Molecular biology Flashcards
Includes: metabolism, water, carbohydrates, lipids, proteins, enzymes, structure of DNA and RNA, DNA replication, cell respiration, photosynthesis.
Define metabolism
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.
What are organic compounds?
molecules that contain carbon and are found in living things.
The function of carbon atoms
form the basis of organic life due to their capacity to form 4 covalent bonds.
What are the main groups of organic compounds in cells?
carbohydrates, lipids, proteins, and nucleic acids
What are carbohydrates, proteins and nucleic acids made of?
monomers- recurring subunits
What are the monomers and polymers of carbohydrates?
monomer: monosaccharide
polymer: polysaccharide
What are the monomers and polymers of nucleic acids?
monomer: amino acid
polymer: polypeptide
What are the monomers and polymers of proteins?
monomer: nucleotide
polymer: DNA or RNA
What are lipids composed of?
Lipids are not composed of repeating monomers, but contain smaller subunits such as triglyceride
- subunits: glycerol + fatty acid (x3)
What are the two types of reactions?
anabolism and catabolism
What is anabolism?
- synthesis of complex molecules from simpler ones
- involves condensation reaction (water is produced)
- example: photosynthesis
What is catabolism?
- synthesis of complex molecules into smaller ones
- involves hydrolysis (water is consumed)
- example: cellular respiration
What is the theory of vitalism?
doctrine that dictated that organic molecules could only be synthesized from living systems.
- it was disproved
What is water made up of?
- two hydrogen atoms covalently bonded to an oxygen atom (H20)
What makes water polar?
oxygen has higher electronegativity and attracts the shared electrons more strongly which results in polarity of water
Hydrogen bonding in water molecule
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
What are the cohesive properties of water?
- water can form intermolecular associations with other molecules that share common properties such as polarity
- water can form hydrogen bonds with other molecules (like molecules stick together)
- those properties result in relatively high surface tension
What are the solvent properties of water?
water is the universal solvent due to its capacity to dissolve a large number of substances
- large quantities of water molecules can weaken forces
Difference between cohesion and adhesion
- cohesion- like molecules stick together
- adhesion- unlike molecules stick together
What adhesive properties of water do?
allow for potential capillary action
- water can form polar associations with charged molecules (unlike molecules stick together)
What are the substances that can dissolve in water?
they are hydrophilic and include glucose, amino acids, sodium chloride, oxygen
What are the substances that cannot dissolve in water?
they are hydrophobic and include lipids such as fats and cholesterol
What are the thermal properties of water?
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
What are other properties of water?
- transparency allows the light to pass through it
- water expands when frozen
What is the example of inorganic molecule?
hydrogen carbonate
Four most common elements used by organisms
oxygen, carbon, nitrogen and hydrogen
What property of water makes it good at transferring heat?
hydrogen bonds
What are monosaccharides?
monomers of carbohydrates that function as the energy source
What are the main examples of monosaccharides?
glucose and ribose
How are monosaccharides joined to form polymers?
they are covalently joined by glycosidic linkages
What are polysaccharides?
polymers of carbohydrate that are used for:
- short term energy storage (glycogen and starch)
- structural components (cellulose)
- recognition/receptors (glycoproteins)
What are the main types of polysaccharides?
- cellulose
- starch
- glycogen
Describe starch
It is the energy storage in plants and it is composed of alpha glucose subunits. It has two forms:
- amylose - linear
- amylopectin - branched
Describe cellulose
It is the component of cell wall in plants. Linear molecule composed of beta glucose subunits.
Describe glycogen
It is the energy storage in animals. Branched molecule composed of alpha glucose subunits.
What is BMI?
Body mass index that can be calculated by:
- BMI= mass in kg/ (height in m)squared
Difference between the carbohydrates and lipids
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
What are lipids composed of?
They contain the elements such as carbon, hydrogen and oxygen.
Lipid relationship with water
They are insoluble in water and behave as “water-hating” molecules.
What is the structure of lipids?
They have the fatty acid group (COOH)
Monoglycerides structure
They have ester bonds and CH3 group
How monoglycerides are formed?
from glycerol that undergo the condensation reaction
What are the saturated fatty acids?
Saturated fatty acids have hydrocarbon chains connected by single bonds only. Rich sources of dietary saturated fatty acids include butter fat and meat fat
What are the unsaturated fatty acids?
Unsaturated fatty acids have one or more double bonds. Sources of it include avocado and peanuts
What are amino acids?
Monomers of a proteim that are linked together to form polypeptides. There are 20 amino acids.
The structure of amino acids
amine group, carboxyl group, variable side chain
Peptide bonds
Amino acids are covalently joined by peptide bonds to form polypeptide chains which required condensation reaction.
