MOLECULAR BIOLOGY TOPIC 2

Transcription

1 MOLECULAR BIOLOGY TOPIC 2

2 TOPIC 2 MOLECULAR BIOLOGY 2.1 MOLECULES TO METABOLISM WATER CARBOHYDRATES & LIPIDS PROTEINS ENZYMES SAMPLE QUESTIONS... 30

3 2.1 MOLECULES TO METABOLISM MOLECULAR BIOLOGY Molecular biology explains in terms of the substances involved. Molecular biologists would identify the in a and break down each step into its. This has allowed us to better understand the processes of cellular respiration and photosynthesis. But there is still a lot that we don t understand about organic molecules and how they act in the body. CARBON COMPOUNDS Carbon is the backbone of every molecule. Carbon atoms can allowing a diversity of stable compounds to exist. Covalent bonds are. This allows, molecules to be formed. eg. Titin protein (contains 539,000 atoms) found within contractile unit of muscle fibres Life is based on carbon compounds. These include: and You need to be able to draw molecular diagrams these compounds: inc. glucose, ribose, a saturated fatty acid and a generalized amino acid You need to be able to identify biochemicals such as sugars, lipids or amino acids from 1

4 CARBOHYDRATES Identify: monosaccharides and disaccharides : Glucose, galactose, fructose : Lactose, maltose, sucrose : Cellulose, glycogen, starch Draw: the ring forms of D-ribose, alpha D-glucose and beta-d-glucose 2

5 LIPIDS Draw: a saturated fatty acid Saturated fatty acid: no double bonds eg. stearic acid Unsaturated fatty acid: double bonds eg. linoleic acid Generalised fatty acid: Identify: lipids : fats, oils, phospholipids and steroids 3

6 PROTEINS Draw: a generalised amino acid a central atom 4 side groups: the group (-NH 2 ) the group (-COOH) an the R standing for the rest Identify: proteins or parts of polypeptides, linked with a peptide bond 4

7 CONDENSATION & HYDROLYSIS Condensation reaction: from two to form a Also known as reactions Also known as reactions Require and Hydrolysis reaction: can break and back into Also known as reactions Require enzymes but 5

8 CONDENSATION & HYDROLYSIS METABOLISM Most use most. Each in each pathway is controlled by a specific. Metabolism is the of all of the pathways used in a particular cell. 6

9 UREA & VITALISM Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized Urea is an chemical compound. It is essentially the produced by the body after. Naturally, the compound is produced when the breaks down or, and. The average person excretes ~ of urea per day, mostly through, but a small amount in. of urea can be created in liquid or solid form, and is often an ingredient found in, animal feed, and diuretics. Falsification of theories with one theory being superseded by another The artificial synthesis of urea helped. Vitalism is the theory that living organisms are fundamentally different from non-living entities because they contain some or are governed by than are inanimate things. Vitalists would theorise that: The synthesis of urea by in 1828 therefore falsified this statement. Vitalism is no longer a generally accepted idea. Complete relevant practice Qs beginning on Page 30 1

10 2.2 WATER STRUCTUREOF WATER Chemical formula: Made up of & bonds exist between the atoms Oxygen nucleus is & than the hydrogen nuclei. This the pair in the covalent bond to the oxygen This means that water molecules are as one part is than the other This means that water molecules can each other form between the molecules 2

11 PROPERTIES OF WATER Theories can be used to explain natural phenomena The theory that hydrogen bonds form between water molecules explains the properties of water Properties of water to be covered: properties properties properties properties Cohesion and adhesion: Water molecules are strongly cohesive ie. they to They also adhesive ie. they to that are or of water molecule allows it to with substances & allows small to be able to on water Allows water to be in plants Thermal properties: Water has a high ie. it takes a lot of energy to the of water Water has a high ie. it takes a lot of energy to it to a Water has a high ie. it needs to a lot of energy to requires to break This allows lakes to lots of heat energy & for organisms. 3

