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unit 2 Flashcards

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1
Q

vitalism theory

A

early idea that organic compounds could only be produced in living cells

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2
Q

falsification of the vitalism theory

A

Friedrich Wohler (German scientist) mixed two inorganic substances (cyanic acid and ammonium) and obtained urea, an organic molecule.

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3
Q

carbon atoms

A
  • The molecules used by living organisms are based on carbon
  • Each carbon atoms forms 4 covalent bonds = allows great diversity of compounds to exist
  • Is the strongest type of bond between atoms = stable molecules = can form large molecules
  • H = 1 bond
  • O = 2 bonds
  • N = 3 bonds
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4
Q

organic vs inorganic compounds

A

organic = compounds that are found in living organisms and contain carbon.

inorganic = compounds that don’t contain carbon

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5
Q

types of carbon compounds

A

carbohydrates
lipids
proteins
nucleic acids

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6
Q

carbohydrates

A
  • can be:
    monosaccharides (glucose, galactose & fructose)
    disaccharides (maltose, lactose & sucrose)
    polysaccharides (starch, glycogen & cellulose)
  • contain C, H & O
  • used for energy or structural purposes
  • general formula = (CH2O)n
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7
Q

proteins

A
  • contain C, H, O and N (sometimes S)
  • large organic compounds made of A.A arranged into one or more linear chains
  • proteins are distinguished by their “R” groups.

e.g. enzymes & antibodies

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8
Q

lipids

A
  • contain C, H and O
  • group of organic molecules that are insoluble in water but soluble in non-polar organic solvents

e.g. triglycerides, phospholipids, and steroids

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9
Q

nucleic acids

A
  • contains C, H, O, N and P
  • composed of smaller units called nucleotides
  • Nucleotides: Base, sugar and phosphate groups covalently bonded together
  • if sugar is ribose = RNA;
    if sugar is deoxyribose = DNA
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10
Q

what is metabolism?

A
  • the web off all enzyme-catalyzed reactions in a cell or organism

can be anabolism (making) or catabolism (breaking)

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11
Q

what is anabolism?

A
  • the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers.
  • by condensation reactions.
  • water is produced
  • energy is required
  • enzymes are needed to catalyze the reaction
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12
Q

give 2 examples of condensation reactions

A
  1. protein synthesis = condensation of amino acids to form a polypeptide:
    amino acid + amino acid —-> dipeptide + water
  2. formation of a disaccharide:
    glucose + glucose —-> maltose + water
    (monosaccharides) (disaccharide)
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13
Q

what is catabolism?

A
  • the breakdown of complex molecules into simpler molecules including the breakdown of macromolecules into monomers.
  • by hydrolysis
  • water is required
  • energy is released
  • enzymes are needed to catalyze the reaction
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14
Q

give 2 examples of hydrolysis reactions

A
  1. . hydrolysis of a disaccharide (lactose) to 2 monosaccharides (glucose & galactose):
    lactose + water —–> galactose + glucose
  2. hydrolysis of a triglyceride to glycerol and 3 fatty acids
    triglyceride + 3 water molecules —-> glycerol + 3 fatty acids
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15
Q

properties of H2O: high specific heat capacity

A

a considerable amount of energy is needed to increase its temperature, due to the strength of the hydrogen bonds which are not easily broken.
this is why the temperature of water tends to remain relatively stable.

Benefit to living organisms: It is beneficial for aquatic animals as they use water as a habitat.

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16
Q

properties of H2O: high latent heat of vaporization

A

water absorbs a great deal of heat to evaporate, due to the H bonds.

Benefit to living organisms: water acts as an excellent coolant; the evaporation of water (sweat/transpiration) cools body surfaces.

