chapter 4,5,6

Question 1

microscopes, magnification, light microscope, electron microscopes,

Answer 1

break through by anton van leeuwenhoek 1674 crafted lenses and saw the first cells- called them animalcules.-light microscope- light passed through specimen and sense refracts the light to magnify it. -magnification-ratio of objects size to image size
electron microscopes- specimens are dead, SEM scanning electron microscope- 3D image of the surface of specimen( surface coated with gold)
TEM transmition electron microscope- beam of electrons shown through into internal structure and it uses magnets to bend the path of electrons

Question 2

fluorescence, confocal, cell fractionation

Answer 2

fluorescence- dye that labels details in cell
confocal-lazor that uses optical sectioning that eliminates out of focus light- sharpening image
cell fractionation- broken up cell put in centrifuge- similar sized components (similar density) bunch together in bulk- helps determine organelle function

Question 3

prokaryotes

Answer 3

DNA in nucleoid ( region where DNA is) no membrane. also in prokaryote ribosomes, cytosol, cell membrane, cell wall, flagella and cilia

Question 4

nucleus

Answer 4

contains genes, the nucleus is a large organelle ( 5microm)
unclear envelope-surrounds nucleus and is made of two lipid bilayer membranes, and pores within the nucleus attach the two membranes.
nuclear pores-proteins that line each pore regulate what comes in and out (8 molecules)
nuclear lamina- fibrillar network in nucleus , it lines the nuclear side of membrane and it is made of protein filaments
chromosomes- present during mitosis they organize DNA (made of chromatin)

Question 5

nucleolus, ribosome, protein synthesis

Answer 5

-present when cell is not dividing, dense ribosomal RNA makes ribosomes.
-ribosome made of ribosomal RNA and protein- two subunits and the make protein
free ribosomes in Cytosol, bound ribosomes attached to rough er
protein synthesis- nucleus makes mRNA, mRNA exits through nuclear pore and goes to ribosome-ribosome translates mRNA message into PRIMARY structure of polypeptide

Question 6

endomembrane system

Answer 6

nuclear envelope, ER, golgi body, lysosome, vesicle, vacuole, plasma membrane

Question 7

ER

Answer 7

-endoplasmic reticulum- made of cisternea(networks of membranous tubules and sacs) the inside of the er cavity called LUMIN
-smooth er- no ribosomes, involved with metabolic process- synthesis of lipids, and detoxification of drugs, metabolism of carbohydrates and it also stores calcium ions.
Rough Er- makes membranes and proteins- has ribosomes attached,
polypeptide is produced by ribosome and is threaded into ER lumen where it is folded into its functional shape (protein complex)- also makes membrane the rough er grows by adding phospholipids to its own membrane.
-glycoproteins- proteins with carbohydrates bonded, these are attached to er by enzymes in er membrane, then it leave by a transport vesicle

proteins that are being secreted are transported in vesicle to golgi body

Question 8

gogli body

Answer 8

molecules arrive from er in vesicles and are modified in the golgi. golgi made of flattened membrane stacks- CISTERNEA, the cisternea are not connected. cis face receives vesicles from ER ( closer to nucleus) trans face dispatches vesicles to membrane
proteins modified from cis to trans region- CISTERNAL MATURATION- the cisternea progress forwards from cis to trans modifying the product as they go. vesicles bud from trans face and go to membrane.
1. vesicles move from er to golgi 2. vesicles join to form new cis face. 3.cisternal masteration. 4.vesicles form and leave trans face carrying product to membrane. 5. vesicles take protein back to gogli body if they function in it. 6. vesicles can also transport product back to er if they function there.

Question 9

lysosomes phagocytosis

Answer 9

sac of hydrolytic enzymes used to digest macromolecules ( these enzymes are made from the ER) the proteins in lysosomal membrane not digested because of their 3D structure
phagocytosis- cell eating, engulfs food in vacuole, vacuole then fuses with
-lysosomal disease-if enzymes aren’t the correct ones in the lysosome the lysosome becomes engorged with molecules that cannot be broken down and example of this is tay sachs disease where the lipid digesting enzyme is inactive and lipids accumulate in the brain

Question 10

vacuoles

Answer 10

large vesicles made from the ER and GA, they are a part of the endomemraue system and they are selectively permeable which gives them a different composition from the cytosol
types; food vacuole-use phagocytosis, contractile vacuole- regulate water
PLANT- have a central vacuole that develops by the coalescence of smaller molecules (join together) the contents are called cell sap, helps support the cell and also stores ions, aids in cell growth when vacuole can grow without cytoplasm increasing in size

