Yr 12 sac 2
What is a biochemical reaction
a singular metabolic reaction
occurs continually in living cells
the energy cycle between ATP (usable nrg) and other organic compounds (non-usable)
What are endergonic reactions
basically endothermic
uses ATP
to produce macromolecules from smaller molecules
What are exogonic reaction
break down macromolecules into smaller molecules
release nrg in form of ATP
Wat is metabolism
the sum of all reactions in living organism
must occur fast to adapt to environment
What are biochemical pathways
interocnnected biochemical reactions
form multistep biochem pathways
NEEDS specific enzyme in all of the many steps, must be exactly complimentary
what occurs from initial reactant to form product in biochem PATHWAYS
reactants (starting molecules) chemically changed to form products
each reactions needs an enzyme
what are reactants
the substrates for a particular enzyme
What is the induced fit model
light change in substrate to fit the enzyme
substrate changes back afterwards
anabolic biochem pathways
endothermic basically
build complex molecules from smaller ones
net input of nrg
thus energy requiring (endergonic)
nrg of products>reactants
catabolic biochem pathways
exothermic basically
breaks down complex molecules into simple, smaller
nrg releasing or exergonic
nrg of reactants>products
Enzymes use in biochem reactions
all reactions require input of nrg
enzymes lower activation nrg
What is rubisco
key enzyme in photosynthesis
acts on just 3-10 substrate per second (high conc combats this)
catalyses fixation of atmospheric CO2
complimentary to substrate
Photosynthesis as an anabolic pathway
sunlight (glucose) -> energy based upon:
- prescence of chlorophyll in plant cells
- CO2 and H20
- enzymes (rubisco)
Enzymes in cellular respiration
generation of energy to usable forms (ATP)
active site caused by tertiary structure
hence if loses structure, no active site
What are cofactors
additional non-protein molecules
needed for enzyme activity and stability
some inorganic, thus no carbon
what are coenzymes
organic cofactors needed for enzyme activity (stability)
carries something necessary
used in cellular respiration/photosynthesis
What do cofactors do
form bonds at active site of enyzyme (also bonds w/substrate)
hence substrate temp held in position which is required for enzyme function
look at diagram for this please
What are organic cofactors/coenzymes comprised of
prosthetic groups:
- cofactors tightly bound to an ezyme
- essential to its function as a catalyst
photosynthesis equation for coenzymes relevant
NADPH (loaded) -> NADP+ (unloaded)
ATP -> ADP + Pi
what does NADPH do
donate H+ ions and electrons and transfer energy
thus it an unload
coenzyme equations in cellular respiration
NADH -> NAD+
FADH2 -> FAD+
both loaded->unloaded
both carry protons and electrons
role of coenzymes in biochemical pathways
transferring of atoms or groups of atoms
enegry transfers
What is a loaded coenzyme
e.g. NADH
can donate hydrogen ions/electrons and transfer energy
high energy
oxidises
formed from unloaded enzyme using high energy electrons (uptake of radient energy of sunlight)
what is unloaded coenzymes
receiver of electrons/hydrogen ions
reduces
lower energy
How ro increase rate in chem reactions
increase temp
increase conc of reagents
increase surface area of reagents
add catalyst
how to increase rate of biochem reactions (enzyme activity)
uses enzymes
increase temp (kinetic energy)
ideal pH
substrat/enzyme conc (enzyme doesnt plataue if enzyme conc>substrate conc as must dissociate before another can bind)
What are competetive inhibitors
bind to site, blocks substrate
slow rate of reaction but eventually same ror
what are non-competetive inhibitors
binds at allosteric site
causes conformation change, no longer complimentary
has more of an effect, lowers reaction rate as increase in substrate conc
what is irreversible inhibition
substrate perma blocked
combines w/another section perma, changes its shape
why is regulation of biochemical pathways necessary
prevent waste
prevent build up in cells of products to harmful levels
prevent depletion of substrate
what is down-regulation in biochem pathways
slowing or stopping activity of enzymes
what is upregulation of biochem pathways
inversing activity of specific enzyme
what is allosteric regulation
conformational changes of active site
caused by regulator molecules binding to allosteric site
