IB Biology - Topic 2 Molecular Biology (2.1-2.5)
End- Product Inhibition
- a non-competitive type of inhibition - the end product of a reaction acts as an enzyme inhibitor by bonding to the allosteric site, slowing/stopping the reaction - reversible and used to regulate reactions - ex: isoleucine, 5 enzymes needed to make it, when it is made it comes back and docks with enzyme one stopping its own production, it undocks to resume
Active site
- arrangement of the molecules in the enzyme produce the active site within which the specific substrate will fit - it recognizes, confines, and orients the substrate in a particular direction
Immobilized Enzyme
- attached to a substance that remains stationary in a container - allows enzyme to be retained to that it can be used - can also be enclosed in calcium alginate beads to contain the enzyme
Cohesion
- attraction of water to itself - causes surface tension
Hydrolysis
- catabolic process - breaks down polysaccharides, triglycerides, and polypeptides into the smaller substances they are made of - adding of water
Amylose
- consist of alpha 1 and 4 linked glucose units - linear section of starch molecules
Benefits of Immobilizing Enzymes
- ease of harvesting - ease of recovering the enzyme - continuous production - extended production time
Lipids
- fats and oils - triglycerides -phospholipids - steroids - animals store as fat, plants store as oil
Fatty Acids
- long chain of carbon atoms joined to hydrogen atoms
Protein
- made up of a chain of amino acids - monomers and polymers
Six Roles of Protein in the body
- structural (ex: collagen) - transport (ex:hemoglobin) - movement (ex: myosin) - hormones (ex: insulin) - defense (ex: immunoglobulin) - enzymes (ex: catalase)
Denaturation of an Enzyme
- structural change that results in a loss, usually permanent, of its biological properties - primary causes: heat and pH - environmental causes: temp, pH, substrate concentration, enzyme concentration - these effect the functioning rate
Amylopectin
- varying structure, straight chain of alpha 1 and 4 linked glucose units with occasional 1 and 6 glycosidic bonds which provide branching points
Thermal Properties
- water is a temp regulator - when it evaporates it carries heat with it acting as a coolant
Adhesion
- when water molecules stick to another substance - plants draw water up from the stems to the shoots through transpiration
Quaternary structure
-2 or more tertiary protein subunits combined to make a single functional protein
amino acids
-20 different types, each with their own R-group -tend to be 50-150 amino acids long -possible combinations of amino acids in proteins are virtually unlimited (in 50 amino acid long protein, possibilities are 20^50
Carboxyl
-C=O-OH
list 3 examples of enzymes, with their functions
-CATALASE: breaks down hydrogen peroxide -LACTASE: digest lactose to glucose and galactose -AMYLASE: digests starch
carbonyl
-CO
carboxyl
-COOH
production of lactose-free milk
-Lactase obtained from commonly from yeast (bacteria is an alternative) -Lactase is bound to the surface of alginate beads -Milk is passed (repeatedly) over the beads -The lactose is broken down into glucose and galactose -The immobilized enzyme remains to be used again and does not affect the quality of the lactose free milk
Amine
-N-H-H
amino
-NH2
Hydroxyl
-O-H
hydroxyl
-OH
phosphate
-PO4
sulfhydryl
-SH
Substrate concentration on enzymes
-as substrate increases, reaction rate increases, more substrate = more frequently collide with enzyme -any more substrate past optimum will have no effect; a'' active sites are used
Immobilization of enzymes
-attached to surfaces (ex. glass) -trapped in gel -aggregations of enzymes bonded together
fatty acids
-building block of most lipids -can be saturated or unsaturated
Saturated fats
-carbons carrying the maximum amount of hydrogen -straight -solid at room temperature -most stable -less healthy
pH on enzymes
-changed pH=altered charge in enzyme and protein solubility and may change shape of molecule -changed shape=lessened ability to bind and catalyze -different enzyme shave different optimum pH levels; changed levels=diminished rate of reaction
describe cis monounsaturated fatty acids (and know how to draw it)
-common in nature -double bond causes a bend in the fatty acid chain -loosely packed -triglycerides formed from cis-isomers have melting points -usually liquid @ room temp
lipids
-contain CHO -have very few O compared to C and H -group of organic compounds -insoluble in water, soluble in non-polar organic solvents
carbohydrates
-contain CHO -organic compounds consisting of one or more simple sugars -monomers (commonly ring shaped molecules) follow the general formula of (CH2O)x
proteins
-contain CHON(S) -large organic compounds -made of amino acids arranged into one or more linear chains
common uses of enzymes
-detergent -biofuels -brewery -textiles -medicine and biotechnology -food -paper
R-groups
-determine amino acids' chemical and physical properties -interactions contribute to creating the 3D shape of a protein (protein shape determines protein function)
Advantages of using immbolized enzymes
-ease of harvesting the product -ease of recovering the enzyme -continuous production is possible -immobolization extend production tike especially when using proteases, which might digest each other in reactions in solution.
enzyme-substrate specificity
-enzymes are specific to their substrates -substrate and active site match in two ways: >structurally >chemically
Thermal properties of water
-has a high specific heat capacity — takes a lot of energy for H20 to change its temperature so water can absorb or give off a great deal of heat without changing temperature very much (the temperature of water remains relatively stable) -has a high latent heat of evaporation — water absorbs a great deal of heat when it evaporates, many organisms use this as a cooling mechanism because evaporating H20 removes a lot of heat from the organism
Structure of an amino acid
-have an amine ground, R group, hydrogen bond, and carboxyl group
denaturation
-heat causes H-bonds to break, warps enzymes -enzymes no longer is able to catalyze reactions, substrate doesn't fit
What role does hydrolysis lay in the relationship between mono, di, and polysaccharides?
-hydrolysis: using water to break a bond -mono: hydrolysis yields glucose and galactose (monosaccharides) -di and poly: made by condensation/dehydration -polysaccharide -> monosaccharide by hydrolysis
induced- fit model
-if lock and key theory were true, each enzyme would only catalyze one reaction -as substrate approaches an enzyme, the active site changes to fit the substrate (conformational change) -this stresses the substrate, which reduces the activation energy of the reaction
Commercial reasons lactose free milk is produced
-increases sweetness of milk -reduce crystallization of ice creams -shortens production times of yoghurt and cheeses
Lactose-free milk
-individuals who are lactose intolerant do not produce lactase -bacteria in the gut are given lactase instead of the monosaccharides glucose and galactose and are thus overfed -pre-digested milk, milk which has had the enzyme lactase already added, is created by isolation lactase from solutions using the calcium alginate bead and then adding the isolate lactase to milk -it is also possible to genetically engineer goats to produce milk that contains the human lactase molecule
Primary structure
-linear sequence of amino acids joined by hydrogen bonds -this sequence will determine a protein's 3-dimensional shape
describe why lipids are better for long-term energy storage than carbohydrates.
-lipids contain more than 2x the energy of carbs (9cal/g vs. 4cal/g) -lipids add 1/6 as much to body mass as carbs do -lipids are not as easily broken down compared to carbs
explain fibrous proteins
-long, thin, linear -insoluble -structural -ex: collagen, keratin, myosin, actin
Temperature on Enzymes
-low temp=not enough energy to catalyze -optimum temp=more collisions -too high temp=denaturation
Structure of a fatty acid
-methyl group, many hydrogen bonds, and a carboxyl group
What is the nature of a channel protein regarding its chemistry?
-middle layer of plasma membrane is non-polar (hydrophobic) -channel proteins — polar, help polar substances get through --channel proteins must be compatible with whatever is trying to pass through
Unsaturated fats
-monounsaturated: 2 carbons are lacking hydrogens consecutively -polyunsaturated: 2 or more carbons are lacking hydrogen -bent -liquid at room temperature -more healthy — can eliminate cholesterol
Carbohydrates
-most abundant type of molecule in living things - plants and animals use them for energy/ structural function
Hydrophobic
-non polar -not charged
Tertiary structure
-often described as globular -dependent upon the composition of each amino acids' R group
Solvent Properties
-other polar substances can dissolve in water - good for transport
Hydrophilic
-polar -charged
How does heat affect proteins?
-proteins are held together by intra-molecular bonds -these bonds are highly susceptible to changes in temp. and pH -high temperature increases molecular motions and places stress on these bonds causing denaturing -pH conditions outside of the acceptable range can prevent normal hydrogen bonding due to the presence of excess ions ( H+ of OH-) -as longs as the covalent (peptide) bonds remain intact the protein retains the ability to return to its normal shape
describe trans monounsaturated fatty acids (and know how to draw it)
-rare in nature (artificially produced) -double bond doesn't cause a bend in the fatty acid chain -closely packed -triglycerides formed from trans-isomers have melting points -usually solid @ room temp
Secondary structure
-repetitive shape either forming a helix or a pleated sheet
explain globular proteins
-round, spherical -soluble -functional -ex: hemoglobin, rubisco, immunoglobulin, and catalase
Water as a Solvent
-small ions dissolve easily into water -allows water to transport ions easily
Enzymes
-speed up the rate of metabolic reactions - help maintain homeostasis - enzymes are PROTEINS - function determined by shape - they can be re-used
Know the parts of an enzyme and how it performs its functions
-substrate (what binds to the enzyme) -active site (area designed to match a specific molecule (the substrate)) -substrate enters activation site --it must enter with a minimum rate of motion that will provide then energy necessary for the reaction (enzymes lower the activation energy of reactions) — enzymes can act as a catalyst many times
Hydrogen Bond
-the bond that gives water its special properties - Electrons are shared, oxygen pulls harder, slightly positive H-atom, slightly negative O-atom -+ and - attract, attraction force - bond between O and H atoms in two water molecules
cohesion
-water molecules are attracted to each other -H-bonds form between water molecules due to their polarity
adhesion
-water molecules are attracted to small, polar molecules -H-bonds form between water molecules and other molecules due to their polarity
Thermal properties
-water requires a lot of energy to change its temperature -when water evaporates it takes heat with it; makes sweat a coolant
The effect of an acid/base on enzyme structure and function
-when a solution has become too acidic, the relatively large number of hydrogen ions can bond with the negative charges of the enzyme or substrate, and prevent proper charge matching between the two -when a solution becomes too basic, the relatively large number of hydroxide ions can bond with the positive charges on the substrate or enzyme and once again prevent proper charge matching between the two -either of these scenarios will result in an enzyme becoming less efficient, and in extreme situations becoming completely inactive -also numerous extra positive and negative charges of acidic and basic solutions can result in the enzyme losing its shape and becoming denatured
collision
-when substrate molecules and active sites come together -when not correctly aligned, collision does not result in catalysis
What does it mean for a protein to become denatured?
-when the temp/pH of a protein is increased/decreased, denaturing occurs -> bonds in proteins are susceptible to change *once bonds break they can't return to original form
glycogen - carbohydrate, adipose - fat
1 gram of glycogen require 2 grams of water to be stored with it while 1 gram of adipose requires none
Lysozyme
1 polypeptide; used in nasal mucus and tears to kill some bacteria by digesting cell walls
1 glycerol + 3 fatty acids=
1 triglycerol
When one bond holding two sugars breaks, how many water molecules are needed?
1 water molecule 1 molecule per bond
organisms assembling polypeptides from 20 aa's the same way - evolution theory
1) The amino acids were produced by chemical processes on Earth before the origin of life 2) Natural selection would favor organisms who used the ideal 20 amino acids 3) All life evolved from a single ancestral species which used the 20 amino acids
Four essential elements in all living things
1) carbon 2) hydrogen 3) nitrogen 4) oxygen
What are the four properties of water due to hydrogen bonding and its polarity?