Question 11

relationship of endomembrane system

Answer 11

nuclear envelope connected to smooth and Rough ER, the membrane or proteins made in rough ER or smooth ER are transported to golgi body in a transport vesicle, the golgi pinches off at the cis face which gives rise to vacuoles, other vesicles, or lysosomes. the lysosomes produced are available for fusion with food, or transport vesicle carries protein to plasma membrane, plasma membrane expands by fusion of vesicle and proteins are secreted from cell

Question 12

endosymbiotic theory

Answer 12

early ancestor of eukaryote engulfed oxygen using bacteria and a relationship formed which was endosymbiotic (cell within a cell). It merged into one organism, a eukaryotic cell with mitochondria. another may have taken in a photosynthetic bacteria which would result in a eukaryotic cell with chloroplasts. the theory is consistent with structural features- the mitochondria and chloroplasts have two membranes- both contain ribosomes and DNA- they reproduce within cell on their own

Question 13

mitochondria chloroplasts and peroxisomes

Answer 13

mitochondria-cellular respiration and they have two membranes made of phospholipid bilayers, the outter membrane and a smooth inner membrane folded into cristae, the matrix is the second membrane and contains enzymes, DNA and ribosomes. the enzymes that are present are built into membrane and catalyze reactions, the folds of cristea increase surface area for more cellular respiration -STRUCTURE FITS FUNCTION
chloroplast- has two membranes - and inter membrane system, the thylakoids are internal membrane sacs a stack of thylakoids is called a granum, the fluid outside thylakoid is called the stoma and it contains DNA ribosomes and enzymes.
peroxisomes- they perform oxidization- single membrane that contains enzymes which remove H from molecules and transfers the H to O to form H2O2 and then that is then converted into H2O by enzymes, peroxisomes grow by incorporating proteins made in the cytosol and ER and by incorporating lipids. *They help detoxify drugs, we don’t know how they duplicate or where they come from

Question 14

cytoskeleton,

Answer 14

a support, mobility,shape maintenance,and anchors organelles- it can reassemble and dismantle quickly
cell motility- changes of cell location movement of organelles outside- whole cell moves along fibres outside the cell
inside-motor proteins walk vesicles or organelles along microtubules
this is how vesicles containing neurotransmitter molecules migrate to axon tips ( axon is a long extension of nerve cell that releases signals to other nerve cells)
cytoskeleton made of centrosome, microfilaments, and intermediate filaments

Question 15

cilia and flagella

Answer 15

microtubule containing extensions (ex sperm or cilia in lungs) cilia also receive signals - the primary cilium- the membrane proteins transmit signals from environment to interior this is important for embryonic development and brain functions
cilia and flagella share the same structure but have different movements
they are made of microtubules in a structure of nine doublets arranged in a ring with two single microtubules in the middle. it has a 9-2pattern. (cilia that don’t move have a pattern 9-0)\
-basal body anchors the microtubules and the pattern is triplets of 9+0( similar to centriole)
-dyniens- large motor proteins that bend the microtubules in cilia or flagella to move them, the two feet walk along the microtubulesand they are powered by ATP
the other doublets are held together by cross linking proteins

Question 16

micro filaments, intermediate filaments

Answer 16

microfilaments-twisted double chain of actin subunits (actin filaments), actin is a globular protein, it can form structural networks wen proteins bind 2 filaments to make microvilli( increase surface area of the cell), the role of microfilaments is to bear tension and support the shape
myosin- thicker filament of motor protein that interacts with actin to cause muscle contraction and it also helps with the amoeboid movement of cells, in plant cells they cause cytoplasmic streaming.

intermediate filaments- larger than microfilaments but smaller than microtubules, they help to bear tension, they are more permanent than microfilaments, fix position of organelles, and they reinforce shape. and each type of intermediate filament is constructed by a particular subunit of a proteins such as keratin. the nucleus sits in a cage of intermediate filaments

Question 17

cell walls

Answer 17

extracellular structure of a plant that protects them and maintains the shape. it also prevents the excessive uptake of water. it holds the plant up and is made of microfibrils of cellulose, the cellulose is made in the cell by cellulose synthase and is secreted out of the cell into the ECM.
primary cell wall- thin flexible young cell wall secreted by young plant cells
middle lamella- between the primary cell walls of adjacent cells it is made of sticky proteins that stick the cells together.
secondary cell wall- added by full gown cell between the membrane and the primary cell wall, it is strong and durable,and is put out there in layers some cells don’t secret cell walls they just secrete hardening substance into primary wall instead