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17
Q

properties of H2O: adhesive

A

water is adhesive, as it can form an attraction to unlike molecules.
e.g. when water molecules are attracted to cellulose molecules by hydrogen bonding

Benefit to living organisms:

  • water exhibits adhesion to the inside of the vascular tubes in plants, which are partially made of cellulose
  • allows the water to be pulled up and move against gravity
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18
Q

properties of H2O: transparent

A

allows light to pass through for photosynthesis

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19
Q

hydrophilic substances

A
  • hydrophilic = “water loving”
  • include all substances that dissolve in water; polar substances
  • examples: charged ions such as Na+/ polar substances such as glucose and fructose
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20
Q

hydrophobic

A
  • hydrophobic means “water fearing”
  • include all substances that are insoluble in water; non polar substances.
  • examples: non polar molecules such as lipids
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21
Q

formation of a polysaccharide examples

A

in plants, many glucose molecules combine through condensation reactions to form the polysaccharide starch

in animals, many glucose molecules combine through condensation reactions to form the polysaccharide glycogen

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22
Q

structure & function of starch

A
  • consists of 2 types of molecules:
    1. amylose which is linear (a straight chain of α-D glucose molecules)
    2. amylopectin which is branched (a branched chain of α-D glucose molecules)
  • the bonds are α-1-4 glycosidic bonds
  • the -OH groups from the glucose molecules are always pointed down, causing starch to have a curved appearance.
  • too large to be soluble in water at room temperature
  • function: store glucose in plants.
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23
Q

saturated fatty acids

A
  • single C-C bonds
  • saturated with hydrogen
  • no double bonds
  • solid at room temperature
  • found in animals
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24
Q

cis - unsaturated fatty acids

A
  • hydrogen atoms on the same side of the C=C double bond.
  • has a twist at the double bond. This causes the fatty acid to pack more closely and lower its melting point.
  • liquid at room temp
  • naturally found.
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25
Q

trans - unsaturated fatty acids

A
  • hydrogen atoms on the opposite side of the C=C double bond.
  • has no twist at the double bond
  • has a higher melting point
  • solid at room temperature.
  • artificially made
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26
Q

what are the 4 levels of proteins?

A
  • primary = the sequence of AA within the protein
  • secondary = repetitive shapes of either a helix or a pleated sheet (e.g. spider silk)
  • tertiary = 3d folding pattern of a protein due to side chain interactions - globular shape
  • quaternary = 2 or more polypeptides combined to make a single functional protein (e.g. haemoglobin)
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27
Q

(proteins) what is the function of collagen

A
  • structural
  • fibrous, rope-like protein
  • main protein component of connective tissue, which is abundant in skin, tendons & ligaments
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28
Q

(proteins) what is the function of immunoglobulin

A
  • defense / immunity
  • recognizes antigens as part of immune response
  • Y shaped proteins produced by B cells
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29
Q

what are enzymes?

A
  • 3d globular proteins
  • act as catalysts; speed up chemical reactions.
  • have an active site to which the specific substrate binds.
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30
Q

what is the active site of an enzyme?

A
  • the region where a specific substrate binds to an enzyme
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31
Q

what is effect of temp on enzyme activity?

A
  • as temp /\ so does the kinetic energy of substrates & enzymes = more collisions between them = increased rate of reaction
  • optimum temp = max rate of reaction
  • beyond optimum temp = enzymes loses it’s shape = cannot fit to substrate = denatured
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32
Q

what is lactase

A

the enzyme that hydrolyses lactose (di) into glucose and galactose (mono) that are easily absorbed by the gut.

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33
Q

what is lactose intolerance?

A

inability to fully digest lactose due to lack of lactase

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34
Q

how is lactose-free milk produced?

A
  1. the milk is treated with the enzyme lactase which breaks lactose down into galactose and glucose
  2. the lactase is immobilised
  3. milk is then repeatedly passed over immobilised enzyme, becoming lactose free
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35
Q

what are nucleotides made of?

A
  • a phosphate group
  • a pentose sugar (ribose in RNA, deoxyribose in DNA)
  • a nitrogenous base - A,G,C,T (U replaces T in RNA)
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36
Q

what are the 5 nitrogenous bases?

