Physiology Biochemistry terms

Absorption of light

Process by which certain wave lengths of light are taken up by a substance by raising electrons to a higher energetic level (excited state)

absorption spectrum

Graph that displays the amount of light absorption with a given pigment at a specific light wavelength

action spectrum

Graph that displays the rate of photosynthesis at specific wavelengths of light

activation energy

The amount of energy required to start a chemical reaction

activation site or active center

Specific region of an enzyme to which the substrate binds and undergoes a specific chemical reaction

aerobic and anaerobic

An aerobic organism can only grow in the presence of O2, anaerobic organisms in the absence of O2

anabolism

Part of the metabolism, which involves all biochemical reaction producing more complex compounds from smaller molecules

facultative or obligate anaerobes

Facultative anaerobes can grow in both oxygenated and deoxygenated environments; obligate anaerobes only deoxygenated environments

Artefact

Something observed in an experiment that is not naturally present, but a result of the experimental procedure

ATP and ADP

Molecules that store energy, ATP carries the energy and ADP is unloaded. ATP can be viewed as the universal currency of energy in cells

ATP synthase

An enzyme that directly generates ATP during the process of cellular respiration. Found on the inner membrane of mitochondria

Baker's yeast, Saccharomyces cerevisiae

A species of yeast. It is a single-celled fungus microorganism

breathing = ventilation

Physical movement of air going from outside environment into the lungs

calcium hydroxide (Ca(OH)2)

In solution, allows detection of CO2

carbon dioxide (CO2)

Gas produced by respiration; it is absorbed by plants for PS

carbonic acid HCO3

Acid formed when CO2 dissolves in water

carotenoids

Red, yellow or orange pigments. They are used as helper pigments during PS; they absorb light and convey the energy to chlorophyll. They cannot conduct PS by themselves

catabolism

Part of the metabolism, it comprises all biochemical reaction breaking down more complex molecules in order to gain energy

catalysis (noun)

The causing of the acceleration of a chemical reaction ^, by reducing the activation energy

catalyst inorganic

Substances (usually metals) which reduce activation energy of a chemical reaction

Catalyze (verb)

The action performed by inorganic catalysts and enzymes, namely reduction of the activation energy

cellular respiration, 4 reaction steps

Opposite of PS, occurs in cells: 6 O2 + C6H12O6 → 6 CO2 + 6 H20 + heat / energy

Glycolysis → Oxidative carboxylation → Citric acid cycle → Electron transport system

chemical bonds, polar and not polar

Chemical bonds found in molecules

Not polar: difference in EN less than or equal to 0.4

Polar: difference in EN larger than 0.4

chlorophyll a and b

Two forms of chlorophyll that absorb violet/blue and red/orange light; released energy drives PS

chloroplast

Organelle within plant cells that conduct PS

chromatography

Technique for separation of a mixture, relying on a mobile and a stationary phase and different solubility and adhesion of the components of the mixture

citric acid cycle (= Krebs cycle)

Third part of cellular respiration: production of ATP and H-Atoms

CO2 trap

Device which allows binding of all the CO2 around a leaf in order to test its requirement in PS

combustion

Burning of a substance

compensation point

Light intensity at which the rate of PS is equal to the rate of respiration. Barely survivable

cristae

Fingerlike infolding of the inner membrane of a mitochondrion with a large amount of surface area

cuticle, lower and upper

Thin, waxy, and transparent layer in plant leaf that is secreted by the epidermis

dark reaction

Cycle of reactions in the second part of PS that does not require light; builds glucose from CO2 and NADPH and ATP

dissolved

becoming incorporated into a liquid and forming a solution

electron or hydrogen carriers

NADP, NAD that transport hydrogen (with its e-) from one molecule to another during PS

electron transport system

A series of protein complexes (e- driven H+ pumps) that create H+ gradient which drives ATP synthesis by ATP synthase

endocytosis

Process by which cells take up material by engulfing part of the cell membrane, forming new membrane vesicles

endosymbiotic theory

The theory that states chloroplasts were free living prokaryotic cells, before being taken up by another prokaryotic cell through endocytosis, forming a union that benefits all. By this principle, eukaryotic cells came into existence

endothermic reaction

A chemical change in which the system absorbs thermal energy from its surroundings, resulting in more chemically bound energy in the products than in the reactants

energy kinetic or potential

Energy: capacity to do work

Kinetic energy: at work

Potential energy: stored

enzyme

A biological catalyst

epidermis, lower and upper

Outer layer of tissue in a plant leaf that protects the inner layers and produces the cuticle. The lower epidermis also contains Guard cells forming the stomata

eukaryote

An organism consisting of a cell or cells with a distinct nucleus and a nuclear envelope

excited state

State of a compound that has absorbed light such that its electrons are at a higher energy stats (shells)

exothermic reaction

Chemical reaction in which energy is released (reaction energy), often upon addition of an activation energy