reversible
types of regulator molecules
allosteric inhibitor:
binding produces change of enzyme shape
which stops enzyme activity
allosteric activators:
shape change resulting from binding
produces increase in enzyme activity
eg trp repressor protein
What is feedback inhibition
abundance of the end product acts as an inhibitor of key enzyme of first step of pathways
eg trp (activates repressor proteins)
what are heterotrophs
organisms that consume other organisms for energy
what are autotrophs
organisms that produce own food using light (photoautotrophs) or chem energy (chemoautotrophs)
Photosynthesis process in terms of autotrophs
initial radiation energy captured by autotrophs cannot be used
thus must be transformed into sugars (glucose)
thuse chemical energy
sugars stored as starch (plants) or glycogen (animals)
simplifies biochem pathway for photosynthesis
6CO2 + 6H2O ->C6H12O6 + 6O2
(light+ chlorophyll)
what is the purpose of chloroplast
location of photosynthesis
contains chlophyll in internal membranes
enables plants to capture radiant energy of sunlight
What is chlorophyll
green pigment in internal membranes
cells w/this only in mesophyll cell layer
what does the structure of the chloroplast contain
stroma (liquid)
thylakoid membranes/grana (individual blobs)
granum (groups of grana)
inner and outer membrane
what is the stroma
fluid inside chloroplast
contains enzymes involved in light-dependant stage (calvin cycle)
what do the thylakodi membranes/grana do
enzyme in light-dependant stage of photosynthesis in thylakoid membranes
provide large surface area for capture of sunlight by chlorophyll
simple sentance for the function of the light dependant stage of photosynthesis
transform light energy captured by chlorophyll into chem energy of loaded coenzymes
simple sentance for function of light independant stage (calvin cycle)
change simple inorganic carbon dioxide molecules into more complex organic glucose
needs high energy coenzymes
function and location of light dependant pathway
transforms sunlight energy captured by chlorophyll
into chem energy of loaded coenzymes
thylakoid membranes
how does the light dependant pathway occur
through ETC (electron transport chain) pathway
series of proteins embedded in thylakoid membranes
thus NADP+ and ADP become loaded
Inputs and outputs of light dependant stage
H20 -> O2 (waste product (specifically the O2 not ATP)
ADP + Pi -> ATP
NADP+ -> NADPH
also must include that sunlight is catalyst of these
explanation of process of the inputs and outputs of the light dependant stage (4 steps)
1. radiant energy from sun absorbed by chlorophyll
2. water becomes 'excited', splits, producing electrons, H+ protons and O2
3. electrons + H+ loaded onto NADP + forms NADPH
-NADP+ + H+ + 2e- ->NADPH
4. energy used to pump protoms from stroma -> inside thylakoid which creates proton gradient
explanation of process of the inputs and outputs of the light dependant stage (4 steps)
1. radiant energy from sun absorbed by chlorophyll
2. water becomes 'excited', splits, producing electrons, H+ protons and O2
3. electrons + H+ loaded onto NADP + forms NADPH
-NADP+ + H+ + 2e- ->NADPH
4. energy used to pump protoms from stroma -> inside thylakoid which creates proton gradient
function and location of light independant pathway
assemble simple inorganic CO2 -> glucose molecules
in the stoma of chloroplast
What is the primary enzyme in the light independant pathway
rubisco which is vital in carbon fixation
Inputs and ouputs for light independant pathway
ATP -> ADP + Pi
NADPH -> NADP
CO2 -> C6H12O6 (important)
how would the calvin cycle be identified in a diagram
known as the CO2 enters
steps to Inorganic CO2 -> Organic
1. CO2 converted to 3-carbon molecule through CARBON FIXATION
2. loaded NADPH coenzymes donate H+ and e-
-bc molecules reduced to higher energy levels
3. ATP supplied energy for anabolic steps of cycle
4. glucose formed as an output
How are C4 plants different to C3
have bundle sheath cells where the majoirt of the cholorplast is (thus photosynthesis)
separate carbon fixation and Calvian cycle by cell type
bundle sheath cells do calvin cycle after the mesophyll cell does carbon fixation
How are CAM plants diff to C3
separate carbon fixation and calvin cycle by day and night
night is carbon fixation
day is calvin cycle
Why do C4 plants separate calvin cycle and carbon fixation by cell