A
  • Adenine
  • Guanine
  • Cytosine
  • Thymine
  • Uracil
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37
Q

what is the structure of a strand of DNA?

A
  • nucleotides are linked into strands via condensation reaction
  • covalent bonds are made between phosphate of 1 nucleotide and the pentose sugar of the next
  • phosphate group attached to 5’C of sugar joins with the hydroxyl group attached to 3’C of sugar = phosphodiester bond + water
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38
Q

what is DNA replication?

A
  • the process by which cells double the quantity of DNA to prepare for division
  • occurs during S-phase of the cell cycle
  • semi-conservative as both DNA molecules are formed from an old strand & a new one
  • depends on complementary base pairing
  • 2 molecules involved: DNA replication enzymes & free floating nucleotides
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39
Q

what is polymerase chain reaction?

A
  • PCR is used to amplify small quantities of DNA to produce multiple copies of DNA
  • it can be useful when only a small amount of DNA is available but a large amount is required to undergo testing.
  • we can use DNA from blood, semen, tissues and so on from crime scenes for example.
  • this is done by DNA replication
  • Taq DNA polymerase enzyme is used (extracted from bacteria)
  • PCR requires cycles of heating and cooling
40
Q

what are the enzymes involved in DNA replication?

A
  • DNA ligase = stick together the fragments on the lagging strand.
  • helicase = separated the 2 DNA strands before replication
  • DNA polymerase = catalyses the formation of a new polynucleotide chain
  • single-strand binding protein = keeps the separated DNA strands apart during replication
41
Q

photosynthesis stage 2: light independent reactions

A
  • ATP and H derived from the photolysis of water during the light-dependent reaction are used to convert CO2 & water into useful organic molecules (e.g. glucose)
  • enzyme rubisco is used
42
Q

what is the structure of water molecules?

A
  • 2 H covalently bonded to 1 O atom
  • each H shared a pair of electrons with the O.
  • O has a greater affinity for electrons that H, so it ‘pulls’ the electron closer = O slightly -, and H slightly +
  • this creates differently charged regions, making H2O a polar molecule, and bcuz it had 2 charged regions it is dipolar
  • the numerous hydrogen bonds in H2O make it a very stable structure
43
Q

properties of H2O: high boiling point

A

it boils at 100 C because the strong hydrogen bonds.

Benefit to living organisms:
the high boiling point of water is vital for making liquid water available to organisms / water is liquid over a range of temperatures.

44
Q

properties of H2O: cohesive

A

water molecules stick to each other because of the hydrogen bonds holding the water molecules together.

Benefit to living organisms:

  • water moves up plants (via xylem) against gravity.
  • creates surface tension which allows some insects to move on water’s surface
45
Q

properties of H2O: solvent

A

water can dissolve many organic and inorganic substances that have charged and polar regions due to its polarity
universal solvent.

Benefit to living organisms:
- water acts as a medium for metabolic reactions: aqueous solutions act as a medium in which specific biochemical reactions take place. Aqueous solutions include the blood plasma, cytoplasm, stroma, etc.

  • water acts as a transport medium.
    In plants, allows dissolved sugars (sap) to be transported in the phloem from the leaves to the stems, roots and flowers of a plant.
    In animals, allows substances to be carried in the blood such as glucose and amino acids.
46
Q

what are the properties of water

A
  • solvent (universal solvent)
  • adhesive
  • cohesive
  • high boiling point
  • high specific heat capacity
  • high latent heat of vaporization
47
Q

use of water as a coolant in sweat

A
  • high temperatures damage tissues and denature proteins
  • the heat needed for the evaporation of water in sweat is taken from the tissues of the skin, reducing their temperature = due to high latent heat of vaporization
  • solutes in sweat are left in the skin surface
48
Q

what is methane?