12 PROPERTIES OF WATER This is also used by animals and plants as a. Plants use heat from their leaves for, thus preventing. This is also true of animals, who use the evaporation of to remove heat from the body. The blood is also. This means that blood can be to other parts in order to cool them down. Thermal properties water vs methane: The key difference between water and methane is their. Methane has, only covalent. As a result, is needed to separate its molecules from each other. This causes the differences in their physical properties, particularly their thermal properties. Solvent properties: Water can many organic and inorganic substances that have or regions. Polar attraction of large quantities of water can : ions will become surround by the region of the water molecules ions will become surround by the 4

13 PROPERTIES OF WATER region of the water molecules Water is often called the because of how well it can act to dissolve substances. Watch this: lve.swf in of water. Water in cells the / for these reactions. Substances that are can therefore be around an organism and be brought into/out of the cells by. All substances that in water are eg. - its positive and negative regions make it polar and soluble All substances that in water are eg. Oil 5

14 MODE OF TRANSPORT THROUGH BLOOD Glucose molecule Freely Carried by the Oxygen molecule in water due to its of oxygen at Carried by protein in has oxygen binding sites Cholesterol (=lipid) molecules Carried by complexes in the blood plasma Fats Hydrophobic molecules Carried by complexes in the blood plasma Sodium chloride (salt) molecule ( ) Freely Carried by the as Complete relevant practice Qs beginning on Page 31 6

15 2.3 CARBOHYDRATES & LIPIDS MONOSACCHARIDES Examples Details Example use in plants Example use in animals Glucose C 6 H 12 O 6 hexose sugar 5C form the ring, with the 6 th corner taken by oxygen Galactose C 6 H 12 O 6 hexose sugar same as glucose but one set of side chains are reversed Fructose C 6 H 12 O 6 pentose sugar Monosaccs à disaccs: reaction is removed formed 7

16 DISACCHARIDES glucose + glucose à + water glucose + galactose à + water glucose + fructose à + water Examples Details Example use in plants Example use in animals Maltose C 12 H 22 O 11 glucose dimer Lactose C 12 H 22 O 11 glucose and galactose Sucrose C 12 H 22 O 11 table sugar glucose and fructose Monosaccs/disaccs à polysaccs: reaction Water is removed (no. of water = ) Glycosidic bonds formed Often and may be Examples: used as an molecule in used as an energy storage molecule in of cell 8

17 POLYSACCHARIDES Cellulose: Function: structural component of plant cell walls Structure: Made of molecules linked together reactions link C1 of one glucose to C4 of the next The molecule is a chain (not curvy) The molecule is Cellulose can to itself through à forming with a It s this strength that allows the cell wall to. Starch: Function: used as an energy storage molecule in plants Structure: Made of molecules linked together reactions link C1 of one glucose to C4 of the next The molecule is a chain (not straight) Starch is, but are due to their There are two forms of starch: contains only C1-C4 bonds and forms linear helices 9

18 POLYSACCHARIDES also contains C1-C6 bonds, which causes branching Glycogen: Function: used as an energy storage molecule in plants Structure: Made of repeating molecules linked together reactions link C1 of one glucose to C4 of the next and potentially C1 to C6. The molecule is a Hydrophilic but therefore does not upset the of the cells 10

19 MOLECULAR VISUALISATION SOFTWARE Go here: 11

20 HEALTH CLAIMS ABOUT LIPIDS could be involved All fatty acids are in of fat in the diet linked to an of link between diets high in and Link between low levels of fatty acids and affected brain and nerve development Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids. Evaluation = Evidence = Strengths? Has a positive or negative been determined? Has the or of the difference between the two means tested? Has the of data been considered? Limitations? What was the of health being tested? What was the? Was the sample of the? Was the data gathered from human or? Was it a study? What were used to gather the data? 12

