Metabolism and Survival Flashcards
(23 cards)
metabolism
METABOLISM is the sum of all of the reactions that occurs in the cell
METABOLIC PATHWAYS are a series of chemical reactions that are controlled by enzymes
[metaboliteA –enzyme1–> metaboliteB –enzyme2–> metaboliteC]
Precursors are a substance needed to start a metabolic pathway
Metabolic reactions can be categorised as either:
- CATABOLIC… breaks down big molecules into small ones, releases energy (ATP)
- ANABOLIC… builds up small molecules into big ones, requires energy (ATP)
METABOLIC RATE is the speed of chemical reactions.
It can indicates the quantity of energy used by the body over a given time, determined by measuring:
- oxygen consumption per unit time
- heat produced per unit time
- using a calorimeter/ respirometer
Factors that affect metabolic rate include:
- size… dependent on surface area to volume ratio (SA:V), due to heat loss
- temperature… as metabolic pathways are enzyme controlled reactions
enzymes
amino acids –> proteins –> enzymes
enzymes are biological catalysts (i.e. they speed up the are of biochemical reactions in the cell by reducing the required activation energy)
enzymes are specific in their function (i.e. they can only carry out one particular reaction, due to the enzyme’s active site being a specific shape that is only complimentary to one substrate)
affinity = attraction (substrate has high affinity for enzyme)
induced fit = since enzymes are made from proteins their structure is slightly flexible, so when the enzyme-substrate complex forms the enzyme’s active site can alter slightly to form a tighter fit with the substrate
factors that affect enzyme activity includes:
- pH… if out-with enzyme’s range it will denature
- temperature… if out-with enzyme’s range it will denature
- product concentration… too much can lead to feedback inhibition
- substrate concentration… increasing concentration equals increasing rate initially but reaches a max. rate as enzyme concentration acts as a limiting factor
Inhibitors
An inhibitor decreases the rate of enzyme controlled reactions
Competitive inhibitors:
- complimentary to enzyme’s active site (has affinity for it)
- binds and doesn’t leave
- prevents enzyme-substrate reaction occurring, so no product is formed, reducing reaction rate
- increasing substrate concentration counteracts effects
Non-competitive inhibitors:
- complimentary to enzyme’s allosteric site
- causes enzyme’s active site to alter shape
- substrate can no longer react with enzyme
- effects counteracted by activator… will bind to allosteric site and cause active site to revert back to substrate-complimetry shape, increasing reaction rate
Feedback inhibition
- end product of metabolic pathway builds up
- product binds to allosteric site of enzyme at start of pathway inhibiting it
- as product concentration decreases inhibition stops and pathways resumes
Enzyme/ gene regulation
Regulation of enzyme is carried out by signal molecules. Enzymes are proteins so are coded for by genes.
Some genes are ‘expressed’ continuously so are always present, and are regulated by their rates of reaction (i.e. feedback inhibition)
Other genes are only required to operate under certain circumstances, so to prevent resources being wasted these genes can be switched on (aka. enzyme induction) or off.
O + S = Operon
occurs in DNA
Gene off:
- R, regulator gene, carries out transcription or translation to produce repressor protein
- repressor protein, binds to O, operator gene
- O switches off S, structural gene, stopping enzyme synthesis
Gene on:
- R, regulator gene, carries out transcription or translation to produce repressor protein
- inducer binds to repressor protein, preventing it binding to O, operator gene
- O switches on S, structural gene, causing enzyme synthesis
ATP
ATP, adenosine triphosphate, is composed of one adenosine molecule and three inorganic phosphates
ADP, adenosine diphosphate, which is comprised of one adenosine molecule and two inorganic phosphates
ATP ADP + Pi + energy
Respiratory substrates
Glucose:
- original substrate
- enters respiration at the start of glycolysis
Starch:
- storage carbohydrate in plants
- can be broken down into chains of glucose
Glycogen:
- storage carbohydrate in animals
- can be broken down into chains of glucose
Sugars (other than glucose):
- can be converted into glucose or glycolysis intermediates, so can enter respiration at start of glycolysis
Proteins:
- can be broken down into amino acids then converted into glycolysis or citric acid intermediates
Fats:
- can be broken down into glycerol and three fatty acids