1) cohesive properties: molecules of water stick to each other 1.5) adhesive properties: water will stick to other surfaces 2) thermal properties: high specific heat capacity and latent heat of evaporation, temperature is stable 3) solvent properties: it's a good solvent because its polar, will dissolve polar solutes easily, good medium for metabolic reactions 4) transport medium: dissolves nutrients, gases and waster products which can be carried in the circulatory system of animals, through the xylem and phloem in vascular plants or through the water in soil or aquatic habitats, water is dense, can transport molecules across membranes in diffusion as well as within the cell or interstitial fluid
Protein structure
1) primary 2) secondary 3) tertiary 4) quaternary
Polysaccharides
1) starch — energy storage (plants) 2) glycogen — energy storage (animals) 3) cellulose — plant cell walls
Design simple experiments to test the effect of temperature, pH and substrate concentration on the activity of enzymes.
1. Prepare a pH 3, pH 7, and pH 10 solution. 2. Cut up some potatoes. Freeze 3 pieces, leave 3 normal, put 3 pieces in the microwave. 3. Place one of each potato in each of the solutions, separately. 4. Record observations
Benefits of enzyme immobilization
1. catalysis can be controlled 2. enzyme concentration can be higher 3. reusable enzymes, save money 4. resistant to denaturation over greater ranges of pH and temperature 5. products are not contaminated with enzymes
explain the 4 levels of protein structure
1. sequence of amino acids 2. alpha helix or beta sheet 3. 3D polypeptide chains 4. two or more globular proteins
what are the three stages of enzyme activity?
1. substrate binds to active site of enzyme 2. while bonding, it changes shape/into a new chemical substance 3. then the products separate from active site
Describe the structure of a single water molecule and how this leads to its dipolar (polar) nature. (and know how to draw it)
2 hydrogen atoms are bonded to one oxygen atom by covalent bonds. However, electrons in these bonds are not shared evenly so the oxygen takes on a partial negative charge and hydrogen takes a partial positive charge.
Quaternary proteins have:
2 or more
Quaternary proteins have:
2 or more different polypeptide chains joined to form a single functional protein and similar bonds to tertiary proteins.
disaccharide
2 sugars ex. maltose-2 glucose molecules connected by glycosidic bond, and sucrose-formed from glucose and fructose
Polypeptide possibilities
20^n n = number of amino acids in the sequence
Describe how the amino acid sequence of polypeptides is coded for by genes.
3 bases are used to form a single amino acid. Each polypeptide is coded based on the genetic code through ribosomes.
triglyceride?
3 fatty acids, one glycerol
explain the 3rd level of protein structure
3D folded structure (polypeptide chains). held in place by ionic bonds, hydrogen bonds, and disulfide bonds
Identify the number of covalent bonds that carbon atoms form, and explain why this is important.
4 bonds and it allows diversity of stable bonds.
Structure of an Amino Acid
4 main groups - carboxylic acid group (COOH) , amino group (NH2), side chain (R), carbon - side chain is extremely important to function
carbohydrates - Ribose (drawing)
5 carbons, 10 hydrogen, 5 oxygen
Ribose molecule
5 carbons, 3 hydroxyl groups (up down down)
Glucose Molecule
6 carbons, 4 hydroxyl groups (down down up down)
Polypeptide
A chain of many amino acids linked together by peptide bonds.
Mono vs Polysaturated fatty acid
A chain with just one double bond is monosaturated and one with two or more double bonds is said to be polysaturated
Ionic Bond
A chemical bond resulting from the attraction between oppositely charged ions. (ex: NH3+O-)
Disaccharide
A double sugar, consisting of two monosaccharides joined by dehydration synthesis.
saturated fatty acid
A fatty acid in which all carbons in the hydrocarbon chain are connected by single bonds, thus, no more hydrogen atom can be added (Generally solid at room temp)
unsaturated fatty acid
A fatty acid possessing one or more double bonds between the carbons in the hydrocarbon chain. Such bonding does not have the maximum number of hydrogen atoms attached to the carbon chain. (tends to be liquid at room temperature, mainly from plants)
glycosidic bond
A glycosidic bond is a covalent bond found between two glucose molecules ex: in maltose.
Amylopectin
A highly branched starch polymer with branches occurring with alpha 1-6 glycosidic bonds
Catabolism
A metabolic pathway where molecules are broken down and produce energy.
Disaccharide
A molecule composed of two monosaccharides. Common disaccharides include maltose, sucrose, and lactose.
Glycogen
A polysaccharide stored in animals; the storage form of glucose in animals.
Anabolism
A process in which large molecules are built from small molecules
High Latent Heat of Vaporization
A property of water that serves a cooling mechanism for living organism due to the fact that it takes a lot of heat to evaporate water from a liquid to a vapor.
Condensation reaction
A reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water; also called dehydration reaction.(creates macromolecule)
Monomer
A simple compound whose molecules can join together to form polymers (found in protein)
Monosaccharide
A single sugar molecule such as glucose or fructose, the simplest type of sugar.
monosaccharide
A single sugar. no covalent bonds. example: galactose
Starch
A storage polysaccharide in plants, consisting entirely of glucose monomers joined by a glycosidic linkages.
Amylose
A straight chain type of starch composed of alpha glucose units.
Cellulose
A structural polysaccharide of plant cell walls, consisting of beta glucose monomers joined by β glycosidic linkages.
enzyme-substrate complex
A temporary complex formed when an enzyme binds to its substrate molecule(s).
Explain how triglycerides are formed by condensation from three fatty acids and one glycerol molecule.
A triglyceride is formed by linking glycerol to 3 fatty acids. Each fatty acid is linked to the glycerol through dehydration synthesis, and 3 water molecules are produced. The bond created is called an ester bond.
Hydrophobic
"Water-hating", non-polar, insoluble in water or non-charged substances like lipids. The heads of phospholipid is an example of th
Hydrophilic
"Water-loving", polar, soluble in water or charged substances like carbohydrates. The tails of phospholipid is an example of this.
what is the attraction between water molecules called?
"hydrogen bond"
low pH
(0-6) means acidic
high pH
(8-14) means a base or alkaline solution
monosaccarides formula
(CH2O)n where n is the number of carbon atom in the molecules.
ATP
(adenosine triphosphate) main energy source that cells use for most of their work
20
*How many* different amino acids?
substrate and active site
*The substrate binds to the active site *They have the same shape and chemical properties *Substrates are converted into products while they are bound to the active sites and then the products are released, freeing the active site to catalyse another reaction
lose H2O
*What* happens to the amine group and carboxyl group of an amino acid when a peptide bond is formed?
between an oxygen atom and two hydrogen atoms
*where* are polar covalent bonds in a water molecule
Carbon
- 4 polar covalent bonds
saturated
All carbons in the hydrocarbon chain are only connected by single bonds, which means that they bond with as many hydrogens as possible (2).
Outline metabolism as the web of all the enzyme-catalyzed reactions in a cell or organism.
All living organisms carry out chemical reactions catalyzed by enzymes-usually occur in cytoplasm, but some are extracellular (digestion in small intestine) metabolism-pathways by which one type of molecule is transformed into another
Metabolism
All of the chemical reactions that occur within an organism.
Outline that there are 20 different amino acids in polypeptides synthesized on ribosomes.
All proteins are formed by the same 20 amino acids.
Proteomes
All the proteins in an organism, genomes show what can happen/ what is there, proteomes show what IS happenING
Inorganic
All things such as air, water, minerals and metals that are neither living organisms nor products produced by living organisms
Alpha Helix vs Beta Sheet
Alpha helix is a coil Beta sheet is like folded paper
folding of proteins into different shapes
Amino acids are added one by one in the same sequence. In globular proteins, they gradually fold up to develop the final conformation. Hydrophobic R groups in the inside, hydrophilic R groups on the the outside.
R-Group
An abbreviation for any group in which a carbon or hydrogen atom is attached to the rest of the molecule.
Protein
An organic compound that is made of one or more chains of amino acids and that is a principal component of all cells
Trans fat
An unsaturated fat, formed artificially during hydrogenation of oils, containing one or more trans double bonds.
Outline anabolism as the synthesis of complex molecules from simpler molecules, including the formation of macromolecules from monomers by condensation reactions.
Anabolism- builds up larger molecules from smaller ones, usually from dehydration synthesis (endergonic) Includes: -The part of metabolism that requires energy -Protein synthesis using ribosomes -DNA synthesis -Photosynthesis -Synthesis of complex carbs including starch, cellulose, and glycogen
Polar Amino Acids
- HYDROPHILIC R group influences where in a cell protein is found and what role it plays. one protein can have both polar and non-polar areas.
Non-polar Amino Acids
- HYDROPHOBIC R group influences where in a cell protein is found and what role it plays. one protein can have both polar and non-polar areas.
Determine the body mass index by calculation or use of a nomogram.
BMI=(mass in kg)/(height in m)²
Why is carbon important?
Because Carbon atoms can form four covalent bonds and allow different elements to be added to carbon and form many stable compounds.
why is water a solvent?
Because of the polarity of its molecules. most reactions take place with all of the substances dissolving in water, making it a medium for metabolic reactions
Amino acids in evolution
Because they are similar, it proves that we all come from a common ancestor
Outline the role of molecular biology in explaining how chemical substances are involved in living processes.
Biological processes are explained through the structure of molecules and how they interact with each other. -Ex. Nucleic acids comprise of DNA and RNA and are used to create genes -Ex. Proteins carry out a large range of tasks in cell enzymes The relationship between genes and proteins is the focus of molecular biology Molecular biology considers various biological processes of living organisms and breaks it down into component parts.
5 roles of proteins in organisms
Blood clotting Cell adhesion Immunity Membrane transport Transport of nutrients and gases\
Ester bond
Bond formed when an acid reacts with the hydroxyl group (OH) in an alcohol Bond in triglyceride because the COOH on the fatty ACID reacts (and condensation reactions) with the OH in the glycerOL
hydrolysis
Breaking down complex molecules by the chemical addition of water, split up into _OH and -H groups glycerides + H2O = fatty acids + glycerol. important as smaller molecules go through intestine and to bloodstream into cells. water helps process. molecules must be smaller.
Hydrolysis
Breaking down polysaccharides, polypeptides and Triglyceride into smaller subunits by the chemical addition of water. (happens when food is digested)
Anabolism
Build up larger molecules from smaller ones including formation of Marco molecules from the monomers by condensation
elements of life
C-4 bonds H-one bond O-2 bonds N-3 (sometimes 4) bonds P-5 bonds S-2 bonds
Ribose
C5H10O5, it has a 5-ring structure and is found in RNA. Deoxyribose is has one less of the OH group than ribose
Glucose
C6H12O6, it has a 6-ring structure and is the main product of photosynthesis. Monomer of starch, glycogen, and cellulose. Monosaccharide that is the energy molecule used in aerobic respiration.
Explain hydrogen bonding and dipolarity, and the link with the cohesive, adhesive, thermal and solvent properties of water.
Cohesive- water is polar, so its polarity causes it to stick to each other through hydrogen bonding Adhesive-water sticks to other molecules due to polarity Thermal- high specific heat: hydrogen bonds restrict motion of water molecules. increase in temp requires broken bonds; energy needed to break bonds is high high latent heat of vaporization: lots of heat energy is needed to break bonds high boiling point: energy needed to break bonds is high Solvent properties: polar nature causes it to form shells around polar and charged molecules
State one example of a benefit to living organisms of each property of water.
Cohesive: water transport in plants-water is sucked through xylem vessels at a low pressure, and can only happen if water will not separate Adhesive: leaves; water adheres to cellulose cell walls Thermal: when ice freezes over,it only freezes on the top due to high specific heat capacity Solvent: cytoplasm is a complex mixture of dissolved substances in which the chemical reactions of metabolism occur
State that enzyme inhibitors can be competitive or non-competitive.
