UNIT 2/8 - Molecular Biology Flashcards
Define condensation reaction of the nucleotide
combination of nitrogenous base, pentose sugar, phosphoric acid to form a nucleotide (and two molecules of water)
State the role of proteins for the DNA
proteins make up more than 50% of chromosome
supporting and packaging role for DNA
List the functions of the nucleosomes
help in packaging of DNA during mitosis or meiosis by supercoiling
markers of particular genes, either to promote gene expression or silence a gene
Define a dehydration reaction
either a hydroxyl group from one molecule combines with a hydrogen atom from the other molecule, or two hydrogen atoms from one molecule combine with an oxygen atom on the other molecule. In either case, water is released, and the two molecules are joined together.
Explain why the hydrogen bonds can form between the atoms within the polypeptide backbone
the oxygen atoms have partially negative charge and the hydrogen atoms attached to nitrogen have partial positive charge
Distinguish fibrous and globular proteins and provide examples for both
fibrous - long and narrow shape, insoluble in water
e.g. collagen, keratin, myosin
globular - round shape, soluble in water
e.g. enzymes (catalase), some hormones - insulin, hemoglobin, immunoglobin
Give examples on how the distribution of non-polar and polar amino acids affect protein function and location
- controlling the position in plasma membranes - non-polar amino acids causing proteins to be embedded in membranes while polar amino acids causing portions of the proteins to protrude from the membrane
- creating hydrophilic channels through membranes - polar amino acids found inside membrane proteins and create a channel through which hydrophilic molecules can pass through
- specificity of active site in enzymes - if non-polar amino acids make up the active site of an enzyme it makes the active specific to non-polar substance and vice versa
Describe how on the example of the sickle-cell disease a slight change in primary structure can affect protein’s shape and ability to function
sickle-cell disease is an inherited blood disorders caused by the substitution of ONE amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin
therefore hydrophobic interactions between sickle-cell hemoglobin proteins lead to their aggregation into fiber and the capacity to carry oxygen is greatly reduced causing the patient anemia, damage nerves and organs, including kidneys, liver and spleen, and can be fatal
Define starch and distinguish its two types
is the stored form of sugars in plants and is made up of a mixture of two polysaccharides:
- amylose and amylopectin (polymers of glucose)
amylose - entirely unbranched chains of glucose monomers connected by 1-4 linkages
amylopectin - branched polysaccharide, most monomers connected by 1-4 linkages but some 1-6 occur periodically causing branched points
Distinguish and define main three polysaccharides
glycogen - storage carbohydrate formed from glucose in the liver, muscle cells and other cells (not in brain) when glucose is not immediately required for cellular respiration, hydrolysis releases glucose from it when the demand for sugar increases, extensively branched, composed of a-glucose linked together by both 1-4 linkages and 1-6 linkages (branching)
cellulose - manufactured in cells and laid down externally, in bundles of fibers, as the main component of the cell walls, linear molecule composed of β-glucose subunits (bound in a 1-4 arrangement)
starch (has its own flashcard lucky bastard)
Explain why are fatty acids such a high-density energy storage
metabolism of fatty acids in cell respiration skips glycolysis and instead Coenzyme A cuts off carbon atoms from the fatty acid in the link reaction and carries them to the Krebs cycle
therefore longer chains are a greater store of potential energy
List the roles of fats and oils in living things
- energy store and metabolic water source
- subcutaneous fat as a buoyancy aid and thermal insulation
- water-proofing of hair and feathers
- electrical insulation
- phospholipid bilayer is a major component of the plasma membrane
Compare and distinguish carbohydrates from lipids as an energy source
CARBOHYDRATE (glycogen)
- short-term energy storage
- more effect on osmotic pressure
- more readily digested- used for aerobic or anaerobic respiration.
- stores half as much ATP per gram
- water soluble as monomers/dimers - easier to transport
LIPID (triglyceride)
- long-term energy storage
- less effect on osmotic pressure.
- less easily digested - can only be used for aerobic respiration.
