Questions for study: 1. What functions do transcription and translation carry out, and where are they carried out in the cell? Transcription: process of creating an equivalent RNA copy of a sequence of DNA Transcription is the first step leading to gene expression. The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. Occurs in nucleus of the cell Translation: Translation is the production of proteins by decoding mRNA produced in transcription.Translation occurs in the cytoplasm where the ribosomes are located. In translation, messenger RNA (mRNA) is decoded to produce a specific polypeptideaccording to the rules specified by the genetic code. This uses an mRNA sequence as a template to guide the synthesis of a chain of amino acids that form a protein. 2. Which of the kingdoms of organisms are characterized by unicellularity (the organism has only one single cell)? Protista 3. Bacteria and archaea are both prokaryotes, but they have very different characteristics. How would you compare archaea and bacteria?Archaea cell membrane contains ether linkages cell wall lacks peptidoglycan genes and enzymes behave more like Eukaryotes have three RNA polymerases like eukaryotes extremophiles 4. What process can lead to shrinkage or swelling of a cell? Osmosis 5. What are the different kinds of fibers that make up cytoskeleton? Cells contain elaborate arrays of protein fibers that serve such functions as: Bacteria cell membrane contains ester bonds cell wall made of peptidoglycan have only one RNA polymerase react to antibiotics in a different way than archea do . 2. 3. 4. 5. establishing cell shape providing mechanical strength locomotion chromosome separation in mitosis and meiosis intracellular transport of organelles The cytoskeleton is made up of three kinds of protein filaments: ? ? ? Actin filaments (also called microfilaments) Intermediate filaments and Microtubules 6. What is a triglyceride? Cholesterol is a type of fat. How is it different from other lipids? What type of lipid makes up the plasma membrane of cells?Triglyceride: glyceride in which the glycerol is esterified with three fatty acids What’s the difference between triglycerides and cholesterol? Triglycerides and cholesterol are separate types of fats (lipids) that circulate in your blood. Triglycerides provide your body with energy, and cholesterol is used to build cells and certain hormones. Because triglycerides and cholesterol can’t dissolve in blood, they circulate throughout your body with the help of proteins that transport the lipids, called lipoproteins.Triglycerides Triglycerides are the basic chemical form of fat. Chemically, the structure of triglycerides is one molecule of glycerol (CHOH2-CHOHCHOH2) attached to three fatty acids, such as oleic acid or linoleic acid. Triglycerides come from either ingestion of dietary fats or through the conversion of unused calories. Triglycerides are stored in the body’s fat cells until the body needs to metabolize them for energy. Cholesterol Cholesterol, with a chemical structure is C27-H4-OH, acts as both a precursor for hormones and as a part of cellular membranes.The human body produces 2 grams of cholesterol per day, making up about 85 percent of blood cholesterol levels. The other 15 percent comes from a person’s diet. Most cholesterol from diet comes from oils and fats in foods. The body produces bile acids from cholesterol; bile acids break down oils and fats. The blood transports cholesterol by lipoproteins, which easily clump together with fats. The two different types of lipoproteins are low-density lipoproteins (LDL) and high-density proteins (HDL). The cell membrane consists of three classes of amphipathic lipids: phospholipids,glycolipids, and steroids. . What are the elements that are generally found in the molecules that make up living organisms (aka “biomolecules”)? CHNOPS elements: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulphur 8. What are nucleotides? What’s the difference between DNA and RNA? Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA DNA RNA 1) mRNA (carries DNA message to cytoplasm) 2)tRNA Types: Single (carries amino acids to mRNA and Ribosomes) 3)rRNA(Ribosomal RNA, workbenchfor protein synthesis) Predominant Typically a double- trandedmolecule with a long chain of A single-stranded molecule in most of it’s biological roles Structure: nucleotides and has a shorter chain of nucleotides 1. Found in nucleus 2. the genetic material 3. sugar is Difference: 1. Found in nucleus and cytoplasm dexyribose 4. Bases are A,T,C,G Pairing of A-T(Adenine-Thymine), G-C(Guanine-Cytosine) A-U(Adenine-Uracil), G-C(Guanine-Cytosine) Bases: Deoxyribose sugar in DNA is less reactive because of C-H Ribose sugar is more reactive because of C-OH (hydroxyl) bonds.Stable in alkaline conditions. DNA has smaller bonds. Not stable in alkaline conditions. RNA on the other Stability: grooves where the damaging enzyme can attach which hand has larger grooves which makes it easier to be makes it harder for the enzyme to attack DNA attacked by enzymes The helix geometry of DNA is of B-Form. DNA is completely The helix geometry of RNA is of A-Form. RNA strands are Unique protected by the body i. e. the body destroys enzymes that continually made, broken down and reused. RNA is more Features: cleave DNA.DNA can be damaged by exposure to Ultraresistant to damage by Ultra-violet rays violet rays Stands for: Deoxyribonucleic acid Ribonucleic acid A nucleic acid that contains the genetic instructions used in A nucleic acid polymer that plays an important role