Competitive: binds to the active site and prevents reaction from happening Non-competitive- binds to another site, the allosteric site, and changes shape of enzyme or stops it from happening.
State one example of competitive and non-competitive inhibitor.
Competitive: dihydropyteroate synthetase Non-competitive: phosphofructokinase
meaning of the name "carbohydrate"
Composed of carbon, hydrogen, and oxygen (two hydrogen atoms to one oxygen)
Organic
Compounds that contain carbon and are found in living things.
Advantages of Immobilization of enzymes
Concentration of substrate increased=faster reaction rate Recycled enzymes can be reused many times; easy to remove when immobilized Separation of products is straightforward Stability of enzymes to temp and pH is higher
Anabolism
Constructive metabolism; the process of building up larger molecules from smaller ones
Define hydrophilic.
Describes molecules that do mix with water molecules.
Structure of a steroid
Diamond shaped thing
Lactose
Disaccharide found in milk
Sucrose
Disaccharide that this used as the transport sugar in plants because of solubility
What defies organic and inorganic molecules
Does it contain carbon
Describe water's solvent properties.
Due to its polarity, water is able to dissolve polar and/or ionic molecules.
Explain enzyme-substrate specificity
Due to the shape/structure of the active site, each enzyme will only catalyze/work with specific types of substrates -LOCK AND KEY MODEL: enzyme & active site are exact match -INDUCED FIT MODEL: enzyme & active site are close match
Lipid
Energy-rich organic compounds, such as fats, oils, and waxes, that are made of carbon, hydrogen, and oxygen.
Lipids
Energy-rich organic compounds, such as fats, oils, and waxes, that are made of carbon, hydrogen, and oxygen. (insoluble in water but soluble in organic solvents)
Enzyme vs. Catalyst
Enzyme remain unchanged at the end of the process
immobilzed enzymes
Enzymes are immbolised by attaching them to a substance that remains stationary in a column or other container
Explain the lowering of activation energy by enzymes (and know how to draw the graph)
Enzymes lower activation energy by bringing substrates into proximity of one another in the proper orientation. lower activation energy allows the reaction to proceed much faster.
Immobilized enzymes
Enzymes that are widely used in industry from commercial purposes, such as lactose-free milk. It aids conveniences and stability within manufactured products.
Outline how immobilized enzymes are widely used in industry.
Enzymes usually attached to aggregate to control its usage, like attaching it to a glass surface. Enzyme can be easily separated, recycled, and exposed to higher substrate concentrations.
factors making experiments with human subjects difficult
Ethics Payment Use animals or humans? Kill animals?
Molecular Biology
Explains living organisms at the molecular level, concerning the chemical processes that occur. (especially the relationship between genes and proteins)
pH
Extreme pHs cause hydrogen ion concentration higher or lower than needed, which affects the active site and causes the enzyme to stop working.
Fat vs. Oil
Fat: -solid at room temperature -made of 3 saturated fatty acids -animals make them Oil: -liquid at room temperature -at least one unsaturated fatty acid -plants (and some animals) make them
fats and cholesterol carried in lipoprotein complexes
Fats - nonpolar, larger than oxygen, and insoluble in water Cholesterol - hydrophobic
Outline that fatty acids can be saturated, monounsaturated or polyunsaturated.
Fatty acids are a chain of carbon atoms with hydrogen atoms linked to each one, with a methyl group on one and and a carboxyl group on the other.
fibrous vs. globular protein
Fibrous - elongated (repeating structure) Globular - intricate shape that includes sheet-like parts
function of RUBISCO
Fixes carbon from CO2 as glucose in photosynthesis
high boiling point
For same reasons as above, water has a high boiling point, which means that liquid water can exist in a wide range of temperatures (enough for all habitats)
Triglycerides
Formed by one glycerol and three fatty acids through condensation reaction Fat in adipose tissue in humans
Galactose
Found as apart of lactose
Saturated Fat
Found in animal fat and are solid at room temperature. Single bonded and full of hydrogen. A type of fatty acid.
Unsaturated Fat
Found in plant fat and are liquid at room temperature. Contains double bonds, which bends the overall molecular structure. Another type of fatty acid.
Define enzyme
Globular protein which acts as a catalyst for biological reactions
most common monosaccharide
Glucose (C6H12O6)
Fats and oil are compounds of __________ and __________
Glycerol and fatty acids
Glycerol vs Fatty Acids
Glycerol has just one structual form and fatty acids have a wide range of structures
Explain the structure and function of cellulose and starch in plants, and glycogen in humans.
Glycogen: used for storage of sugar in animals Globular structure with lots of branching (makes getting glucose easier and quicker) with alpha 1-4 bonds and alpha 1-6 bonds Starch: used for energy storage in plants Amylose-20-30%, helix shape with alpha 1-4 bonding, typically used quicker and not stored. Amylopectin-70-80%, somewhat globular with less branching, alpha 1-4 and 1-6 bonds Cellulose: used for plant cell walls Beta 1-4 bonds, no branching, straight chain
water
H2O polar (H is positive, O is negative)
Example of a quaternary protein
Haemoglobin, collagen
Alpha Glucose
Has the H arranged starting from C1 as UUDU
Beta Glucose
Has the H arrangement DUDU starting from C1
Effect of a denatured protein
Have different properties from the original molecule. For example texture change, or aggregate to form clumps
Amino acids
Have one carbon in the middle; this carbon is connected to a hydrogen, an R group, a carboxyl, and an amine group (NH2)
two things that can cause denaturation
Heat - causes vibrations within the molecule that can break intermolecular bonds or interactions Extremes of pH - changes charges on R groups, breaking ionic bonds within the protein causing new ionic bonds to form
Explain the denaturation of proteins by heat or by deviation of pH from the optimum.
Heat-can break intermolecular bonds within a protein and causes it to lose its function pH-deviation from the usual +H/-OH concentration can cause a protein to attract itself/divert itself from the surrounding ions.
Why aare fats and oil important to bodies of plants and animals
High Energy Content Less dense than water Non-polar and therefore Insoluble in water insulating
glycogen
Highly branched Kidneys, brain and white blood cells Stores energy for animals
Cis fat
Hydrogens on the same side of the double bond; Examples: most natural fats and oils
Hydrophilic vs. Hydrophobic
Hydrophilic- water loving Hydrophobic- water fearing
Describe how substances can be hydrophilic or hydrophobic.
Hydrophilic-polar molecules that dissolve in water, charged molecules, and substances water adheres to (cellulose) Hydrophobic-non polar molecules, all lipids are hydrophobic. Hydrogen bonds form between the water molecules surrounding a hydrophobic substance, but not between the substance and the water; water is more attracted to itself than it is to the non polar molecule
pH effect on enzyme activity
If increases OR decreases beyond the enzyme's pH optimum, enzyme activity decreases and eventually stops
Evaluate the evidence and methods used to obtain the evidence for health claims made about lipids.
Implications-do the results support the claim strongly, moderately, or not at all? Limitations-what could have affected the experiment in which the results could have been affected by an outside force, therefore throwing off the results. Is there a correlations between lipid intake and the rate of the disease/health benefit? How large is the difference between mean rates of the disease with different lipid intake levels? How spread apart is the data? How large was the sample size? How similar were the samples? (sex, age, weight) Were results adjusted? Are the measurements reliable?
Trans-isomer
In context of unsaturated fatty acids, if the hydrogen are on opposite side of the double bond, the isomer is this. They do not have a kink at the double bond, have a higher melting point, solid at room temperature. Often associated with bad nutrition due to it being found in processed foods like margarine.
Cis-isomer
In context of unsaturated fatty acids, if the hydrogen atoms are on the same side of the double bond this the isomer is this. They have 'kinks' in the double bonds.
amino acids differences
In each amino acid, the R group is different; there are 20 amino acids
temperature effect on enzyme activity
In liquids, high temperature give particles more kinetic energy which increases the chance of a substrate molecule colliding with an active site (enzyme activity increases) Heating of enzymes can cause denaturation which decreases enzyme activity
where is the polypeptide produced?
In living cell, they are synthesised by ribosomes in the cytoplasm
high latent heat of vaporization
In order to evaporate, a substance must break apart to float; it is hard for water to do this because they have hydrogen bonds; it takes a lot of heat for water to vaporize, which makes it a good coolant ex: sweating
Outline that unsaturated fatty acids can be cis or trans isomers.
In unsaturated fatty acids, if the hydrogen atoms are on the same side of the two carbon atoms, it is cis. If the hydrogen atoms are on opposite sides, it is trans.
substrate concentration effect on enzyme activity
Increasing Substrate Concentration increases the rate of reaction. This is because more substrate molecules will be colliding with enzyme molecules, so more product will be formed.
Explain the effect of substrate concentration on rate of an enzyme controlled reaction
Increasing substrates increases frequency of collisions & enzyme activity. Eventually a max rate is reached when active sites are saturated by substrates, and at this point adding any addition substrate has no effect on rate of reaction.
Outline how a protein may consist of a single polypeptide or more than one polypeptide linked together.
Integrin-membrane protein with 2 polypeptides where one is embedded in the other Lysozyme is a single polypeptide protein
alpha-D-glucose and Beta-D-Glucos are known as
Ismoers (having slightly different arrangements of the side groups, giving them a slightly different property)
impossible
It is *what* to make hemoglobin in the lab without using ribosomes and other components of cells
State the use of immobilized enzymes in industry. Describe methods of production of lactose-free milk and its advantages.
Lactase is obtained from K. Lactis, and can be extracted from it. It is used to produce lactose free milk.
function of RHODOPSIN
Light receptor in eye cells that send signals to brain
Fats and Oil are an example of which organic compound?
Lipids
Triglycerides
Lipids formed by the condensation of three fatty acids and one glycerol that forms the backbone.
Temperature and enzymes
Low Temp = Low rate High Temp = too fast (denatured/ no longer catalyuse reaction) optimal Temp = 37C
Lipids
Macromolecule composed of carbon, hydrogen, and oxygen and is used for insulation and long-term energy storage. They are insoluble in water (triglycerides, steroids, waxes and phospholipids).
Carbohydrates
Macromolecule composed of carbon, hydrogen, and oxygen.Used for short-term energy storage or structural support.
Proteins
Macromolecule composed of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. They are distinguished by the "R" group and basic/ base unit is called an amino acid.
Cellulose
Made by beta glucose; linked by carbon atom 1 and 4; OH is up of carbon 1 and down on carbon 4; unbranched and form bundles because OH are opposite, it is a straight chain; this is used to keep the structure and tensile strength of the cell wall in plants
Cellulose
Main component (carbohydrate) in plant cell walls
Explain how databases can be used to identify potential new anti-malarial drugs.
Malaria is caused by Plasmodium fulciparum It is growing resistance to drugs like choloquine Malaria tries to inhibit metabolism Scientific study tested 310,000 chemicals to sensitive and resistant strains. The results showed that 19 new chemicals inhibited the enzymes normally targeted by anti-malarial drugs and 15 chemicals that bound to a total of 61 different malarial proteins.
Maltose
Malt sugar found in barley and is made up of two glucose molecules
Catabolism
Metabolic pathways that break down molecules, releasing energy.
Outline that metabolic pathways consist of chains and cycles of enzyme-catalyzed reactions.
Metabolism-chemical reactions that occur in cells to maintain life Usually occur in chains of reactions; the product of one reaction will be the reactant of the next
water vs methane (5)
Methane does not form hydrogen bonds and is nonpolar Methane has a lower specific heat, which means it takes less energy to heat. This results from the lack of H-bonds which prevent vibration. Methane has lower heat of vaporization Methane has lower melting and boiling points
Comparing methane
Methane is a waste product of anaerobic -can be used as a fuel -contributes the Greer house has Water is polar, methane is polar
Water
Molecule that has high specific heat capacity, high latent heat of vaporization, strong cohesive and adhesive properties, and is the universal solvent. These properties derive from its structure of two positively charged hydrogen atoms and one negatively charged atom and are extremely helpful to many living organisms.
