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Study Guide to Review for Test 1

by: CatLover44

Study Guide to Review for Test 1 101-NYA-05

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Hi! This is a compilation of all the notes I typed for the first seven lectures of the course (aka material on test 1).
General Biology 1
Virginia Hock
Study Guide
cells, organelles, Biological, hierarchy, Proteins and Enzymes, functions of proteins, organisms, DNA, RNA
50 ?




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This 44 page Study Guide was uploaded by CatLover44 on Thursday September 22, 2016. The Study Guide belongs to 101-NYA-05 at Dawson Community College taught by Virginia Hock in Fall 2016. Since its upload, it has received 17 views. For similar materials see General Biology 1 in Biology at Dawson Community College.


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Date Created: 09/22/16
General Biology Test 1 Study Guide Lecture 1 Review Organizing Forms of Life 1. Molecules. Molecules are the building blocks of life. While molecules are non -living, they make up cells which ultimately make up all forms of life. 2. Cells. Cells are fundamental to biology as they provide a clear distinction between organisms and non-living things. They are the smallest organisms, and are the basis for all forms of life. Cells also contain organelles, which are various functional components in cells: consider them as the organs of a cell. The human body contains trillions of cells which are organized into various types of tissues. All cells have several things in common: they are all enclosed by a membrane, which regulates the passage of materials between a cell and its surroundings; they all use DNA as their genetic information; and they all contain RNA. Note: what are DNA and RNA, and how are they different? • DNA (deoxyribonucleic acid) provides instructions for making proteins. • RNA (ribonucleic acid) is a messenger that controls the synthesis of proteins. In some viruses, it carries genetic info instead of DNA. 3. Tissues. Tissues are comprised of cells of a specific type that work together for the same purpose. For example, muscle tissues are made of one type of cell. There are four types of tissues in humans: epithelial tissue (which lines the cavities of our bodies, the surfaces of blood vessels, and our organs), connective tissues (fibrous tissues, fat, cartilage, bone, bone marrow, and blood), muscle tissues (strong tissues that contract, and let us move our bodies), and nervous tissue (found in the nervous system, they're composed of neurons that send information from our nerves to our spinal cords, allowing us to see, touch, taste, smell, and hear). 4. Organs. Organs are made up of tissues. They are body parts that carry out b odily functions. 5. Organ Systems. Organ systems are comprised of at least two organs that work in conjunction with each other to perform a bodily function. There are 11 organ systems in humans. Some examples of organ systems are the digestive system , respiratory system, and the nervous system. 6. Individuals. Individuals are single organisms. Some examples of individuals are plants, animals, and people. 7. Populations. Populations are groups of individuals of the same species which all live in some area. For example, there are populations of moose, dear, and geese in forests. 2 8. Communities. Communities are an entire group of organisms that make up an ecosystem. Examples of biological communities are: trees, plants, animals, mushrooms, fung i, and bacteria. All these organisms are called species. 9. Ecosystems. Ecosystems contain all organisms in a particular area. They also include non -living beings in the environment with which organisms interact: soil, gas, light, etc. 10. The Biosphere. The biosphere contains all life on Earth, as well as everywhere life exists on Earth. This includes land, bodies of water, and several kilometres above and below the Earth’s surface. Properties of Organisms 1) All living things are made of cells. Cells are an organism’s smallest and functional components. All cells are made of the same things; they are all enclosed by a membrane, use DNA as its genetic information, and use RNA to create proteins. Cell theory entails three important points about cells: (1) cells are the smallest units of life, (2) they make up all living things (bacteria, plants, fungi, animals and protists, which can be single-celled or multicellular), (3) new cells are only made from existing cells. 2) All living things metabolize energy. Organisms cannot survive without energy because living (i.e. maintaining cells) requires energy. Plants metabolize energy in 3 the form of light during the process of photosynthesis, while humans and animals acquire energy from eating food. For instance humans use adenosine triphosphate (ATP) for energy so they can perform tasks, and cells metabolize energy to develop larger membranes. 3) Living things respond to their environment. Organisms respond to physical and chemical changes to the external or internal environment. For example, they respond to changes in smell, temperature, and light. Internal responses help to maintain homeostasis. 4) Living things adjust themselves to survive in their environments. Organisms maintain their internal health through a stabilizing process called called homeostasis. For example, whenever an organism's temperature is too high or low, their body works to regulate their temperature to bring it back to normal so it can function properly. 5) Living things grow, and develop their characteristics. Organisms grow and develop their characteristics with time. For example, their cells grow in size and in numbers. Organisms display two different types of growth: determinate and indeterminate. Determinate growth is growth that ends after a certain point in development is reached, while indeterminate growth is growth that doesn’t seem to end. 6) Living things reproduce. Organisms are created through reproduction, which may be either sexual or asexual. Humans reproduce sexually, and pass on their genetic traits to their offspring. A child’s characteristics are not identical to those of their siblings and parents. On the other hand, organisms that reproduce asexually create offspring that are identical to themselves. Side note: evolution occurs in populations, not individuals. 