in the Definition: the development and functioning of all known living process that translates genetic information from organisms deoxyribonucleic acid(DNA) into protein products Medium of long-term storage and transmission of genetic Acts as a messenger between DNA and the protein Job/Role: information synthesiscomplexes known as ribosomes DNA is a long polymer with a deoxyribose and phosphate RNA is a polymer with a ribose and phosphate backbone Bases ; backbone and four different bases: adenine, guanine, and four different bases: adenine, guanine, cytosine, and Sugars: cytosine and thymine uracil 9. What are some special properties of water molecules? High Heat Capacity High Heat of Vaporization Cohesive and Adhesive High Surface Tension Frozen water less dense than liquid water 10. The electron transport chain in mitochondria is carried out in steps. What is the advantage of this? Why aren’t electrons transferred directly onto Oxygen?Electron transport chains are the source of energy for all known forms of life. They are redox reactions that transfer electrons from an electron donor to an electron acceptor. The transfer of electrons is coupled to the translocation of protons across a membrane, producing a proton gradient. The proton gradient is used to produce useful work. Minimise loss of energy as unusable heat. What kinds of molecules transport the electrons? NADH Dehydrogenase, Ubiquinone, Cytochrome b-c1, Cytochrome c, Cytochrome Oxidase, ATP Synthase, NADH How is ATP finally generated, and from what energy source? Chemiosmosis: Generation of ATP by ATP Synthase by using proton gradient.The only way for proton to move from high concentration (intermembrane space) to low concentration (matrix) is through the ATP Synthase. The proton spins the turbine of the enzyme, and this causes the phosphorylation of ADP to ATP. Energy Source: Proton Gradient Why do we breathe out CO2 and breathe in Oxygen? CO2: from oxidative decarboxylation of sugar. By-product of respiration O2: to supply the oxidation reactions in the cell 11. What does mitosis do? The main functions of mitosis are growth and repair. 12. Think of a molecule that is used for long-term energy storage, a) in animal cells, and b) plant cells. Think of a molecule that is used for providing energy in quick bursts.Animal: Fats Plant: Oil Carbohydrates function in short-term energy storage, providing energy in quick bursts. 13. Which of the following animals have the most conserved genome (% similarity) to the human genome? Mice, worms, flies, yeast. 14. What happens to various cellular membranes (i. e. nuclear membrane, ER, lysosomes, endosomes, mitochondria) during cell division? Replication during G1 phase. Each copy attach to cell membrane on the side of new daughter cells before cytokinesis. 15. Compare meiosis and mitosis. Which one gives a lower chromosome number in the daughter cells? Meiosis What are these cells called? Gametes 16. What is meant by dominance in Mendel’s law of dominance?Mendel’s law of dominance When an organism has two different allels for a trait, the allele that is expressed, overshadowing the expression of the other allele,is said to be dominant. The gene whose expression is overshadowed is said to be recessive. Mendel’s law of segregation When gametes are formed by a diploid organism, the alleles that control a trait separate from one another into different gametes, retaining their individuality. Mendel’s law of independent assortment Members of one gene pair separate from each other independently of the members of other pairs. What’s a heterozygote? An organism that has different alleles at a particular gene locus on homologous chromosomes. Why were Mendel’s “true breeding” strains true breeding (i. e. the phenotype was the same from generation to generation)?Referring to organisms for which sexual reproduction produces offspring with inherited traits identical to those of the parents. The organisms are homozygous for the characteristics under consideration. What is a hybrid? offspring of parents that differ in genetically determined traits. The parents may be of different species, genera, or (rarely) families. The term hybrid, therefore, has a wider application than the terms mongrel or crossbreed, which usually refer to animals or plants resulting from a cross between two races, breeds, strains, or varieties of the same species. 17. What was the blending hypothesis, and why did blending not occur in Mendel’s crosses with pea plants? One mechanism for this transmission is the “blending” hypothesis. · This hypothesis proposes that the genetic material contributed by each parent mixes in a manner analogous to the way blue and yellow paints blend to make green. Over many generations, a freely mating population should give rise to a uniform population of individuals. However, the “blending” hypothesis appears incorrect as everyday observations and the results of breeding experiments contradict its predictions. 18. What did Watson and Crick propose, based on Rosalind Franklin’s X-ray diffraction picture? Watson and Crick refers to the duo of James D. Watson and Francis Crick who, using x-ray data collected by Rosalind Franklin, proposed the double helix structure of the DNA molecule in 1953. 