Monomers and Polymers of Proteins
Monomers- amino acids Polymers- polypeptides
Galactose
Monosaccharide that is the nutritive sweetener in foods
Fructose
Monosaccharide that is the type of sugar found in fruit
Explain how monosaccharide monomers are linked together by condensation reactions to form disaccharides and polysaccharide polymers.
Monosaccharides link through a process called condensation, or dehydration hydrolysis. One molecule loses -OH and the other loses -H and forms water as a byproduct. The bond between the two monosaccharides is called a glycosidic linkage.
Concentration of subtrate
More the better but when there is too much substrate, the enzyme work as their fastest rate at the given condition. Adding more substrate at that point have no effect on reaction
Amino Acid
Nitrogen compounds that are the building blocks of protiens
What key organic molecule contains nitrogen
Nuleuc acids and protein
Explain how amino acids are linked together by condensation to form polypeptides.
OH from one molecule and H from the other molecule (amine and carboxyl groups) forms peptide bond and 1 water molecule through dehydration synthesis.
unsaturated
One or more carbons have a double bond, so those can only bond with one hydrogen instead of 2
Anabolism
Part of metabolism; building large molecules from smaller ones.
trans fats
People who consume more *what* tend to have higher rates of coronary heart disease
oxygen dissolved in blood plasma vs. transport in hemoglobin
Plasma (where it is dissolved) can only carry a little amount of oxygen. Hemoglobin (where it does not dissolve) has binding site for oxygen, so it is able to carry more.
Glucose transport
Polar; soluble
Glucose
Primary fuel source for cell fpe cellular respiration
exogenous
Produced outside the body
Enzyme
Protein that catalyzes chemical reactions and causes less energy to be required
Identify biochemicals, such as sugars, lipids or amino acids from molecular diagrams.
Proteins contain N and sometimes S, but carbs and lipids do not Carbon contains O and H in a ratio of 1:2 Lipids generally contain less oxygen
Denaturation
Proteins lose their shape because the bonds break Due to heat or pH level Also effected by substrate concentration
What are enzymes made of?
Proteins with long polypeptide chain that are folded into specific shapes. ( The shape of the enzyme are very precise and gives each enzyme it's ability to catalyst one specific reaction)
Outline that every individual has a unique proteome.
Proteome-all the proteins produced by a cell, tissue or organism. It is usually identifies using gel electrophoresis. Proteomes can vary between different cells and even within a cell at a different time, so it shows what is happening in a cell at a certain time.
pH and enzymes
Require optimum pH level to function at the right rate. (different enzyme have different optimum pH) and if not H+ ion or OH- ion can attach to active site and prevent reaction
receptors
Rhodopsin
Explain how amino acids can be linked together in any sequence, giving a huge range of possible polypeptides.
Ribosomes link polypeptides together and can make a bond between any two amino acids. # of possible amino acid sequences: 20^n
Fibrous protein
elongated with a repeating structure; amino acid sequence prevents folding, and remains elongated
product
end result of the reaction that is released from the active site
hydrogen bonds in water (chemical)
energy is released when a H bond is made and used when it is broken.
explain function of galactose
energy molecule
explain function of fructose
energy molecule (found mostly in fruit)
fat molecules transport
entirely non polar; carried on lipoprotein
lysozyme
enzyme in secretions (like nasal mucus and tears) that kills bacteria by digesting the peptidoglycan in their cell walls; made from 1 polypeptide
catalysts
enzymes
substrate concentration
enzymes affected by substrate concentration. As substrate concentration keeps increasing all active site are being saturated & therefore the enzymes reaction rate can only go so fast so it never reaches a max.
Explain the effect of pH on rate of an enzyme controlled reaction
enzymes all have optimal pH levels- variation from optimal pH will reduce activity and eventually cause denaturation. when pH levels are too low or too high, rate of reaction will be low as well.
water in enzyme reactions
enzymes and substrates float around, allowing for collisions
Immobilized enzymes
enzymes can be easily separated from the products to stop reaction at ideal time & prevent contamination. enzymes can be recycled. increase stability of the enzymes to change in temp. & pH (denaturing). substrates can be exposed to more enzymes concentration therefore speeding up reaction rates
Outline that enzymes have an active site to which specific substrates bind.
enzymes can only catalyze 1 reaction with 1 substrate
what is true of enzymes activity and pH?
enzymes have an optimum pH
Disulfide Bridge
The covalent bond between two sulfur atoms (-S—S-) linking two molecules or remote parts of the same molecule.
Carbon
The element that forms the basic building blocks due to its ability to form four, strong covalent bonds. This element can form single, double and triple bonds.
Primary Structure
The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.
Quarternary Structure
The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.
Protein structure
The function of a protein depends on the protein's 3D shape. stabilized by intermolecular bonds between AA brought together in folding process.
Lock and Key Model
The model of the enzyme that shows the substrate fitting perfectly into the active site
lock and key model
The model of the enzyme that shows the substrate fitting perfectly into the active site
Why are lipids better for long term energy? Why are carbohydrates better for short term energy?
The same amount of energy is stored in both lipids and carbohydrates, but less fats are needed to store this energy. This is good bc for long term you have to carry it with you. Near our skin and kidneys because it is a good heat insulator and shock absorber Glycogen is good for short term because it can be broken down into glucose quickly and easily transported. It can also be used in aerobic and anaerobic cellular respiration, but lipids can only be used in aerobic
Secondary Structure
The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain.
Define anabolism
The set of reactions that assemble large molecules from smaller parts
What is molecular biology
The study to explain the role of chemical substances involved in the life processes
theory of vitalism
The theory that living organisms have a "vital force" that allows them to be alive and create organic molecules.
Tertiary Structure
The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.
Metabolism
The web of all enzyme catalyzed reaction in q cell or organism. Mostly happens in the cytoplasm
Discuss the scientific evidence for health risks of trans fats and saturated fatty acids.
There has been a correlation found between consumption of saturated fatty acid intake and coronary heart disease. However, many pieces of evidence disprove this fact. There is also a correlation related to trans fats, which seems to be more related to coronary heart disease.
Conformation
Three dimensional structure of a protein determined by amino acid sequence and polypeptides
Classes of Lipids
Triglycerides-either fats or oils Phospholipids-make up plasma membrane Steroids-testosterone, progesterine, estrogen, cholesterol, cortisol
Describe what occurs in Condensation reactions.
Two molecules are bonded together to create one larger molecule. water is released as a product.
cellulose
Unbranched Cell wall Structure and cell wall
polyunsaturated
Unsaturated fat that contains more than one double carbon bond
monounsaturated
Unsaturated fat that contains one double carbon bond
cis
Unsaturated fat where both hydrogens on the carbons sharing the double bond are on the same side; often turn into oils because there is a bend there. The bend makes them not as good as sticking together, so they melt quicker; healthier
trans
Unsaturated fat where each hydrogen on the carbons sharing the double bond are on different sides; no bend; unhealthy
Describe urea as an example of a compound that is produced by living organisms, but can also be artificially synthesized.
Urea is a nitrogen-based compound that is a component of urine. It is produced when there is an excess of amino acids in the body, to try and extract the nitrogen from the amino acids. It is synthesized in the liver and passed through the kidneys.
State the main application of artificially produced urea.
Urea was believed to only be able to be produced through the kidneys. In 1828 Friederich Wohler synthesized urea using silver isocyanate and ammonium chloride, which was the first organic compound artificially synthesized.
triglycerides
Used as energy stores (energy can be released by aerobic cell respiration), heat insulators Twice as much energy per gram available because it adds half as much (of carbohydrates) to body mass due to the lack of water associated
Outline the theory of Vitalism and how Wohler's synthesis of Urea disproved the theory.
Vitalism was a theory that organic compounds could only be made by living things due to their "vital force." When Wohler was able to produce Urea (an organic compound) artificially in his lab it showed that organic compounds could still be found without the "vital force" of life.
Methane
Waste product found in the guts of animals It is different than water because it is less dense, has a lower temp for all 3 thermal properties, and has a smaller molecular mass
adhesive
Water can stick to other polar molecules, because of the hydrogen bonds that can stick to them example: in leaves, water can adhere to cellulose, and if it evaporates the leave can pull up more from the nearest xylem to use for cell wall moisture
Hydrophobic
Water fearing (substances that does not dissolve in water)
Hydrophobic
Water fearing, non polar all substance that insoluble in water
Outline that water molecules are polar and that hydrogen bonds form between them.
Water is formed by 2 covalent bonds between 1O and 2H Oxygen has more valence electrons, therefore it pulls more electrons toward itself, making the water molecule partially charged Hydrogen is partially +, oxygen is partially - Water forms hydrogen bonds with itself, which gives water its properties
Hydrophilic
Water loving, polar molecule, all substance that dissolve in water (sugar, salt)
Water
Water molecules are polar and hydrogen bonds form between them.
Universal Solvent
Water property to dissolve many substances because of it polarity. This allows water to act as a transport medium of important molecules in biological organisms
Condensation
Water releasing, energy supplies by AT
cohesive
Water sticks to other water molecules because of hydrogen bonding example: in plants, water is sucked up through the xylem, but water does not break
Explain how enzymes lower the activation energy of the chemical reactions that they catalyze.
When an enzyme bonds with a substrate, it changes the substrate to reach the transition state, thus lowering activation energy.
Outline how enzymes can be denatured.
When the bonds between an enzyme break it changes shape and can no longer have a functional active site
Explain the use of water as a coolant in sweat.
When the hypothalamus senses that the body is too hot, it stimulates the sweat glands to start producing sweat. It is carried to the surface of the skin where it spreads out. The energy needed to vaporize the sweat comes from the skin, which cools it. Blood flowing through the skin is cooled, which lowers body temperature. Due to water's high latent heat of vaporization, this is affective in cooling the body.
substrate concentration
When there is more substrate it increases at first, but then the graph levels off because they are all taken so it can't get any faster; it does not decrease, just levels off
quarterary structure of a protein
When two or more polypeptide link together
glycosidic bond
a bind between two carbohydrates
polar covalent bond
a bond with unequal sharing of electrons; in water, the nucleus of the oxygen is more attractive to electrons than the hydrogens; gives hydrogen a partial positive charge and oxygen and partial negative charge; the molecule is bent and the two hydrogens end up at one ending forming a pole and oxygen is at the other end forming a pole
Unsat Fat
a chain contains a double bond between two of the carbon atoms
fatty acids
a chain of hydro carbons w/a carboxyl group at the end. Most fatty acids used by living organisms are between 12-20 carbons. saturated - all single bonds. unsaturated - one or more double bonds.
dimer
a compound whose molecules are composed of two identical monomers
Define organic molecule.
a molecule that contains carbon (with the exception of carbonates -CO2 and -CO3
Lactose
a naturally present sugar in milk composed of glucose and galactose
urea
a nitrogen-containing compound with a relatively simple molecular structure (component of urine); was synthesized artificially without a vital principle
denaturation
a protein has gone through a change to its conformation
What is matabolism?
