Ib Biology Sl Molecular Biology

Front 1

Vitalism

Back 1

Theory that the phenomena of life is due to a vital principle. (requires living things to be made).

Front 2

Example of Vitalism

Back 2

Urea production in a living organism (thought only able to be produced by the kidney)

Ammonia (NH3) + carbon dioxide (CO2) = Ammonium Carbonate (NH4CH2O2N)

= Urea (CH2ON2) + Water (H2O)

Front 3

types of bonds carbon can form

Back 3

Single Bond - one pair of shared electrons.

Double Bond - two pairs of shared elections.

Triple Bond - three pairs of shared electrons.

Front 4

Define macromolecules and examples.

Back 4

Four main classes of Carbon Compounds

- carbohydrates

- lipids

- proteins

- nucleic acids

Front 5

Glucose

Back 5

Six membered rings with one side chain

Front 6

What does metabolism consist of

Back 6

Anabolism and Catabolism

Front 7

Anabolism

Back 7

synthesis of complex molecules from simpler molecules including the formation of macromolecules by condensation reactions.

e.g. protein and DNA synthesis

Front 8

Catabolism

Back 8

breakdown of complex molecules into simpler molecules including hydrolysis of macromolecules into monomers.

e.g. digestion of food

Front 9

What are the four things a carbon atom will bond with.

Back 9

Amine Group (NH2)

Carboxyl Group (COOH)

A hydrogen atom (H)

the R group (Protein)

Front 10

Properties of water

Back 10

cohesion

thermal

adhesion

solvent

Front 11

Cohesion

Back 11

Hydrogen bonding causes water molecules to stay close to each other.

Front 12

Adhesion

Back 12

this property occurs as a result of the polarity of a water molecule and its ability to form hydrogen bonds

Front 13

High specific heat capacity

Back 13

The amount of heat needed for 1g of a substance to change its temperature by 1 degree.

Front 14

High heat of vaporization

Back 14

the quantity of heat a liquid must absorb for 1g to be covered to the gaseous state.

Front 15

solvent

Back 15

dissolving agent

Front 16

solute

Back 16

the substance that is dissolved

Front 17

solution

Back 17

a liquid that is a homogenous mixture of two or more substances

Front 18

aqueous solution

Back 18

water is the solvent

Front 19

Hydrophilic

Back 19

Water loving.

All substances that dissolve in water are hydrophilic, including polar molecules

Front 20

Carbohydrates

Back 20

a monosaccharide, disaccharide or polysaccharide.

Front 21

Monosaccharide

Back 21

a single sugar unit.

e.g. glucose, fructose, ribose

Front 22

disaccharide

Back 22

consists of two monosaccharides joined by a covalent bond.

linked by condensation reaction (creation of water).

glucose + glucose = maltose + water.

Front 23

polysaccharides

Back 23

consist of many monosaccharide units linked together.

e.g. starch, glycogen, cellulose all are composed of glucose molecules linked in different ways.

Front 24

starch

Back 24

made by plant cell and used to store large amounts of glucose.

energy store (glucose molecules can be added or removed).

Front 25

two forms of starch

Back 25

amylose (unbranched)

amylopectin (branched).

Front 26

Cellulose

Back 26

Unbranched chains of beta-glucose.

hydrogen bonds link the molecules together. linked molecules form bundles called cellulose microfibrils

Front 27

What is different about cellulose compared to other carbohydrates?

Back 27

very high tensile strength. we can’t break it down.

Front 28

Glycogen

Back 28

similar to amylopectin, but more branching. made by animals and some fungi

stored in the liver and some muscles in humans

functions to store energy in the form of glucose

Front 29

Fatty acids

Back 29

chain of carbon atoms linked by a covalent bond contain a carboxyl group at one end.

Front 30

Three types of fatty acids

Back 30

can be saturated, monounsaturated or polyunsaturated

Front 31

Saturated

Back 31

if there are only single bonds between the carbon atoms, then each carbon atom is bonded to as many hydrogen atoms as possible.

Front 32

Unsaturated

Back 32

if there are one or more double bonds between the carbon atoms.

Front 33

monounsaturated

Back 33

one double bond

Front 34

polyunsaturated

Back 34

more than one double bond

Front 35

isomer

Back 35

molecules with the same number and type of atom, but with a different arrangement of those atoms

Front 36

trans isomer

Back 36

hydrogens are on the opposite end of the double bond

Front 37

difference between isomer and trans isomer

Back 37

trans isomers are rare in nature and usually artificially produced to produce solid fats

e.g. margarine from vegetable oils

Front 38

cis isomer

Back 38

hydrogens are on the same side of the double bond. opposite of trans isomers

Front 39

Triglycerides

Back 39

formed by condensation from three fatty acids and one glycerol.

Front 40

what makes lipids more advantageous to animals than carbohydrates?

Back 40

suitable for long term energy storage in humans than carbohydrates. a gram of fat stores more than twice as much energy as a gram of polysaccharide (starch). animals must carry their energy stores with them, so it is advantageous to have a more compact reservoir of food.

Front 41

Where is fat stored in animals.

Back 41

fat is stored in adipose cells, which form adipose tissue.

adipose tissues cushion vital organs like kidneys.

adipose tissue beneath the skin also serves as a layer of insulation

Front 42

Equation for Body Mass Index (kgm^2) (BMI)

Back 42

mass (kg) / (height (m)^2

Front 43

Nomogram

Back 43

alternative to calculating BMI

ruler is used to draw a line from the body mass to height.Where the drawn line intersects the W/H2 line is the BMI.