A
  • waste product of anaerobic respiration in methanogenic prokaryotes living in anaerobic conditions = wetlands, swamps and guts of animals
  • can be used as a fuel
  • contributes to the greenhouse effect
49
Q

examples & function of monosaccharides

A 
glucose = energy molecule used in aerobic respiration
galactose = nutritive sweetener in foods
fructose = fruit sugar
50
Q

examples & function of disaccharides

A 
maltose = malt sugar found in barley
lactose = sugar found in milk
sucrose = transport sugar found in plants because of its solubility
51
Q

examples & function of polysaccharides

A 
starch = storage carbohydrate in plants
glycogen = storage carbohydrate in animals
cellulose = main component in plant cell walls
52
Q

structure & function of cellulose

A
  • straight chains of β glucose molecules, held together with 1-4 glycosidic bonds.
  • it forms a straight unbranched chain because the -OH groups point out in opposite directions and every other β glucose is flipped 180 degrees.
  • made of bundles (fibrils) due to the H-bonds forming between the parallel chains of beta glucose.
  • function: to provide tensile strength for cell walls in plant cells
53
Q

structure & function of glycogen

A
  • a multi-branched polysaccharide
  • consists of many α glucose molecules linked by 1-4 and 1-6 glycosidic bonds
  • it is highly branched (due to many 1-6 bonds), making the molecule more compact and a perfect molecule for energy storage
  • function: stores energy in the liver and some muscles of humans
54
Q

unsaturated fatty acids

A
  • contains one double bond or more
  • not saturated with hydrogen (can be hydrogenated)
  • liquid at room temperature
  • found in plants

a) Mono-unsaturated fatty acids: has one C=C double bond.
b) Polyunsaturated fatty acids: has two or more C=C double bonds.

55
Q

compare carbohydrates and lipids

A

lipids are more suitable for long-term energy storage in humans

similarity = both can be used as energy storage

differences:

  • carbs = stored as glycogen (liver), lipids = stored as fat (adipose tissue)
  • carbs = fast release of energy (easily digested), lipids = slow release of energy (less digested)
  • carbs contain less energy per gram
56
Q

how do amino acids form polypeptides?

A
  • condensation reaction = water produced
  • forms polypeptide bond between right carbon of 1 and the nitrogen of the other
  • energy is released
57
Q

amino acids and polypeptides

A
  • 20 different AA in polypeptides
  • AA link by condensation reactions to form polypeptides
  • polypeptides are synthesized on ribosomes
  • the different “R” groups are what makes the AA different and allow the proteins to form a wide array of structures and functions
  • some AA are polar, others are non-polar
58
Q

genes and amino acids / polypeptides

A
  • the AA sequence of polypeptides is coded for by genes
  • each 3 bases codes for 1 AA in a polypeptide
  • most organisms use the same 20 AA in the same genetic code although there are some exceptions.
59
Q

proteins and polypeptides

A
  • a protein may consist of a single polypeptide or more than one polypeptide linked together.
    e. g. hemoglobin has 4 linked polypeptides, which are folded into a globular protein to carry oxygen in the blood.
  • the AA sequence determines the three-dimensional conformation of a protein.
60
Q

what is a proteome?

A

all of the different kinds of proteins produced by a genome, cell, tissue or organism at a certain time.

61
Q

(proteins) what is the function of hemoglobin

A

transport

- transports O2 throughout the blood system

62
Q

(proteins) what is the function of insulin

A
  • hormone
  • regulates blood glucose levels
  • produced in beta cells in the pancreas
63
Q

(proteins) what is the function of pepsin

A
  • enzyme
  • speeds up reactions
  • breaks down protein in the stomach to polypeptides / dipeptides
64
Q

what is the lock and key model?

A
  • a specific substrate fits the active site; the shape of the substrate corresponds to the shape of the active site.
  • the bonds in the substrate (s) are weakened making a reaction easier.
  • the unchanged enzyme and product(s) are released.
  • the enzyme is to be reused.
65
Q

what is the induced-fit model?