a series of reactions, catalyzed by enzymes, which occurs in a living organism
Competitive Inhibition
a substance that is similar in shape to the substrate bonds with the active site, occupying the space, and preventing the substrate from bonding ex: prontosil, an antibiotic that inhibits the enzyme that makes folic acid for bacteria
lactose
a sugar that is digested by lactase
Urea
accidentally synthesized in 1828 by Friedrich Wöhler, and helped disprove the theory of vitalism, as urea is found in urine, therefore should only have been able to be created by living organisms
give examples of named proteins
actin, myosin, fibrin, hemoglobin, insulin, FSH, LH, histone
denaturation
active site is altered so substrate can no longer bind so reaction does not occur. can be altered by high temps. or high/low pH
Enzymes are immobilized by
adsorption onto solid resins or by bnonding them to collagen or synthetic polymer
compare the structures of amylose starch, amylopectin starch, glycogen, and cellulose
all are made up of many units of glucose bonded together
saturated fatty acid
all carbons connected by single covalent bonds. fixed number of hydrogen atoms
genome
all of the genes of a cell, a tissue, or an organism (fixed, smaller)
Proteomes
all of the proteins produced by a cell, a tissue or an organism
proteome
all of the proteins produced by a cell, a tissue, or an organism (variable, larger), better representation
what is a proteome?
all the proteins produced by a cell, each individual has a unique proteome
Starch
alpha glucose; atom 1 and 4; both point downwards, which causes it to be curved; does not have a fixed size amylose: unbranched and forms a helix amylopectin: branched and more globular Storage in plants because there would be osmosis problems if starch did not store the glucose; stores things like seeds
difference between a-D-glucose and b-D-glucose
alpha has H- OH beta has OH-H
Secondary protein structure
alpha helixes or beta pleated sheets and are connected by hydrogen bonds (reactions between amine and carboxyl groups)
Polypeptide are built up from
amino acid monomers during condensation reaction
amino acids
amino acids are the monomer of proteins. r groups is differ in every amino acids. the r group is what gives the polypeptide its characteristics which makes amino acids very chemically diverse.
describe the difference between an amino acid molecule and protein molecule
amino acids make up proteins, therefore a protein is a chain of multiple amino acids. the type of protein depends on the variable group of the amino acids
high specific heat capacity
amount of energy need to raise the temperature of water is relatively large, (demonstrated by stable temperature of large bodies of water because amount of energy needed to lose for water to cool down is large)
why are lipids better than carbohydrates in Long term energy storage?
amount of energy released per respiration in lipids in double of carbs. lipids add half body mass
examples of enzymes
amylase: starch->glucose and maltose maltase: maltose->glucose sucrase: sucrose->glucose and fructose
reductionist approach
an approach to studying a system in which the focus is on each part of the system in isolation
Lactase
an enzyme obtained from a yeast that naturally grows in milk
immobilized enzymes
an enzyme that is attached to a material that restricts its movement
Proteome
an organism's complete set of proteins
polysaccharides
are made up of glucose but differ in the type of linkage
quaternary structure of a protein
association of two or more polypeptides (globular) (ex: hemoglobin)
Explain the effect of temperature on rate of an enzyme controlled reaction
at low temps, may not be enough energy for reaction to occur. increasing temp increases enzyme-substrate collisions and reaction rate/activity until extreme heat causes denaturation
hydrophilic
attracted to water (all substances that dissolve in water)
Cohesion
attraction between two of the same molecules
ahesion
attraction between water molecules of different substances, due to eletrostatic charge of the substance
Why is water adhesive?
because of the dipolarity of water molecules causing them to stuck to hydrophilic/polar surfaces in xylem vessel between water and cellulose. keep moisture and gas exchange surface
Why is hydrogen bonds form
because they are polar molecules, and the slight negative charge from oxygen form weak bond with slight postive charge from hydrogen
solvent properties
because water is polar, it forms a shell around polar molecules and separates them; it also creates hydrogen bonds with them, so they dissolve water can digest polar because the positive part of the molecule splits from the negative and the positive goes to the oxygen and the negative goes to hydrogen.
What are enzymes
biological catalysts
Hydrogen bonds
bond between water MOLECULES (like two different molecules) positive and negative charges attract, so normally this would produce an ionic bond Water only has partial charges, so instead, it forms a hydrogen bond. An intermolecular force that forms when a hydrogen atom in one polar molecule is slightly attracted to an oxygen in another molecule give water its properties
peptide bond
bond formed between two amino acids
Beta Bond
bond forms between the one and four carbon in cellulose
Ester Bond
bond that forms between glycerol and the fatty acid chains in a triglyceride
Alpha Bond
bond that occurs between two glucose molecules when water is pulled out leaving behind a shared oxygen molecule (Starch and Glycogen)
condensation of amino acids
bonding 2 amino acids together to form a dipeptide, forming water
Catabolism
break down large molecules and release ATP. Examples are: digestion of food, cell respiration and digestion by decomposers
catabolism
breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers (ie digestion of food, respiration)
define catabolism w examples
breakdown of complex molecules into simpler molecules: digestion of food, cell respiration, digestion by decomposers
Protease
breaks down proteins --> used in baby food production to make foods easier to digest
Anabolism
build up larger molecules like (proteins, DNA, Glucose in photosynthesis, and complex CHO's like starch, cellulose and glycogen. Requires ATP.
Proteins
build up of amino acids in condensation reaction
explain function of cellulose
builds up plant cell wall
What is the structure of a carboxyl group
c = O, - O,H
carboxyl group?
c = O, - O,H
what is the peptide bond?
c-n
energy in chemical reactions
can be either exothermic (release of heat) or endothermic (absorption of heat)
Carbon
can form four bonds; this causes a lot of compounds to exist because this is a lot of bonds; forms covalent bond (it shares an electron with something else); the up to four bonds can be single or double bonds
temperature
can increase enzyme activity because they will move around faster and collide more also decreases it because the enzymes vibrate, which breaks bonds and causes the enzymes to denaturize
List the four major categories of biomolecules.
carbohydrates ,lipids, proteins, and nucleic acid.
what are the main types of molecules used by the organism?
carbohydrates, lipids, proteins and nucleic acids
Saturated Fat
carbon chain linked to maximum amount of H-atoms without double bond
fatty acid
carbon compounds also known as hydrocarbon chains; insoluble in water
lipids
carbon compounds made by living organisms that are mostly/entirely hydrophobic. two or three hydrocarbon chains
amino acid molecule
carbon in the middle that is connected to a hydrogen, a nitrogen (connected to the amine group), and R group, and a carboxyl group
steroids
carbon skeleton consisting of four fused rings ex: cholesterol, progesterone, estrogen and testosterone
what are the 4 most commonly occurring elements in organisms?
carbon, hydrogen, nitrogen, oxygen
What do carbohydrates contain?
carbon, hydrogen, oxygen
what elements are in fatty acids AND glycerol?
carbon, hydrogen, oxygen
Most common elements in Living organisms
carbon, hydrogen, oxygen, nitrogen
what elements are present in amino acids?
carbon, hydrogen, oxygen, nitrogen
which are the most frequently occurring chemicals in living things?
carbon, hydrogen, oxygen, nitrogen
cholesterol transport
carried on lipoprotein
Protein functions
catalysis: enzymes Muscle contration Cytoskeletons: microtubules that give shape and pull apart chromosomes (tubulin) Tensile strengthening: fibrous proteins Blood clotting Transport Cell adhesion: membrane proteins; adhere within tissues Membrane transport Hormones: chemically very diverse Receptors: binding sites in membranes and cytoplasm for hormones, etc. Packing of DNA: histones Immunity: antibodies Cats Might Climb Puny Trees, But Turtles Climb Mountains and Hairy Rodents Climb Puny Icebergs
Enzyme
catalyze biochemical reactions by lowering the activation energy needed for the reaction to take place. Each one of these only works for a specific substrate to form a desired product
Polypeptide
chains of amino acids that are linked together by condensation reaction; main component of proteins, there can be one or more
polypeptides
chains of amino acids that are made by linking together amino acids by condensation reactions; main component of proteins
Denaturation of Proteins
change in heat or pH will cause the protein to lose hold of its folds and the function of the protein is lost. Primary structure will remain, but secondary etc. will be lost.
chemical reaction
change substance into different substance by breaking & forming chemical bonds
Van der Waals Interaction
clusters of hydrophobic groups away from water
Why is water cohesive?
cohere (stick to each other) because the negative end of one molecule's oxygen can form a hydrogen bond with the positive hydrogen of another molecule. used in xylem vessels as forces pull water up trees
tensile strengthening
collagen
insoluble in water
common characteristic of all lipids
inhibitors
competitive are similar to substrate and compete for active site. non competitive don't.
Differentiate between a competitive and a non-competitive inhibitor.
competitive binds to active site, non competitive binds to another site away from active site
Carbohydrates
composed of carbon, hydrogen, and oxygen (thats why carbohydrate its chem); first energy source
Urea
compound found in urine that contains nitrogen; it takes the excess nitrogen away when there are excess amino acids; made in the liver and transported to the kidney to leave; this can be artificially made, which disproves the theory of vitalism
if a scientist wanted to combine two molecules of glucose, what reaction would occur?
condensation
by what reaction type are amino acids linked?
condensation (to form polypeptides)
Macromolecules are built up from monomer by
condensation reaction durin an anabolic reaction
Triglycerides are formed by
condensation reaction from three fatty acids and one glycerol
what are amino acids linked together by?
condensation to form polypeptides
what is it called when water is lost?
condensation/dehydration
Explain how the amino acid sequence determines the three-dimensional conformation of a protein.
conformation-a protein's 3d structure; it is determined by the amino acid sequence of a protein and its polypeptides Amino acids are always added in the same sequence to make a particular polypeptide. The order the amino acid is in determines the shape the protein will be. Structures can also form based on interactions between the R groups.
Metabolic Pathways
consist of chains or cycles of reactions that are catalyzed by enzymes
protein
consists of either a single polypeptide or more than one polypeptides linked
polarity of water
covalent bonds are formed when two atoms share a pair of e-. the nucleus may be more attracted to one e- so they are not shared equally.
peptide bond
created when the carboxyl group and amino group join together and do condensation reaction with amino acids; produces water and makes a polypeptide
explain how changes in pH and temperature lead to DENATURATION of proteins
denaturation occurs when environmental factors disrupt protein structure and, as a result, impair their function. Hydrogen ion changes associated with pH can disrupt ionic/hydrogen protein bonds. Increased molecular motion associated with high temps. can also destroy structure. also various chemicals can denature protein.
Effect of pH on enzymes
different for different areas. optimum is 7 for most enzymes. extremes from opt. will cause denature due to alterations in enzymes conformation. pepsin in stomach has optimum 2.5.
explain function of maltose
dimer of glucose, broken down for starch
1 amino acid+ 1 amino acid=
dipeptide
hydrolysis of carbohydrates
disaccharides and polysccarides break down using hydrolysis
unsaturated
double bonds that break up chains of hydrogen
why is water thermal?
due to H- bonds, water has high mp/bp/latent heat of vaporization/SHC. causes water to be liquid and slowly change temperature. crucial for animals to live
secondary structure of a protein
due to hydrogen bonding, a helical or pleated shape is formed. not all proteins have this structure
Describe water's cohesive & adhesive properties.
due to hydrogen bonding, water molecules stick to each other (cohesion) and other molecules (adhesion).