Question 18

extracellular matrix

Answer 18

ECM, outside of cell, glycoproteins present- proteins with covalently bonded carbohydrates. collagen present- it is a type of glycoprotein that forms strong fibres outside the cell
proteoglycans- molecule tat consists of a small protein with many carbohydrates attached
proteoglycan complex-hundreds of proteoglycan molecules bonded to a long polysaccharide.
fibronectin-glycoprotein that attaches ECM to integrin proteins in plasma membrane
integrin- made of two subunits and transmit signals from ECM to cytoskeleton, the ECM communicates with cell through integrins and regulates behaviour of the cell and can even influence the activity of genes in the nucleus, the signal reaches the nucleus through cell signalling.
ex: cells in embryo move along specific pathway by matching orientation of microfilaments to gain fibres of ecm

Question 19

Cell junctions

Answer 19

-cell to cell communications
plasmodesmata-PLANTS, they are pores in the cell wall lined with membrane and filled with cytosol, they are tunnels that connect adjacent cells and allow molecules to pass through

tight junctions ANIMAL membrane of neighbouring cells are very tightly packed together and bound by specific proteins , they form continuous seals that prevent leakage of extracellular fluid across epithelial cells

desmosomes- anchor junctions, rivets fastening cells together into strong sheets , intermediate filaments made of keratin proteins anchor desmosomes in cytoplasm
ex. attache muscle cells together when you tear your muscle you rupture your desmosomes

gap junctions- communicating junctions provide cytoplasmic tunnels from cell to the adjacent cell (similar to plasmodesmata), proteins surround pore and they are necessary for communication between cells ex, tissue heart muscle and embryonic cells

Question 20

macrophage

Answer 20

ingest bacteria into phagocytic vesicle its a white blood cell that crawls across the surface and reaches out to bacteria with filopodia which are pseudopodia extensions
actin filaments interact with other elements of the cytoskeleton to move ti, the bacteria in the phagocytic vesicle are killed by enzymes from lysosomes that fuse with it the lysosomes are produced by ribosomes and the synthesis of these enzymes are programmed by the DNA in the nucleus. ATP drives these reactions and it is made in the mitochondria

Question 21

microtubules

Answer 21

hollow tables the structure is 13 columns of tubular molecules, tubular dimer consists of alpha tubular and beta tubular they maintain the cells shape and movement (cilia and flagella) they also help wth chromosome and organelle movement

Question 22

membrane characteristics

Answer 22

proteins and phospholipids are act as a fluid, proteins clustered in specialized patches. the membrane is not static the movement of phospholipids is rapid although proteins are stationary. the membrane can solidify and this results in permeability changes and it cannot support protein function. -unsaturated lipids prevent membrane from solidifying at low temperatures but keeping space between the lipids.-cholesterol regulates membrane- in-between phospholipids, and keeps membrane more static when hot and fluid when cold.
membranes have evolved adaptations according to temperature they are in ex: fish have unsaturated membranes when they live in cold lakes *winter wheat, number of unsaturated bonds in membrane increases in fall and decreases in the summer.

• proteins in membrane determine membrane function
• phospholipids amphipathic meaning the have hydrophobic and hydrophilic regions

Question 23

membrane proteins + membran protein functions

Answer 23

• integral proteins- amphipathic (hydrophobic interior- Matches lipids) hydrophilic exposed to ecm or cytosol. (some have hydrophilic channels and some only go part way into the membrane)
• peripheral proteins- loosely bound to surface of membrane and held by cytoskeleton, they are often exposed to integral proteins and some are attached to extracellular fibres

functions of membrane proteins

1. transport-movement of molecules in or out of cell
2. enzyme activity-enzymatic pathway
3. attachment to ECM/ cytoskeleton-helps with support of cell
4. cell-cell recognition-glycoproteins are antigen and used for identification
5. intercellular joining-cells joined by proteins-gap junctions etc
6. signal transduction-receptor protein in membrane

Question 24

carbohydrates

Answer 24

cell-cell recognition(important for cell embryos and immune system)- cells recognize other cells by binding to carbohydrates on the surface.