21 LIPIDS FOR LONG-TERM ENERGY STORAGE Functions of lipids include: S : phospholipids in cell membranes H : steroid hormones are lipids (eg. oestrogen) I : fat is an insulator; lipids also insulate neurons P : fats protect internal organs from damage S of : fats can be used as a energy storage source Carbohydrates and lipids contain a lot of and can be used for energy Lipids so they are more suitable for long-term storage These lipids are stored as in (cf. Topic 1) under the skin and around organs, including the. Lipids release than sugars (or proteins). Lipids are therefore than sugars of equal yield: Lipids add as much to body mass as sugars Glycogen is (b/c it s soluble), while fats are not Why use glycogen at all???? Breakdown of sugars is much, making them for energy storage Sugars are in water (cf. ), making them to sites of use Glucose can be used aerobically (with O 2 ) or anaerobically (without O 2 ) but fats 13

22 BODY MASS INDEX (BMI) CALCULATION Body Mass Index (BMI) is a to identify potential weight issues. It is should be used with other measures, such as: a test evaluations assessments and BMI is calculated in the same way for kids and adults. Units for BMI =, You can also use a BMI chart to assess BMI An alternative method uses a : Draw a line between the weight and weight. It will cross a third axis, a BMI scale. Complete relevant practice Qs beginning on Page 33 14

23 2.4 PROTEINS POLYPEPTIDES Amino acids are linked together by to form polypeptides. The bonds formed are. The bonds formed are bonds. The bonds form in the. ESSENTIAL AMINO ACIDS There are essential amino acids found in polypeptides synthesised by the ribosomes. The source of these amino acids would be the absorbed products of. 15

24 POLYPEPTIDE SYNTHESIS Ribosomes are the molecules (structures) within cells that the of. There are possibilities for polypeptides amino acids or or A amino acid peptide has 1,280,000,000 possible combinations. Some polypeptides (eg. ) are in length! The sequence of amino acids is coded for by. DNA stored in the is read and into an. This RNA message ( ) can leave the nucleus and head to the. Here, the instructions contained within the message are into a. Each amino acid has unique properties. side chains can be polar/non-polar, hydrophilic/hydrophobic, acidic/basic, etc The properties of each amino acid influence how a will be able to up into a. There are levels of structure in proteins: structure structure structure ß 16

25 PROTEIN STRUCTURE Primary (1 ) structure: Involves Secondary (2 ) structure: Repeating local structures Generally found in proteins These include: o : peptide chain wound into a helix o : peptide strands lie in a plane Tertiary (3 ) structure: Single protein into a Generally form proteins Important for of the protein Quaternary (4 ) structure: Two or more polypeptide chains together eg. Hemoglobin becoming haemoglobin 17

26 PROTEIN STRUCTURE Proteins can be separated into two groups based on their : FIBROUS PROTEINS GLOBULAR PROTEINS SOLUBILITY SHAPE SENSITIVTY TO CHANGES ROLE EXAMPLES 18

27 PROTEIN FUNCTION Proteins have a variety of uses in organisms: speeds up chemical reactions give animal cells their shape provide strength of and binding sites in membranes and cytoplasm for hormones, neurotransmitters, tastes, smells and receptors for light of Rubisco: Full name = ribulose bisphosphate carboxylase It is an involved in It from a state to one able to be by the plant. Insulin: It is a involved in levels in the blood within narrow limits. It is secreted by the in the. Insulin signals the liver cells to and convert it to. This takes it out of the. Not produced by people with. 19

28 PROTEIN FUNCTION Immunoglobulins: Also known as Produced by the in response to the presence of an The of the protein is allowing them to respond to a of. They also other immune cells to help the pathogen once it has been identified. Rhodopsin: A that can. Found in within the at the back of the eye. The absorption of light causes a and change to the molecule. This results in a being sent to the. Rods work well in even, and are responsible for vision. Collagen: A protein. Forms a in skin and in the blood vessel walls that. Gives tendons, ligaments, skin and blood vessel walls their. Forms part of teeth and bones,. Spider silk: proteins Spiders can produce different types of silk with different for different. Some of the silk is comparable to in regards 20