Describe water's thermal properties.
due to strength of hydrogen bonding, it takes large amounts of energy to break apart water molecules and heat them up. as a result, water has a high specific heat capacity and high latent heat of vaporization.
immobilized enzymes
enzymes that are attached to a material or aggregations that restricts its movement can happen by attaching an enzyme to glass, trapping them in alginate gel, or bonding them together to form aggregates Often used in industry because they can... 1. be easily separated from the products of the reaction 2. recycled 3. be more stable to temperature and pH 4. there can be higher enzyme concentrations, so it speeds up reaction rate
proteins
essential for cell processes (build, signal, fight disease, etc) C,H,O,N
sweat coolant
evaporation of water from body cools it down as H bonds break for molecule to evaporate. heat energy is used to do this.
example & function of catalyst/enzyme proteins
ex: catalase breaks down toxic hydrogen peroxide in cells
example & function of structure/tensile strength proteins
ex: collagen builds up skin, bone, and other tissues
example & function of gas/nutrient transport proteins.
ex: hemoglobin binds oxygen molecules to red blood cells
example & function of DNA packaging proteins
ex: histones super-coil DNA to package into chromosomes
example & function of immunity/defense proteins.
ex: immunoglobulin/antibodies marks pathogens for immune system attack
example & function of hormones
ex: insulin lowers blood-glucose levels
example & function of movement/muscle contraction proteins
ex: myosin/actin muscle fibers that contract
urea synthesis
example of a compound that is produced by living organisms but can also be artificially synthesized. helped falsify vitalism
molecular biology
explains living processes in terms of the chemical substances involved
Two groups of proteins
fibrous and globular
function of SPIDER SILK
fibrous proteins with incredibly high tensile strength
explain the 2nd level of protein structure
folding of amino acid chain into an alpha helix or beta sheet. held in place by hydrogen bonds. looks like a curly fry or a flattened curly fry.
intermolecular forces
forces of attraction between molecules
Water molecules
formed by polar covalent bonds between two hydrogen and one oxygen
how many bonds can carbon atoms form?
four, allowing a diversity of stable compounds to exist
Sodium Chloride transport
freely soluble in water; dissolves to Na and Cl ions that are carried in the blood
Tertiary protein structure
globular protein structure that is formed by interactions in protein R groups causing them to further fold from the alpha helixes or beta pleated sheets. Otherwise creating an active protein (polypeptide)
enzyme
globular proteins that speed up chemical reactions without being altered
enzymes
globular proteins that work as catalysts (speed up chemical reactions without being altered themselves); have an active site to which specific substrates bind; made by living cells (found in all of them, and also secreted by some cells to work outside)
what are the building blocks of carbohydrates?
glucose, fructose, and galactose
list three examples of a monosaccharide
glucose, galactose, fructose
which carbohydrate in animals functions to store energy till needed by its metabolism?
glycogen
molecules
group of two or more atoms held together by covalent bonds (single, double or triple)
protein denaturation
heat (breaks intermolecular bonds), optimum pH; protein uncoils, loses its shape, and loses its function
high latent heat of vaporization
heat required when a molecule evaporates and separates from other molecules in a liquid to become a vapour molecule (demonstrated by waters use as a coolant because of vaporation's cooling effect
denaturing proteins
heat, strong acid or alkalis disturb the bonds between different part if a protein molecule and disrupt it's structure. The primary structure will remain but secondary, tertiary and quaternary structure will be lost
transport of nutrients & gases
hemoglobin
water's thermal properties
high heat capacity and high heat of vaporization due to the large amount of energy needed to break the hydrogen bond
explain structure of glycogen
highly branched and compact
packing of dna
histones
Nature of science
humans can produce 10 of the 20 amino acids needed to build proteins
fatty acids have what?
hydrocarbon chain with a carboxyl group
Lipids
hydrocarbon tails; insoluble in water
The bonds that hold the beta pleated sheets together
hydrogen
positive side of water molecule
hydrogen
trans unsaturated
hydrogen atoms are bonded to carbon atoms on opposite sides of a double bond
trans unsaturated fatty acids
hydrogen atoms are bonded to carbon atoms on opposite sides of a double bond
cis unsaturated
hydrogen atoms are bonded to carbon atoms on the same side of a double bond
cis-fatty acid
hydrogen atoms are nearly always on the same side of the two carbon atoms that are double bonded
cis unsaturated fatty acid
hydrogen atoms are nearly always on the same side of the two carbon atoms that are double bonded, low melting point, oils/liquids
txx rans unsaturated fatty acid
hydrogen atoms are on alternate sides or opposite from each other, produced artificially
trans unsaturated fatty acid
hydrogen atoms are on alternate sides or opposite from each other, produced artificially. Solid at room temperature
trans-fatty acid
hydrogen atoms are on the opposite sides of the carbon atoms that are double bonded
significance of bipolarity in water molecules
hydrogen atoms have partial positive charge and oxygen has a partial negative charge
cohesive
hydrogen bond between molecules hold them together in a network, which results in water's cohesiveness.
what causes the folding and twisting of amino acid chain
hydrogen bonds between different parts of the chain
adhesion
hydrogen bonds form between water and other polar molecules causing water to stick to them (demonstrated by transpiration of water off the surface of a leaf because water can adhere to the cellulose in the walls of xylem vessels)
high specific heat capacity
hydrogen bonds make it harder for water molecules to move, but in order for temperature to rise, molecules move faster A lot of energy is needed to raise the temperature of water (aka get water molecules to move) To cool down, water must lose a lot of energy Example: ocean is livable and stable for animals because the temperature doesn't not change drastically
which end of water molecule contains positive charge?
hydrogen side
Macromolecules are broken down to monomer by
hydrolysis during catabolic reaction
List examples of hydrophilic and hydrophobic substances.
hydrophilic-glucose, salt, cellulose hydrophobic-fats and oils
polar
hydrophilic: attractive to water. dissolve in water as their ions are more attracted to water than to each other.
non-polar
hydrophobic: not attractive to water, insoluble in water.
pH
if the enzyme goes above/below the pH it won't work, it'll denature. most enzymes have an optimum pH, activity is the highest. if it changes from the optimum pH, enzyme activity decreasing and eventually stop
immunity
immunoglobulin/ anti bodies
function of triglycerides
important role in structure of membranes when they combine with a phosphate group in the form of phosphoric acd to form phospholipids
Explain how metabolic pathways can be controlled by end-product inhibition.
in a metabolic chain, the last end product can be an inhibitor to the starting enzyme. this ensures that equilibrium is reached and that chemical reactions are controlled, to prevent product buildup
where do most enzymatic reactions occur?
in water as dissolved substances
saturated fatty acid
includes a hydrocarbon chain with all single bonds
unsaturated fatty acid
includes a hydrocarbon chain with one double bond
Enzyme experiment
independent variable: pH 1-14 dependent variable: how long until substrate is used control variable: constant temperature
describe hydrophobic v. hydrophillic RE: solubility
insoluble in water vs. soluble in water
hydrophobic v. hydrophillic
insoluble in water vs. soluble in water
hormone
insulin estrogen
what causes the tertiary structure of the protein
interactions between the R groups of amino acids present
hydrogen bonds in water
intermolecular bond can form between the positive pole of one water molecule and the negative pole of other. form in liquid water, giving H2O its properties
Globular
intricate shape that folds up during final conformation
An example of a bond in a tertiary protein
ionic, disulphide, hydrogen, hydrophobic
water
is the medium of life
metabolism
is the web of all the enzyme-catalyses reactions in a cell or organism
why is water a stable habitat for aquatic life?
it has a high heat capacity, its temperature remains relatively constant
why is water a stable habitat for aquatic life?
it has a high heat capacity, its temperature remains relatively constant. Also has strong surface tension so can provide a surface for insects to live on.
fibrous
its long and narrow, its purpose is structural, its amino acids are repetitive. its less sensitive, its insoluble in water - collagen, myosin,fibrin, actin
What determines the function of a protein?
its shape
globular
its shape is round, it purpose is functional, its amino acids sequence is irregular,its soluble in water -enzymes, hemoglobin, insulin
glucose + galactose
lactose
lactose/ milk
lactose is a sugar in milk made by glucose and galactose; people can't digest if they don't have lactase, so thats what lactase it only digest 250 mL, if more, it will have to sit and wait and it will hurt.
Production of lactose free milk
lactose is hydrolysed with lactase giving glucose and galactose during immobilization.
glucose + galactose
lactose is made up of
lactose free milk
lactose is natural milk sugar. enzyme lactose breaks lactose into glucose & galactose. isolate lactose from yeast
state two examples of disaccharide
lactose, maltose
3 examples of disaccharides
lactose, sucrose, maltose
explain 2 advantages of lactose-free milk
lactose-free milk is sweeter and makes a creamier ice cream since glucose/galactose are sweeter sugars and do not crystallize the same way as lactose.
Polymers
large compound formed from combinations of many monomers
polysaccharide
large macromolecule formed from +3 (usually 100) monosaccharides. many bonds. example: cellulose in cell wall, glycogen stores extra glucose in liver and bone marrow
rubisco
likely the most abundant protein on earth; catalyses the reaction that fixes carbon dioxide from the atmosphere, which provides the source of carbon from which all carbon compounds needed by living organisms can be produced
difference between lipid and carbohydrate chemically
lipids contain much less oxygen than carbohydrate of the same size. and lipid can also contain small amount of other elements.
Fatty acids consist of
long chains of carbon atoms that are joined to hydrogen atoms call hydrocarbon chain (the number of carbon atom is a fatty acid are usually between 14 and 22, although shorter and longer chain do exist)
Polysaccharide
long chains of monosaccharides held together with glycosidic linkages made by condensation reactions
Polysaccharides
long molecules consisting of chains of monosaccharides linked together
state 4 functions of lipids
long term energy storage -thermal insulation -protection of internal organs -cell membrane structure
Lipids
long term energy stored not easily moved more difficult to break down only used in aerobic
fibrous proteins
long, insoluble molecules made up of polypeptide chains
Fibrous Proteins
long, narrow, mostly insoluble in water
explain function of glycogen
long-term energy storage in animals
explain function of starch
long-term energy storage in plants
temperature in enzymes
low temp has low rate. higher temp increases kinetic energy, more rate of collision and more energy exerted. optimum 37C above will denature, losing 3D shape
oils rich in cis-fats
lower melting point → liquid at room temperature
Catabolism
macromolecules being broken down or digested into monomers through hydrolysis; gives off energy that the cell can use ex: cellular respiration, food digestion
Triglycerides
made by condensation from 3 fatty acids and one glycerol= 3 hydrocarbon tails ex: fats and oils
polysaccharides
made by linking together glucose molecules; three main - starch, glycogen, and cellulose
glycogen
made of alpha glucose, carbon and all point downward. the chain has many branches and is made by animals and some fungi, stores energy.
Starch are made up of
made of long chains of glucose that coil into a helical shape
proteins
made of one or more chains of amino acids
Proteins
made of one or more chains of amino acids; carbon hydrogen oxygen nitrogen, but two also contain sulphur
Glycogen are made up of
made up of branching chains of glucose monomers
explain function of glucose
main energy molecule of respiration
R groups
make amino acids different; what allows organisms to make/use proteins
glucose + glucose =
maltose
glucose + glucose =
maltose is made up of
list three examples of a disaccharide
maltose, lactose, sucrose
polysaccharide
many sugars
function of IMMUNOGLOBULIN (antibodies)
marks pathogens for destruction by immune system
body mass index
mass in kilograms/ height in meters ^2. below 18.5 underweight. over 30 obese
Calculate BMI.
mass/height squared
integrin
membrane protein used to make connections with other cells
membrane transport
membrane proteins are used for facilitated diffusion and active transport and for electron transport during cell respiration and photosynthesis
cell adhesion
membrane proteins cause adjacent animal cells to stick to each other within tissues
Explain the industrial production of lactose-free milk
milk is poured through immobilized lactase enzymes to make lactose-free milk.
explain structure of amylopectin starch
moderately branched with a helix shape
What is a monosaccharide?
monomers , single sugar made up of just one subunit
carbohydrate monomer
monosaccharide
what are the building blocks of carbohydrates?
monosaccharides (glucose, fructose, and galactose)
condensation of carbohydrates
monosaccharides combine using condensation.