19. What does the endolysosomal trafficking system (i. e. ndosomes and lysosomes) do that is different from the Golgi? Lysosomes are membrane-enclosed organelles that contain an array of enzymes capable of breaking down all types of biological polymers—proteins, nucleic acids, carbohydrates, and lipids. Lysosomes function as the digestive system of the cell, serving both to degrade material taken up from outside the cell and to digest obsolete components of the cell itself. In their simplest form, lysosomes are visualized as dense spherical vacuoles, but they can display considerable variation in size and shape as a result of differences in the materials that have been taken up for digestion (Figure 9. 34).Lysosomes thus represent morphologically diverse organelles defined by the common function of degrading intracellular material. The primary function of the Golgi apparatus is to process and packagemacromolecules, such as proteins and lipids, after their synthesis and before they make their way to their destination; it is particularly important in the processing of proteins for secretion. 20. What is molecular cloning? What are two common techniques used in cloning? Molecular cloning refers to the procedure of isolating a defined DNA sequence and obtaining multiple copies of it in vivo. Recombinase-based cloning Restriction/ligation cloning 21.Where do oncogenes come from? Proto-oncogenes are genes whose products promote cell growth and division. They do this by encoding transcription factors that stimulate the expression of other genes, signal transduction molecules that stimulate cell division, or cell cycle regulators that move the ell through the cell cycle. Proto-oncogene products may be located in the plasma membrane, cytoplasm, or nucleus, and their activities are controlled in various ways, including regulation at the transcpritional, translational, and protein-modification levels. When cells become quiescent and cease division, they repress the expression of most proto-oncogene products.In cancer cells, one or more proto-oncogenes are altered in such a way that tier activities cannot be controlled in a normal fashion. This is sometimes due to a mutation in the proto-oncogene resulting in a protein product that acts abnormally. In other cases, proto-oncogenes may encode normal protein products, but the genes are overexpressed or cannot be transcriptionally repressed at the correct time. In these cases, the proto-oncogene product is continually in an “on” state, which may constantly stimulate the cell to divide. When a proto-oncogene is mutated or aberrantly expressed, and contributes to the development of cancer, it is known as an oncogene. Oncogenes are those that have experienced a gain-of-function alteration.As a result, only one allele of a proto-oncogene needs to be mutated or mis-expressed in order to trigger uncontrolled growth. Hence, oncogenes confer a dominant cancer phenotype. 22. What are the molecular causes of breast cancer? Mutation of BRCA1 and BRCA2 (tumour suppressor genes) 23. What happens to the ends of chromosomes when they replicate? What kind of special structure is involved? A telomere is a region of repetitive DNA at the end of a chromosome, which protects the end of the chromosome from destruction. 24. What normal cellular process goes out of control in tumor cells (cancer cells)? Cell division and apoptosis 25. Certain chemicals are carcinogenic (cancer-causing).How do they do this? A carcinogen is any substance, radionuclide or radiation that is an agent directly involved in the exacerbation of cancer or in the increase of its propagation. This may be due to the ability to damage the genome or to the disruption of cellular metabolic processes. Several radioactive substances are considered carcinogens, but their carcinogenic activity is attributed to the radiation, for example gamma rays and alpha particles, which they emit. 26. What is a transgene?  A transgene is a gene or genetic material that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. 27.What is gene therapy? Gene therapy is the insertion of genes into an individual’s cells and tissues to treat a disease, such as a hereditary disease in which a deleterious mutant allele is replaced with a functional one. 28. Think of a condition (a genetic disorder) that is caused by a chromosomal duplication. Inv dup 15 syndrome, Williams Syndrome 29. How big is a virus compared to a bacterium? -6 bacteria size ranges in micrometer i. e. 10 m virus size ranges in nanometer i. e. 10 m Bacteria Yes Present DNA and RNA. Eixsts as double-stranded Nucleic acid: and circular in shape. Peptidoglycan cell wall or capsule/slime Outermost structure: layer in some.Size: Larger (1000nm) Living attributes: Living organism Cause disease? : Ribosomes: Virus Yes Absent DNA or RNA. can be double-stranded or singlestranded, circular or linear. Protein coat or viral envelope Smaller (20 – 400nm) Considered living and non-living -9 Bacteria Beneficial? : Enzymes: Some beneficial bacteria (e. g. certain bacteria required in the gut) Yes Virus Viruses are not beneficial. However, a particular virus may be able to destroy brain tumors. http://www. technologyreview. com/Biotech/20363/ Viruses can be useful in genetic engineering. Yes, in some 30. What are the steps of influenza virus replication? Are there any drugs that interfere with it? ReplicationViruses can only replicate in living cells.  