Biology Notes regarding Cells and Related topics

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1. The ability of ice to float because of the expansion of water as it solidifies is an important factor in the fitness of the environment. If ice sank, then eventually all ponds, lakes, and even oceans would freeze solid, making life as we know it impossible on earth. During the summer, only the upper few inches of the ocean would thaw. Instead, when a deep body of water cools, the floating ice insulates the liquid water below, preventing it from freezing and allowing life to exist under the frozen surface.

2. Carbon atoms are the most versatile building blocks of molecules. A covalent bonding capacity of four contributes to carbon’s ability to form diverse molecules. Carbon can bond to a variety of atoms, including oxygen, hydrogen, nitrogen, and sulfur. Carbon atoms can also bond to other carbons, forming the carbon skeletons of organic compounds.

3. Most macromolecules are polymers. Carbohydrates, lipids proteins, and nucleic acids are the four major classes of organic compounds in cells. Some of these compounds are very large and are called macromolecules. Most macromolecules are polymers, chains of identical or similar building blocks called monomers. Monomers form larger molecules by condensation reactions in which water molecules are released, dehydration. Polymers can disassemble by the reverse process, hydrolysis.

4. Monosaccharides are the simplest carbohydrates. They are used directly for fuel, converted to other types of organic molecules, or used as monomers for polymers. Disaccharides consist of two monosaccharides connected by a glycosidic linkage. Fats are constructed by joining a glycerol molecule to three fatty acids by dehydration reactions. Saturated fatty acids have the maximum number of hydrogen atoms. Unsaturated fatty acids have one or more double bonds between their carbons. The primary structure of a protein is its unique sequence of amino acids. Secondary structure is the folding or coiling of the polypeptide into repeating configurations, such as the a helix and the pleated sheet, which result from hydrogen bonding between parts of the polypeptide backbone. Tertiary structure is the overall three-dimensional shape of a polypeptide and results from interactions between amino acid side chains. Proteins made of more than one polypeptide chain have a quaternary level of structure. The structure and function of a protein are sensitive to physical and chemical conditions. Protein shape is ultimately determined by its primary structure, but in the cell chaperone proteins may help the folding process. Each nucleotide monomer consists of a pentose covalently bonded to a phosphate group and to one of four different nitrogenous bases.

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RNA has ribose as its pentose; DNA has deoxyribose. RNA has U and DNA T. In making a polynucleotide, nucleotides join to form a sugar-phosphate backbone from which the nitrogenous bases project. The sequence of bases along a gene specifies the amino acid sequence of a particular protein.

5. Prokaryotic cells have no nuclei or other membrane-enclosed organelles. Eukaryotic cells have membrane-enclosed nuclei and other specialized organelles in their cytoplasm. However, both prokaryotic and eukaryotic cells are bounded by a plasma membrane.

6. The evolutionary relationships between prokaryotic and eukaryotic cells are that the nucleus contains most of the genes that control the eukaryotic cell. Many of the different membranes of the eukaryotic cell are part of an endomembrane system. These membranes are related either through direct physical continuity or by the transfer of membrane segments as tiny vesicles. These relationships, however, do not mean that the various membranes are alike in structure and function. The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, various kinds of vacuoles, and the plasma membrane.

7. The current model of the molecular architecture of membranes is the fluid mosaic model. S. J. Slinger and G. Nicolson advocated a revised membrane model that placed the proteins in a location compatible with their amphipathic character. They proposed that membrane proteins are dispersed and individually inserted into the phospholipid bilayer to be exposed to water. This molecular arrangement would maximize contact of hydrophilic regions of proteins and phospholipids with water while providing their hydrophobic parts with a non-aqueous environment. According to this model, the membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids; hence the term fluid mosaic model.

8. Membranes have distinct inside and outside faces. The two lipid layers may differ in specific lipid composition, and each protein has directional orientation in the membrane. The plasma membrane also has carbohydrates, which are restricted to the exterior surface. This asymmetrical distribution of proteins, lipids, and carbohydrates is determined as the membrane is being built by the endoplasmic reticulum. Molecules that start out on the inside face of the endoplasmic reticulum end up on the outside face of the plasma membrane. A single cell may have membrane proteins performing several functions, and a single protein may have multiple functions.

9. Membrane carbohydrates are usually branched oligosaccharides with fewer than fifteen sugar units. Some of these oligosaccharides are covalently bonded to lipids, forming molecules called glycolipids. Most, however, are covalently bonded to proteins, which are thereby glycoproteins. The oligosaccharides on the external side of the plasma membrane vary from species to species, among individuals of the same species, and even from one cell type to another in a single individual. The diversity of the molecules and their location on the cell’s surface enable oligosaccharides to function as markers that distinguish one cell from another.