- stores twice as much ATP per gram
- not water soluble (hydrophobic) - more difficult to transport
Define the term monosaccharides, state its general chemical formula and list examples
monomers of carbohydrates linked together by condensation reactions to form disaccharides and polysaccharides polymers,
small, sweet taste, water soluble
CnH2nOn
e.g. glucose, galactose, fructose
Define the term disaccharides and list examples
carbohydrates mase of two monosaccharides combined together in condensation reaction via glycosidic linkage
small enough to be soluble in water, transport form commonly
e.g. lactose, maltose, sucrose
Define the term polysaccharides and list examples
macromolecules polymers with a few hundred to a few thousand monosaccharides joined together in condensation reaction via glycosidic linkages
used for energy storage or cell structure, play a role in cell recognition
e.g. cellulose, glycogen, starch
State on what does the type of polymer formed depend on
monosaccharide subunits involved
Determine why is cellulose indigestible for most animals and state ones that have the ability to digest it
its composed of β-glucose and most animals lack the enzyme required to break it down
the misfits:
- Ruminants (e.g. cows) may digest cellulose due to the presence of helpful bacteria in a specialized stomach
- Chaecotrophs (e.g. rabbits) will re-ingest specialized feces that contain digested cellulose (broken down in the caecum)
Classify monosaccharides depending on the amount of carbon atoms
trioses - contain 3 carbons, formula C3H6O3
pentoses - contain 5 carbons, formula C5H10O5
hexoses - contain 6 carbons, formula C6H12O6
State another name for condensation reaction
dehydration synthesis reaction
State when does monosaccharides form rings
in aqueous solutions
Define what is glycosidic linkage
covalent bond between two subunits of polysaccharides formed by dehydration
Distinguish α-glucose from β-glucose
differ in placement of the hydroxyl group attached to number 1 carbon
(alpha has it down, beta up)
List reasons for why glucose is an especially important monosaccharide
in animals:
- glucose is transported to cells in blood plasma
- glucose is used as a respiratory substrate for cellular respiration or converted to glycogen (storage carbohydrate)
in plants:
- a first product of photosynthesis
Distinguish dehydration reaction from hydrolysis
dehydration - synthesizing a polymer
removes a water molecule forming a new bond
hydrolysis - breaks down a polymer
adds a water molecule, breaking a bond
Distinguish 3 most popular disaccharides and show their functions
lactose - produced in mammary glands, secreted into the milk as an important component in the diet of very young mammals(galactose + glucose)
sucrose - produced in green leaves from glucose and fructose, transported in plant in solution in the vascular bundles (glucose + fructose)
maltose - breakdown product in the hydrolysis of starch (glucose +glucose)
Define fatty acids
long hydrocarbon chains found in certain types of lipids (triglycerides and phospholipids), all have a hydroxyl group (-COOH), methyl group (CH3-) and chains of hydrocarbons (11-23 carbon long)
insoluble in water, soluble in organic solvents
List and define types of fatty acids
saturated fatty acids - are saturated with hydrogen (carbons carry as many hydrogen atoms as they can), found in animal products (butter, bacon, red meat), solid at room temp, straight AF = no double bonds, high density energy store=high CHD risk
monounsaturated fatty acids - one double bond, typically liquid at room temp, kinked
polyunsaturated fatty acids - have at least two double bonds in the carbon chain, come from plants, tend to be liquids in room temp, very kinked, bended
Define the term hydrogenation
complete or partial elimination of the double-bonds by adding hydrogen atoms
straightens out the natural bent of unsaturated fatty acids
present in many heavily processed fatty acids
Distinguish two distinct structural configurations of unsaturated fatty acids
cis - hydrogen atoms attached to carbon double bond on the same side, less CDH risk, oils at room temp
trans - unsaturated but linear structure, solid at room temp, hydrogen atoms attached to carbon double bond on opposite sides, ULTRRA HIGH CHD RISK
Characterize omega-3 fatty acids and explain their name origin
cis fatty acids, found in plant and fish oil = v healthy because -> reduce tendency to form blood clots and provide healthy plasma membranes around cardiac muscles
name: first carbon double bond is to be found at third carbon counting backwards from the omega end (methyl group)
Define triglyceride lipids
largest class of lipids and function primarily as long-term energy storage molecules (animals tend to store it as fats - solid, plants as oils - liquid)
consist of glycerol and three fatty acids formed in condensation reaction between fatty acids and glycerol fats in animal cells, oils, plant cells
What determines the overall characteristic of the triglyceride lipid
identity of the fatty acids
What characteristic bond occurs in triglycerides
ester linkage
State why being insoluble in water is beneficial for the fatty acids as human energy storage
they do not upset osmotic balance in the cells
Explain why are lipids such a good energy storage
they have 2x energy content per gramme than any other type of storage
because triglyceride lipids can by hydrolyzed into two carbon segments that can enter into cell respiration at a chemical sequence point and is v efficient for the production of ATP
Distinguish LDL from HDL
LDL - low density lipoproteins - carry cholesterol from the liver to the rest of the body - they raise blood cholesterol levels - increased by saturated and trans fats