- glycerol can then be converted into fragments that can enter respiration during the citric acid cycle
Aerobic respiration
GLYCOLYSIS (occurs in cytoplasm):
- glycose (6C)
- intermediate stages [2ATP-> 2ADP+Pi (energy investment phase) ]
- [2NAD –(dehydrogenase enzyme)–> 2NADH, 4ADP+Pi->4ATP (energy payoff phase - net gain of 2ATP) ]
{ to 2pyruvate }
KREB’S/ CITRIC ACID CYCLE (occurs in central matrix of mitochondria):
- 2pyruvate (3C)
- [ 2NAD –(dehydrogenase enzyme)–> 2NADH, 2Cdioxide ]
- 2 acetyl (2C) coA
- 2 citrate
- [ 2NAD –(dehydrogenase enzyme)–> 2NADH, 2Cdioxide ]
- 2x intermediate (5C)
- [ 2NAD –(dehydrogenase enzyme)–> 2NADH, 2Cdioxide ]
- 2x intermediate (4C)
- [2NAD–dehydrogenase enzyme)–> 2NADH]
- [2NAD–dehydrogenase enzyme)–> 2NADH]
- 2oxaloacetate (4C)
{ back to 2acetyl coA }
ELECTRON TRANSPORT CHAIN (occurs on cristae in mitrochondria):
- all NADH->NAD, releasing hydrogen ions and high energy electron
- flow of hydrogen ions provides ATP synthase enzyme with energy which catalyses the synthesis of ATP from ADP + Pi [36 ATP]
- Oxygen is the final electron acceptor, it combines with the H+ ions and electrons forming water (+low energy electrons)
can be NAD/FAD -> NADH/FADH
= 38ATP in total produced
Anaerobic respiration
ANIMAL CELLS =
Glycolysis (occurs in cytoplasm):
- glycose (6C)
- intermediate stages [2ATP-> 2ADP+Pi (energy investment phase) ]
- [2NAD –(dehydrogenase enzyme)–> 2NADH, 4ADP+Pi->4ATP (energy payoff phase - net gain of 2ATP) ]
{ to 2pyruvate }
Lactic acid fermentation:
- 2pyruvate (3C)
- [2NAD–dehydrogenase enzyme–>2NADH]
- 2lactate (3C) (lactic acid)
This process can be reversed by introducing oxygen
PLANT CELLS =
Glycolysis (occurs in the cytoplasm):
- glycose (6C)
- intermediate stages [2ATP-> 2ADP+Pi (energy investment phase) ]
- [2NAD –(dehydrogenase enzyme)–> 2NADH, 4ADP+Pi->4ATP (energy payoff phase - net gain of 2ATP) ]
{ to 2pyruvate }
Fermentation stage:
- 2pyruvate (3C)
- 2ethanol (2C) + carbon dioxide (1C)
Cell membrane
The cell membrane forms a barrier around the cell and controls the movement of substances in and out of the cell - it is selectively permeable.
Membrane is comprised of proteins and phospholipids. The phospholipids are arranged in a fluid bilayer structure, with proteins dispersed and embedded throughout. The phospholipids have a hydrophilic phosphate head and a hydrophobic lipid tail. The proteins have many functions such as forming pores, pumps, enzymes and acting as receptors.
Mitrochondria
Mitochondria is the site of cellular respiration and is located in the cytoplasm.
It possesses a double membrane - the outer one acts as a semi-permeable barrier around the cell and the inner one is extensively folded to create cristae, which provide a large surface area. The cristae project into a fluid-filled interior known as the central matrix.
Microorganisms
Microbiology is the study of microorganisms
Microorganisms are useful for industrial use (e.g. production of medicines and foods) due to their adaptability, speed of population growth and ease of cultivation
Generation time = the time taken for microorganisms to divide (reproduce)
Population growth of microorganisms:
(1) Lag… slow increase in numbers, microorganisms are adjusting to the conditions, only a few to begin with
(2) Log/ exponential… rapid increase, optimum conditions, fastest rate of growth
(3) Stationary… stabilised growth, birth rate = death rate
(4) Death… build up of toxic waste products, decrease in resources
Growth can be estimated by:
- taking a count at the time of inoculation and at known time intervals
- counts can be either total cell counts (all cells living and dead) or viable cell counts (counting only live cells)
Culture of microorganisms = requires appropriate growth medium and environmental factors
- environmental factors… control of temperature/oxygen levels (via aeration) /pH (via buffers or addition of acids/alkaline), sterility (via aseptic techniques - eliminates contaminating organisms)
- growth medium… provides a source of energy and simple chemical compounds for biosynthesis. Can be solid agar plate or liquid broth
Chemical requirements (+ source), use:
- Carbon (carbohydrate), ATP production
- Hydrogen (water), found in all organic materials
- Oxygen (water/air), aerobic respiration
- Nitrogen (compounds containing ammonium/ nitrate groups), synthesis of nucleic acids/ amino acids/ proteins
- Phosphorus (compound containing a phosphate group), synthesis of nucleic acids/ ATP
- Sulphur (compound containing sulphate group), synthesis of amino acids
Dormancy
Since food is scare animals can go into a state of dormancy to survive adverse conditions.