7) Living things can biologically evolve. When organisms with adaptive traits reproduce with each other, their offspring will inherit those adaptive traits. This allows future generations to survive in certain environments. Eventually, the organisms with characteristics that are harmful die off, and only those with the beneficial traits survive. 4 Lecture 2 Review Concept no. 2: DNA is the Cell’s Blueprint According to cell theory, all cells: - are the smallest unit of life; - constitute all life forms; - come from pre-existing cells. - DNA is essential to life because it oversees the cell’s activities, such as its metabolism. It contains four different nucleotides, which are abbreviated as A, T , C, G. - Nucleotides are essentially chemical building blocks. You can think of them as a four-letter alphabet of inheritance. Specific arrangements of the four nucleotides encode information into genes. - Our genes determine traits like hair colour and eye colour. - RNA (ribonucleic acid) helps DNA to complete its tasks. For example, when our bodies produce melanin, RNA is activated. - RNA copies DNA into a form that it can use: RNA is a messenger, meaning it can leave the cell’s nucleus. DNA can't leave the cell’s nucleus. Evidently different cellular processes take place in different compartments of the cell. - DNA is made up of genes, which are the units of inheritance that transmit genetic information from parents to their offspring. - Genes have different lengths, and are made of different lengths and sequences of the 4 nucleotides. 5 Lecture 3 Review • There are two main types of scientific experiments: 1) Discovery scientific experiments, which entail watching natural phenomena without altering them in any way. Qualitative data is obtained from these types of experiments. 2) Hypothesis-based experiments, which entail explaining nature by manipulating natural phenomena using experimental procedures and control parameters. o Most scientific experiments combine discovery and hypothesis-based experimentation. Ordered Steps of the Scientific Method Step 1. Make an observation about a natural occurrence that scientists would want to explain. Research the work of other scientists that was done on th e phenomenon you observe. Step 2. Ask yourself questions about what you notice from your observations. Step 3. Form a hypothesis (a falsifiable statement). Step 4. Predict what types of results you will likely obtain from your experiment (based on your hypothesis). Step 5. Test your predictions: (a)Plan what types of experiments you'll conduct, and what your controls will be; (b)Perform your experiments; (c)Collect data and analyze it. Step 6. Interpret your data: does it support or fail to support your hypothesis? Step 7. Draw conclusions. Proper Experimental Design • Variables are the parts of a scientific experiment which may or not be controlled. Scientific experiments may have different amounts or types of variables. 6 o Independent variables are those that are manipulated by the experimenter. o Dependent variables are obtained through changes to the independent variable. They're also referred to as the output or response. The experimenter has no control over the dependent variables. o Control variables are the factors of the experiment that are kept the same between the experimental and control groups. o The control group is the group that does not receive the main treatment that's provided to the experimental group. All the other experimental conditions are the same between both groups. The results obtained from this group are compared to the results obtained from the experimental group. • Use proper scientific methods when conducting your experiments in order to avoid biases, which impact the validity of your results. o The experiment must be repeated in order to ensure accurate re sults. • Biases occur when extraneous factors affect the data you're collecting. o For example, if someone volunteers for an experiment and they think that taking a certain drug will improve their mood, they may actually end up feeling more cheerful through no fault of the medication provided to them as part of the experiment. This is called the placebo effect. o Double-blind experiments are experiments where the experimental group and the control group are not told whether they are going to receive the placebo or the actual treatment. These experiments reduce the chances of obtaining biased results. o Use large sample sizes and several replicates to get dependable data from your experiment. • Using a sufficient sample size allows us to draw more accurate conclusions from the data procured from an experiment. Repeating the experiment several times also yields the same result: data that is credible. 7 Lecture 4 Review Macromolecules • All organisms contain: o nucleic acids; o proteins; o carbohydrates; o lipids. • Organic compounds contain a carbon backbone. o Carbon is a very important element: § Carbon can form four covalent bonds, and it can form with other carbon atoms, as well as many other elements. • Most organic compounds contain oxygen (O) and hydrogen (H), but can also contain nitrogen (N), phosphorus (P), and sulfur (S). • The properties of organic molecules depend on two things: o the arrangement of carbon atoms in a molecule (carbon skeleton); o the other atoms attached to the carbon skeleton (functional groups). § These properties define a molecule’s distinctive chemical properties. § Pay special attention to the carboxyl, amino and hydroxyl groups. 