HDL - high density lipoprotein - scavenge excess cholesterol and carry it back to the liver for disposal - lower blood cholesterol levels - increased by cis fats
Explain the health risk of high cholesterol
high cholesterol levels lead to hardening and narrowing of arteries (atherosclerosis)
because LDL particles will form deposits in the walls of the arteries and their accumulation leads to the development of atherosclerotic plaques that restrict blood flow and therefore leading to coronary heart disease (CDH) if the coronary arteries become blocked
State the formula for Body mass index
BMI=mass in kg/ (height in m)^2
State general functions of lipids in cell
- Storage of energy for long-term use (e.g. triglycerides)
- Hormonal roles (e.g. steroids such as estrogen and testosterone)
- Insulation – both thermal (triglycerides) and electrical (sphingolipids)
- Protection of internal organs (e.g. triglycerides and waxes)
- Structural components of cells (e.g. phospholipids and cholesterol)
Define how polypeptides are formed
synthesized from naturally occurring 20 amino acids, each from a specific gene in a condensation redaction at ribosomes
each has its own amino acid sequence and three-dimensional shape and carries out a specific function
List common elements of the basic amino acid structure
- central carbon atom (alpha carbon)
- amine group (NH2)
- carboxylic acid group (COOH)
- hydrogen atom (H)
- variable side chain (R)
Name 2 amino acids that are modified variants found only in certain organisms
- selenocysteine
- pyrrolysine
Define a peptide bond
a covalent bond between amino acids (the amino group and the carboxyl group) formed by dehydration reactions
AMINE GROUP LOSES HYDROGEN ATOM
CARBOXYLIC ACID LOOSES HYDROXYL OH
Define a polypeptide
polymer of amino acids linked by peptide bonds, with single c-terminal end and t-terminal end
if capable of carrying out its function its synonymous with protein
Define the R amino acid group and state its other name
variable group
group differentiating amino acids by different bonding location around the central carbon atom
Define an amino acid
organic molecule with both an amino group and a carboxyl group
List specific examples of proteins and their functions
rubisco - enzyme catalyzing the first reaction of the carbon-fixing reactions of the photosynthesis
insulin - hormone produced by the pancreas that results in a decrease of blood sugar levels and an increase of sugar body cells
immunoglobulin - antibody that recognizes an antigens as part of the immune response
rhodopsin - pigment found in the retina of the eye that is particularly useful in low light conditions
collagen - main protein component of the connective tissue, which is abundant in skin, tendons and ligaments
spider silk - fibrous protein spun by spiders for making webs, drop lines, nest building etc.
State what happens to amino acids in aqueous solutions (like cytoplasm or blood plasma)
amine and carboxyl group gets ionized, which does not alter the covalent bonding but makes the functional groups look different because each amine group has gained a hydrogen ion and each hydroxyl group has lost one
List the non-polar amino acids
- glycine
- alanine
- valine
- cysteine
- proline
- leucine
- isoleucine
- methionine
- tryptophan
- phenylalanine
List the +charge amino acids
- lysine
- arginine
- histidine
List the polar amino acids
- serine
- threonine
- tyrosine
- asparagine
- glutamine
List the -charge amino acids
- aspartic acid
- glutamic acid
Define the polypeptide backbone
repeating sequence of atoms with extending side chains of the amino acid
Define the term protein
biologically functional molecule made up of one or more polypeptides, each folded and coiled into 3D structure,
an organic substance consisting of covalently bonded amino acids and ready to carry out its function
Characterize the primary protein structure
the sequence and number of amino acids within the protein, determined by the base sequence of the gene, dictates secondary and tertiary structure due to the chemical nature of the backbone and R group
Characterize the secondary protein structure
repetitive shapes of either a helix or a pleated sheet, stabilized by the hydrogen bonds between groups in the main chains of a polypeptide
e.g. beta-pleated = spider silk, alpha-helix = myosin
- Alpha helices occur when the amino acid sequence folds into a coil / spiral arrangement
- Beta-pleated sheets occur when the amino acid sequence adopts a directionally-oriented staggered strand conformation
Both α-helices and β-pleated sheets result from hydrogen bonds forming between non-adjacent amine and carboxyl groups
What happens when there is no secondary structure in the polypeptide
it will form a random coil
Characterize the tertiary protein structure
three-dimensional conformation of a polypeptide, caused by interactions between the amino acids when polypeptide folds up after translation
bonds present: hydrogen, van der Waals forces, disuphide bridges, ionic
e.g. enzymes
Characterize the quaternary protein structure
two or more polypeptide chain combined together to make a single functional protein
e.g. hemoglobin, insulin, collagen
Alternatively, proteins may have a quaternary structure if they include inorganic prosthetic groups as part of their structure
Not all proteins will have a quaternary structure – many proteins consist of a single polypeptide chain
Justify hemoglobin’s quaternary protein structure
- Hemoglobin is composed of four polypeptide chains (two alpha chains and two beta chains)
- It is also composed of iron-containing haeme groups (prosthetic groups responsible for binding oxygen)
Define the prosthetic group
non-polypeptide structure found in some proteins (conjugated proteins), often play an important role in enzyme catalysis