10. One mechanism by which substances cross membranes is diffusion. Diffusion is the tendency for molecules of any substance to spread out into the available space. Each molecule moves randomly, yet diffusion of a population of molecules may be directional. The diffusion of a substance across a biological membrane is called passive transport, because the cell does not have to expend energy to make it happen. The diffusion of water across a selectively permeable membrane is a special case of passive transport called osmosis. The direction of osmosis is determined only by a difference in total solute concentration. Water moves from a hypotonic, low concentration, solution to a hypertonic, high concentration, solution even if the hypotonic solution has more kinds of solutes. Some transport proteins can move solutes against their concentration gradients, across the plasma membrane from the side where they are less concentrated to the side where they are more concentrated. This transport is “uphill” and therefore requires work. To pump a molecule across a membrane against its gradient, the cell must expend its own metabolic energy; therefore, this type of membrane traffic is called active transport.

11. In addition to the plasma membrane, a eukaryotic cell has the extensive and elaborately arranged internal membranes, which partition the cell into compartments. These membranes also participate directly in the cell's metabolism; many enzymes are built into the membranes. Because the cell's compartments provide local environments that facilitate specific metabolic functions, incompatible process can go on simultaneously inside the same cell.

12. The endoplasmic reticulum is a membranous labyrinth so extensive that it accounts for more than half the total membrane in many eukaryotic cells. The endoplasmic reticulum consists of a network of membranous tubules and sacs called cisternae. The endoplasmic reticulum membrane separates its internal compartment, the cisternal space, from the cytosol. Also because the endoplasmic reticulum is continuous with the nuclear envelope, the space between the two membranes of the envelope is continuous with the cisternal space of the endoplasmic reticulum.

13. The chromatin in the nucleus consists of DNA, which carries genes along with proteins. Nucleoli are involved in the production of particles called ribosomes. Ribosomes synthesize proteins. The endoplasmic reticulum, a labyrinth of membranes forming flattened sacs and tubes that segregate the contents of the endoplasmic reticulum from the cytosol. The endoplasmic reticulum takes two forms: rough, studded with ribosomes, and smooth. Many types of proteins are made by ribosomes attached to endoplasmic reticulum membranes, and the endoplasmic reticulum also plays a major role in assembling the cell’s other membranes. The Golgi apparatus, another type of membranous organelle, consists of stacks of flattened sacs active in synthesis, refinement, storage, sorting, and secretion of a variety of chemical products. Another membrane-enclosed organelle is the lysosome, which contains mixtures of digestive enzymes that hydrolyzes macromolecules. Peroxisomes are a diverse group of organelles that contain enzymes that perform specialized metabolic processes. Vacuoles have a variety of storage and metabolic functions. Mitocondrias carry out cellular respiration, which generates ATP from organic fuels such as sugar.

14. The factor which limits cell size is the surface-area-to-volume ratio. The smaller the cell, the greater the surface area while the volume remains constant. Cells need a large surface area in order to absorb essential nutrients and expel wastes.

15. Organic compounds store energy in their arrangements of atoms. With the help of enzymes, a cell systematically degrades complex organic molecules that are rich in potential energy to simpler waste products that have less energy. Some of the energy to simpler waste products that have less energy. Some of the energy taken out of chemical storage can be used to do work; the rest is dissipated as heat.

16. Enzymes regulate the rate of chemical reactions by regulatory molecules that change an enzyme’s shape and function by binding to an allosteric site, a specific receptor site on some part of the enzyme molecule remote from the active site. The effect may be either inhibition or stimulation of the enzyme’s activity.

17. The specificity of an enzyme depends on its structure because enzyme inhibitors resemble the normal substrate molecule and compete for admission into the active site. These mimics, called competitive inhibitors, reduce the productivity of enzymes by blocking the substrate from entering active sites. Noncompetitive inhibitors do not directly compete with the substrate at the active site. Instead, they impede enzymatic reactions by binding to another part of the enzyme. This interaction causes the enzyme molecule to change its shape, rendering the active site unreceptive to substrate, or leaving the enzyme less effective at catalyzing the conversion of substrate to product.