How is maltose formed ?
glucose + glucose
How is lactose formed ?
glucose + galactose
How is sucrose formed ?
glucose + fructose
What are the protein structures?
primary, secondary, tertiary, quaternary
Describe the primary structure of a protein
- order of amino acid sequence and formed by covalent peptide bonds
Describe the secondary structure of a protein
- folding into repeat patterns such as alpha helix or beta plated sheet
- formed by hydrogen bonds between the amine and carboxyl groups
Describe the tertiary structure of a protein
- overall three dimensional arrangement of polypeptide
- determined by interactions between variable side chains
Describe the quaternary structure of a protein
- presence of multiple polypetides
What are the main functions of proteins?
- enzymatic (rubisco)
- movement (actin, myosin)
- transport (haemoglobin)
- immunity (immunoglobulins)
- hormonal (insulin, glucagon)
- structure (spider silk, collagen)
What is proteome?
The totality of all proteins that are expressed within a cell, tissue or organism at a certain time.
Define denaturation and its causes
Structural change in protein that results in the loss of its biological properties. Causes:
- temperature (heat breaks bonds)
- pH (alters protein change)
Enzymes
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
What is the substrate?
It binds to a complementary region on the enzyme’s surface called active site.
What are the two models of enzyme activity?
- lock and key model
- induced fit model
Explain the lock and key model
enzyme and substrate complement each other precisely in terms of both their shape and chemical properties
- active site and the substrate will share specificity
Explain the induced fit model
- 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
Factors that affect the enzyme activity
- temperature
- pH
- substrate concentration
How temperature affects the enzyme activity?
- increases the enzyme activity
- enzyme activity peaks at an optimal temperature
- higher temperature will decrease its activity because it causes denaturation
How pH affects the enzyme activity?
- enzyme activity is at its highest at an optimal pH range
- activity decreases outside of this range due to denaturation
How substrate concentration affects the enzyme activity?
- increases the enzyme activity
- at a certain point, the activity stays constant
Explain the concept of enzyme kinetics
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.
What is the application for immobilised enzymes?
production of lactose-free milk and associated dairy products.
- lactase digests lactose into glucose
- lactase is fixed to an inert surface
What are the benefits associated with lactose-free milk?
- source of dairy for lactose-intolerant people
- increases sweetness of milk
-reduces crystallization and production time for cheese
What are the enzyme inhibitors?
chemical substances that reduce the activity of enzymes or prevent it.
What are the two types of enzyme inhibitors?
competitive and non-competitive inhibitors
Competitive inhibitors
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
Non-competitive inhibitors
The inhibition that does not resemble the substrate bind to the enzyme at different site from 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
What are nucleotides?
The monomer of a nucleic acid
What nucleotide consists of?
- pentose sugar
- phosphate groups
- nitrogenous base
Difference between purines and pyrimidines
Purines (adenine and guanine) are two-carbon nitrogen ring bases while pyrimidines (cytosine and thymine) are one-carbon nitrogen ring bases.
How polynucleotide is created?
- 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
What is the structure of DNA?
- two complementary strands that line up in opposite directions with the bases facing inwards and connected by hydrogen bonds
What is the structure of RNA?
The polynucleotide chain that is single stranded
Difference between RNA and DNA
DNA sugar is deoxyribose, RNA sugar is ribose. DNA has thymine and RNA has uracil. DNA is double stranded and RNA is single stranded.
Who and how elucidated DNA structure ?
- 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
Cell respiration - describe
Controlled release of energy from organic compounds to produce ATP.
What are the main compounds used in cell respiration?
carbohydrates, lipids, and proteins
What is ATP?
Adenosine triphosphate is a molecule that functions as an immediate source of energy when hydrolysed to form ADP.
- ADP + Pi = free energy
Glycolysis
It is the break down of glucose that occurs in the cytoplasm of the cell.
Steps of glycolysis
- glucose is broken down into two pyruvates (C3)
- 2 ATP molecules are created
- the reduction of NAD+ to 2NADH + H+
What if the oxygen is absent in the cell?
Fermentation leads to production of lactic acid.
Anaerobic respiration
- 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
Aerobic respiration
- 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
Fermentation
Reversible anaerobic process that allows ATP production to continue without the oxygen. It restores NAD+ stocks to ensure the production of ATP in glycolysis.
Fermentation in animals
Produces lactic acid and is used to maximise muscle contractions when oxygen is limited
- this reaction can be reversed when oxygen is restored
Fermentation in plants
Produces ethanol and carbon dioxide gas which can be use in baking.
What is the respirometer
determines an organism’s respiration rate by measuring carbon dioxide production or oxygen uptake.
What types of work cells require energy for?
- chemical work- synthesis of polymers
- transport work - pumping substances across the membrane
- mechanical work- concentration of muscle
What are the important features of ATP?
- moving within cells and organisms
- takes part in many steps of cellular respirations
- delivers energy in small amounts
Oxidation in cell respiration
Oxidation describes chemical reactions where electrons are lost
Reduction in cell respiration
Reduction refers to reactions where electrons are gained.
Steps of link reaction
- 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.