• glycoprotein- carbohydrate covalently bonded to protein and they vary from species to species and from individual to individual ex: blood type is according to glycoproteins; type A, AB, O, B
• glycolipid- carbohydrate covalently bonded to lipid

Question 25

membrane synthesis/ sidedness

Answer 25

asymmetric arrangement of proteins is determined as membrane built from ER and golgi

1. membrane proteins and lipids made in ER and carbohydrates can be added to proteins to make glycoproteins.
2. gogli body modifies glycoproteins and some lipids get carbohydrates making glyolipids.
3. glycoproteins and lipids transported in vesicle to membrane
4. vesicle fuses with membrane, these glycoproteins and glycolipids are now on the outside of the cell

Question 26

membrane permeability, transport proteins, channel proteins, aquaporin, carrier protein

Answer 26

hydrophilic substances cannot diffuse across membrane without the assistance of a protein (hydrophobic molecules can due to the hydrophobic interior)
transport protein-move hydrophilic molecules across membrane
channel protein-hydrophilic channel specific molecules can diffuse through(passive no atp required and they go with concentration gradient) ex; aquaporin, water diffuses through this molecule, they are made of four identical subunits and only one water molecule can fit through at a time.
carrier protein- molecules bind to protein and the protein then changes shape allowing molecule to enter cell
*proteins so specific that rbc have a glucose transport protein that rejects fructose
the permeability of a given membrane is determined by specific transport proteins present in the membrane its self.

Question 27

passive transport
dynamic equilibrium
water

Answer 27

diffusion, no energy required, molecules flow with concentration gradient
dynamic equilibrium is when the concentration of solute is equal on both sides
osmosis- diffusion of water across a membrane, it depends on the concentration of solutes that cannot cross membrane.
isotonic- solute concentration equal on both sides, no net gain of water, movement of water is equal
hypertonic- cell in hypertonic solution will shrivel, higher concentration of solute outside cell drawing the water out.
hypotonic- cell in hypotonic solution will expand and in animal cells lyse, water is moving from region of high to low concentration and due to the amount of high concentration of solute in the cell it pulls the water in
osmoregulation- control of solute of concentrations, controlling the water balance of cells, so animal cell won’t lyse- paramecium have a contractile vacuole to do this

Question 28

conditions

cell wall

Answer 28

animal cell- in hypotonic solution the cell becomes lysed(unhealthy), in isotonic solution the cell is normal(healthy), in hypertonic solution, cell is shrivelled( unhealthy)
plant cell, hypotonic solution, plant cell is turgid( healthy), isotonic, the plant cell is flaccid, and in a hypertonic the cell is plasmolyzed (plasmolysis) which is unhealthy
retains water balance and prevents cell from lysing by exerting turgor pressure back to the water pressure

Question 29

facilitated diffusion

Answer 29

passive transport aided by proteins, there are two types, channel proteins and carrier proteins. a type of channel proteins are ion channels, which are gated channels that open and close responding to stimuli, ex, nerve cells ion channels open in response to electric stimuli and k+ ions diffuse out
in passive transport molecules go with concentration gradient therefore no energy required

Question 30

active transport

sodium potassium pump

Answer 30

goes against concentration gradient therefore energy is required, this type of transport allows cell to maintain a certain concentration despite environment of cell
ex; animal cell has a NAK pump which pumps out three Na molecules for every two K molecules, P from ATP transfers to protein which triggers a shape change allowing sodium to be released
affinity- attraction or force between particles that causes them to combine
NAK PUMP-1. cytoplasmic Na+ binds to pump 2.Na+ stimulates protein phosphorylation of pump. 3.new shape, and now has affinity for K ions, and Na is released into ECM. 4. K ions bind to extracellular side of protein which then triggers the release of the phosphate group and the original shape of the protein is restored, and the k ions are released into the cell.

Question 31

membrane potential

Answer 31

cells have voltage, or electric potential due to difference of charge in cytoplasm and ECM. results from unequal distribution of cation(+) and anions(-). the membrane potential can be a source of energy and it also effects the traffic of charged particles across membrane- cells that have a negative charge favour the transport of cation ions into the cell and anion ions out of the cell, therefore this is one of the two forces driving molecules across a membrane; electric force and concentration gradient, these two combined are the electrochemical gradient.(specifically for ions). ions diffuse along electrochemical gradient, ex:nerve cells stimulated and protein channels open allowing Na to fall down concentration gradient