8 § Estradiol and testosterone have similar structures, but they serve completely different purposes. The slightest change in the structure of a molecule can change its function (form fits function). • O, C, H, and N make up 96% of our body’s wet weight percentage. • Biological molecules are made of smaller components that are connected to each other. • An organic compound is a macromolecule, or large molecule. o Macromolecules are made when two large molecules bond together. Examples of macromolecules are RNA, sugars, and fats. o Alpha = starch, Beta = cellulose • A single unit of a biomolecule is called a monomer, and a string of monomers is called a polymer. o A protein is a string of monomers, not a single monomer. • Chains of polymers are built via dehydration synthesis; a bond forms with the removal of a water molecule. • Chains of polymers are broken via hydrolysis; a bond is broken with the addition of a water molecule (one monomer gets H+, the other gets OH-) • There are four main classes of biological molecules: 1. Carbohydrates 9 2. Lipids 3. Proteins 4. Nucleic acids 1. Carbohydrates • The class of carbohydrates includes sugars, which can be simple or complex. • Sugars are broken down for energy via cellular respiration, which is demonstrated by the following chemical equation: C H O + 6O = 6CO + 6H O 6 12 6 2 2 2 o CO and H O are formed with the aid of 36 ATP (adenosine triphosphate). 2 2 o Our liver stores sugar as glycogen. Glycogen is insoluble, and must be broken down into smaller parts before it can enter and leave our cells, while glucose is soluble and can therefore easily be used by out bodies for energy. Also, glycogen is a monosaccharide, and glucose is a disaccharide. o Carbohydrates are found in insects, fungi, animals, bread, starch and sugars. • Sugars are stored as long chains, for short-term energy reserves in muscles and the liver in animals. • Carbohydrates have the following functions in biological systems : o Sugar is a source of energy; o Cellulose provides structure and support. 10 o Sugar is stored as starch in plants. • Carbohydrates have a specific structure: o The chemical formulas for carbohydrates usually have ratios of 1:2:1 for C, H, and O atoms. o Monomers are simple sugars, while polymers are complex sugars. • There are two types of simple sugars: 1. Monosaccharides, monomers of carbohydrates, that share the same molecular formula (C H O ). Examples of monosaccharides are glucose, 6 12 6 galactose, and fructose. Glucose, galactose, and fructose are isomers, meaning the arrangement of atoms is different in each structural formula. 2. Disaccharides, two linked monosaccharides. Examples of disaccharides are sucrose, lactose, and maltose. Memorize this table! Sucrose Glucose + Table sugar Fructose Lactose Glucose + Milk sugar Galactose Maltose Glucose + Brewing sugar Glucose 11 • You have to be able to recognize the different types of disaccharides from their structures. The three disaccharides above are all made of the same elements, but they're arranged in different ways so they're different compounds. • There are two types of complex sugars (or polysaccharides): 1. Storage carbohydrates (starch and glycogen) a. Starch allows for energy storage in plants, and converts excess glucose into starch. b. Animals store excess glucose as glycogen. 12 c. Important: Starch has a branched structure, and glycogen had a highly- branched structure. d. Note: a polysaccharide is a string of many sugar molecules. 2. Structural carbohydrates (cellulose and chitin) a. Cellulose provides structure in plants b. Chitin is found in fungal cell walls, and the skeletons of insects and other arthropods. c. Important: the complex structure of cellulose gives rigidity to the structure of plants. d. Herbivores eat only plants, which contain cellulose in their cell walls, but they don't produce the enzymes that decompose cellulose. Instead, they have bacteria in their digestive systems which contain the enzymes that break down cellulose. i. Termites have protests that contain the enzyme they need to break down cellulose. ii. Note: all the parts of a plant or tree contain cellulose. 13 2. Lipids • ATP is used by our cells for energy. Our bodies make it from food. Food is converted into sugar, which is converted into fats, which make up proteins, which eventually make ATP. o In a protein cell, the cell uses ATP to release ions. • All lipids are non-polar, meaning they are insoluble in water. o They have little to no affinity to water (hydrophobic). • Lipids are very different from each other with respect to their forms and functions, even though they are mostly made of C and H atoms. • There are three different types of lipids: 1. Neutral fats: a. have different structures and functions, but they are all hydrophobic (water-fearing) and are therefore non-polar. b. Include fats, but also phospholipids and steroids. c. The functions of fats in animals are long-term energy reserves in fat tissues, the maintenance of body temperature (insulation), protection of vital organs, and buoyancy. i. Fat provides our kidneys with the property of shock absorbency. 14 ii. Neutral fats are found in hormones and steroids, such as Estradiol and progesterone. • Fat is constructed from two kinds of smaller molecules; 1 molecule of glycerol, and 1 to 3 molecules of fatty acids, o The number of fatty acids ranges from 1 to 3. o 3 fatty acids strung together make up a triglyceride. Triglycerides are made via dehydration synthesis. • Saturated fats are easily stacked together, and are solid at room temperature. Stearic acid is an example of a saturated fat. • Unsaturated fats don't stack well, and are liquid at room temperature. Oleic acid is an example of an unsaturated fat. 2. Phospholipids: a. Are the main constituent of cell membranes in biological systems; i. Cell membranes are made of phospholipids, which have hydrophilic heads and hydrophobic tails. ii. This particular structure prevents certain things from entering our cells. 