Types of carbohydrates
monosaccharides: single sugar units ex: glucose, fructose, and ribose disaccharides: 2 monosaccharides linked ex: maltose (2 glucose), sucrose( glucose and fructose) polysaccharides: many monosaccharides ex: starch, glycogen, cellulose (all made from glucose)
tertiary structure of a protein
more folding occurs from disulphide bonds - globular shape
substrate concentration effect in enzymes
more has more chance of collision. until plateau where there are no more enzymes available to react.
function of COLLAGEN
most common structural protein. builds bone, skin, etc.
transport in blood
most substances are transported in the blood plasma. mode of transport depends on its solubility in water
Quaternary Protein structure
multiple polypeptides folded together to create larger globular protein.
muscle contraction
myosin, actin
what makes living organisms different from non-living matter
natural selection
amino group in fatty acids?
no
amino group in glycerol?
no
are fats soluble in water?
no
carboxyl group in glycerol?
no
is cholesterol soluble in water?
no
is nitrogen in fatty acids?
no
is nitrogen present in glycerol?
no
saturated
no double bonds, max hydrogens
Oxygen transport
non polar; but small enough to be soluble; carried on hemoglobin because increases the capacity sine it is non polar
hydrophobic
not attracted to water (all substances that are insoluble in water)
where is the active site?
on the enzyme
Saturated fatty acid molecule
one end has a carboxyl group, other end has a third hydrogen
induced fit model (?)
one enzyme can bind more than one substrate. conformational change in active site to fit substrate, improving binding. can specify more than one substrate. as active site changes, rate of reaction increases.
Describe what occurs in hydrolysis reactions.
one molecule is split into smaller parts by the addition of water molecules.
unsaturated
one or more double bonds between carbons
Monosaccharides
one ring ie glucose, fructose, galactose
monosaccharide
one sugar ex. glucose, fructose
starch
only made by plants and used for large amounts of energy storage
monounsaturated
only one double bond between carbon atoms
enzymes have a what where their activity is highest?
optimum pH
Temperature and pH
optimum temperature: 37 degrees C (below this the process occurs too slowly optimum pH: neutral occurs at 7 (not all enzymes have the same optimum pH)
negative side of water molecule
oxygen
disaccharide
pair of monosaccharides linked through condensation example: glucose + galactose = lactose + H2O
Define active site
part of enzyme structure where the substrate binds
aerobic respiration
part of the cell respiration cycle are lipids used
consequence of unequal polarity
part of the molecule has a slightly positive charge and another a slightly negative charge
The bonds in a polypeptide chain that join the amino acids together
peptide
lipoprotein
phospholipids on the outside, fatty acids carried on the inside; cholesterol in between phospholipid
blood clotting
plasma proteins act as clotting factors that cause blood to turn from a liquid to a gel in wounds - use of fibrin
State the function of polar regions of amino acids on the active site of the enzyme
polar amino acid side chains help attract substrates to active site
dipolarity
polar molecules have a slight positive and slight negative charge
solvent
polar natures means that it forms shells around charged and polar molecules, preventing them from clumping together and keeping them in solution; (demonstrated by its ability to dissolve salt and glucose)
the process of turning monomer into polymer
polymerisation
Polypeptides
polymers of amino acids that make up proteins
globular proteins
polypeptide chains folded into a compact, almost spherical shapes
glycogen
polysaccharide found in animals -long highly branched chains of alpha glucose connected by alpha 1,4 and alpha 1,6 glycosidic bonds
cellulose
polysaccharide found in plant cell walls -long strands of beta glucose connected by beta 1,4 glycosidic bonds -forms very strong sheets of fibre due to H-bonding between cellulose strands
starch
polysaccharide found in plants -amylose: long chain of alpha glucose connected by alpha 1,4-glycosidic bonds -amylopectin: branched chains of alpha glucose connected by alpha 1,4 and alpha 1,6 glycosidic bonds
many monosaccharides linked together =?
polysaccharides, linked together by condensation reactions
Health risks of trans fats
positive correlation in causing coronary heart diseases due to linear structure that builds up over one another and blocks veins.
macromolecules
produced by living organisms, broken down into monomers
endogenous
produced from within; due to internal causes
secondary structure of protein
protein structure is formed by folding and twisting of amino acid chain
tertiary structure of protein
protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure
transport of nutrients and gases
proteins in blood help transport oxygen, carbon dioxide, iron, and lipids
immunity
proteins make huge numbers of different antibodies
define ENZYME
proteins which act as biological catalysts of chemical reactions, speed up metabolic reactions, do not become part of end product
carbohydrates
provides energy for cell processes, allows storage for energy (although in quick and short releases, unlike lipids), ex: monosaccharides, disaccharides, poly, glucose, etc. C,H,O
explain function of lactose
quickly-digested energy molecule (found in milk)
Calculating Reaction Rates
rate of reaction is (S^-1)=1/time taken (s) - time taken in enzyme experiments is commonly the time to reach a measurable end point
Substrate
reactant of an enzyme-catalyzed reaction
carbon
referred to as the "backbone" of organic molecules because it can be used to make a huge range of different molecules
4 examples of monosaccharides.
ribose, glucose, galactose, fructose
characteristics of polypeptides
ribosomes linked amino acids together by peptide bonds. polypeptides can have from 20 amino acids to ten of thousands amino acids.
Globular Proteins
rounded shape, often soluble in water
isomer
same chemical formulas, different atom arrangement ex. fructose and glucose
Saturated fats vs unsaturated fat
saturated fat can increase risk of coronary heart disease, unsaturated fat can decrease risk of coronary heart disease,
Primary protein structure
sequence of amino acids that creates other folded protein structures
explain the 1st level of protein structure
sequence of amino acids. held in place by peptide bonds (from condensation). bunch of little amino acids circles together in a chain.
immunoglobulin
serve as an antibody in the immune system; bind to antigens on bacteria/other pathogens, cause a response
covalent bond
sharing of electrons between atoms, usually formed by carbon
Carbohydrates
short term energy used both aerobic and anaerobic easily dissolved easily broked down transported quicker
Explain why water has a much higher melting and boiling temperature than methane.
since water molecules are polar, the network of hydrogen bonds that they form causes them to resist changes in temperature, i.e. it takes more energy to break apart water molecules and eventually melt, boil, or vaporize them. Methane is non polar and forms no hydrogen bonds.
atom
single particle of an element
Monosaccharides
single sugar unit
lipoproteins
small droplets of cholesterol and fat when transporting in blood due to insolubility. coated by phospholipids and proteins
what is Monomers
small subunits used to build large and complex molecules called polymers
Anabolism
smaller molecules are brought together to made bigger molecules through condensation reaction; requires energy through ATP ex: protein synthesis, photosynthesis
explain function of sucrose
soluble energy store for plants
Amino acids transport
soluble; solubility varies for different R groups, but all are soluble enough to get through
organic compound
something containing carbon
is oxygen soluble in water?
somewhat (due to small size)
enzyme
speeds up the chemical reactions of the substrate that binds to its active site
hydrolysis of amino acids
splitting water and separating a dipeptide into 2 amino acids. just the opposite from above
Storage carbohydrates
starch (plants) and glycogen (animals)
list four examples of a polysaccharide
starch, cellulose, glycogen
list three examples of a polysaccharide
starch, cellulose, glycogen are examples of
polysaccharides consist of which monosaccharides linked together?
starch, chitin, glycogen, cellulose
3 examples of polysaccharides
starch, glycogen, cellulose
Second group of lipids
steroids, consist of four rings of carbon (vitamin D and cholesterol are the best-known steroids)
collagen
structural protein in tendons, ligaments, skin, and blood vessel walls, high tensile strength with limited stretching
Collagen
structural protein that is the main protein found in connective tissues such as tendons and ligaments.
protein functions
structural support, storage, transport, cellular communications, movement, and defense against foreign substances
Non-Competitive Inhibitor
substance that binds to the allosteric site, changing the shape of the enzyme and the active site, preventing the substrate from bonding ex: cyanide (CN-) will bond to -SH group of an enzyme and destroy disulfide bonds
Substrate
substance that connects to the enzyme to be catalyzed in the reaction
product
substance that is created after the reaction
Hydrophobic
substances that are "water-hating", don't dissolve in water
Hydrophilic
substances that are "water-loving", dissolve well
substrate
substances that enzyme converts into products
glucose +fructose
sucrose
glucose +fructose
sucrose is made up of
"ase"
suffix commonly attached to enzyme names
metabolism
sum of all chemical reactions that occur in a living thing, catalyzed reactions, how fast it takes to grow things like hair, nails, etc
Metabolism
sum of all reactions that occur in the organism; consists of pathways where molecules are transforms; can be catabolic or anabolic
define anabolism w examples
synthesis of complex molecules by condensation reactions: protein synthesis, photosynthesis, DNA synthesis
anabolism
synthesis of complex molecules from simpler molecules, including the formation of macromolecules from monomers by condensation reactions (ie photosynthesis, protein synthesis)
three factors that can alter an enzyme's activity
temperature, pH levels, substrate concentration
Benedict's Reagent
test for reducing sugars
as substrate concentration rises...
the # of active sites on the enzymes are occupied, reaction rate increases at first, then slows and stops once active sites are occupied
Activation Energy
the amount of energy it takes to start a reaction
Active site
the area or the pocket on the enzyme where the substrate binds
Vitalism
the belief that carbon compounds cannot be made without a living organism/ vital force; disproved by Urea
cohesion
the binding together of two molecules of the same type, for instance two water molecules (in plants when these forces push the water against gravity )
catabolism
the breakdown of complex molecules into simpler molecules, including the hydrolysis of macromolecules into monomers; hydrolysis=water molecules are split
Define denaturation
the deterioration of a protein's structure from high temps and deviating from optimum pH
Proteome
the different kinds of proteins produced by a genome, cell, tissue or organism at a certain time. This found by extracting a mixture of proteins and using gel electrophoresis with antibodies specific to those proteins with fluorescent markers. They can vary between different types of cells and different individuals.
proteome
the entire set of proteins expressed by a given cell or group of cells. different for all, except for identical twins (may differ with age)
Induced Fit Model
the enzyme changes shape slightly when bonding to the substrate, this activates the substrates, and product(s) are released
what define a polypeptied's squence
the gene of the organism
when an enzymatic reaction is heated, what happens?
the kinetic energy is increased and the rate of reaction increases
primary structure of protein
the order of amino acids (held together by peptide bonds) in a chain. all proteins have this
Define metabolism
the overall network of chemical reactions that occur in cells
Hydrogen bonding
the partial +ve charge is attracted to the partial -ve charge creates an intermolecular attraction between the water molecules
solvent property of water
the polarity of water makes it an excellent solvent for other polar molecules since the hydrogen bond has both a positive and negative side, which allows water to dissolve both positive charge molecules and negatively charged molecules. (therefore molecules with no charge don't dissolve in water)
Metabolism
the process of building or breaking molecules in order to keep the body alive
Metabolic rate
the rate at which materials in the body build and break - homeostasis requires a higher metabolic rate - if materials were left on their own to build and break, the metabolic rate would be too slow to sustain life
Active site
the region on the surface of the enzyme which matches up w/the shape & chemical properties of substance. the active enzyme only allows one specific substrate & the enzyme to bind together. the substrate are changed & can not be reused but the enzyme can be used over again.
molecular biology
the science that explains biological processes from the structure of molecules and how they interact with each other
Define catabolism
the set of reactions that break larger molecules down to smaller ones.