29 PROTEOME Every individual has a. Proteome: The proteome is a function of both the organism s (genes) and. Environmental factors such as,, etc can affect a cell s activities eg. DNA methylation can stop translation of a protein! Epigenetics: Watch this: PROTEIN DENATURATION or ( ) can cause of proteins. Denaturation affects the holding the, and structures together. This will result in an loss of and therefore. eg. Cooking an egg denatures its proteins, causing them to harden Complete relevant practice Qs beginning on Page 34 21

30 2.5 ENZYMES ENZYME BASICS, which the of chemical without becoming a part of the Enzymes are proteins with a shape. Without enzymes, chemical reactions. Enzymes work by the needed for a reaction. Many enzyme names end in eg. amylase, lipase, sucrase, lactase, catalase Active site: The active sites are : ie. enzymes are designed to fit the shape of their substrate This is known as the The active site is simply a on the surface of the enzyme 22

31 ENZYME-SUBSTRATE SPECIFICITY Lock and key model Active site and substrate each other in terms of both and (e.g. opposite charges). Binding to the active site brings the substrate into close, creating an -. The enzyme the of the into a (or products), creating an -. As the enzyme is in the reaction, it can continue to work once the product is completed. Induced fit model The lock and key model of enzyme action does not fully explain enzyme activity. There are some enzymes that are capable of reactions eg. some have quite a broad specificity The Induced Fit Model proposes that the the substrate precisely. 23

32 ENZYME-SUBSTRATE SPECIFICITY As the substrate binds to the active site, the to better fit the substrate. This the in the substrate, thus the required for the reaction. ENZYME CATALYSIS Catalysis involves and the of with the. Collisions between the free moving enzymes and substrates are the result of. Successful collisions will the active site and substrate correctly, allowing to occur. Go here: 24

33 ENZYME DENATURATION Enzymes, like all proteins, can become. Denaturation is usually. Can be caused by and Denaturation holding the of a protein together à resulting in loss of FACTORS AFFECTING ENZYME ACTIVITY 25

34 FACTORS AFFECTING ENZYME ACTIVITY Temperature Low temps result in for the of a reaction to be achieved Increasing the temp will increase the and of both and, resulting in higher enzyme activity This is because a will result in between enzyme and substrate At an temp, the of enzyme activity will be at its Higher temps will, as the thermal energy the bonds holding the enzyme together This causes the (particularly the ) to, resulting in a loss of enzyme ( ) ph Changing the ph will alter the of the enzyme, which in turn will change and may change the of the molecule Changing the shape or charge of the active site will diminish its ability to to the substrate, Enzymes have an ph 26

35 FACTORS AFFECTING ENZYME ACTIVITY Substrate concentration Increasing substrate concentration will increase enzyme activity More substrate means there is an increased of enzyme and substrate and So more will be formed in a period. After a certain point, the rate of reaction will despite further increases to substrate concentration, because as the environment has become with substrate and are in use SUBSTRATATE TEMPERATURE ph CONCENTRATION Too low Too high ENZYME IMMOBILISATION Immobilised enzymes are widely used in industry. Methods: Aggregations of enzymes bonded together Attached to a surface eg. glass Entrapped in gels eg. Advantages: Enzyme is not dissolved so concentration of substrate can be increased Enzymes can be many times, saving time and money Collection of products is straight forward to changing temp and ph Examples: Used for medical diagnostic tests Used for food production eg. 27

36 PRODUCTION OF LACTOSE-FREE MILK of adult humans are lactose intolerant They have lost the ability to in after early childhood. A allows lactase production to continue through to adulthood. It is the of this that results in lactose intolerance. Ingestion of milk will lead to &. The food industry has produced lactose-free milk. Use enzyme to break down into and. Milk tastes but will not cause reaction in lactose-intolerant adults. Steps: 1. Lactase is (from or ) 2. Lactase is to an substance (such as beads) 3. Milk passed over enzymes becomes lactose-free Other uses: Source of milk for lactose-intolerant individuals Increases the sweetness of milk, thus the need for the of ice-creams the time for or Complete relevant practice Qs beginning on Page 34 28