15 b. Their structures are similar, but not the same as those of neutral fats (2 molecules of fatty acids, 1 glycerol molecule,and 1 phosphate molecule); c. Consist of hydrophilic (water-loving) heads, and hydrophobic (water- fearing) tails, so when they are placed in water, they form a bi-layer with a shield of water-loving heads protecting the water-fearing tails. d. The diagram below demonstrates the structures of phospholipids in the cell membranes of plants, animals, bacteria, and protists: 3. Steroids 16 a. Cholesterol, a type of steroid, makes up cell membranes, and the components of vitamins and hormones, such as growth hormones, and the sex hormones (estrogen, progesterone, testosterone); b. Are made from sterol, which are multiple rings of carbon atoms. Several types of molecules are made in our bodies from sterol. i. You don't need to memorize steroids, but you should recognize their structures. 3. Proteins • Proteins are the workhorses in the cell. o Their functions include coordinating the movement of substances in and out of cells, catalyzing reactions in cells, acting as messengers or receptors, and protecting our bodies from diseases § Enzymatic proteins accelerate certain chemical reactions. For example, digestive enzymes catalyze hydrolysis of bonds in food molecules. § Defensive proteins provide protection from diseases. For example, antibodies deactivate to help destroy viruses and harmful bacteria. 17 § Storage proteins store amino acids. For example, casein (protein found in milk) is he major source of amino acids for baby mammals. Plants have storage systems in their seeds. Ovalbumin is he protein found in egg whites, which is used as the amino acid for developing embryos. § Hormonal proteins direct an organism's activities. For example, insulin is produced by the pancreas and causes other organs to absorb glucose which allows it to regular blood sugar concentration. § Receptor proteins let cells communicate with each other. They respond to chemical stimuli. For example, receptors in a nerve cell detect signalling molecules released by other nerve cells (think of neurotransmitters). § Contractile and motor proteins are what allow us to move. Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin are responsible for muscle contraction. § Structural proteins provide support. For example, keratin makes up hair, feathers and horns, while insects and spiders use silk to make their cocoons and webs. § Collagen and elastin proteins provide a fibrous support for connective tissues in animals. 18 • Proteins are made of amino acids (monomers). o Proteins are found in meat and nuts. o Cartilage is a protein, and glucagon is a protein hormone that's made by the pancreas. o Proteins allow muscle tissues to contract and expand. o Proteins are very complex polypeptides that are formed when two polypeptides are combined. • All amino acids have the same basic structures which can be classified by: o The amino group, the carboxyl group, and the R-group, which is variable. o Amino acids have the amino and carboxyl groups. • There are 20 common amino acids which all contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. You don't need to memorize them. Just remember that their forms are all the same except for R-groups; R-Groups are the only 19 functional groups that change. Proline is different from the other amino acids listed below because it's the only one that doesn't contain H N. 3 • Polypeptides are chains of amino acids that were created via dehydration synthesis. As the chain grows, a polypeptide is created. • Many amino acids are connected by peptide bonds, and eventually form polypeptides. • The repeating structure of atoms forms the polypeptide backbone with side chains (R-Group) coming out of it. • All polypeptides have an N-terminus, which is a free amino end, and a C-terminus, which is a free carboxyl end. o These make polypeptides polar (soluble in water, hydrophilic) • The shape of a protein is essential to its function. Amino acids are linked together in specific ways to create distinct patterns. 20 • Proteins can spontaneously change their shapes depending on the order and arrangement of amino acids. • There are 4 structural levels of proteins: o Primary structure: the specific unique sequence of amino acids that make up a protein (polypeptide). The order of the amino acid is determined by the nucleotide of the gene that encodes the protein; they are genetically determined. Even a small change in the primary structure of a protein can change the way it works. Remember: form determines function. § Proteins with primary structures are made of amino acids that are bound together by peptide bonds in a linear fashion. This structure is the most important of all structures because it determines the form and function of the protein by determining how its amino acids are arranged. § Sickle-cell anemia occurs when one amino acid is substituted for another (glutamic acid is replaced by valine, which is less polar than glutamic acid, in hemoglobin, causing some blood cells to be smaller than others. Since there aren't enough healthy red blood cells to carry oxygen in our bodies, we become ill). 21 o Secondary structure: classified by the coiling or folding of amino acids within a polypeptide. Coiling and folding occurs because hydrogen bonds form at regular intervals within a molecule. Hydrogen bonds (H-bonds) form between the amino and carboxyl groups in the polypeptide’s backbones. § Coiling and folding: • contributes to a protein’s conformity; • can be in the alpha helix (coiling) or beta sheet form (folding). Alpha helix (coiled) § Hydrogen bonds hold cells in shape in alpha helix structures, and hold neighbouring strands of sheet together in beta sheet structures. (No covalent bonding, and the hydrogen bonds are stronger when many hydrogen bonds are present. Like a telephone cord, once tension is released, the fivers can recoil and hydrogen bonds can reform. § alpha helix bonds are mostly common in keratin (alpha keratin), which makes up our hair and nails as well as wool. Beta pleated sheet (folded) 22 § Beta sheets are strong, but not elastic. The distance between folds is fixed by the covalent bonds in the polypeptide backbone; they can stretch but can't twist (these are stronger than alpha helixes). H-bonds bond the adjacent length of polypeptides for beta sheets. • Folded sheets make up the core of