Steps of krebs cycle
- Acetyl-CoA combines with oxaloacetate to form citrate.
- Citrate is converted and that leads to production of NADH and CO₂.
- Alpha-ketoglutarate is oxidized to succinyl-CoA, producing NADH and CO₂.
- Succinyl-CoA generates ATP and forms succinate.
- Succinate is oxidized to fumarate, producing FADH₂.
- Fumarate is hydrated to form malate.
- Malate is oxidized to regenerate oxaloacetate, producing NADH.
Electron transport chain
- 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.
- Electrons from both complex are transferred carrier called Coenzyme Q. This molecule carries the electrons to complex III.
- 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
What is the terminal electron acceptor in mitochondrial respiration?
O2
Most CO2 is released where?
Krebs Cycle
What is the function of redox reactions?
providing the energy that establishes the proton gradient
The immediate energy source that drives the ATP synthesis in oxidative phosphorylation is…
H+ concentration gradient across the membrane holding ATP synthase
Final electron acceptor of the electron transport chain is…
oxygen
Chemiosmosis
Formation of ATP by the movement of hydrogen ions (H+) across a membrane during cellular respiration.
Photosynthesis
involves the use of light energy to synthesize organic compounds from inorganic molecules.
Explain the concept of light spectrum
Visible light has a range of wavelengths. Violet has the shortest wavelength (further), red has the longest one (closer).
Photosynthesis reaction
6 Carbon dioxide + 12 Water = Glucose + 6 Oxygen + 6 Water
Why are pigments important in photosynthesis?
they are required for light energy conversion into chemical energy
Define chlorophyll
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
What is the absorption spectrum?
Indicates the wavelengths of light absorbed by each photosynthetic pigment
What is the action spectrum?
Indicates the overall rate of photosynthetic activity at each wavelength of light
What are the two stages of photosynthesis?
- light dependent reaction
- light independent reaction
Light dependent reaction
- 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.
Light independent reaction
- CO₂ combines with RuBP to form 3-PGA.
- ATP and NADPH convert 3-PGA into G3P.
- Some G3P regenerates RuBP.
-Remaining G3P forms carbohydrates. - ADP, NADP⁺, and Pi are released for reuse in the light reactions.
Photosystem I
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.
Photosystem II
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.
Where the light and dark reaction take place?
Light reaction takes place in grana and the dark reaction takes place in stroma regions of the chloroplast.
Two chain pathways
glycolysis and link reaction
Two ring metabolic pathways
Krebs cycle and Calvin cycle
What is the net energy yield from glycolysis for one glucose molecule?
2 ATP
Hydrogen carrier in the glycolysis reaction
NADH
Why the inner mitochondrial membrane is folded?
Increases the capacity of the mitochondria to synthesize ATP -> those folds are called cristae
Two molecules that transport electrons to ETC
NADH and FADH2
how many proton pumps are in oxidative phosphorylation?
3
Final enzyme in ETC
cytochrome oxidase
Function of intermembrane space
Allows for rapid build-up of H+ concentration
Phosphorylation
Phosphate is added to a compound
Lysis reaction
Breakdown of the membrane of the cell
Transfer of protons from the intermembrane space to matrix
Diffusion
Differences between the oxidative phosphorylation and photophosphorylation
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.
function of granum
they are made up of stacks of thylakoids to increase the surface area available for the ETC
Function of thylakoid
maximizes the electrochemical gradient that results from proton accumulation
function of stroma
contains suitable enzymes and an appropriate pH for calvin cycle to occur
Function of outer membrane in mitochondria
contains necessary transport proteins for shuttling pyruvate into mitochondria
What mitochondrial matrix contains?
suitable enzymes and appropriate pH for the Krebs cycle to occur
What is the electron tomography?
technique in which a 3 dimensional image of an internal cellular structure can be generated
What is the exergonic reaction?
if reactants contain more energy than the products, the energy is releases (catabolic reactions)
What is the endergonic reaction?
if reactants contain less energy than the products, the energy is absorbed (anabolic reactions)
Example of competitive inhibition
treating influenza with neuraminidase inhibitor
Example of non-competitive inhibition
cyanide as an inhibitor of cytochrome oxidase
How to calculate the reaction rate?
reaction rate = 1/ time taken
Feedback inhibition
matabolic pathways can be controlled by feedback inhibition where a product inhibits an earlier step.
What is the use of inhibitors?
inhibitors can be used to treat infectious diseases by targeting the enzymes involved in pathogenesis.
What is the function of the electron carriers?
transfer chemical energy via redox reactions
Oxidation is associated with
loss of electrons, loss of hydrogen but gain of the oxygen
Reduction is associated with
gain of electrons, gain of hydrogen, and loss of the oxygen
What was the lollipop experiment
- light independent reactions were elucidated by Melvin Calvin using a lollipop-shaped apparatus
- radioactive CO2 was incorporated to identify the different carbon compounds
