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Chlorophyll me up :) > Molecular Biology > Flashcards

Molecular Biology Flashcards

1
Q

Define metabolism

A

The totality of chemical processes that occur within a living organism in order to maintain life. It is the web of all enzyme-catalysed reactions that occur within a particular cell or organism.

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2
Q

What are organic compounds?

A

molecules that contain carbon and are found in living things.

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3
Q

The function of carbon atoms

A

form the basis of organic life due to their capacity to form 4 covalent bonds.

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4
Q

What are the main groups of organic compounds in cells?

A

carbohydrates, lipids, proteins, and nucleic acids

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5
Q

What are carbohydrates, proteins and nucleic acids made of?

A

monomers- recurring subunits

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6
Q

What are the monomers and polymers of carbohydrates?

A

monomer: monosaccharide
polymer: polysaccharide

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7
Q

What are the monomers and polymers of nucleic acids?

A

monomer: nucleotides
polymer: RNA and DNA

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8
Q

What are the monomers and polymers of proteins?

A

monomer: amino acids
polymer: polypeptides

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9
Q

What are lipids composed of?

A

Lipids are not composed of repeating monomers, but contain smaller subunits such as triglyceride
- subunits: glycerol + fatty acid (x3)

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10
Q

What are the two types of reactions?

A

anabolism and catabolism

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11
Q

What is anabolism?

A
  • synthesis of complex molecules from simpler ones
  • involves condensation reaction (water is produced)
  • example: photosynthesis
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12
Q

What is catabolism?

A
  • synthesis of complex molecules into smaller ones
  • involves hydrolysis (water is consumed)
  • example: cellular respiration
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13
Q

What is the theory of vitalism?

A

organic molecules could only be synthesized from living systems.
- it was disproved

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14
Q

What is water made up of?

A
  • two hydrogen atoms covalently bonded to an oxygen atom (H20)
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15
Q

What makes water polar?

A

oxygen has higher electronegativity and attracts the shared electrons more strongly which results in polarity of water

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16
Q

Hydrogen bonding in water molecule

A

The dipolarity of the water molecule enables it to form polar associations with other charged molecules
Water molecules can form hydrogen bonds with other water molecules

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17
Q

What are the cohesive properties of water?

A
  • water can form intermolecular associations with other molecules that share common properties such as polarity
  • water can form hydrogen bonds with other molecules (alike molecules stick together)
  • those properties result in relatively high surface tension
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18
Q

What are the solvent properties of water?

A

water is the universal solvent due to its capacity to dissolve a large number of substances
- large quantities of water molecules can weaken forces

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19
Q

Difference between cohesion and adhesion

A
  • cohesion- alike molecules stick together
  • adhesion- unlike molecules stick together
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20
Q

What adhesive properties of water do?

A

allow for potential capillary action
- water can form polar associations with charged molecules (unlike molecules stick together)

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21
Q

What are the substances that can dissolve in water?

A

they are hydrophilic and include glucose, amino acids, sodium chloride, oxygen

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22
Q

What are the substances that cannot dissolve in water?

A

they are hydrophobic and include lipids such as fats and cholesterol

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23
Q

What are the thermal properties of water?

A

water absorbs large amounts of heat energy before undergoing a resultant change in state
- extensive hydrogen bonding has to be broken first
- these properties make water a very effective coolant - high specific heat capacity

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24
Q

What are other properties of water?

A
  • transparency allows the light to pass through it
  • water expands when frozen
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25
Q

What is the example of inorganic molecule?

A

hydrogen carbonate

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26
Q

Four most common elements used by organisms

A

oxygen, carbon, nitrogen and hydrogen

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27
Q

What property of water makes it good at transferring heat?

A

hydrogen bonds

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28
Q

What are monosaccharides?

A

monomers of carbohydrates that function as the energy source

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29
Q

What are the main examples of monosaccharides?

A

glucose and ribose

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30
Q

How are monosaccharides joined to form polymers?

A

they are covalently joined by glycosidic linkages

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31
Q

What are polysaccharides?

A

polymers of carbohydrate that are used for:
- short term energy storage (glycogen and starch)
- structural components (cellulose)
- recognition/receptors (glycoproteins)

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32
Q

What are the main types of polysaccharides?

A
  1. cellulose
  2. starch
  3. glycogen
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33
Q

Describe starch

A

It is the energy storage in plants and it is composed of alpha glucose subunits. It has two forms:
- amylose - linear
- amylopectin - branched

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34
Q

Describe cellulose

A

It is the component of cell wall in plants. Linear molecule composed of beta glucose subunits.

