimidines | T, U and C have one ring in their structure |
| Condensation polymerisation of nucleotides - step 1 | • The hydroxyl group (OH) on the 3' carbon atom of the sugar of one nucleotide joins with the phosphate on the fifth carbon of the pentose sugar (5') of the other nucleotide to form water, which is released. |
| Condensation polymerisation of nucleotides - step 2 | • Free nucleotides can then be continuously added to the 3' carbons in this way, forming a long sugar– phosphate–sugar–phosphate backbone strand. |
| Condensation polymerisation of nucleotides - step 3 | • The nucleotides in the sugar–phosphate chain are joined by phosphodiester bonds (a type of strong covalent bond). |
| Structure of DNA | DNA is double helix structure (two chains of nucleotides). Primary structure of DNA is a single strand of polynucleotides, consists of a sequence of bases. Hydrogen bonds between pairs of nitrogenous bases stabilise the secondary structure of the DNA |
| The genetic code | The genetic code in DNA of protein-encoding genes typically contains info for joining amino acids to form polypeptides. 1 genetic instruction consists of a group of 3 bases (e.g AAT, GGC). Because of this the genetic code is referred to as a triplet code. |
| Main features of the genetic code part 1 | • One genetic instruction consists of three- base sequences. DNA = triplet code. DNA triplet is transcribed into mature mRNA= codon. • code in non-overlapping. • code is essentially the same in bacteria, in plants and animals |
| Main features of the genetic code part 2 | As the genetic code uses four nucleotides and three nucleotides code for an amino acid, the combinations of these nucleotides make a total of 64 possible codons (43 = 64), to code for the total 20 amino acids |
| Main features of the genetic code part 3 | The code is said to be redundant or degenerate because, in many cases, more than one triplet of bases codes for one particular amino acid. Differences in codons encoding the same amino acid usually occur at the second or third base. |
| Main features of the genetic code part 4 | The information in the DNA template strand also includes a START instruction and three STOP instructions |
| The structure of genes part 1 | • stop and start triplet sequences—regions where encoding DNA begins and ends for a specific gene • promoter regions—an upstream binding region for the enzyme that is involved in the encoding process (which is RNA polymerase) |
| The structure of genes part 1 | exons—DNA regions that are the coding segments • introns (or spacer DNA)— DNA regions that are non- coding segments. |
| Start and stop codons | Start triplet indicates where the first stage of gene expression will begin, becoming AUG when transcribed, initiating translation. Stop triplet indicates where transcription will end.. When transcribed into mRNA they become the codons UAA, UAG and UGA. |
| Promoter regions part 1 | Sections of a gene that are found before the start triplet, at the 5' end of the site where transcription will begin. Is the location where the RNA polymerase attaches to the gene & identifies which DNA strand will be transcribed |
| Promoter regions part 2 | • identifies where transcription of the gene will start • identifies in which direction transcription will occur. In many eukaryotic genes, the promoter region is coded for by the sequence of bases TATAAA, which is sometimes called the TATA box. |
| Exons | Exons are regions of a gene that are usually ‘expressed’ as proteins or RNA. Exons come together to make up mRNA, which is then translated into proteins. |
| Introns | Non-coding regions of a gene. Introns are spliced out of the mRNA during the stage of gene expression called RNA processing. There are no rules about the number of exons and introns in a gene. In some genes 99% of the length can be made up of introns. |
| Gene Expression | process by which the information stored in a gene is used to synthesise a functional gene product such as a protein. Gene expression leading to protein synthesis in eukaryotic cells occurs in 3 stages: • transcription • RNA processing • translation |
| Transcription | production of single-stranded pre-mRNA from DNA, controlled by RNA polymerase (enzyme). Transcription occurs within the nucleus of eukaryotic cells. |
| Transcription process part 1 | • The DNA in the relevant region unwinds, and then unzips, exposing the nucleotide bases of both strands • Only one of these strands is used directly for synthesis of mRNA called the template strand. The one not used is called the non-template strand |
| Transcription process part 2 | • As RNA polymerase moves along the template strand of DNA (from 3' →5'), nucleotides are added to the growing RNA molecule according to the DNA-RNA base-pairing rules (A-U, T-A, G-C, C-G). • The RNA produced is called pre-mRNA |
| Transcription process part 3 | • Transcription ends when RNA polymerase reaches the stop codon. • The RNA polymerase detaches, releasing the mRNA and allowing the DNA molecule to reform |
| RNA Processing | pre-mRNA is processed further to become mRNA. Occurs within the nucleus. |
| RNA Processing process | • methylated cap added at the 5' end •poly-A tail added to the 3' end • splicing of the introns by spliceosomes that cut out the regions that corresponded to the introns (non-coding) of the gene and join the remaining pieces back together (RNA splicing) |
| Alternative splicing | A primary transcript can be spliced in many different ways, resulting in alternative mature mRNA strands from a single gene and, thus, create different proteins. This is the result of some exons being removed along with the introns during RNA processing |
| Translation | Process in which the codons on mRNA are translated into a sequence of amino acids resulting in a polypeptide. Occurs on ribosomes that are free in the cytoplasm or located on the rough ER. The ribosomes provide a scaffold for the mRNA to assemble |
| mRNA | mRNA codons are a 3 base code. The 'instructions' for assembling a polypeptide are coded as three base codons in the mRNA. For a genetic code based on triplets of four bases (a, c, g, u) there are 64 possible codons. |