e.g. carbohydrate in glycoproteins
Define protein denaturation
structural change, unraveling and loss of proteins native shape due to pH, salt, temperature alterations
IS PERMANENT
will alter proteins activity
Determine why temperature higher than physiological optimum causes proteins to loose their structure and function
the stress is put on the intra-molecular bonds and therefore the primary structure remains intact but hydrogen bonds not really
but if covalent bonds remain intact the protein will return to its normal shape in normal temp
same happens in abnormal pH because of extra charge
Explain why amino acids are called zwitterions
bc they are neutral molecules possessing both negatively and positively charged regions
Define the term proteome
totality of proteins expressed within a cell, tissue, organism at a certain time
State why the proteome is always significantly larger than the number of genes
Gene sequences may be alternatively spliced following transcription to generate multiple protein variants from a single gene
Proteins may be modified (e.g. glycosylated, phosphorylated, etc.) following translation to promote further variations
List and explain the various functions of proteins with examples
Structure - support
- Collagen: A component of the connective tissue of animals (most abundant protein in mammals)
- Spider silk: A fiber spun by spiders and used to make webs (by weight, is stronger than Kevlar and steel)
Hormones - coordination of organisms activities
- Insulin: Protein produced by the pancreas and triggers a reduction in blood glucose levels
- Glucagon: Protein produced by the pancreas that triggers an increase in blood glucose levels
Immunity - protection against disease
- Immunoglobulins: Antibodies produced by plasma cells that are capable of targeting specific antigens
Transport of substances
- Hemoglobin: A protein found in red blood cells that is responsible for the transport of oxygen
- Cytochrome: A group of proteins located in the mitochondria and involved in the electron transport chain
Sensation - response of cell to chemical stimuli
- Rhodopsin: A pigment in the photoreceptor cells of the retina that is responsible for the detection of light
Movement - transport proteins
- Actin: Thin filaments involved in the contraction of muscle fibres
- Myosin: Thick filaments involved in the contraction of muscle fibres
Enzymes - selective acceleration of chemical reactions
- Rubisco: An enzyme involved in the light independent stage of photosynthesis
Define the term metabolism
integrated network of all biochemical reactions of life
Define anabolic reactions and give an example
larger molecules being built up from smaller molecules
e.g. synthesis of proteins from amino acids, synthesis of polysaccharides from simple sugars
Define catabolic reactions and give an example
larger molecules are broken down, energy-releasing = exergonic
e.g. digestion of complex foods, breakdown of sugar in respiration
Define denaturation
changing the structure of a protein so that it cannot carry out its function
usually caused by high temperatures, pH,
usually irreversible
Characterize enzymes
- proteins = made of long chains of amino acids in a three dimensional shape
- biological catalysts = possess an active site
- substrate specific (only catalyze one biochemical reaction)
- found in all living cells and secreted to work outside by some
- effective in small amounts
- remain unchanged by the end of a reaction
Explain how do enzymes work
by lowering the energy of activation
Define an active site
area of an enzyme designed specifically to match a particular substrate
Define the energy of activation
minimal amount of energy needed to activate the reacting molecules by breaking the bonds between them
List and explain the enzyme-substrate binding analogies
lock and key model = enzyme fits the active site perfectly
induced fit model = initially the substrate doesn’t fit the active site perfectly but substrate binding changes the shape of an active site therefore weaking the bond of the substrate thus reducing the activation energy
List the factors affecting the work of the enzymes
- temperature
- pH
- substrate concentration
- inhibitors
Explain how the temperature affects enzyme activity
temp increases = rate of reaction increases (bc the molecules have more energy = collide more)
optimum temp approx. 35 degree Celsius
afterwards the rate of reaction declines bc of the active site change and lost of function
Define a thermophile
organisms that are able to withstand a much higher temperature before denaturation
e.g. bacteria at deep-sea vents
Explain how the pH affects enzyme activity
enzymes only operate within a narrow range of pH
any deviation from it causes the hydrogen bonds between the amino acids of an enzyme to break causing lost of shape and function (usually permanent)
List the appropriate pH values for the enzymes: pepsin, trypsin, urease
pepsin pH = 2
trypsin pH = 8
urease pH = 7
Explain how the substrate concentration affects enzyme activity
increasing it increases the rate of an reaction
up to a point of active site saturation where no further addition of substrate will alter the rate of the reaction
Provide a reason for lactose intolerance
organisms inability to produce lactase in sufficient quantities
usually visible with ageing
Define enzyme inhibitors
chemical substances reducing the activity of enzymes or preventing it completely
List and define the two types of enzyme inhibitors and give examples
- competitive inhibitors = molecules sufficiently resembling the substrate in shape so that they may compete with it to occupy the active site, prevents the substrate from entering.