A
  • the substrate is specific to the active site, does not fit perfectly
  • when the substrate binds to the active site, the shape of the active site changes and only then it perfectly fits the substrate.
  • the substrate induces the active site to change slightly.
  • this weakens the bonds in the substrate and therefore reduces the activation energy.

this model is a more precise version of the lock and key one as it explains why some enzymes can bind to many different substrates. That is why some enzymes can have broad specificity.

66
Q

what is effect of pH on enzyme activity?

A
  • optimal pH = enzyme works most efficiently = max rate of reaction
  • there is no one optimal pH for all enzymes - some are more acidic, some neutral, etc.
  • /\ or \/ optimum pH = rate of reaction decreases
  • too acidic or too basic = less efficient & inactive
  • too many + or - charges = ionic bonds are disturbed = loses shape = denatured
67
Q

what is effect of substrate concentration on enzyme activity?

A
  • substrate conc /\ = more collisions = /\ rate of reaction
  • at a certain point, increased substrate conc will no longer /\ rate of reaction bcuz all enzymes become fully saturated with substrates = no active sites available = constant rate of reaction
68
Q

nucleotide bonds

A
  • between bases = hydrogen

- between sugar of 1 and phosphate group of other = covalent

69
Q

what is the general structure of DNA?

A
  • double helix
  • made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs.
  • A forms 2 hydrogen bonds with T, G forms 3 hydrogen bonds with C.
  • sugar phosphate backbone provides the stable backbone of one of the helices.
  • bases projecting into the centre.
  • at one end there is pentose with 5’ (said “five prime” ) carbon which is free from bonding.
  • at the other end there is a 3’ carbon free from bonding to other nucleotides.
  • additional nucleotides are joined to the 3’ end of the existing polynucleotide chain
70
Q

compare DNA & RNA

A

similarities:

  • both are nucleic acids
  • both consist of nucleotides

differences:

  • DNA = double stranded, RNA = single stranded
  • DNA = deoxyribose sugar, RNA = ribose
  • DNA = A,T,G,C RNA = A,U,G,C
71
Q

Watson & Crick DNA models

A

First model
- triple helix-
- bases outside of the molecule
- magnesium holding 2 strands together
- ionic bonds between phosphate groups
Failed because:
- didn’t take into account Chargaff’s finding: the amount of A=T and amount of C=G
- would not be enough magnesium available
Through Rosalind Frankin’s X-ray diffraction that showed a double helix + spacing between subunits
Second Model
- figured out the 2 strands were anti-parallel
Their model quickly suggested:
- possible mechanisms for replication
- information was encoded in triplets of bases

72
Q

explain Meselson and Stahl’s experiments

A
  1. bacteria were grown in heavy isotope 15N
  2. then these bacteria were transferred to light isotope 14N
  3. after each replication, samples were collected and centrifuged to determine their density.
  4. first-generation DNA was of medium density, which shows that one strand was grown in 15N (old) and the other strand was grown in 14N (new). This shows that DNA replication is semi-conservative.
73
Q

why is the genetic code universal?

A

the same specific base triplets (codons) code for the same amino acids in all living things

74
Q

what is cell respiration?

A

the controlled release of energy from organic compounds (mainly glucose) in cells to produce ATP

75
Q

what is glycolysis?