| tRNA | Form a cloverleaf structure. Different types produced by transcription from the DNA template of a different tRNA gene. Act as transfer molecules, bringing the correct amino acid to the ribosome for assembly into the polypeptide. |
| specific sites on the tRNA where binding occurs - amino acid attachment site | where the amino acid attaches to the tRNA. For each tRNA this site is specific for a particular amino acid e.g. A glycyl tRNA will only attach for the amino acid glycine |
| specific sites on the tRNA where binding occurs - anticodon site | tRNA molecule is necessary to ensure that the correct amino acid is added to the growing polypeptide. Composed of 3 bases that are complementary to the codon on the mRNA. Eg the codon for glycine is GGU and the matching anticodon of the glycyl tRBA is CCA |
| Translation process part 1 | • To begin protein synthesis, a small ribosomal subunit attaches to the 5' end of an mRNA strand. • The ribosome subunit bonds to the methylated cap on the mRNA and moves along it 'scanning' for an AUG start. |
| Translation process part 2 | • The ribosome then passes along the mRNA strand and, as it passes each codon in the mRNA, a tRNA, carrying the appropriate amino acid, moves to the ribosome, attaching by complementary base pairing between the codon (mRNA) and anticodon (tRNA) |
| Translation process part 3 | • The order in which amino acids are added to the polypeptide is therefore determined by the codon sequence of the mRNA. • The mRNA is read in a 5' → 3' direction as the ribosome moves along it. |
| Translation process part 4 | • Once aligned, the amino acid joins by a peptide bond to the first amino acid through CPR • Once the job of the tRNAs is complete, they detach themselves from the mRNA and return to the cytoplasm, from where they can be drawn upon again when required. |
| Translation process part 5 | • Attachment of amino acids continues until a stop codon is reached. • The polypeptide chain is then released from the ribosome into the cytoplasm or the endoplasmic reticulum. |
| Transcription process summary | • RNA polymerase copies the DNA template strand by adding complementary base pairing of free nucleotides. • pre-mRNA is produced. |
| RNA processing process summary | • introns are removed, • poly-A tail or methyl cap added. • mRNA is produced. |
| Translation process summary | • ribosomes use/read the mRNA code • tRNA brings a specific amino acid to the ribosome with the tRNA anticodons joining to complementary mRNA codons • an amino acid is added to the growing polypeptide chain. |
| Constitutive genes | Constitutive genes are always switched on: they are transcribed continually. For other genes, transcription may be induced or repressed by transcription factors as needed, depending on the cell type, stage or environmental conditions. |
| Regulatory genes | code for transcription factors. The actions of these genes determine whether other genes are active (‘on’) or not (‘off’) and, if active, the rate at which their products are made. |
| Transcription factors | Proteins that control gene expression at the transcription stage, or control the action of other genes. They bind to DNA sequences close to the promoter region of a gene or to the RNA polymerase to induce or repress the expression of specific genes |
| Structural genes | code for proteins and RNAs that are not involved in gene regulation, they produce proteins that become part of the structure and the functioning of the organism (eg. enzymes, protein channels, protein components) |
| The LAC Operon—A prokaryote model for gene regulation | An operon is a unit of DNA under the regulation of a single promoter that codes for several proteins. An iducible operon that expresses three structural genes that code for three enzymes, but only when the sugar lactose is available. |
| Lactose in the LAC Operon | The enzymes break down lactose into the useable forms glucose and galactose. Producing the enzymes that break down lactose constitutively would be a misuse of energy for the bacteria because lactose is not the preferred energy source for E. coli |
| The lac operon consists of - promoter | short DNA segment where RNA polymerase can attach and start transcription of the three downstream lac genes. Thee three lac genes are transcribed as a single entity with one long mRNA transcript being produced. |
| The lac operon consists of - operator | An operator is a short DNA segment that provides a binding site for a repressor. |
| The lac operon consists of - 3 structural genes | lacZ (β-galactosidase), lacY (β-galactoside permease) and lacA (β-galactoside transacetylase)—that code for three different enzymes. |
| The lac operon consists of - lac repressor | transcription factor binds to the operator in the lac operon, blocking the RNA polymerase from binding to and transcribing the structural genes in the lac operon, thereby preventing the synthesis of the three enzymes involved in lactose metabolism |
| lac repressor when lactose present | lactose binds to the lac repressor, inhibiting the transcription factor from binding to the operator enabling RNA polymerase to attach to the promoter and transcribe the 3 structural genes. Results in production of the enzymes in lactose metabolism |
| Secretory proteins | produced to be exported out of a cell. The movement of secretory proteins occurs by exocytosis, also known as secretion. Before reaching the plasma membrane for exocytosis, secretory proteins must first be synthesised and modified. |
| Ribosomes and Rough endoplasmic reticulum | Proteins that are to be secreted are synthesised by ribosomes that stud the outer surface of the rough endoplasmic reticulum. The protein is transported through the tubules of the rough endoplasmic reticulum, where it is modified. |
| Exocytosis | secretory vesicle membrane and plasma membrane come into contact, the fluid and dynamic nature of the plasma membrane enables these membranes to fuse. Once the two membranes are fused, the contents of the secretory vesicle are released out of the cell |
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