e.g. O2 competing with CO2 for Rubisco’s active site, malonate
- non-competitive inhibitors = not resembling the substrate and thus binding to the allosteric (different site) and causing a conformational change so that the substrate is unable to react
e.g. cyanide ions competing with cytochrome oxidase in terminal oxidation in cell aerobic respiration
Where and when does lactic acid respiration occur in humans?
in muscle fibers when demand for energy for contraction is very great and cannot be fully met by aerobic respiration
Define a lactic acid fermentation
is a biological process by which glucose, fructose and sucrose are converted into cellular energy and the metabolite lactate
State the bacteria that create such foods soy sauce, cheese and yogurt, beer, wine and bread
aspergillus - soy sauce
lactobacillus - cheese, yogurt
saccharomyces - beer, wine, bread
Describe the phosphorylation in glycolysis and its function
two phosphate groups are added to a molecule of glucose to form hexose biphosphate, two molecules of ATP provide the phosphate groups
this raises the energy level of hexose by subsequent reactions possible
Describe the lysis in glycolysis and its function
hexose biphosphate is split to form two molecules of triose phosphate
Describe the oxidation in glycolysis and its function
2 atoms of hydrogen are removed from each triose phosphate molecule
the energy released by this oxidation is used to link on another phosphate group, producing a 3-carbon compound carrying two phosphate groups. NAD+ is the hydrogen carrier that accepts the hydrogen atoms
Describe the ATP synthesis in glycolysis and its function
pyruvate is formed by removing the two phosphate groups and by passing them to ADP and results in ATP formation
Summarize the Krebs cycle goal
oxidizes organic fuel derived from pyruvate
State the full name of coenzyme FAD and what is it derived from
flavin adenine dinucleotide
derived from riboflavin, a B vitamin
State the role of NADH and FADH2 in citric acid cycle
shuttling their cargo of high-energy electrons into the electron transport chain
What makes the citric acid cycle a cycle?
regeneration of the oxaloacetate by decomposition of the citrate back to oxaloacetate
Define is the electron transport chain?
a collection of molecules embedded in the inner membrane of the mitochondrion in eukaryotic cells (in plasma membrane in prokaryotes)
mostly composed of proteins in multiprotein complexes (I-IV) with prosthetic groups bound to them
State and explain happens to the electron carriers as electrons travel down the chain?
electron carriers alternate between reduced and oxidized states as they accept and then donate electrons
each component becomes reduced when it accepts electrons from its “uphill” neighbor (which has lower affinity for electrons) and returns to its oxidized form as it passes electrons to its “downhill” more electronegative Neighbour
Explain the difference in energy efficiency between NADH and FADH2 in terms of electron transport chain
while donating an equivalent number of electrons for oxygen reduction the FADH2 provides one-third less energy for ATP synthesis
State the purpose of electron transport chain
it makes no ATP directly, instead it eases the fall of electrons from food to oxygen breaking a large free-energy drop into a series of smaller steps that release energy in manageable amounts
What causes the part of ATP synthase - the rotor to spin?
protons moving one by one into binding sites behaving somewhat like a rushing stream that turns a waterwheel
State what is the ATP synthase powered by and how is it maintained
by the H+ gradient established by the exergonic flow of electrons from NADH and FADH2 from ETC
they want to go back tho
which is prevented by the passage of H+ through ATP synthase to move them across the membrane but also drive the phosphorylation of ADP
Explain when it might be beneficial to reduce the efficiency of cellular respiration?