Question 32

electrogenic pump

Answer 32

generates voltage across a membrane and produces stored energy that can be used to drive cellular work. the major electrogenic pump in animals is the sodium potassium pump, it creates a positive charge in the ECM
*proton pump is the main one in plants and it actively transports hydrogen ions out of the cell, the proton gradient can be used for ATP synthesis or cotrransport
cotransport- atp powered pump that a specific solute out of cell can indirectly drive the transport of other substances into the cell. the solute is pumped out against gradient and can do work when it diffuses back in
*plants use the hydrogen ion gradient established from the proton pump to bring sucrose into the cell ( for example in veins of cells) this goes against sucroses concentration gradient.
* cotransport is active transport driven by a concentration gradient.
cotransport and diarrhea in animal cells- Na+ is not reabsorbed because waste is expelled so fast so patients are given a Na Cl glucose solution which is taken up by a Na-glucose pump which acts as a cotransporter in the intestine

Question 33

bulk transport in cell

Answer 33

exocytosis- cell secretion, transport vesicle from gogli fuses and contents spill out of cell, the vesicle becomes a part of the membrane ex, pancreas secretes insulin this way.
endocytosis- takes in molecules and forms new vesicle( opposite of exocytosis and has different proteins involved, but both remodel the plasma membrane) endocytosis has three types:
1. receptor mediated endocytosis(specialized pinocytosis) proteins with receptor sites bind to specific solutes, when the receptors are full a vesicle pinches off from plasma membrane . receptors are recyled. ex human cells take in cholesterol for steroids- LDL( low density lipoprotein) in blood binds to LDL receptors and enter by receptor mediated endocytosis
2.phagocytosis- cell eating, cell engulfs larger molecules into food vacuole, the food vacuole then fuses with a lysosome and digests the contents
3.pinocytosis- cell drinking-cell obtains dissolved solutes that are not specific and are just in the solution outside the cell-into vesicles that are coated by protein coat.

Question 34

cell signalling , and three stages

Answer 34

coordinates a cells activities-
LOCAL SINGALLING- communication through gap junctions (plasmodeta). other type **paracrine signalling which is when a secreting cell discharges local regulators that act on nearby cells ex; growth factor stimulates nearby cells to grow and divide.
-synaptic signalling-nervous system- and electrical signal triggers the secretion of neurotransmitters, molecules diffuse across the synapse(which is a long narrow space between nerve cells)

LONG DISTANCE SIGNALLING- which is known as ENDOCRINE SIGNALLING or hormonal, specialized endocrine cells secrete hormones into blood and reach target cells which recognize them and respond to the I plant hormones travel in the vascular tissue or air)

first stage. reception- outside molecule binds to receptor protein, target cells detection of the signalling molecule
second stage. transduction- steps that convert signal into a form that can bring about a cellular response. molecules involved are known as relay molecules. signal transduction pathway is the sequence of changes in a series of different molecules
third stage. response of cell ( can be anything) - ensures cellular activities occur at the correct time.

Question 35

reception

Answer 35

certain cells respond to the signal ( they must have specific receptor protein). signalling molecules bind as ligand(which is a molecule that specifically binds to a larger molecule) protein changes shape which means the receptor is activated and can now act on other molecules.

• receptor in membrane- transmits info into the cell
• G-protein coupled receptor(GPCR) uses GTP for energy. A signalling molecule binds to the receptor site causing a shape change, the cytoplasmic side activates a gprotein, the g protein carries GTP as it leaves the receptor site and diffuses across the membrane, it then binds to an enzyme, activating it temporarily, this reaction is reversible.
• ligand gated ion channel- membrane receptor is a gate for ions, a signal molecule binds to receptor as a ligand, this causes the receptor to change shape and either open or close for ions. (nervous system)
• intracellular receptors- these proteins are in the cytoplasm or nucleus. signal molecule is a hydrophobic molecule and can therefore pass through the membrane– testosterone secreted by testes get response from specific cells with the correct receptors. testosterone binds to the receptor proteins inside cell then the protein and testosterone enter the nucleus together and turn on male sex genes. the testosterone receptor when activated acts as a transcription factor( protein that turns genes on and off)

intracellular receptors carry out complete transduction

Question 36

transductio multistepts, phosphorylation

Answer 36

MULTIPLE STEPS- receptor in membrane, and the molecules that usually relay the signal are proteins. the signal molecule does not enter the cell. (more steps= larger signal) , each step signal is transducer into a different form, usually by phosphorylation.
phosphorylation/ dephosphorylation (acts as a switch)- protein kinase(enzyme that transfers P from ATP. protein kinase is involved in signal transduction pathway -protein phosphatase-removes P from proteins inactivating protein kinase, they turn off the signal transduction pathway and make protein kinase available again.