globular proteins, and also make up some fibrous proteins such as fibroid, which is the silk that spiders use to spin webs. • Globular structures are formed from hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions. o Tertiary structure: formed when more forces are holding the protein together. Examples of these forces are hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions. o All of the above forces between amino acids can occur in one protein. o The 3-D structure of a protein is determined by which forces are acting between the R-groups of amino acids. § Hydrogen bonds occur between hydrogen and fluorine, hydrogen and oxygen, and hydrogen and nitrogen; § Ionic bonds result from charged particles (ions with + or – charge) § Hydrophobic interactions occur between two non-polar molecules 23 § Covalent bonds occur when atoms share electrons. Disulfide bonds are covalent. o Quaternary structure: the fusion of two or more polypeptides. § Quaternary structures are formed by interactions between polypeptide chains that contain protein. • Hemoglobin in a globular protein with 4 polypeptide subunits • Collagen is a fibrous protein made of 3 helical polypeptides coiled together to create a strong rope-like structure. • Many proteins have 2 or more polypeptide chains that form one macromolecule. Ø Proteins are affected by their environment, and they can break down (disruption or destruction). This is denaturation, which can be temporary or permanent. o Denaturation can disrupt the normal alpha-helix and beta sheets in a protein, and uncoil them it into a random shape. o Denaturation reactions aren't strong enough to break the peptide bonds, so the primary structure remains intact. 24 o Alcohol, heat, acids, and bases can denature proteins. In most cases, once a protein is denatured, it doesn't work properly anymore (its functionality is compromised). Disinfecting alcohols work by denaturing bacteria. o H-bonds, which occur in both the secondary and tertiary structures, can be denatured by alcohol. Ø Ribosomes are very important: they have a quaternary structure, use RNA to make other proteins, and are made in the nucleolus of cells. o Our bodies need RNA and some proteins to produce proteins. Lecture 5 Review Nucleic Acids and Flow of Genetic Information • Nucleic acids make DNA and RNA o DNA gives instructions, and RNA follows those instructions o DNA has oxygen in its sugar molecules, RNA doesn't • Nucleic acids are made of nucleotides that connect and form polynucleotides • Easy ways to distinguish between RNA and DNA: o DNA is double-stranded, RNA is single-stranded o RNA doesn't contain thymine (T), it's version of thymine is uracil (U), so if you see U, you know you're looking at RNA. o MEMORIZE THIS TABLE! 25 • There are three types of RNA: mRNA, tRNA, and rRNA. o mRNA = messenger RNA, tRAN = transfer RNA, rRNA = RNA + protein. • We need DNA for cell replication: it contains genes that determine which proteins are made. DNA Assembly: Complementary Base Pairing • Recall: A only binds with T, and C only binds with G (DNA TO RNA) . This forms the basis of complementary base pairing. Examine the diagram below: • DNA will not exit our nucleus, mRNA is DNA’s “helper” in this sense because it leaves the nucleus for it. • Note: DNA’s double-stranded structure makes it more stable than RNA. • Our height, eye colour, hair colour, and muscle mass are determined by nucleotide sequences. o A change in a nucleotide sequence causes a different protein to be made. • We need DNA, RNA, and genes to make proteins. • Remember the four structures of proteins, and their properties! o 1. Primary structure: monomers that connect to each other to make polymers. Controls shape and function (most important structure) o 2. Secondary structure: alpha coils and beta pleated sheets. Beta pleated sheets make up the core of globular proteins. 26 o 3. Tertiary structure: held together by many attractive forces (hydrogen bonding, ionic bonding, non-polar interactions, disulfide bridges), and contains one polypeptide. o 4. Quaternary structure: fusion of two or more polypeptides. This structure is forms by the interactions within the polypeptide chains that comprise the protein. Many proteins are made of two or more polypeptide chains that stick together to make one macromolecule . Transcription and Translation Transcription • In the transcription process (inside the nucleus), a strand of DNAs copied (template strand). o DNA is copied, and turned into a form that RNA understands. o The part of the gene that is meant to be copied is separated before transcription occurs. o Transcription of a RNA molecule that's complementary to DNA according to the base pair rule. • To make a protein properly, genes must control how amino acids are arranged. • There is no thymine (T) in RNA, so T is replaced by U (uracil). • Note: proteins are made outside of the cell's nucleus. • In the translation process (outside the nucleus), DNA is copied into mRNA. • Coding tells the nucleotides when to start and stop copying DNA. • Note: DNA’s double-stranded structure makes it stronger than RNA, which is only single-stranded. • mRNA is synthesized in the nucleus with the help of enzymes and DNA. It contains the information from one gene. • The nucleotides arranged into groups of three are called codons, which tell nucleotides when to start and stop copying. o AUG (methionine) is always the start codon; o The last three codons are stop codons which don't code for anything, they just mark the end of the coding process. o Codons determine how cells decide which amino acid to add. o Each codon indicates an amino acid. 27 o The transcription process is over when mRNA is released from the enzyme. • In the transcription process (in or outside nucleus?) the primary structure of proteins are made according to the codon sequence on the mRNA. o mRNA is turned into protein; o Codons on mRNA provide the sequence that amino acids must be arranged in; o Results in 7 amino acids; o The start codon, AUG, is called methionine; o mRNA has the formation, but doesn't do the work ( don't shoot the messenger); o Amino acids are not nucleic acids so they have nothing to do with the base pair rules; o The cell needs a way to match up amino acids with the codons on mRNA to thE anti-codons on tRNA; o tRNA is the second type of RNA. It's called the decoder. o Transfer RNA communicates between mRNA and amino acids. Each mRNA codon has its own specific anti-codon that it can bind to (complementary tRNA anti-codon). Each tRNA has a unique anti-codon that carries a corresponding amino acid. o There are many different kinds of tRNA, but they are all different because they have their own unique anti-codons, and they can only bind to one type of amino acid. § So only one kind of amino acid can be placed at a particular codon site by a single tRNA molecule. § Many amino acids can have several codons: 1 start codon and 3 stop codons, and 61 codons code for 20 amino acids. 