hibernating mammals lowering their metabolism in the state of inactivity
Define water
a molecule formed by polar covalent bonds between an oxygen atom and two hydrogen atoms
is a dipole with unequal charge distribution
Explain why is water a polar molecule (dipole) and state what does it enable
has different charges at each end and exhibits dipolarity as oxygen with higher electronegativity and lone electron pairs attracts the electrons more strongly than hydrogen
enable formation of hydrogen bonds with other water molecules
State the angle between hydrogen atoms in a water molecule
104.5 degrees
List the properties of water
- cohesive properties
- adhesive properties
- thermal properties (high specific heat, high heat of vaporization, good coolant)
- solvent properties
Define the cohesive properties of water
molecules of the same type are attracted to each other
explains: droplet formation, surface tension, capillary action
Define the adhesive properties of water
attraction between two unlike molecules
Define the thermal properties of water (3)
high specific heat - can absorb and give off great deal of heat without great temperature change
high heat of vaporization - water absorbs great deal of heat when evaporating
good coolant - evaporating water removes a lot of heat
Define the solvent properties of water
excellent solvent of other polar molecules, is a medium in which biochemistry occurs
e.g. aqueous solutions are cytoplasm, stromae, blood plasma
List some water advantages as a habitat
- stable temperature
- thermal properties
- solvent; diffuses nutrients and oxygen
- currents; transports
- transparent; light can go through so photosynthesis can occur
Define cell respiration
cellular process by which sugars and other organic compounds are broken down in order to release energy (ATP) for other cellular processes
State a full name and define ATP and state basic elements of its structure
adenosinotriphosphate
a nucleotide carrying 3 phosphate groups, which it can loose and release energy
3 phosphate groups, one ribose sugar, one adenine
State the function of ATP
powering of cellular work by coupling exergonic reaction with endergonic reactions
e.g. hydrolysis with condensation
State the function and two most popular types of electron carriers
accept hydrogen atoms removed from substrates shuttling them to the place where they are needed
NAD+ - nicotinamide adenine dinucleotide
FAD - Flavin Adenine Dinucleotide
State two types of anaerobic respiration, their general equations and the places where they occur
Alcoholic fermentation:
glucose -> ethanol + CO2 +energy
in yeast (Saccharomyces) used in wine and beer production
Lactic acid fermentation:
glucose -> lactate + energy
in some bacteria
(Lactobacillus) and in humans muscles
State the main difference in anaerobic vs aerobic respiration
instead of oxygen as the final electron acceptor other, less electronegative substances serve as such
for example SO42-
Describe the steps of alcoholic fermentation
- glucose is converted to pyruvate (glycolysis)
- release of carbon dioxide from the pyruvate and thus conversion into two-carbon compound acetaldehyde
- reduction of acetaldehyde by NADH to ethanol (which regenerates the supply of NAD+)
Describe the steps of lactic acid fermentation
- glycolysis
- pyruvate directly reduced by NADH to form lactate thus no CO2 release
List the steps of aerobic cellular respiration
- glycolysis
- the link reaction
- citric acid cycle
- the oxidative phosphorylation
Define the process of glycolysis
glucose (6carbon sugar) is split into two 3carbon sugars and rearranged to form two molecules of pyruvate
List the processes happening during glycolysis and two phases of it
phase 1 - energy investment phase
- phosphorylation - transfer of phosphate group from ATP to glucose in order to make it more chemically reactive.
- lysis - phosphorylated 6-carbon sugar is split into two 3-carbon sugar phosphates (triose phosphate)
phase 2 - energy payoff phase
- oxidation by transfer of electrons to NAD+ and using energy from this exergonic redox reaction to attach a phosphate group making it a high-energy product
- ATP synthesis - phosphate groups are transferred to ADP in an exergonic reaction (substrate-level phosphorylation) in an exergonic reaction, remaining phosphate groups are relocated and another substrate-level phosphorylation takes place forming pyruvate
State the net energy yield from glycolysis, one glucose molecule
2 ATP
(4 ATP formed - 2 ATP used = 2 ATP)
State the function of link reaction
most energy remains stockpiled in two molecules of pyruvate after glycolysis, when O2 is present the pyruvate enters the mitochondrion matrix where the oxidation of glucose is completed
List the processes occurring during link reaction
- pyruvate enters the mitochondrion via active transport.
- pyruvates carboxyl group (-COO-) which is already fully oxidized and thus has little chemical energy is removed and given off as CO2 molecule.
- remaining two carbon fragment is oxidized into acetate, extracted electrons are stored in the form of NADH.
- coenzyme A, derivative of B vitamin is attached via its sulfur atom to the acetate, forming acetyl CoA which has a high potential energy.
all of it occurs with the help of enzymatic pyruvate dehydrogenase complex
Summarize the function of citric acid cycle
a metabolic furnace oxidizing organic fuel derived from pyruvate
State the net ATP gain per one turn of Krebs cycle
1 ATP, most of the chemical energy is transferred to NAD+
List and explain he steps of citric acid cycle
- The acetyl CoA (4C) joins the cycle by combining with the compound oxaloacetate and forms citrate (6C).
- Decarboxylation - 2xCO2 is removed as a waste product and excreted.