phosphorylation cascade- signal molecule binds to receptor and relay molecule activates protein kinase 1. this protein kinase then activates protein kinase 2, and protein kinase 2 then phosphorylates a protein that will bring about the cellular response. protein phosphatase then catalyzes the removal of P making it inactive

Question 37

second messengers

Answer 37

these are small molecules or ions that are a part of the signal transduction pathway, the first messenger is extracellular and binds to a receptor. the second messenger is spread by diffusion. the most common is cyclic AMP or camp (also Ca+). cAMP- cyclic adenosine monophosphate.
the first messenger in series binds to a G COUPLED PROTEIN RECEPTOR which activates the g protein that moves across the membrane and activates adenylyl cyclase which is an enzyme that converts ATP to cAMP and cAMP acts as a second messenger which activates protein kinase A.

Question 38

response

Answer 38

signal transduction pathways lead to cellular activities. a slow process is when the final activated molecule in the pathway is a transcription factor, it is slow because and entire protein is being synthesized for the intended cellular activity. a transcription factor turns on or off specific genes (usually on) which enables protein synthesis ex: growth factor binds to a receptor which triggers phosphorylation cascade, last kinase enters nucleus and activates the transcription factor that stimulates transcription of a gene, and mRNA is created to direct the synthesis of proteins.
fast process, signalling pathway regulate a protein activity instead of its actual synthesis. this directly effects the activity of the cell outside the nucleus.

Question 39

Evolution and signalling

Answer 39

same signalling mechanisms in diverse species due to the fact that they have similar biological processes such as hormone action or embryonic development or even cancer. scientists think that cel signalling mechanisms evolved before multicellular organisms. this makes sense because how would a multicellular organism thrive or even function if the cells cannot coordinate their functions.

Question 40

why are cells small?

Answer 40

larger cells put to big of a demand on the DNA, this would limit cells activity, also, the surface area must be large relative to the volume or else important nutrients would not be able to get into and around the cell in time for cell to function ( also wastes out) a cell must have a large surface area and small volume, meaning the cell must be small to function efficiently

Question 41

must know process, molecules involved and structure for simple diffusion, facilitated diffusion, protein pump, cotransport, endocytosis

Answer 41

passive diffusion(no atp, requires gradient)
-simple diffusion is the process, requires gradient, molecules involved, alcohol and gases (hydrophobic molecules so they can pass through hydrophobic interior of membrane) structure- phospholipids 

-facilitated diffusion is the process, it also requires gradient structure- protein carriers or protein channels (aquaporin) molecules- glucose, amino acids, and urea out.

active transport- against gradient, atp
protein pump- is the structure used and also the process it goes against the gradient and requires ATP -molecules- iodine, glucose and amino acids (when needed like the veins of plants) IONS- sodium potassium hydrogen(protons)

• cotransport- is the process the structure is an ion pump such as a proton pump, and the cotransporter protein, molecules involved; protons and glucose

endocytosis- vesicle fuses with membrane- phagocytosis(wbc cell eating larger molecule) pinocytosis- cell drinking, small molecules that cannot get through pumps
receptor mediated endocytosis (exocytosis- secretion)

Question 42

protein phosphorylation/ dephosphorylation (understanding)

Answer 42

activity of proteins in a cell regulated by the addition or removal of P from ATP

• phophorylation- protein kinase, delivers phosphate group from ATP to a protein
• dephosphorylation- protein phosphatase, remoces P from protein - protein acts as switch that can turn off signal transduction pathway when ligand no longer present

Question 43

metabolism, metabolic pathway, anabolic vs catabolic

energy, kinetic, thermal, heat, potential, chemical

Answer 43

metabolism- all organisms chemical reactions- transforms matter into energy
metabolic pathway- molecule changed in a series of steps that are catalyzed by an enzyme.
catabolic- break down of molecules (exergonic, cellular respiration)
anabolic- make molecules endergonic, photosynthesis)
energy ability to do work
kinetic- energy of movement
thermal- total kinetic energy
heat- thermal energy transfer
potential- matter due to position/location/structure
chemical energy- potential energy available in a chemical reaction (glucose)