37 EXPERIMENTAL DESIGN Catalase is an enzyme that catalyses the conversion of hydrogen peroxide into water and oxygen. Choose a research question and design an experiment to be run in class. Possible research Qs: What is the effect of substrate concentration? What is the effect of temperature? What is the effect of ph? Does the source of catalase influence the rate of reaction? Things you must consider about your IV: How are you going to vary your IV across a sufficient range? What units will you be measuring your IV in? Have you selected concentrations of chemicals that are safe to handle? Things you must consider about measuring your DV: Measuring increase of product or disappearance of substrate? Direct or indirect measurement? (eg. concentration or product or change in ph) Units and uncertainty of equipment? Time period needed? How many repeats are needed? Things you must consider about designing a fair test: What else could affect your DV? How/why would they affect your DV? How could you eliminate or reduce their influence on the DV? Do you need to monitor them throughout to be sure that they were controlled? Is there anything that was beyond your control? Safety and ethics of your method and equipment? 29

38 SAMPLE QUESTIONS MOLECULES TO METABOLISM Q1 State the number of covalent bonds formed by a carbon atom. Q2 Define anabolism. Q3 What is meant by the term dimer? Q4 Which describes these molecules correctly? A. I = ribose; II = amino acid B. I = glucose; II = amino acid C. I = ribose; II = fatty acid D. I = glucose; II = fatty acid Q5 What is meant by the term dimer? A. Glucose and galactose are examples of monosaccharides. State one other example of a monosaccharide. (1) B. The equation below shows the production of glucose and galactose from lactose. i. There are several different types of carbohydrate. State which type of carbohydrate lactose is. (1) ii. State the type of chemical reaction that occurs when lactose is digested into glucose and galactose. (1) 30

39 WATER Q1 Which diagram represents the polarity of a water molecule? Q2 Which diagram best illustrates the interactions between water molecules? 31

40 WATER Q3 Explain how the properties of water are significant to living organisms. [9] 32

41 CARBOHYDRATES & LIPIDS Q1 A woman has a mass of 72kg and a height of 1.69m. a. Calculate her BMI. b. Deduce the body mass status of this man using the table. c. Outline the relationship between height and BMI for a fixed body mass. Q2 A man has a height of 150cm and a BMI of 40. a. Calculate the minimum amount of body mass he must lost to reach normal body mass status. Show your working. b. Suggest 2 ways in which the man could reduce his body mass. Q3 What is the difference between galactose and lactose? A. Lactose is a disaccharide and galactose is a monosaccharide. B. Lactose is the product of anaerobic respiration in humans and galactose is the product of anaerobic respiration in yeast. C. Lactose is an enzyme and galactose is a hormone. D. Galactose is a sugar found in milk but lactose is not found in milk. Q4 What chemical is shown in the diagram below? A. Saturated fatty acid B. Cis-monounsaturated fatty acid C. Trans-monounsaturated fatty acid D. Polyunsaturated fatty acid 33

42 PROTEINS Q1 Which best describes the tertiary structure of a protein? A. The interaction of polypeptide subunits and prosthetic groups B. Interactions forming hydrogen bonds between the amino acids C. The sequence of amino acids in the polypeptide chain D. The structure formed from interactions between the amino acid side groups ENZYMES Q1 The graph below shows the effect of substrate concentration on enzyme activity. What conclusion can be drawn about section X of the graph? Which best describes the tertiary structure of a protein? A. The enzyme has started to denature and the reaction slows down. B. The reaction has finished and the substrate has been used up. C. The enzyme is saturated and is working at its maximum reaction rate. D. Some of the enzyme has been consumed and the reaction has reached a plateau. Q2 Which of the following will cause an enzyme to permanently lose its properties? I. Hydrolysis II. Freezing to 20 C III. Dissolving it in water A. I only B. II only C. I and II only D. I and III only 34

43 ENZYMES Q3 Discuss factors that affect enzyme activity. [9] 35