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35
Q

Describe glycogen

A

It is the energy storage in animals. Branched molecule composed of alpha glucose subunits.

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36
Q

What is BMI?

A

Body mass index that can be calculated by:
- BMI= mass in kg/ (height in m)squared

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37
Q

Difference between the carbohydrates and lipids

A

carbohydrates:
- short term storage
- smaller ATP yield
- easy to digest
- soluble in water
lipids:
- long term storage
-larger ATP yield
- harder to digest
- insoluble in water

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38
Q

What are lipids composed of?

A

They contain the elements such as carbon, hydrogen and oxygen.

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39
Q

Lipid relationship with water

A

They are insoluble in water and behave as “water-hating” molecules.

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40
Q

What is the structure of lipids?

A

They have the fatty acid group (COOH)

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41
Q

Monoglycerides structure

A

They have ester bonds and CH3 group

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42
Q

How monoglycerides are formed?

A

from glycerol that undergoes the condensation reaction

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43
Q

What are the saturated fatty acids?

A

Saturated fatty acids have hydrocarbon chains connected by single bonds only. Rich sources of dietary saturated fatty acids include butter fat and meat fat

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44
Q

What are the unsaturated fatty acids?

A

Unsaturated fatty acids have one or more double bonds. Sources of it include avocado and peanuts

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45
Q

What are amino acids?

A

Monomers of a protein that are linked together to form polypeptides. There are 20 amino acids.

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46
Q

The structure of amino acids

A

amine group, carboxyl group, variable side chain

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47
Q

Peptide bonds

A

Amino acids are covalently joined by peptide bonds to form polypeptide chains which required condensation reaction.

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48
Q

How is maltose formed ?

A

glucose + glucose

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49
Q

How is lactose formed ?

A

glucose + galactose

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50
Q

How is sucrose formed ?

A

glucose + fructose

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51
Q

What are the protein structures?

A

primary, secondary, tertiary, quaternary

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52
Q

Describe the primary structure of a protein

A
  • order of amino acid sequence and formed by covalent peptide bonds
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53
Q

Describe the secondary structure of a protein

A
  • folding into repeat patterns such as alpha helix or beta plated sheet
  • formed by hydrogen bonds between the amine and carboxyl groups
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54
Q

Describe the tertiary structure of a protein

A
  • overall three dimensional arrangement of polypeptide
  • determined by interactions between variable side chains
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55
Q

Describe the quaternary structure of a protein

A
  • presence of multiple polypetides
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56
Q

What are the main functions of proteins?

A
  • enzymatic (rubisco)
  • movement (actin, myosin)
  • transport (haemoglobin)
  • immunity (immunoglobulins)
  • hormonal (insulin, glucagon)
  • structure (spider silk, collagen)
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57
Q

What is proteome?

A

The totality of all proteins that are expressed within a cell, tissue or organism at a certain time.

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58
Q

Define denaturation and its causes

A

Structural change in protein that results in the loss of its biological properties. Causes:
- temperature (heat breaks bonds)
- pH (alters protein change)

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59
Q

Enzymes

A

globular protein which speeds up the rate of chemical equation by lowering the activation energy
- the molecule, the enzyme reacts with is called the substrate

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60
Q

What is the substrate?

A

It binds to a complementary region on the enzyme’s surface called active site.

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61
Q

What are the two models of enzyme activity?

A
  • lock and key model
  • induced fit model
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62
Q

Explain the lock and key model

A

enzyme and substrate complement each other precisely in terms of both their shape and chemical properties
- active site and the substrate will share specificity

63
Q

Explain the induced fit model

A
  • active site is not a rigid fit for the substrate and changes its conformation to better accommodate the substrate
  • this stresses the substrate bonds and induces catalysis
64
Q

Factors that affect the enzyme activity

A
  • temperature
  • pH
  • substrate concentration
65
Q

How temperature affects the enzyme activity?

A
  • increases the enzyme activity
  • enzyme activity peaks at an optimal temperature
  • higher temperature will decrease its activity because it causes denaturation
66
Q

How pH affects the enzyme activity?

A
  • enzyme activity is at its highest at an optimal pH range
  • activity decreases outside of this range due to denaturation
67
Q

How substrate concentration affects the enzyme activity?

A
  • increases the enzyme activity
  • at a certain point, the activity stays constant
68
Q

Explain the concept of enzyme kinetics

A

the rate of enzyme catalysis can be increased by increasing the frequency of enzyme-substrate collisions. The rate of enzyme catalysis is decreased by denaturation.