18. The activity of an enzyme is regulated by the microenvironment that is conductive to a particular type of reaction. If the active site has amino acids with acidic side chains, the active site may be a pocket of low pH in an otherwise neutral cell. An amino acid may facilitate hydrogen transfer to the substrate as a key step in catalyzing the reaction. Still another mechanism of catalysis is the direct participation if the active site in the chemical reaction. Sometimes this process even involves brief covalent bonding between the substrate and a side chain of an amino acid of the enzyme. Subsequent steps of the reaction restore the side chains to their original states, so the active site is the same after the reaction as it was before.

19. An organism at work uses ATP continuously, but ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP. The ATP cycle moves at an astonishing pace. A working muscle cell recycles its entire pool of ATP about once each minute. That turnover represents 10 million, molecules of ATP consumed and regenerated per second per cell. If ATP could not be regenerated by the phosphorylation of ADP, humans would consume nearly their body weight in ATP each day.

20. Chemiosmosis functions because most of the ATP made in cellular respiration is produced by oxidative phosphorylation when NADH and FADH donate electrons to the series of electron carriers in the electron transport chain. At the end of the chain, electrons are passed to oxygen, reducing it to water. Electron transport is coupled to ATP synthesis by chemiosmosis. At certain steps along the chain, electron transfer causes electron-carrying protein complexes to move hydrogen from the matrix to the intermembrane space, storing energy as a proton-motive force. As hydrogen diffuses back into the matrix through ATP synthase, its exergonic passage drives the endergonic phosphorylation of ADP.

21. First, light enters photosystem II and electrons split from water replace the electron lost from photosystem II which then activates the chlorophyll of photosystem II. Electrons are emitted and are passed along a series of electron acceptors. As electrons pass through this series, ATP is generated. The electrons from chlorophyll of photosystem II are passed to the chlorophyll of photosystem I replacing those lost from photosystem I. Light and electrons activate the chlorophyll of photosystem I and more electrons are emitted. The electrons are passed along a series of electron acceptors. Electrons are finally passed to NADP. NADP plus electrons plus protons from water yields NADPH2.

22. The ATP and NADPH from the light reactions is later used in dark reactions along with carbon dioxide. This forms a 5-carbon sugar to form a short lived 6-carbon sugar which immediately breaks down into 2 molecules of 3-carbon PGA which is reduced to PGAL which can be used to make fructose, glucose, starch, complex organic compounds, or it can even regenerate more 5-carbons.

23. C3 plants use an initial fixation of carbon that occurs via rubisco. The first organic product of carbon fixation is a three-carbon compound, 3-phosphoglycerate. C4 plants preface the Calvin cycle with an alternate mode of carbon fixation that forms a four-carbon compound as its first product. CAM plants open their stomata during the night and close them during the day, just the reverse of how other plants behave.

24. Organic compounds are broken down with the help of enzymes. A cell systematically degrades complex organic molecules that are rich in potential energy to simpler waste products that have less energy. Some of the energy taken out of chemical storage can be used to do work; the rest is dissipated as heat.

25. Oxygen and organic compounds yield carbon dioxide, water, and energy. The organic compounds oxidize to carbon dioxide. The organic compounds lose electrons to the carbon dioxide. The oxygen reduces to water. The oxygen gains electrons to the water.

26. Cells generate ATP in the absence of oxygen by fermentation. Fermentation is an extension of glycolysis that can generate ATP solely by substrate-level phosphorylation, as long as there is a sufficient supply of NAD to accept electrons during the oxidation step of glycolysis. Fermentation consists of glycolysis plus reactions that generate NAD by transferring electrons from NADH to pyruvate or derivatives of pyruvate.

27. Photosynthesis uses water in the light reaction in order to make ATP and carbon dioxide in the Calvin cycle to make ADP. The products of photosynthesis are oxygen and organic molecules. Cellular respiration uses organic molecules and oxygen to make ATP. The products of cellular respiration are carbon dioxide and water which can be used for photosynthesis.

28. The cell cycle assures genetic continuity because when a cell divides, both daughter cells will have the exact same genetic material.

29. Mitosis allows for the even distribution of genetic information to new cells by duplicating the chromosomes of the cell. Then the microtubules attach themselves to the chromosomes and pull them to opposite sides. Each side will have an equal number of chromosomes.

30. Cytokinesis occurs by a process known as cleavage. The first sign of cleavage is the appearance of a cleavage furrow, which begins as a shallow groove in the cell surface near the old metaphase plate. On the cytoplasmic side of the furrow is a contractile ring of actin microfilaments associated with molecules of the protein myosin. Actin and myosin are the same proteins that are responsible for muscle contraction, as well as many other kinds of cell movement. The contraction of the dividing cell’s ring of microfilaments is like the pulling of drawstrings. The cleavage furrow deepens until the parent cell is pinched in two, producing two completely separated cells.