Front 44

Ribosomes

Back 44

the molecules within cells that facilitate the formation of peptide bonds.

Front 45

Polypeptide

Back 45

linked amino acids forming proteins, coded by an R group.

Front 46

Genes

Back 46

unit of inheritance consisting of a specific DNA sequence.

Front 47

How many amino acids are there in a polypeptide?

Back 47

4 to thousands

Front 48

Central Dogma of Genetics

Back 48

DNA -> RNA -> Polypeptide

or basically

Gene -> Message -> Product

Front 49

Four levels of protein structure

Back 49

Primary

Secondary

Tertiary

Quaternary

Front 50

Primary Protein Structure

Back 50

- Amino acid sequence

- peptide bonds

- the order/number of amino acids in a polypeptide chain

- the primary structure is read from the NH2— terminal to the —COOH terminal.

- each amino acid is identifies by its specific R group

- most polypeptides are between 50-1000 amino acids long

Front 51

Secondary Protein Structure

Back 51

- repeating local structures

- held by H-bonds

- local folding of the polypeptide backbone

- stabilized by H-bonds

- three types of secondary structures:

- alpha (helix)

- beta (pleated sheet)

- open loops

Front 52

Tertiary Protein Structure

Back 52

- folding of a single protein

- R-group interactions

- hydrophobic core

- 3D conformation of a polypeptide

- amino acid chain (in the helical, pleated or loop form) links itself in places to form the unique twisted or folded shape of the protein.

- stabilized by R-group interactions

- hydrophobic core

- 3D structure gives proteins their functional properties such as active sites on enzymes.

Front 53

Quaternary Protein Structure

Back 53

- Protein complex

- Made of two or more subunitsnumber of tertiary polypeptides are joined together.

- composed of four different polypeptide chains

- each chain forms a tertiary structure called a haem group.

- e.g. haemoglobin

Front 54

Prosthetic Groups

Back 54

proteins are often bound to inorganic groupse.g. Haemoglobin has four polypeptide “haem” groups each associated with and FE2+

Front 55

What are the two types of proteins and their functions?

Back 55

Fibrous - structural roles

Globular - functional

Front 56

Denaturation

Back 56

process in which the protein unravels and loses its native state.

Front 57

What happens during denaturation?

Back 57

- Protein becomes inactive

- interactions between R-groups are interrupted

- heat causes denaturation by breaking interactions between r-groups

- pH affects charges in R-groups, which disrupts interactions.

Front 58

Functions carried out by proteins

Back 58

Catalysis -> Tensile Strengthening

Muscle Contraction -> Blood Clotting

Cytoskeleton -> Transport of nutrients and gases

Cell Adhesion -> Receptors

Membrane Transport -> Hormones

Immunity -> Packing of DNA

e.g. rubisco, insulin, immunoglobins, rhodopsin, collagen and spider silk

Front 59

Proteome

Back 59

all the proteins produced by a cell, a tissue, or an organism

a proteome is variable as different cells will make different proteins

Front 60

Genomes

Back 60

what proteins an organism can make

Front 61

Enzymes

Back 61

globular proteins used as catalysts for biochemical reactions

speeds up reactions without being consumed

Front 62

Substrate

Back 62

Reactant in a biochemical reaction

Front 63

Active Site

Back 63

region on the surface of an enzyme to which substrates bind and which catalyses the reaction

Front 64

Collision

Back 64

the coming together of an active site and substrate

Front 65

How do active sites and substrates match each other?

Back 65

structurally, the 3d structure of the active site is specific to the substrate. substrates that don’t fit won’t react

chemically, substrates that are not chemically attracted to the active site won’t be able to react.

Front 66

Effects of Temperature on Collisions

Back 66

- as temperature increases, rate of reaction increases

- as molecules have more energy, move faster and collide and react more frequently

- optimum temperature = maximum rate of reaction

- balance between enzyme stability and kinetic energy of reactants

- at too high of a temperature however, enzyme is denatured

Front 67

Substrate Concentration

Back 67

- increase in concentration of substrate molecules results in increase in rate of reaction.

- levelled makes optimal

- too high, makes full saturation, rate becomes constant, any increase beyond the optimum will have no added effect because no extra active site to be used.

Front 68

Denaturation

Back 68

- loss of r group interactions

- change in structure means change in active site - if it changes shape, no longer able to bind to substrates

Front 69

Lactose

Back 69

The natural sugar found in milk.

Some people are lactose intolerant

using enzymes, lactose free milk can be made

Front 70

Commercial Uses

Back 70

- many enzymes have commercial uses

- e.g. detergents - proteases and lipases, breakdown protein and fat stains.

- biofuels - breakdown starch in grains

- brewing - clarification

- medicine and bioengineering - diagnostics, contact lens cleaner.

- always immobilized enzymes

- attached to a material so movement is restricted

Front 71

Common ways to immobilize enzymes

Back 71

- aggregations of enzymes bonded together

- attached to surfaces like glass

- entrapped in gels, like alginate gel beads.

Front 72

Advantages of immobilizing enzymes

Back 72

- enzymes are easily separated from the product - retrieved enzymes can be used again

- increases stability of enzymes

- substrates can be exposed to higher enzyme concentration