69
Q

What is the application for immobilised enzymes?

A

production of lactose-free milk and associated dairy products.
- lactase digests lactose into glucose

70
Q

What are the benefits associated with lactose-free milk?

A
  • source of dairy for lactose-intolerant people
  • increases sweetness of milk
  • reduces crystallization and production time for cheese
71
Q

What are the enzyme inhibitors?

A

chemical substances that reduce the activity of enzymes or prevent it.

72
Q

What are the two types of enzyme inhibitors?

A

competitive and non-competitive inhibitors

73
Q

Competitive inhibitors

A

Molecules that sufficiently resemble the substrate in shape may compete to occupy the active site. It blocks the active site, preventing the substrate from entering.
- it reduces the rate of reaction slightly

74
Q

Non-competitive inhibitors

A

The inhibitor that does not resemble the substrate and does not bind the with active site. They bind to allosteric site on the enzyme. The active site is altered and the substrate cannot attach to it and react.
- it reduces the rate of reaction more than competitive enzymes

75
Q

What are nucleotides?

A

The monomer of a nucleic acid

76
Q

What nucleotide consists of?

A
  • pentose sugar
  • phosphate groups
  • nitrogenous base
77
Q

Difference between purines and pyrimidines

A

Purines (adenine and guanine) are two-carbon nitrogen ring bases while pyrimidines (cytosine and thymine) are one-carbon nitrogen ring bases.

78
Q

How polynucleotide is created?

A
  • nucleotides are linked together into a single strand via condensation reaction
  • this polynucleotide arrangement results in formation of sugar-phosphte backbone that is covalently linked together by phosphodiester bonds
79
Q

What is the structure of DNA?

A
  • two complementary strands that line up in opposite directions with the bases facing inwards and connected by hydrogen bonds
80
Q

What is the structure of RNA?

A

The polynucleotide chain that is single stranded

81
Q

Difference between RNA and DNA

A

DNA sugar is deoxyribose, RNA sugar is ribose. DNA has thymine and RNA has uracil. DNA is double stranded and RNA is single stranded.

82
Q

Who and how elucidated DNA structure ?

A
  • Watson and Crick
  • they developed a DNA model that demonstrated a double helix structure composed of antiparallel DNA strands and it is internally facing bases with complementary pairing
83
Q

Cell respiration - describe

A

Controlled release of energy from organic compounds to produce ATP.

84
Q

What are the main compounds used in cell respiration?

A

carbohydrates, lipids, and proteins

85
Q

What is ATP?

A

Adenosine triphosphate is a molecule that functions as an immediate source of energy when hydrolysed to form ADP.
- ADP + Pi = free energy

86
Q

Glycolysis

A

It is the break down of glucose that occurs in the cytoplasm of the cell.

87
Q

Steps of glycolysis

A
  • glucose is broken down into two pyruvates (C3)
  • 2 ATP molecules are created
  • the reduction of NAD+ to 2NADH + H+
88
Q

What if the oxygen is absent in the cell?

A

Fermentation leads to production of lactic acid.

89
Q

Anaerobic respiration

A
  • occurs in cytoplasm
  • results in small energy yield (2ATP from glycolysis)
  • forms lactic acid (animals) or ethanol and CO2 (plants)
  • fermentation and it is reversible
90
Q

Aerobic respiration

A
  • occurs in mitochondria and requires oxygen
  • results in large energy yield (around 36 ATP per glucose)
  • forms carbon dioxide and water
  • uses hydrogen carriers to make ATP
91
Q

Fermentation

A

Reversible anaerobic process that allows ATP production to continue without the oxygen. It restores NAD+ stocks to ensure the production of ATP in glycolysis.

92
Q

Fermentation in animals

A

Produces lactic acid and is used to maximise muscle contractions when oxygen is limited
- this reaction can be reversed when oxygen is restored

93
Q

Fermentation in plants

A

Produces ethanol and carbon dioxide gas which can be use in baking.

94
Q

What is the respirometer

A

determines an organism’s respiration rate by measuring carbon dioxide production or oxygen uptake.

95
Q

What types of work cells require energy for?

A
  • chemical work- synthesis of polymers
  • transport work - pumping substances across the membrane
  • mechanical work- contraction of muscle
96
Q

What are the important features of ATP?