Influenza infection and replication is a multi-step process: firstly the virus has to bind to and enter the cell, then deliver its genome to a site where it can produce new copies of viral proteins and RNA, assemble these components  into new viral particles and finally exit the host cell. Influenza viruses bind through hemagglutinin onto sialic acid sugars on the surfaces of epithelial cells; typically in the nose, throat  and lungs of mammals and intestines of birds (Stage 1 in infection figure). After the hemagglutinin is cleaved by a protease, the cell  imports the virus byendocytosis.Once inside the cell, the acidic conditions in the endosome cause two events to happen: first part of the hemagglutinin protein fuses the viral envelope with the vacuole’s membrane, then the M2 ion channel allowsprotons to move through the viral envelope and acidify  the core of the virus, which causes the core to dissemble and release the viral RNA and core proteins. The viral RNA (vRNA)  molecules, accessory proteins andRNA-dependent RNA polymerase are then released into the cytoplasm(Stage 2). The M2 ion  channel is blocked by amantadine drugs, preventing infection. These core proteins and vRNA form a complex that is transported into thecell nucleus, where the RNA-dependent RNA polymerase  begins transcribing complementary positive-sense vRNA (Steps 3a and b). The vRNA is either exported into the cytoplasm and translated (step 4), or remains in the nucleus.Newly synthesised viral proteins are either secreted through the Golgi apparatus onto the cell surface (in the case of neuraminidase and hemagglutinin, step 5b) or transported back into the nucleus to bind vRNA and form new viral genome particles (step 5a). Other viral proteins have multiple actions in the host cell, including degrading cellular mRNA and using  the released nucleotides for vRNA synthesis and also inhibiting translation of host-cell mRNAs. Negative-sense vRNAs that form the genomes of future viruses, RNA-dependent RNA polymerase, and other viral proteins are assembled into a virion. Hemagglutinin and neuraminidase molecules cluster into a bulge in the cell membrane. The vRNA and viral core proteins leave the nucleus and enter this membrane protrusion (step 6). The mature virus buds off from the cell in a sphere of  host phospholipid membrane, cquiring hemagglutinin and neuraminidase with this membrane coat (step 7). As before, the viruses adhere to the cell through hemagglutinin; the mature viruses detach once their neuraminidase has cleaved sialic acid residues from the  host cell. Drugs that inhibit neuraminidase, such as oseltamivir, therefore prevent the release of new infectious viruses and halt viral  replication. After the release of new influenza viruses, the host cell dies. Because of the absence of RNA proofreading enzymes, the RNA-dependent RNA polymerase that copies the viral genome makes an error roughly every 10 thousand nucleotides, which is the approximate length of the influenza vRNA.Hence, the majority of newly manufactured influenza viruses are mutants; this causes “antigenic drift”, which is a slow change in the antigens on the viral surface  over time. The separation of the genome into eight separate segments of vRNA allows mixing or reassortment of vRNAs if more than one type of influenza virus infects a single cell. The resulting rapid change in viral genetics produces antigenic shifts, which are sudden changes from one antigen to another. These sudden large changes allow the virus to infect new host species and quickly overcome protective immunity.  This is important in the emergence of pandemics, as discussed below in the section on Epidemiology. Host cell invasion and replication by the influenza virus. The steps in this process are discussed in the text.Neuraminidase inhibitors Antiviral drugs such as oseltamivir (trade name Tamiflu) and zanamivir (trade name Relenza) are neuraminidase inhibitors that are  These drugs are often effective against both influenza A and designed to halt the spread of the virus in the body.   The Cochrane Collaboration reviewed these drugs and concluded that they reduce symptoms and complications. Different B. strains of influenza viruses have differing degrees of resistance against these antivirals, and it is impossible to predict what degree of  resistance a future pandemic strain might have. M2 inhibitors (adamantanes) The antiviral drugs amantadine and rimantadine block a viral ion channel (M2 protein) and prevent the virus from infecting  cells. These drugs are sometimes effective against influenza A if given early in the infection but are always neffective against  Measured resistance to amantadine and rimantadine in American influenza B because B viruses do not possess M2 molecules.  This high level of resistance may be due to the easy availability of amantadines as isolates of H3N2 has increased to 91% in 2005.  and their use to prevent outbreaks of influenza in part of over-the-counter cold remedies in countries such as China and Russia,  farmed poultry. 31. Think of some types of virus and where they are propagated. Influenza – Tropics 32. Go over the malaria life cycle. What are two types of plasmodium that infect humans? What is a key difference between them? Plasmodium falciparum and Plasmodium vivax ?Whereas the number of chromosomes is the same in both species, P. vivax has a comparably larger genome size. The difference in genome size (of about ~3mb) might be due to slightly larger average introns and the intergenic regions in P. vivax, thus, the total coding regions of the two genomes are roughly comparable. ? The major difference between the two genomes is the A+T nucleotide content: P. falciparum contains 23% higher A+T content than P. vivax. ? There is significant distributional difference of A+T nucleotides; as in P. vivax high A+T content is seen in the sub-telomeric regions, whereas, in P. falciparum the distribution is almost even across chromosomal locations.