Dormancy = period when growth, development and activity are temporarily suspended. Metabolic rate is reduced to its minimum to conserve energy.
Predictive = organism becomes dormant before the onset of adverse conditions, indicated by changes in day length and temperature
Consequential =
- Organism becomes dormant after/ in response to the onset of the adverse conditions
- More common in regions where climate is unpredictable and conditions change rapidly.
- Advantages… organisms can remain active longer n use more of remaining available resources
- Disadvantages… high mortality rate if conditions change too unexpectedly, organisms cannot find shelter and become dormant in time
Types of dormancy =
Hibernation:
- response to the onset of winter
- can be predictive or consequential
- uses fat stores
- body temp, breathing rate, heart rate drops so less energy is required
- metabolism drops
Aestivation:
- consequential response to periods of high temps/ drought
- metabolism drops to minimum rate
- retreat into shells/ cocoon
Torpor:
- occurs daily
- is a physiological state
- metabolism drops to minimum rate
- activity of organism, heart rate, breathing rate drops so less energy is required
Extremophiles
Extremophiles are organisms that thrive in conditions which would provide lethal to almost any others (e.g. very high/ low temperatures/pH/pressure)
This is as they possess extremely tolerant enzymes
They are usually part of the archaea group
Migration
Some animals are unable to tolerate conditions because they cannot regulate their metabolic rate so instead must expend energy to relocate to a more suitable environment (avoiding metabolic adversity = low/high temperatures, scarcity of food).
For some organisms migration is an innate behaviour (determined by their genes) whereas for others it is a learned behaviour (influenced by environment/ experiences)
Tracking migration:
- radio transmitters
- satellite tracking
- ultrasound transmitters
- ringers (metal band with unique number)
Conformers and regulators
Conformers:
- cold blooded organisms
- low metabolic rate (reduced ATP usage) so require less food less frequently
- internal body temperature varies with external environment (therefore cannot alter their metabolic rate)
- can carry out certain behaviours to a limited extend to maintain metabolic rate… vaporisation (getting wet), convection (losing or gaining heat due to an airflow), conduction (lying next to a cooler or warmer surface), radiation (finding shade or lying on hot rocks
- can only live in a narrow ecological niche
Regulators:
- warm blooded organisms
- high metabolic rate as requires high ATP supply so required a frequent and high food supply
- able to maintain a constant internal body temperature (as can alter metabolic rate via homeostasis)
- large range of possible ecological niches
Circulatory systems
Single circulatory system:
- e.g. fish
- blood flows through a two chambered heart (one ventricle, one atrium) once for each complete circuit of the body (single circulation)
Incomplete double circulatory system:
- e.g. amphibians, reptiles
- blood flows through a three chambered heart (two atria, one ventricle) twice for each complete circuit of the body (double circulation)
- oxygenated and deoxygenated blood mix together in the ventricle
Complete double circulatory system:
- e.g. birds, mammals
- blood flows through a four chambered heart (two atria, two ventricles) twice for each complete circuit of the body (double circulation)
- oxygenated and deoxygenated blood do not mix together
Anatomical lung arrangement
Amphibians:
- can exchange gasses through their skin and mouth cavity
- primitive lungs, small, thin walled, some alveoli
- diffusion is slow, air is forced in and out by gulping
Reptiles (simular to mammals):
- lungs have bronchi, bronchioles, alveoli
- thin walls
- some have diaphragm, other use locomotory muscles to breath
- air flow is bidirectional (forced in two directions - in, out)
Birds:
- as flying uses up so much energy they must maximise their oxygen uptake
- birds possess large air sacs that keeps air flowing through the lungs
- air flow is said to be unidirectional (air is forced in one continuous direction)
Physiological adaptions to low oxygen niches
High altitude habitats:
- increased pulmonary capacity and breathing rate to allow for increased diffusion of gases
- increased levels of haemoglobin and number of red blood cells to maximise oxygen transport
Deep diving marine habitats:
- slowing heart rate to lower metabolic rate to cope with reduced ATP levels due to anaerobic respiration
- possesses partially collapsable lungs to cope with high pressure and decrease buoyancy
- blood is diverted to essential organs such as heart, brain, lungs
- increased haemoglobin level and number of red blood cells to maximise oxygen transport
- increased myoglobin (provides a store of oxygen for muscle cells) concentration in muscles
Measuring fitness in humans
VO2max is the maximum rate at which the body is able to take up and use oxygen
Unit: cm^3kg^-1min^-1
The higher the VO2max the fitter the person is (increases as the person improves their cardiovascular fitness)
Physiological homeostasis
Regulators maintain homeostasis via a negative feedback loop.