extraction

Removal of a compound or several compounds from part of a living being using a solvent

fermentation, alcoholic and lactic acid

Breaking down of glucose in the absence of O2 to produce ethanol or lactic acid respectively

gas washing bottle

Laboratory device whose primary use is to inject a stream of gas through a liquid

germinating

a seed or spore beginning to grow and sprout

glowing splint test

Detection reaction for oxygen

glucose

C6H12O6, simple sugar that is an important energy source in living organisms

glycogen

Similar to starch; long threadlike molecules with glucose as building blocks; insoluble in H2O and therefore osmotically inactive

glycolysis

First step in the break-down of glucose to extract energy for cellular metabolism

grana thylakoid

Stack of thylakoids that are the site of the light reaction during PS

ground state

Lowest energy state of an atom

guard cell

Pairs of epidermal cells that control gas diffusion by regulating the opening and closing of stomatal pores

H-Bond

Attraction between a partially positive H-Atom attached to a highly electronegative atom (F, O, N)

high energy compound

Compounds that have a lot of chemical energy stored → e.g. glucose and starch

hydrogen oxygen reaction

Chemical reaction of hydrogen with oxygen to produce H2O

intermembrane space

small compartment between the inner and the outer membrane of a mitochondria and chloroplasts

iodine

I2, molecule used to detect starch

law of the limiting factor

If a chemical process is affected by more than one factor, then its rate will be determined by the factor which is furthest away from the optimum

Leaf sun and shade

Sun leaves: thicker (bigger cuticle and longer palisade layer)

Shade leaves: thinner but larger to collect the more sparse light

light reaction

First part of PS; chlorophyll absorbs light and upon releasing it H2O is split into O2 and H bound as NADPH and ATP. The latter two are used in the subsequent dark reaction

lock and key principle

Enzymes have a specific shape that directly correlates to the shape of the substrate

low energy compound

Compound that contains little energy, e.g. H2O and CO2

matrix

The former bacterial cytoplasm found in mitochondria

metabolism

The chemical reactions in cells and entire organisms (catabolism + anabolism)

mitochondrion (mitochondria)

Organelles found in large numbers in essentially all eukaryotic cells, in charge of the biochemical process of respiration

mixture

Aggregate of at least two pure substances

mobile phase

Solvent in the fractionation method called chromatography. It migrates up the stationary phase and pulls along components of the mixture (according to their solubility in the solvent and the adhesion strength to the stationary phase)

NADPH and NADP

Molecules, NADPH carries H-atoms and NADP is unloaded, produced by light reaction during PS

Oxidative decarbonxylation

Second step of cellular respiration

palisade layer

Tightly packed cells in a plant leaf that perform PS

Photosynthesis, real and apparent

Real PS: all the oxygen produced at a certain light intensity

Apparent PS: all oxygen produced by PS that is not consumed by cellular respiration at a certain light intensity

prokaryote

microscopic single-celled organism that does not have a distinct nucleus + no nuclear envelope

pure substance

liquid that is made up of one type of particle; it cannot be fractionated by another

reactant

Substance that undergoes change during a reaction

reaction energy

Energy that is released in an exothermic reaction

reflection

Sending back of light by a surface without absorbing it

respiration

Process in living organisms that involves the production of energy through the uptake of oxygen and glucose and the release of carbon dioxide and water

ribosome

cellular structure made of RNA and protein, that performs protein synthesis

sample line

Where we place mixture onto stationary phase

solubility

Ability to be dissolved in water

soluble

adjective to solubility

solvent

A liquid able to dissolve other substances

spongy mesophyll layer

Layer in plant leaf that contains air space for gas exchange

starch

Substance which consists of long chains of glucose

stationary phase TLC plate

Thin material layer, coated onto a plate, that does not move with the sample

stomatum = stoma

Pores in the lower epidermis of a plant leaf that allows the movement of gases; made by guard cells

stroma

Former prokaryotic cytoplasm of a chloroplast

stroma thylakoid

Part of the chloroplast: Infold of the inner membrane that contains green pigment and where light reaction of PS takes place

substrate

Reactant that binds to the active site or center of an enzyme and will undergo a chemical reaction

thylakoid membrane

Inner membrane that carries out light reaction of PS infolding of the cell membrane in bacteria

transmission

Waves of light travelling through one medium into another

transpiration

Evaporation, water leaving the plant through stomata

vascular bundle with xylem and phloem

Vascular bundle = vein

Xylem = cells that carry water and minerals from the roots through the stem to the leaves

Phloem = cells that carry glucose from the leaves through the stem to the roots

visible light

Segment of electromagnetic spectrum that human eyes can see

detection reaction

Discovering or noticing something through a reaction

CO2 detection test

Test that helps us discover CO2; it is a Ca(OH)2 solution which turns cloudy when in the presence of CO2