Question 44

energy transformation

Answer 44

organisms are open systems that absorb and release energy

• first thermodynamics law, energy consideration- not created or destroyed just changes form- transferred or transformed
• second thermodynamics law- when energy is transferred/transformed, it increases entropy( which is disorder) heat released it warms nearby matter which is why we can’t reuse it.

spontaneous reaction-occur without energy they are favourable and release energy
nonspontaneous reaction- requires energy to occur
biological order/ disorder- living systems increase energy of surroundings by releasing heat and adding entropy

Question 45

free energy+ metabolism , chemical equilibrium+ metabolism

Answer 45

free energy in a system is the energy that can perform work ( kind of similar to potential energy but its either released or absorbed)
- a system changes either to -deltaG which is the release of energy or +deltaG( which is the energy used in the reaction.
change in free energy = energy final - energy initial.
metabolism/free energy-exergonic- negative value of free energy because energy is released. the size of deltaG or change in free energy shows the amount of energy released. Endergonic- requires energy so there is a positive deltaG- the energy “lost” is actually stored in molecules- size of delta G is the amount of energy required
chemical equilibrium-forward and reverse reactions occur at the same rate, they reach an equilibrium when there is not enough energy to continue, when there is no change of concentration of the reactants and products the free energy (G) is at its lowest value, and to change it from an equilibrium energy is required. (systems never move away from equilibrium on their own) if a system is at an equilibrium, no work can be done
metabolism/equilibrium- if reaction is isolated and equilibrium will occur and no more free energy- therefor cell would die so they must have open systems. cells maintain a lack of equilibrium by not allowing products to accumulate- they become reactions again quickly, the reactions cycle and keep going by a large difference in free energy, for example- glucose and oxygen.

Question 46

energy coupling, atp, 3 types of work

Answer 46

exergonic process drives an endergonic process, ATP drives most endergonic reactions
ATP hydrolysis is exergonic (water added, phosphate group is lost) ATP+ H20— ADP+ P+ a change in free energy of -7.3kcal
this works because the reactant has higher chemical energy relative to the product- the energy does not actually come from the bond breaking, it comes from the chemical change to a lower state of energy.
atp hydrolysis- three types of work it can drive: mechanical, chemical, and transport
-chemica- glutamine synthesis- (endergonic) when coupled with ATP occurs in two steps 1. atp phosphorylates glutamic acid-making it less stable (higher potential energy)
2.ammonia displaces the phosphate group forming glutamic acid
-transport- atp phosphorylates transport proteins and changes their shape and ability to bind with other molecules
mechanical-motor proteins move along cytoskeleton, atp drives them, atp binds covalently to protein water hydrolyses atp to adp and p and the free energy released moves protein

Question 47

phosphorylated intermediate + endergonic reaction and energy coupling

Answer 47

reactant with P group covalently bonded to it making it less stable and more likely to react. glutamic acid synthesis on own has a value of +3.4kcal but the atp hydrolysis has a value of -7.3kcal, so the total free energy produced is released as -3.9 kcal making the endergonic reaction exergonic– if the free energy of endergonic reaction absorbed is less than the free energy released in the coupled exergonic reaction, the reaction now exergonic

Question 48

regeneration of ATP

Answer 48

energy is required to phosphorylate adp, meaning it is endergonic- this comes from another exergonic reaction- the break down of glucose (cellular respiration)
ATP cycle- atp couples cells exergonic processes to endergonic processes, adp loses phosphate group to reaction when H20 hydrolyzes it, then cellular respiration provides energy for dehydration synthesis of adp back into atp. the ATP can be used again for more coupling reactions

Question 49

enzymes/ activation energy

Answer 49

they do not increase energy produced in a reaction, they just increase the rate of reaction. they re biological catalysts meaning they are a chemical agent that speed up the rate of reaction without being used up. activation barrier- starting molecule bus absorb energy (which is activation energy) in order to get over the barrier so the action can start- this is the initial investment of energy in the form of heat usually - even exergonic reactions require this.
* enzymes lower activation energy required and therefor lower the energy barrier, this allows reactions to occur in organisms at a sustainable temperature.