A
  • the first stage of cell respiration in all living organisms (in both aerobic and anaerobic)
  • occurs in the cytoplasm
  • does not require oxygen.
  • glucose is broken down into two molecules of pyruvate with a small yield of ATP.
76
Q

anaerobic cell respiration

A
  • respiration in the absence of oxygen
  • glycolysis is the first step
  • gives a small yield of ATP

in humans = pyruvate converted to lactate (removed from the cell when O2 is available + used to maximize muscle contraction)

in yeast = pyruvate converted to carbon dioxide

77
Q

aerobic cell respiration

A
  • requires oxygen
  • gives a large yield of ATP from glucose
  • occurs in the mitochondrion
  • the pyruvate is taken up into the mitochondria and is broken down into carbon dioxide and water.
78
Q

cell respiration formula

A

glucose + oxygen –> CO2 + water + ATP

C6H12O6 + 6O2 –> 6CO2 + 6H20 + ATP

79
Q

compare anaerobic & aerobic cell respiration

A

similarities:

  • both start with glucose
  • both produce ATP & pyruvate

differences:

  • aerobic needs O2, anaerobic doesn’t
  • aerobic = mitochondrion, anaerobic = cytoplasm
  • aerobic = large amount of ATP, anaerobic = small amount
80
Q

what is a respirometer?

A
  • a device used to measure the rate of respiration of a living organism by measuring its rate of exchange of O2 and/or CO2
  • an alkali is used to absorb CO2, so reductions in volume are due to oxygen use.
  • temp should be kept constant to avoid volume changes due to temp fluctuations.
81
Q

what is respiratory rate?

A
  • the rate at which an organism converts glucose into CO2 & water
  • calculated by measuring rate of oxygen consumption using a respirometer
82
Q

what is photosynthesis?

A
  • the production of carbon compounds in cells using light energy.
  • involves the conversion of light energy to chemical energy
83
Q

photosynthesis equation

A

6CO2 + 6H20 —> C6H12O6 + 602

carbon dioxide + water —light energy absorbed by chlorophyll—> glucose + oxygen

84
Q

what is chlorophyll?

A
  • a green pigment found in the chloroplasts of plants, algae, and some bacteria
  • main pigment of photosynthesis
  • absorbs red & blue light most effectively
  • reflects green light more than others
85
Q

what is the action spectrum of photosynthesis?

A
  • a graph showing the rate of photosynthesis for each wavelength of light.
  • the rate of photosynthesis is not the same for every wavelength of light.
86
Q

what is the absorption spectrum of photosynthesis?

A

a graph showing the percentage of light absorbed by pigments within the chloroplast, for each wavelength of light

87
Q

what is photolysis?

A

splitting water into hydrogen and oxygen using ATP

88
Q

photosynthesis stage 1: light dependent reactions

A
  1. chlorophyll absorbs light energy & converts that energy to ATP (chemical energy)
  2. light energy is also used in the photolysis of water
  3. oxygen that is split by photolysis is released as a waste product
89
Q

what are the limiting factors of photosynthesis?

A
  • temp
  • light intensity
  • CO2 concentration
90
Q

what is the effect of temperature on photosynthesis?

A
  • as temp /\ so does the kinetic energy of reactants = more collisions = increased rate
  • at the optimum temp = max rate
  • above optimum temp = rate \/ rapidly because enzymes denature
91
Q

what is the effect of CO2 concentration on photosynthesis?

A
  • low CO2 conc = low rate
  • as CO2 conc /\ , so does the rate
  • at high levels of CO2, there is no further increase in photosynthesis & rate reaches a plateau
  • this is due to reaching the saturation level
92
Q

what is the effect of light intensity on photosynthesis?

A
  • low light = low rate
  • as light /\, so does the rate
  • at a certain point further /\ in light will not /\ photosynthesis = at high light, rate reaches a plateau
  • this is because enzymes are working at their max rate
93
Q

globular proteins

A
  • round / spherical shape
  • functional purposes
  • soluble in water
  • irregular AA sequence
    e. g. enzymes and haemoglobin
94
Q

fibrous proteins

A
  • long and narrow
  • structural purposes
  • insoluble in water
  • repetitive AA sequence
    e. g. collagen and fibrin
95
Q

what is the function of rubisco

A

catalyzes the first reaction of the carbon-fixing reactions of photosynthesis

96
Q

what is rhodopsin

A

a pigment found in the retina of the eye which is useful in low light condition

IB biology sl (6 decks)

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