28 • You need to know how to read this table for tests and quizzes! • tRNA anti-codons must always match correctly to mRNA codons. If one tRNA existed for each codon, there should be 61 codons but there are more than 61. Some tRNA are able to bind to more than 1 mRNA codon. • Ribosomes are large RNA and complex proteins. They link mRNA and tRNA to make other proteins. They continue link them to each other until the whole length of mRNA has been read. You can think of them as tiny machines. • The third type of RNA is rRNA, which are made of proteins and RNA. o The first tRNA attaches to a P site on the ribosome o The next tRNA attached to an A site o Each tRNA caries an amino acid • As the ribosome moves along (reads) the mRNA it aligns their tRNA and their amino acids. o The amino acids from the tRNAs are transferred from one tRNA (at the P site) to the other (at the A site), and are then joined by an enzyme, which is a growing polypeptide. o After this is done, the tRNA at the P site moves to the E site (exit site) and detaches itself from the ribosome. At his point the tRNA at the A site 29 moves to the P site, and a new tRNA with the next amino acid attaches to the empty A site. o These steps repeat until the end of the mRNA molecule is reached, and then the amino acid chain is released into the cytoplasm. o Elongation occurs until the stop codon arrives at the A site (UAG, UAA, or UGA), then a protein (release factor) binds to the A site, which causes a water molecule to be added to hydrolyze the chain from the tRNA at the A site. It releases a polypeptide. o Once this process is complete, the ribosome detaches itself and waits for a new mRNA to “read”. • Note: remember that rRNA helps with the assembly of amino acids to make proteins. Lecture 6 Review Recall Cell Theory: A cell is the smallest unit of life; Cells make up all organisms; New cells come from pre-existing cells. Cells are small because the size of a cell is directly proportional to its metabolic needs: bigger cells require more energy to maintain homeostasis. As a cell becomes larger, it's volume increases at a greater rate than its surface area. Larger organisms don't have larger cells, they have more cells. Cells cannot grow indefinitely due to their metabolic needs. Cells absorb nutrients and release them as waste. Oxygen enters our cells via diffusion. In small cells, certain molecules can enter and leave cells quickly (fast and effective communication between organelles and the nucleus). The speed of this communication would slow down if cells were to increase in size. A decrease in the surface area of a cell would impede the entrance and exit of nutrients. The size of cells is therefore optimized for these operations: fast communication between the nucleus and organelles, and fast absorption of nutrients. 30 Recall: bacteria, archaea, and (some) protists are single-celled, while (some) protists, plants, animals, and fungi are multi-cellular. Note: viruses are not organisms because they do not contain proteins or membranes and are unable to reproduce on their own (they need hosts to survive). All cells: are surrounded by membranes; Contain genetic information in the form of DNA; Contain internal mass (cytoplasm); Contain ribosomes which aid in the process of protein synthesis. Note: The size of eukaryotes vary between 10 and 100 micrometers, while prokaryotic cells range in size from 1 to 10 micrometers. Prokaryotic cells do not have a nucleus. Their DNA is kept in a region within the cell called the nucleoid (DNA is free in the cytoplasm). The walls of prokaryotic cells are very strong in order to protect it from bursting, and to help the cell maintain its shape. In Domain bacteria, the cell wall is made of peptidoglycan, which is essentially a protein and a carbohydrate. Their cell walls do not contain cellulose. Domain Bacteria Cell walls can be either gram positive ( gram + ) or gram negative ( gram - ). Gram + cell walls have thick layers of peptidoglycan above their plasma membranes that absorbs purple gram stain (positive reaction). Gram - cell walls have one thin layer of peptidoglycan above their plasma membrane, but on top of this thin layer they have an outer membrane that contains polysaccharides and lipoproteins. Adding purple stain to these types of cell walls doesn't have any effect (negative reaction). The outer layer prevents absorption of the stain. The polysaccharides in the diagram of a gram - cell 31 wall are purple because another type of stain was applied that turned them purple. The diagram on the left represents a gram + cell wall, and the one on the right represents a gram - cell wall. Gram staining is a valuable tool in medicine; it helps to determine whether a patient's infection is caused by gram +'or gram - bacterium, allowing the doctors to choose the right medication for their ailments. Penicillin kills gram + bacteria. Domain Archaea Some prokaryotes produce a capsule. Capsules protect the cell from drying out, and help cells stick to things. They also protect the cell from being destroyed by white blood cells. Prokaryotes = Bacteria + Archaea no membranes around the nucleus, DNA is found in the nucleoid region. The cell walls of prokaryotic cells in Domain Bacteria contain peptidoglycan (protein+carbs), while the cell walls of prokaryotic cells in Domain Archaea contain polysaccharides and proteins (no peptidoglycan!). Only immature red blood cells (RBC's) contain nuclei. Once a RBC matures, it expels its nucleus so that it can carry more oxygen. Two Major Categories of Organelles 1) membranous organelles: surrounded by a membrane Includes the plasma membrane, cytoplasm, nucleus, endoplasmic reticulum (ER), Golgi apparatus, vesicles, lysosomes, peroxisome, mitochondria, chloroplasts, and vacuoles. 