A
  • moving within cells and organisms
  • takes part in many steps of cellular respirations
  • delivers energy in small amounts
97
Q

Oxidation in cell respiration

A

Oxidation describes chemical reactions where electrons are lost

98
Q

Reduction in cell respiration

A

Reduction refers to reactions where electrons are gained.

99
Q

Steps of link reaction

A
  • Pyruvate enters mitochondrial matrix
  • Pyruvate loses carbon (as CO2) and hydrogen, forming acetyl-CoA and NADH.
  • Acetyl-CoA joins with coenzyme A.
  • Acetyl-CoA is ready for the Krebs Cycle.
100
Q

Steps of krebs cycle

A
  • Acetyl-CoA from link reaction enters Krebs Cycle and it is converted to CoA
  • C6 is converted and that leads to production of NADH and CO₂ from NAD+
  • C5 is oxidized to C4, producing NADH and CO₂ from NAD+
  • C4 generates GTP from GDP and Pi
  • The electron carrier from FAD is reduced, producing FADH₂.
  • C4 is regenerated producing NADH.
101
Q

Electron transport chain

A
  • takes place in the inner mitochondrial membrane
  • In complex I, NADH from glycolysis and Krebs cycle is oxidized to NAD+ and it passes 2 electrons and H+ ions are pumped into intermembrane space
  • FADH2 from Krebs cycle and glycolysis is oxidized to FAD by complex II. It releases the H+ ions into intermembrane space and passes off electrons.
  • Complex III accepts the electrons and pumps more H+
  • Electrons in the complex III are picked by cytochrome C. This molecule transports electrons to complex IV.
  • In Complex IV, reaction with oxygen produces water. More H+ ions are pumped and now this concentration is very high
  • H+ ions need to cross the membrane to balance the concentration gradient. They use ATP Synthase and as those ions pass, the pump makes ATP
102
Q

What is the terminal electron acceptor in mitochondrial respiration?

A

O2

103
Q

Most CO2 is released where?

A

Krebs Cycle

104
Q

What is the function of redox reactions?

A

providing the energy that establishes the proton gradient

105
Q

The immediate energy source that drives the ATP synthesis in oxidative phosphorylation is…

A

H+ concentration gradient across the membrane holding ATP synthase

106
Q

Final electron acceptor of the electron transport chain is…

A

oxygen

107
Q

Chemiosmosis

A

Formation of ATP by the movement of hydrogen ions (H+) across a membrane during cellular respiration.

108
Q

Photosynthesis

A

involves the use of light energy to synthesize organic compounds from inorganic molecules.

109
Q

Explain the concept of light spectrum

A

Visible light has a range of wavelengths. Violet has the shortest wavelength (further), red has the longest one (closer).

110
Q

Photosynthesis reaction

A

6 Carbon dioxide + 12 Water = Glucose + 6 Oxygen + 6 Water

111
Q

Why are pigments important in photosynthesis?

A

they are required for light energy conversion into chemical energy

112
Q

Define chlorophyll

A

Main photosynthetic pigment that is located in the chloroplasts in plant cells.
- it absorbs the red and blue lights more efficiently
- it reflects the green light

113
Q

What is the absorption spectrum?

A

Indicates the wavelengths of light absorbed by each photosynthetic pigment

114
Q

What is the action spectrum?

A

Indicates the overall rate of photosynthetic activity at each wavelength of light

115
Q

What are the two stages of photosynthesis?

A
  • light dependent reaction
  • light independent reaction
116
Q

Light dependent reaction

A
  • Chlorophyll molecules in the thylakoid membranes absorb light energy.
  • The absorbed light energy stimulates electrons in chlorophyll.
  • Electrons are passed through an electron transport chain (ETC), generating a proton gradient and releasing oxygen through water splitting.
  • Excited electrons from PSII replenish those lost in PSI, where they’re used to reduce NADP⁺ to NADPH.
    -Proton gradient created by ETC powers ATP synthesis through ATP synthase complexes.
  • ATP and NADPH are used in the Calvin cycle to convert carbon dioxide into carbohydrates.
117
Q

Light independent reaction

A
  • 3 molecules of CO₂ enter Calvin cycle
  • CARBON FIXATION: 3CO2 combines with RuBP to form 2 molecules of 3-PGA, 6 molecules of ATP are converted to 6 ADP
  • REDUCTION: 6 NADPH are converted to 6 NADP + H+, ATP and NADPH convert 3-PGA into G3P which forms glucose
  • REGENERATION: G3P is recycled, it regenerates rubisco and 3ATP form 3 ADP
118
Q

Photosystem I

A

Photosystem I absorbs light energy and excites electrons, which are then transferred through an ETC. Electrons ultimately reduce NADP⁺ to NADPH, providing the reducing power necessary for the Calvin cycle.