Question 50

enzyme-substrate complex, induced fit theory, how enzymes work,

Answer 50

enzyme and substrate bind together, once joined the enzyme helps convert substrate to product.
enzyme specify results from shape
active site- site where substrate fits and is changed
induced fit- active site of an enzyme can move when a substrate enters the active site. the active site changes slightly and this brings it into a position that an enhance its catalyzing ability
how enzyme works- substrate heard in active site by weak bond(vanderwaal,h bonds, ionic bonds) r groups of enzyme catalyze conversion substrate to product, the product produced has a different shape and leaves shape

Question 51

how enzymes lower activation energy (4)

Answer 51

1. reaction has 2 or more reactants ( substrates) , that need to come together in the proper orientation in order to react, the enzyme provides the proper template so they can join in the proper orientation
2. enzyme holds substrate and stretches the substrate into a transition state resulting in a lowered activation energy because the substrate is now reactive ( stresses bonds reducing activation energy
3. active site acts as a micro environment which is more conductive for the substrate.- ex: acidic R groups create acidic environment in an otherwise neutral cell
4. direct participation of active site in a chemical reaction- brief covalent bond between substrate and side chain of amino acids. steps of reaction restore the enzyme to the original state and the enzyme is the same after the reactions it was before

Question 52

factors effecting enzyme (4)

Answer 52

• concentration- rate of reaction( amount of substrate being converted to product is related to the concentrations of substrate and enzyme. enzyme saturated- all of the active sites are filled at all times and the only way to speed up this reaction is to add more enzymes ( assuming reaction is at optimum temperature. if not, temperature increase can also speed up the rate of reaction)
• temp- slight increase (towards optimal temperature) the reaction rate will increase because of the increase in particle collisions (the enzymes are able to find the substrate faster and once the enzyme is in the substrate the reaction will be faster because the molecules kinetic energy is higher) however if the temperature increases above the optimal temperature, the enzyme will become denatured and drop (even though the parties are moving faster)
• pH- optimal ph for an enzyme is important or else the enzyme will not function- too acidic or basic it can denature the enzyme, the enzyme must start in the proper pH it cannot go into it, because the enzyme will still be denatured.
• cofactors- bind to enzyme and they perform a crucial function (inorganic) * coenzyme does the same thing but it is organic (vitamin)
• enzyme inhibitors- chemicals that restrain enzymes specifically ( if the inhibitor binds covalently its irreversible (not if its a weak bond) -competitive inhibitors-bind to active site, non competitive- binds to allosteric site of enzyme ( back)

Question 53

evolution of enzymes

Answer 53

mutation in DNA sequence results in different amino acid which could make and enzyme act in a different way. such as enzyme binding to a new substrate. natural selection favours the mutated gene and they persist in the population.

Question 54

regulation of metabolism/allosteric inhibitors and activation

Answer 54

cell regulates metabolism by controlling when and where an enzyme is active, 1. switches gene on and off 2. regulate activity once enzyme is made

*allosteric regulation- enzyme has two subunits composed of polypeptides chain with its own active site. it changes between active and inactive ( two different shapes) , the regulatory molecule binds to the allosteric site where subunits connect.
activator- stabilizes shape creating functional active sites
inhibitor- stabilizes inactive form of enzyme
*one regulatory molecule changes all active sites of all subunits
EX: atp inhibitor is also the adp activator- both same for enzymes. - ATP exceeds demands for cell and it starts to bind to other substrates that are making atp, inhibiting them. in contrast, when there is not enough atp, ADP binds to the same enzyme and activates it.

Question 55

cooperativity

Answer 55

substrate binds to one active site of a multisubinit enzyme triggering a shape change in all the other subunits. it increases the catalytic activity at all of the other sites.1 substrate primes enzyme to act on all other substrates. EX: hemoglobin- made of four subunits each with an active site that binds with oxygen. once oxygen binds to subunit of hemoglobin, it primes all of the other subunits for more oxygen. The less Oxygen there is the less Oxygen will bind to the hemoglobin, so oxygen molecules are released where the body needs oxygen.

Question 56

feedback inhibition

Answer 56

metabolic pathway shut off y inhibitory binding of the end product to an enzyme earlier in the pathway (JUST LIKE THE ATP ONE) another example is the process of threonine being converted into isoleucine( which is many steps), isoleucine, as the product accumulates , and starts to slow down its own production by binding allosterically to the enzyme and inhibiting it at the first step of the pathway.

Question 57

location of enzymes

Answer 57

organelles organize enzymes and substrates in a multi enzyme complexe- product of enzyme is now a substrate for another enzyme.
enzymes are in a fixed location within a cell( cellular respiration-mitochondria)

Question 58

parts of enzyme

Answer 58

active site- where substrate binds
cofactor- may form active site
apoenzyme- protein part of enzyme (regular enzyme)
allosteric site- back of enzyme