32 2) non-membranous organelles: no membrane present Includes: nucleolus, ribosomes, cytoskeleton, centrosome, cilia, flagella, cell junctions, cell wall, and extracellular matrix. Cells are surrounded by a plasma membrane. It's the boundary between the cell contents and its surroundings. Everything that enters and leaves a cell passes through the cell membrane. The functions of the cell membrane include: cell adhesion, cell recognition and communication, and protection from harmful viruses and bacteria. Cells want to keep their constituents in tact (organelles, cytoplasm), and protect themselves from anything that could harm them. Plasma Membranes Consist of Two Components: phospholipid molecules protein molecules Phospholipid molecules have: Hydrophilic heads Hydrophobic tails When placed in water, they form a cell membrane that is selectively semipermeable (allows only certain molecules to enter and leave). 33 Fluid Mosaic Model Proteins are spread out among the lipid molecules like tiles in a mosaic. they can move side-to-side through the bilayer. Cytoplasm and Cytosol Cytoplasm is the region between the nucleus and the plasma membrane. Cytosol is the fluid that fills up the space between the nucleus and the plasma membrane. It contains most of the cell's mass, and contains organelles. The cytoplasm is filled with cytosol. The Nucleus Is wrapped in a double-membrane (not a true double-membrane, because the membrane is folded on itself. The mitochondria and chloroplasts have true double membranes) which is a nuclear envelope. It has pores that let the nucleus exchange materials with the cytoplasm. Contains DNA and protein. DNA and protein can be loose (chromatin) or compact (chromosomes, histone proteins). Endoplasmic Reticulum The ER membrane is continuous with the nuclear envelope. It weaves in sheets, creating a network of membrane tubules and sacs (lipid bilayer) called cisternae. There are two kinds of ER membranes: rough (with ribosomes) and smooth (no ribosomes). 34 Functions of Rough ER membranes: Produce proteins (with ribosomes); Distribute proteins and lipids with transport vesicles. Rough ER Functions: Synthesis and transport of proteins secretory proteins that exit the cell; Proteins destined for other organelles (certain cells in the pancreas secrete insulin into the blood). Rough ER functions: Modification and Distribution of Proteins The ER folds into its 3D conformation. Enzymes can modify the proteins by adding carbs or lipids to them. Smooth ER Functions Synthesize fats (lipids, proteins, steroids). Detoxify poison (liver cells). Metabolizes carbs. Stores some types of minerals. Is rich in enzymes, and helps carry out many types of metabolic processes: Synthesize and transport lipids (oils, phospholipids, steroids). In the liver, enzymes help to detoxify poisons and drugs such as alcohol. 35 Metabolizes carbs (sugars, starches, etc.) Stores calcium. Main Functions of the Golgi Apparatus manufacturing, warehousing (packaging and transporting) centre for cell products. Synthesis, modification, storage, packaging and export of various cell products. Structurally similar to ER. 5-20 membranous sacs (cisternae). Chemical modification of cells (refines molecules). Packaging and export of various molecules (storage and transportation of molecules). Synthesizes carbs. Main Functions of Vesicles Vesicles are hollow spherical organelles surrounded by a membrane identical to plasma membranes. They're membrane-enclosed sacs. There are two types of vesicles produced by the ER and the Golgi apparatus: Transport vesicles (made by the ER). Secretory vesicles (made by the Golgi apparatus). Lecture 7 Review Lysosomes: Vesicles that contain digestive enzymes 36 destroy certain substances (pathogens, damaged organelles, etc.) Formed by the Golgi, their enzymes are only acidic when they're inside the acidic membrane (pH = 5). This prevents any changes in the pH level in the cell if they rupture and leak. Macrophages are types of white blood cells that digest bacteria and other dangerous substances that could cause illnesses. This process is called phagocytosis. Phagocytosis digests materials that are taken in from outside of the cell, while autophagy involves the digestion of organelles taken from inside of the cell. Peroxisomes metabolize fatty acids Detoxify alcohol and other harmful compounds (in the liver) Can self-replicate Contains an enzyme that converts peroxide (H2O2) into water (O2) Mitochondria the power plant of the cell Sites of aerobic respiration (convert food energy into a form of energy that cells can use) Turns glucose into ATP Has two membranes, each composed of a phospholipid bilayer and embedded with its own unique collection of proteins Endosymbionts 37 the mitochondria in eukaryotic cells may have come from bacteria-like endosymbionts integrated into the cell millions of years ago Nucleolus located inside the nucleus Production and assembly of ribosome components No membrane separates the nucleolus from the rest of the nucleus. It's just a dark spot inside the nucleus. Ribosomes synthesize proteins Are free-floating in the cytoplasm, and make proteins for the cell Are attached to the rough ER, which makes proteins that can be stored and released as needed. Cytoskeleton is made up of microtubules, microfilaments, and intermediate filaments. makes the form and internal framework that supports (and gives shape to) a cell. Is a network of fibres extending throughout