- Oxidation - removal of the hydrogens (4 times) accepted by 3NAD+ and FAD which releases energy that is later stored by oxidized carriers and released by ETC.
- substrate level phosphorylation produces 1 ATP.
- Regeneration of oxaloacetate
State the total amount of CO2, ATP, NADH, FADH2 molecules at the end of Krebs cycle from one glucose molecule
6 CO2 (2x1 link, 2x2 krebs)
4 ATP (1x2 glyco, 2x1 krebs)
10 NADH (1x2 glyco, 2x1 link, 2x3 krebs)
2 FADH2 (1x2 krebs)
State the alternative name and summarize the aim of the electron transport system
oxidative phosporylation
hydrogen atoms or their electrons, removed from earlier stages of respiration, are transported along a series of carriers to be combined with oxygen and form metabolic water, which generates energy used to make ATP
State the name of two processes and summarize their aims occurring during oxidative phosphorylation
- electron transport chain - electron transport and pumping of protons which create a proton gradient (electrochemical gradient) across the membrane.
- chemiosmosis - ATP synthesis powered by the flow of protons back across a membrane through the ATP synthase
List the steps of electron transport chain, include the name of the last complex
- electrons from previous steps are transferred from NADH to the first molecule of complex 1.
- passing of an electron reduces the complex they are on and oxidizes as they leave.
- in-between complexes electrons are transported on a small hydrophobic molecules (not proteins) or cytochromes.
- FADH2 from citric acid cycle starts from complex II at lower energy.
- last complex (cytochrome oxidase) passes electrons to a very electronegative oxygen that also picks up a pair of hydrogen ions forming metabolic water.
Define chemiosmosis
an energy-coupling mechanism that uses energy stored in the form of H+ gradient across a membrane to drive cellular work
Define ATP synthase
protein complex embedded in the inner mitochondrial membrane or prokaryotic plasma membrane making ATP from ADP and inorganic phosphate
State the energy yield from one glucose if all the proton-motive force generated by ETC were used to drive ATP synthesis
1 glucose = 4ATP (substrate-level phosphorylation) +28 ATP (oxidative phosphorylation) = 32 ATP
Describe the process of chemiosmosis in detail
- before an electrochemical gradient must be established.
- H+ ions flowing down their gradient enter a channel in a stator of ATP synthase anchored in a membrane.
- protons enter binding sites within the rotor changing the shape of each subunit so that the rotor spins within the membrane.
- each proton makes one complete turn before leaving the rotor and passing through a second channel in the stator into the mitochondrial matrix.
- spinning of the rotor causes an internal rod to spin as well which extends into the knob below it which is held stationary by part of the stator.
- turning of the rod activates catalytic sites in the knob that produce ATP from ADP and inorganic phosphate.
Define autotroph
“self-feeders”
organisms that sustain themselves without eating anything derived from other living beings but rather produce organic molecules from CO2 and other inorganic raw materials
Define photoautotrophs
organisms that use light as a source of energy to synthesize organic substances
Define heterotrophs
unable to make their own food, live on compounds produced by other organisms
Define photosynthesis and state its basic equation
production of sugar from carbon dioxide and water, occurring in chloroplasts and using light energy and producing oxygen as a waste product
6 CO2 + 6 H2O + Light energy –> C6H12O6 + 6 O2
List and briefly define the two phases of photosynthesis
- light-dependent reactions - light energy is used to split water providing a source of electrons and protons in thylakoids.