119
Q

Photosystem II

A

Photosystem II absorbs light energy, exciting electrons within its chlorophyll molecules. These electrons are then transferred through an ETC, generating a proton gradient and releasing oxygen through the splitting of water molecules. PSII replenishes the electrons lost by PSI, ensuring a continuous flow of electrons during the light-dependent reactions of photosynthesis.

120
Q

Where the light and dark reaction take place?

A

Light reaction takes place in grana and the dark reaction takes place in stroma regions of the chloroplast.

121
Q

Two chain pathways

A

glycolysis and link reaction

122
Q

Two ring metabolic pathways

A

Krebs cycle and Calvin cycle

123
Q

What is the net energy yield from glycolysis for one glucose molecule?

A

2 ATP

124
Q

Hydrogen carrier in the glycolysis reaction

A

NADH

125
Q

Why the inner mitochondrial membrane is folded?

A

Increases the capacity of the mitochondria to synthesize ATP -> those folds are called cristae

126
Q

Two molecules that transport electrons to ETC

A

NADH and FADH2

127
Q

how many proton pumps are in oxidative phosphorylation?

A

3

128
Q

Final enzyme in ETC

A

cytochrome oxidase

129
Q

Function of intermembrane space

A

Allows for rapid build-up of H+ concentration

130
Q

Phosphorylation

A

Phosphate is added to a compound

131
Q

Lysis reaction

A

Breakdown of the membrane of the cell

132
Q

Transfer of protons from the intermembrane space to matrix

A

Diffusion

133
Q

Differences between the oxidative phosphorylation and photophosphorylation

A

photophosphorylation takes place in chloroplast not in the mitochondrion. Oxidative phosphorylation takes place in the cellular respiration, the other one in the light reaction. Photophosphorylation gains ATP by sun radiation and the other one by organic compounds.

134
Q

function of granum

A

they are made up of stacks of thylakoids to increase surface area of thylakoids

135
Q

Function of thylakoid

A

maximizes the electrochemical gradient that results from proton accumulation

136
Q

function of stroma

A

contains suitable enzymes and an appropriate pH for calvin cycle to occur

137
Q

Function of outer membrane in mitochondria

A

contains necessary transport proteins for shuttling pyruvate into mitochondria

138
Q

What mitochondrial matrix contains?

A

suitable enzymes and appropriate pH for the Krebs cycle to occur

139
Q

What is the electron tomography?

A

technique in which a 3 dimensional image of an internal cellular structure can be generated

140
Q

What is the exergonic reaction?

A

if reactants contain more energy than the products, the energy is releases (catabolic reactions)

141
Q

What is the endergonic reaction?

A

if reactants contain less energy than the products, the energy is absorbed (anabolic reactions)

142
Q

Example of competitive inhibition

A

treating influenza with neuraminidase inhibitor

143
Q

Example of non-competitive inhibition

A

cyanide as an inhibitor of cytochrome oxidase

144
Q

How to calculate the reaction rate?

A

reaction rate = 1/ time taken

145
Q

Feedback inhibition

A

matabolic pathways can be controlled by feedback inhibition where a product inhibits an earlier step.

146
Q

What is the use of inhibitors?

A

inhibitors can be used to treat infectious diseases by targeting the enzymes involved in pathogenesis.

147
Q

What is the function of the electron carriers?

A

transfer of chemical energy via redox reactions

148
Q

Oxidation is associated with

A

loss of electrons, loss of hydrogen but gain of the oxygen

149
Q

Reduction is associated with

A

gain of electrons, gain of hydrogen, and loss of the oxygen

150
Q

What was the lollipop experiment

A
  • light independent reactions were elucidated by Melvin Calvin using a lollipop-shaped apparatus
  • radioactive CO2 was incorporated to identify the different carbon compounds
151
Q

What is pentose sugar?

A
  • ribose
  • deoxyribose
  • has two OH groups at the bottom
152
Q

What is hexose sugar?

A
  • glucose
  • fructose
  • galactose
  • has two OH groups on the right side
153
Q

Difference between alpha glucose and beta glucose

A
  • alpha glucose- glucose molecule where the OH is oriented downwards
  • beta glucose- OH is oriented upwards

Chlorophyll me up :) (7 decks)

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