When a factor affecting the body’s internal environment deviates from its normal optimum level the change is detected by receptors which sends out nerve/hormonal messages to the effectors. The effectors then cause a corrective mechanism to counteract the original deviation and return the system to normal.
Negative feedback control for body temperature:
- important so enzymes can remain working at optimum temperatures
- Hypothalamus is located in the brain and (thermoreceptors located within) detect blood temperature and water levels, then communicates with skin via nerves to regulate body temperature
- correction to increase in body temp… vasodilation (skin arteries widen, blood goes to capillaries at skin’s surface, heat loss via radiation), increased sweating (water in sweat heats up on skins surface and evaporates), effoctor pills muscles relax - hairs lowered (minimises insulation effect), metabolic rate decreases (reducing heat production)
- correction to decrease in body temp… vasoconstriction (skin arteries narrow, blood is diverted away from skins surface, reduces heat loss by radiation), effector pills muscles contract - hairs raised (traps layer of air to insulate the body), shivering (increased muscle activity generates heat), metabolic rate increases (generates heat)
Microbial products
Microbial products are often classified as either primary or secondary metabolites
Primary metabolites:
- compounds related to the synthesis of microbial cells
- are produced in the log (exponential) growth phase
Secondary metabolites:
- compounds produced in the stationary phase of growth of microorganisms
- often compounds are produced as a result of an inducer in the environment
- compounds are not associated with growth and may even be toxic
Altering/ proving microorganisms
Mutagenesis: exposing microorganisms to mutagenic agents so a mutation occurs, possibly producing improves strains
The mutant strains are often genetically unstable and with continued cell divisions the DNA base sequence can revert back to the original type
Selective breeding can improve microorganisms:
- In fungi and yeast new genotypes can arise via sexual reproduction, allowing them to adapt better to new environments
- Bacteria cannot sexually reproduce, but can carry out horizontal transfer (so can transfer plasmids or pieces of chromosomal DNA between one another), some others can take up DNA from their environment and incorporating it into their genome
Recombinant DNA technology
Recombinant DNA technology involves the manipulation of an organism’s genome by transferring genes from one organism into a microorganism. In order to do this a vector (agent which can introduce DNA into a cell) is required.
Artificial chromosomes and plasmids (small circular pieces of DNA) can be used as vectors. Useful features of these that allows gene expression includes:
- marker genes… allow cells that have taken up the plasmid to be identified (e.g. fluorescence)
- restriction sites… allow plasmid to be cut so a DNA fragment can be inserted
- origin of replication… sequence of DNA at which replication is initiated
- self replication genes… allow vector to be copied once it is inserted into the new cell
- regulatory sequences… these control expression of the inserted gene and cause multiple copies of the plasmid to be made within the cell
- Safety mechanisms… prevent survival of microorganism in an external environment (so cannot contaminate wild populations)
In recombinant DNA technology the restriction endonuclease enzyme recognises the restriction site and makes cuts, cutting out the desirable genes out of the donor DNA, and creating ‘sticky ends’. It is also used to open the plasmid where the gene is to be inserted. The enzyme DNA ligase is used to combine the vectors with complementary sticky ends to the target sequences (desired gene)