- light-independent reactions - sugars are built up from carbon dioxide in stroma
Define light in terms of energy
electromagnetic energy traveling in rhythmic waves
List the wavelengths of visible light
380 nm - 750 nm
Define pigments
substances that absorb visible light
Define an action spectrum for photosynthesis
the relative effectiveness of different wavelengths of radiation in driving the process of photosynthesis
State an important function of at least some carotenoids in photosynthesis and define it
photoprotection
absorption and dissipation excessive light energy that would otherwise damage chlorophyll or interact with oxygen forming reactive oxidative molecules
Describe what happens while excitation of chlorophyll by light
absorption of a photon of boosts an electron in the chlorophyll molecule to an orbital of higher energy -> excited, high-energy electron instantenously drops back down to ground state releasing excess energy as heat and fluorescence
State why each pigment has its own absorption spectrum
photons absorbed are only those whose energy is exactly equal to the energy difference between the ground state and an excited state (different for each molecule) -> therefore each pigment has a unique absorption spectrum
Define a photosystem
organised association of photosynthetic pigments (chlorophyll a,b, carotenoids) grouped together, that absorb the light energy and use it to boost electrons to an excited state
composed of a reaction-center complex surrounded by several light-harvesting complexes
Define a primary electron acceptor
molecule capable of accepting electrons and becoming reduced
List and distinguish between two types of photosystems in the thylakoid membrane
photosystem II (PSII) (P680) - reaction center activated by light of wavelengths 680 nm - red part of the spectrum
photosystem I (PSI) (P700) - reaction center activated by light of wavelengths 700 nm - far- red part of the spectrum
What is the best absorption wavelength on the action spectrum
400-525 nm - violet-blue
625-700 nm - orange-red
Define chlorophylls structure
flat, light-absorbing head with magnesium (porphyrin ring) and a long hydrocarbon tail
Briefly state how the light drives the synthesis of ATP and NADPH
by energizing the two photosystems embedded in the thylakoid membranes of chloroplasts
Define linear electron flow
flow of electrons through the photosystems and other molecular components built into the thylakoid membrane during the light reaction of photosynthesis
State and describe the steps of the photosynthesis light reaction
I. Photoactivation of PSII
absorption of light energy by pigment molecules in PSII and excitation of electrons in chlorophyll which are later accepted by primary electron acceptor at the start of ETC
II. Photolysis
replacement of the lost electron in PSII by splitting of water by light energy, oxygen as a waste product
III. Photophosphorylation
transport of the excited electrons along ETC (in between the photosystems) to PSI, proton gradient creation and the ATP synthase produces ATP
IV. Photoactivation in PSI
light energy transferred via light-harvesting complex pigments, absorption of light energy causes more electrons to excite in PSI, which are used to reduce NADP+
Describe cyclic phosphorylation and state when occurs
electrons cycle back from the ferredoxin to the cytochrome complex and from there continue on to a P700 chlorophyll in the PS I reaction - center
present in bacteria who only have one photosystem, organisms living in intense light (photoprotective)
List the differences between cyclic and non-cyclic phosphorylation
NON-CYCLIC
- electrons do not come back to the same molecule.
- first electron donor is water
- involves both PSI and PSII
- last electron acceptor is NADP
- the net products are ATP, NADPH and O2.
CYCLYIC
- electrons come back to the same molecule.
- first electrons donor is p700 (PSI)
- involves PSI only
- last electron accept is p700 (PSI)
- the product is ATP only.
List and briefly describe the processes occurring during Calvin cycle
I. Carbon fixation
Ribulose biphosphate (RuBP) is added CO2 with RUBISCO assisting creating 2 glycerate 3-phosphate (GP)
II. Reduction
GP is reduced to triose phosphate - glyceraldehyde 3-phosphate (G3P) using NADPH+H+ and ATP
III. Product Synthesis
one triose phosphate is further metabolized to produce a carbohydrate (triose)
IV. Regeneration of the CO2 acceptor (RuBP)
5 molecules of G3P and 3 ATP molecules are used to regenerate RuBP
List the limiting factors of photosynthesis
- light
- carbon dioxide
- temperature
Describe the effect of light intensity on photosynthesis
without light - no photosynthesis
photosynthesis rate increases with increasing light intensity (light is limiting) up to compensation point where light stops being the limiting factor
Define compensation point
reached when all the CO2 produced in respiration by the plant is re-used in photosynthesis and there is no net loss or gain in O2
Describe the effect of carbon dioxide concentration on photosynthesis
because of low and medium CO2 concentrations it is a limiting factor when CO2 in the Calvin cycle is fixed to produce G3P and RuBP and NADPH accumulate
Describe the effect of temperature on photosynthesis
because of many enzymes present it works just like in enzymes
Make connections between the structure of a chloroplast and its function in photosynthesis
double membrane bounding the chloroplast - is permeable to CO2,O2, ATP, sugars and other products of photosynthesis
photosystems with chlorophyll pigments arranges on thylakoids membranes of grana - provide huge surface area for maximum light absorption
thylakoid spaces within grana - restricted regions for accumulation of protons and establishment of the gradient
fluid stroma with loosely arranged thylakoid membranes - site of enzyme fixation, site for light-independent reactions
List the 3 different plant types and their characteristic photosynthesis
C3 plants - normal ones like rice, wheat, soybeans - initial fixation of carbon occurs via rubisco and the first organic product of carbon fixation is 3-phosphoglucerate (GP).
C4 plants - plants present in hot regions with intense sunlight where stomata close partially during the day - PEP carboxylase adds CO2 to PEP (phosphoenolpyruvate) forming the four-carbon oxaloacetate.
CAM plants - crassulacean acid metabolism - plants whose stomata opens at night only, minimizing the transpiration, CO2 is fixed into the organic acid malate and stored during the night in vacuoles and at night used to make starch