Denature
the structural change in a protein, usually enzymes, that results in the loss of it biological properties. The bonds that hold the enzyme shape begin to vibrate and eventually break, the unfolding and losing its ability. This can be caused if the conditions for enzyme are not optimal(temperature or pH)
Molecular Biology
the study of the chemical substances involved in living processes
Collision
the substrate collides with the enzyme they are floating in liquid (water?) and bc of this they float around randomly, and bump into each other by chance
enzyme activity
the substrate meets the active site of the enzyme by collision or random movements. the substrate binds with the active enzyme. the enzyme weakens the binds of the substrate. while attached to the active site the substrate is changed into the product. the products separate from the active site , leaving the enzyme to be used again
anabolism
the synthesis of complex molecules from simpler ones; living organism have macromolecules which are formed from monomers; anabolism uses a condensation reaction (water is produced)
vitalism
the theory that the origin and phenomena of life are due to a vital principle, which is different from purely chemical or physical forces (proven by Urea)
condensation reaction
the two molecules are joined to form a larger molecule + water. two amino acids can join to form a dipeptide bond
how do the structural formulas for all the amino acids differ?
the variable groups (usually depicted as R) determine the specific type of amino acid
metabolsim
the web of all enzyme-catalyzed reactions in a cell or organism
Metabolism
the web of all the enzyme catalyzed reactions in a cell or organism.
if a protein becomes denatured, what has happened to it?
their bonds have broken and reformed. Overall shape will change and its function will be different.
if a protein becomes denatured, what has happened to it?
their bonds have broken due to high heat, enzyme shape and overall structure is disrupted and no longer the same
Vitalism
theory that only living organisms are composed of organic chemicals, that could only be created by living organisms, due to their "vital force"
Explain the trends apparent in enzyme activity graphs.
there are optimum temperatures and pH, thus it has a peak. Substrate concentration is logistic because reaction slows when it hits a certain point.
if triglycerides are solid at room temp...
they come from animals, saturated fatty acid chains, ex butter n lard
if triglycerides are liquid at room temp..
they come from plants, unsaturated fatty acid chains, ex olive oil, corn oil
how can a polypeptide differ from another?
three things: SIZE (how many AA), sequence of AA, type of folding
conformation of a protein
three-dimensional structure of a protein that is determined by the amino acid sequence of a protein and its constituent polypeptides
Explain the end-product inhibition of the pathway that converts threonine to isoleucine.
through a series of 5 reactions, threonine is converted to isoleucine. as the concentration of isoleucine builds up, it binds to allosteric sire of the first enzyme.
unsaturated fatty acids
trans produced human manipulation -hydrogen next to the double bond are on opposite -behaves like a saturated acid cis was found in nature -hydrogen next to the double are both on the same side -causes the molecule to bond and be rather inflexible
hemoglobin
transport protein for carrying oxygen in red blood cells
hemoglobin
transport protein in red blood cells that binds oxygen in the lungs and releases it in tissues with a reduced oxygen concentration; made from 4 polypeptides
Hemoglobin
transportation protein that transports oxygen throughout the blood system
function of INSULIN
triggers uptake of glucose by cells, lowering blood sugar
3 fatty acid chains and 1 glyceride
triglyceride
condensation of triglycerides
triglycerides are former by condensation from three fatty acids and one glycerol. - condensation reaction between glycerol and fatty acids
phospholipids
two fatty acids and a phosphate group are attached to glycerol. partly hydrophobic
disaccharide
two monomers linked together; maltose (two glucose molecules), sucrose (glucose + fructose)
polyunsaturated
two or more double bonds
explain the 4th level of protein structure
two or more globular proteins. held in place by ionic bonds, hydrogen bonds, and disulfide bonds.
Disaccharides
two rings bonded together - maltose
explain structure of cellulose
unbranched and a straight chain (unlike amylose starch which is helical)
explain structure of amylose starch
unbranched and forms a straight helix
polypeptide
unbranched chain of amino acids. (>40 are peptides). coded by genes. the sequence of bases in the DNA of the gene determines the sequence of the amino acids in the polypeptide.
cellulose
unbranched chains of linked beta glucose, carbon & alternate upwards & downwards. it makes up plant cell walls
polar covalent bonds
unequal sharing of electrons
cellulose
used to build cell walls of plants and is made up of long, straight chains of glucose molecules with hydrogen bonds formed between parallel chains
Pectinase
used to get a higher yield of juice as more will separate from the pulp in juice production
lipids
used to store energy: fat in humans (saturated, solid at room temp), oils in plants (unsaturated fats, liquid at room temp), C,H,O
what chemical substance is formed when the H+ and OH- ends are joined?
water
hydrophilic
water loving (things that dissolves well in water)
define metabolism
web of all enzyme catalyzed reactions in a cell or organism, sum of all chemical reactions that occur in a living thing
Collsions
when a substrate comes close to an active site, it does this to bind. Successful reactions only occur if substrate and the active site do this with sufficient kinetic energy.
Adhesion
when water forms hydrogen bonds with other polar molecules.
amino acid
which organic compound is this?
carbohydrate (alpha glucose)
which organic compound is this?
hydrocarbon
which organic compound is this?
Are amino acids soluble in water?
yes
amino group in amino acids?
yes
can the enzyme be used again and again?
yes
carboxyl group in amino acids?
yes
carboxyl group in fatty acids?
yes
is glucose soluble in water?
yes
is sodium chloride soluble in water?
yes
molecules join to form fats in fatty acids?
yes
molecules join to form fats in glycerol?
yes
nitrogen in amino acids?
yes
Amino acids
The base unit of peptides and there twenty different types of that are synthesized by the ribosomes. They contain a NH2 group, carboxyl and "R" group. Determined based on mRNA copied from DNA.
Glycosidic Bond
The bond formed when carbohydrate molecules are joined together in condensation reactions. Can be 1-4 or 1-6.
ester bond
The bond formed when fatty acid molecules are joined to glycerol molecules in condensation reactions.
Condensation Reaction
The building of polymers by the removal of water molecules when monomers combine.
Metabolism
The building up or breaking down of molecules based on: 1) identity 2) orientation 3) speed of collision
Peptide bond
The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid
peptide bond
The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid
Elements found in all the key organic molecules (Protein, Carbohydrate, nuleic acids and lipid)
Carbob, Hydrogen, Oxygen
most abundant group of biological molecules
Carbohydrate
Polysaccharide
Carbohydrates that are made up of more than two monosaccharides
Polysaccharides
Carbohydrates that are made up of more than two monosaccharides -starch, glycogen, cellulose
State that life is based on carbon compounds, including carbohydrates, lipids, proteins and nucleic acids.
Carbohydrates- C,H,O with O and H in a 1:2 ratio; includes monosaccharides, disaccharides, and polysaccharides Lipids-C.H,O insoluble in water, soluble in nonpolar solvents, and used for energy storage; includes steroids, waxes, fatty acids, and triglycerides (fats if solid at room temp, oils if liquid at room temp) Proteins-C,H,N,O,(P) chains of amino acids, distinguished by their R groups Nucleic acids-C,H,N,O,P chains of subunits called nucleotides. Includes DNA and RNA. Contains a base, sugar, and a phosphate group.
Why is carbon the ideal building block for large molecules?
Carbon can make covalent bond with up to 4 other atoms.
Describe how carbon atoms can form four covalent bonds, allowing a diversity of stable compounds to exist.
Carbon is the 15th most abundant element, and it has 4 valence electrons which allows it to create up to 4 other covalent bonds. With 4 covalent bonds, carbon can form a large variety of different compounds Carbon can also form double and triple covalent bonds.
What is found at the two ends of a hydrocarbon chain for fatty acids
Carboxyl group (COOH) and methyl group (CH3)
Describe how carbohydrates, proteins, and lipids can each be identified from each other.
Carbs have a 2:1 ratio between hydrogen and oxygen.
Outline catabolism as the breakdown of complex molecules into simpler molecules, including the hydrolysis of macromolecules into monomers.
Catabolism-larger molecules are broken down into smaller ones through hydrolysis (exogonic) Includes: -The part of metabolism that releases energy -Digestion of food in the mouth, stomach and small intestine -Cellular respiration -Digestion of carbon compounds by decomposers
2 types of metabolic reactions
Catabolism: hydrolysis Anabolism: condensation/dehydration
State that living organisms synthesise many different proteins with a wide range of functions.
Catalysis-enzymes Muscle contraction-actin and myosin cause muscle contrations Cytoskeletons-tubulin gives animal cells their shape
enzymes
Catalysts for chemical reactions in living things
induced fit model
Change in the shape of an enzyme's active site that enhances the fit between the active site and its substrate(s)
Carbohydrate
Class of organic compounds containing oxygen, carbon and hydrogen. They includes monosaccharides, disaccharides, polysaccharides
proteome
The complete set of proteins expressed by a genome
Outline the functions of the following proteins: rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk.
Rubisco-catalyzes reaction that fixes CO2 from the air and is the source for all carbon compounds needed by organisms. Insulin-produced as a signal to many cells in the body to absorb glucose and to help reduce the glucose concentration in the blood. Secreted by Beta cells in the pancreas and is transported through blood. Immunoglobin-Y shaped antibodies produced by plasma Beta cells; has sites at the tip of their two arms that bind to antigens on bacteria/pathogens, acts as markers to identify these pathogens to be destroyed by large white blood cells called phagocytes. Rhodopsin-membrane protein present in the retina that absorbs light. It contains a retinal molecule surrounded by an opsin polypeptide. When it absorbs light it changes shape, and sends a signal to the brain. Collagen-structural protein made from 3 polypeptides wound together, most abundant protein in the body. Spider Silk-different types of silk have different functions. It contains polypeptides in parallel arrays.
Cohesive
Same molecules sticks to each other
Metabolism
Set of life sustaining chemical reactions within the cells of living organisms. Can also refer to the sum of all chemical reactions that occur in living organisms
Glycogen
Similar to the branched for of starch (amylopectin), but made in animals alpha glucose, 1 and 4, both down=curved; does not have a fixed size stores short term glucose in humans
Outline the modes of transport of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in blood, in relation to their solubility in water.
Sodium chloride and glucose-dissolved in water, so it is transportable through blood Amino acids-solubility depends on R group Oxygen-dissolves sparingly in water, if oxygen levels are too low, hemoglobin has binding sites for transport Fat molecules and cholesterol-insoluble in water, travels through lipoprotein
starch
Somewhat branched Amyloplasts Stores energy for plants
Functions of the 3 main polysaccharides
Starch: stores energy in plants Glycogen: stores energy in animals Cellulose: major component of plant cell walls, helps give rigidity/support to plant parts such as roots, stems, and leaves
Glycogen
Storage carbohydrate in animals. It is multi-branched which the molecule more compact and is made up of alpha glucose
Starch
Storage carbohydrate in plants
Protein Functions
Structure (collagen, keratin) Hormones (insulin, glucagon, thyroxine) Immune (antigens on cell) Transport (cell membrane transport, O2 transport) Movement (actin+myosin in muscles) Enzymes (many, many, many enzymes)
Explain that enzyme catalysis involves molecular motion and the collision of substrates with the active site.
Substrates can only bind to an active site if they are close to it-collision Substrates are usually dissolved in water and movement is usually rapid and random
Fructose
Sugar found in fruit
List of some inorganic substance found in living things
Sulfer, Calicum, Phosphorus, Iron,and Sodium
Explain that temperature, pH and substrate concentration can affect the rate of activity of enzymes.
Temp-higher heat=higher kinetic energy, which can lead to more collisions, but also denaturation. pH-deviation from optimum pH can cause denaturation Substrate concentration-higher concentration means more collisions, but as the active sites get filled up the rate of reaction slows.
enzyme substrate specificity
The active site of an enzyme can only attach to one substrate at a time, and one substrate type
Explain why lipids are more suitable for long-term energy storage in humans than carbohydrates.
The amount of energy released in cellular respiration per gram of lipid is double that of carbs. The same amount of energy in a lipid adds to half of body mass compared to carbs. Fat also forms pure droplets with no water present, in contrast to glycogen's two grams per gram. Therefore 1 lipid=6 carbs in terms of energy storage efficiency.
