IB Biology - Topic 2 Molecular Biology (2.1-2.5)

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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.


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