31. Aberrations in the cell cycle can lead to tumor formation if the density-dependent inhibition is not exhibited. Density-dependent inhibition is a phenomenon in which crowded cells stop dividing. If cells do not exhibit density-dependent inhibition, then the cell will keep on dividing and a dense tumor will begin to form.

32. It is important that in meiosis each cell can only have the haploid number of chromosomes and not the diploid number of chromosomes. It is also important that crossing over occurs or their would be a limited number of genetic combinations for the sex cells.

33. Meiosis is important in heredity because it allows the offspring to acquire genes from the parents by inheriting chromosomes. This is important because the offspring will only acquire some of the genes but not all of the genes.

34. In gametogenesis, meiosis makes diploid sporophytes into haploid spores. Then spores turn into haploid gametophytes which by gametogenesis turn into haploid gametes. In spermatogenesis, meiosis divides one diploid sex cell into two, and then into four haploid sperm cells. In oogenesis, meiosis divides one diploid sex cell into a haploid cell and a polar nucleus. Then the haploid cell divides into another haploid egg cell and another polar nucleus.

35. A similarity between gametogenesis in animals and in plants is that in both cycles haploid gametes are produced. Some differences are that in animals, gametes are directly created by meiosis. In plants, meiosis creates spores and then the spores create gametes.

36. Mendel’s work laid the foundation of modern genetics because his work consisted of traits passed on by genes. It’s also based on the dominance and recessiveness of traits.

37. The principle patterns of inheritance are dominance and recessiveness, segregation, and independent assortment. The law of dominance and recessiveness states that one allele that’s dominant will express the phenotype over a recessive allele. The law of segregation states that two alleles for each character segregate during gamete production, and also that 50% of the gametes will receive one allele and the other 50% will receive the other allele. The law of independent assortment states that gametes are produced in every single possible combination of alleles.

38. In eukaryotic genomes, most of the DNA, about 97% in humans, does not encode protein or RNA. Some of it is known to be regulatory sequences, but much of it consists of sequences whose functions are not yet understood. This DNA includes introns; the stretches of noncoding DNA that often interrupt the coding sequences of eukaryotic genes. Even more of the noncoding of DNA consists of repetitive DNA, nucleotide sequences that are present in many copies in a genome, usually not within genes.

39. This organization contributes to continuity of genetic information because the parts of the DNA that are expressed continue to be the same and do not change. The organization contributes to variability of genetic information because the parts that are not expressed can vary, although the repetitive DNA would still be similar.

40. A sex-linked trait is carried on the X chromosome. Therefore, males are affected a lot more than females since sex-linkage only requires one chromosome in males and two in females. In a monohybrid trait, only one gene comes from the father and only one comes from the mother. The two possibilities are either dominant or recessive. In a dihybrid trait, there are two genes given from the father, and two genes given from the mother. Now there are four possible phenotypes: dominant in a gene, dominant in the other gene, dominant in both genes, or recessive in both genes.

41. An inheritance pattern exhibiting autosomal dominant is Huntington’s disease, a degenerative disease of the nervous system, which is caused by a dominant allele. An inheritance pattern exhibiting autosomal recessive is cystic fibrosis, which causes mucus build up in the pancreas, lungs, digestive tract, and other organs, which is caused by recessive alleles. An inheritance pattern exhibiting a sex-linked trait is fruit fly color, in which red eyes are dominant and white eyes are recessive.

42. Nucleic acids relate to their functions of information storage and protein synthesis because the double helix shape allows for more information to be stored and also allows the strand to become stronger.

43. In prokaryotes, most of the DNA in a genome codes for protein, with the small amount of noncoding DNA consisting mainly of regulatory sequences such as promoters. The coding sequence of nucleotides along a prokaryotic gene proceeds from start to finish without interruption. In eukaryotic genomes, by contrast, most of the DNA, about 97% in humans, does not encode protein or RNA. Some of it is known to be regulatory sequences, but much of it is not yet understood.

44. Protein synthesis controls many functions within the cell because most of the parts in a cell are made of protein, so protein synthesis must make all of these parts. It also makes RNA which gives functions to other parts of the cell.

45. Gene expression is regulated in prokaryotes and eukaryotes by operons. An operon is basically the operator, the promoter, and the genes they control. The operator is positioned within the promoter or between the promoter and the enzyme-coding genes, the operator controls the access of RNA polymerase to the genes.

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