the cytoplasm. Contains protein rods, which may extend or contract, allowing cells to change s hape. Protein rods are very dynamic, so they can quickly be diskmantled on one part of the cell and reassembled at a new location. Microtubules are the thickest of the 3 components of the cytoskeleton (microtubules, microfilaments, intermediate filaments) They support the cell and give it rigidity 38 They transport chromosomes during cell division (on cell tracks), and contain cilia and flagella for cell motility. Vesicles act as railroad tracks; they are involved in the movement of organelles in the cell (vesicle transport). Centrosome a non-membranous organelle In animal cells, centrosome a are made of pairs of centrioles that are perpendicular to each other. Centrosome a are made of microtubules Their main functions are: Microtubule-organizing center Movement of chromosomes during cell division Flagella & Cilia Flagella are long, and there are only a few of them on a cell Cilia are short and cells have many of them Cytoskeleton: intermediate filaments maintain the cell cite and stabilize cell shape Larger than microfilaments, but smaller than microtubules Each type is made of different protein subunits They don't bind ATP or serve as tracks for transport 39 Cytoskeleton: microfilaments have strings of actin (2 chains) Maintain the shape and size of the cell Allow the cell to move (muscle cell contraction) Extracellular Matrix holds cells together Regulates cell behaviour (homeostasis?) Cell signalling Cell receptors Consists of gel-like substance that's made of carbs and fibrous proteins Abbreviated ECM Other Eukaryotic Cells Protists (Paramecium) -contain contractile vacuole, which: - exports excess water from inside the cell - maintains cytoplasmic concentration of chemicals Plant Cells generally similar to animal cells, but with some important differences: 40 Contains a cell wall with plasmodesmata, a central vacuole, and chloroplasts Does NOT contain centrioles or lysosomes Cell Wall the cell walls of plant cells are hard and rigid, which allows for the cells (and the plant) to be supported. By physical support, we mean the plant is able to be held upright and water loss is prevented. The plasmodesmata are pores in the cell wall. They're similar to gap junctions in animal cells which directly connect the cytoplasm of two cells. These pores permit movement of fluids between cells (osmosis: water and small solutes can pass freely from cell to cell). Central Vacuole Supports plant cells and the plant itself, like cellulose Makes up 90% of the plant cell's volume Maintains tugor (fruit of the plant) Is the site of storage for various products and waste: Stores various compounds: proteins, inorganic ions, defensive compounds (defen d the plant against herbivores) Disposes of metabolic wastes that would otherwise ends bed the cell if they accumulated in the cytoplasm Chloroplasts the site of photosynthesis 41 Found in green parts of a plant Each plant cell contains a lot of chloroplasts Chloroplasts contain pigments (i.e. chlorophyll, which makes the leaves or stems of a plant green, and traps light energy for photosynthesis) Energy-converting Organelles: the Mitochondria & Chloroplast the mitochondria converts food into ATP (requires O2, waste product is CO2) the chloroplasts convert solar energy into food (requires CO2 and solar energy to create glucose, and O2 is released) Both mitochondria and chloroplasts are double-membrane bound organelles that contain their own DNA and proteins that are made by their own ribosomes. They both can self-replicate Differential Gene Expression every cell in an organism has the same genetic composition, with the exceptions of gametes (egg) and sperm cells All cells have specific functions: Every cell in the body has some genes turned on, and others turned off The genes that are turned on in a white blood cell (WBC) will not be the same as t he 'on' genes in a nerve cell The specific components of a given cell provides its unique characteristics by expressing different subsets of genes (2 cells can contain different subsets of gene products, or proteins) Even though all cells have the same genes, they only express the genes that they require. They will not express OTHER tissue-specific genes! 42 A typical human cell probably expresses about 20% of its genes at any given time Both neuron and epithelial cells have genes (DNA / chromosomes ) encodin g for neural and epithelial specific proteins (they contain the exact same genes, but only the neuron can express the nerve genes, and thus will only make nerve proteins. Neurons don't make epithelial proteins) Epithelial cells can only express epithelial genes, and will only make epithelial proteins. They can't make nerve proteins. What is a virus? viruses are acellular infectious particles Viruses (i.e. toxins or poisons) are not members of any of the domains or kingdoms They are obligate intercellular parasites: cannot reproduce or carry out metabolic activities outside of a host cell Consist of either DNA or RNA, not both, and proteins. They dint have ribosomes so they can't make their own proteins. They are host-specific because they have specific receptors where they bind Measles bind to skin cells HIV bind to immune cells once inside the cell, the viral nucleic acids take it over, and force it to make more of the virus Once a virus binds to a receptor, it either enters the cell or injects nucleic a cid into the cell In either case, the protein coat is released and the viral nucleic acid will replicate via the machinery of the host cell 43 The Life Cycle of Viruses viral genes are able to take command of the host's metabolic pathways, and direct it to make new copies of the original virus Once the viral nucleic acid and the protein coat are made, the virus is assembled and then released The virus then kills the host cell, and hen newly released viruses infect other cells Treatment for bacterial viruses is antibiotics, while vaccines treat viruses and bacteria 44


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