minimises photorespiration which would occur in the warm weather that the C4 plants live in
this is done as diff enzyme is used instead of Rubisco in carbon fixation which means that Oxygen cannot be preferntially binded to as the enzyme cannot bind to Oxygen
Why do CAM plants separate calvin cycle and carbon fixation by day and nigth cycles
CO2 can be taken in at night, which in its dry and hot climate, prevents the water loss that would occur if the stomata opened during the day
What is the simple process of C3 plants
CO2 enters the mesophyll cell through the stomata
calvin cycle occurs
glucose is produced and exits the cell
simply process in C4 plays
CO2 enters the mesophyll cell
transformed into C4
this enters the bundle sheath cells
goes back into CO2 and performs calvin cycle
glucose is produced and exits the cell
simple process in CAM plants
CO2 enters mesophyll at night, goes to C4 and then during day CO2 goes into Calvin cycle which produces glucose withought the CO2 entering during the day
What is photorespiration
when plants uptake O2 and not CO2
this is less efficient and produces CO2 instead of glucose
How does photorespiration occur in terms in rubisco
it can bring bind with both CO2 and O2
thus O2 is a competetive inhibitor
when rubisco binds with oxygen, photorespiration occurs
photorespiration when in high temp
rubisco fixed O2 more often
this is because CO2 is LESS SOLUBLE
thus more O2 available in mesophyll
if prolonged then rate of photorespiration faster that photosynthesis (death)
photorespiration when in dry conditions
stomata prevents H2O loss
blocks entry of CO2
limits exit of O2 produced in light-dependant
more O2 and less CO2
thus rubisco binds more O2 than CO2 and photorespiration rates increase
stages in minimising photorespiration for C4 plants
stage one (in mesophyll)
carbon dioxide ->malic acid
use of PEP Carboxylase to fix carbon
PEP can only bind to CO2 which means no photorespiration
Stage two (in bundle sheath cells)
glucose production via calvin cycle
malic acid convrted into pyruvate and CO2
steady CO2 production
thus Rubisco preferentially binds to the CO2, not O2
Night stage of CAM plants
CO2 is taken in (optimal)
carbon fixation occurs when stomata open
reaction catalysed by PEP carboxylase
malic acid stored in vacuoles in plant cell for daytime
Day stage of CAM plants
calvin cycle occurs during the day (needs water to be excited by radient sunlight)
stomata is closed (no water loss)
steady production of CO2
thus Rubisco has affinity for CO2
photoresp reduced
Light availability's impact on rate of photosynthesis
as light intensity increase - photosynthesis rate increases
- until maximum point (similar to substrate conc graph)
further increase has no effect
this point is called the light saturation point
water defecit impact on rate of photosynthesis
plants can close stomata quick to preventfurther water loss
prevents gas exchange (bad)
lack of supply of CO2 to mesophyll cells (no calvin cycle -> no photosynthesis)
no H2O for long time mean death
water logging (too much) impact on rate of photosynthesis
roots need O2 to grow
lack of O2 due to excess H2O in air spaces
thus ASPHYXIATION
plant root cells unable to respire
Temperature impact on rate of photosynthesis
same graph as enzymes as that is what it is
low temp ->lack of kinetic energy
high temp -> denaturisation
has optimal point
CO2 conc impact on rate of photosynthesis
as it increases, photo- increases
until limited by limiting factors
- rubisco working at max rate (enzyme conc)
- lack of coenzymes (such as NADPH)
interrelationships between factors impacting on rate of photosynthesis
they do not act in isolation
amt of CO2 limits max rate of ps at optimal light intesity (light saturation point)
temp also limits this and others
Role of cellular respiration
produces ATP (necessary for life)
What processes need ATP
protein synthesis
extretory processes (removes metabolic waste)
production of antibodies
ways to produce ATP
anaerobic respiration (some bacteria use)
aerobic respiratio (almost all use this)
fermentation (some bacteria/yeast use this)
What is the equation for cellular respiration
C6H12O6 + 6O2 ->6CO2 + 6H2O
ADP+Pi->ATP
Where does glycolysis occur
in cytosol
first stage
equation in glycolysis
Glucose-> -> ->2 Pyruvate (half of glucose)
2ADP+Pi->2ATP
2NAD+->2NADH
No O2 required
if confusing check book
net yeild of ATP and loaded coenzymes in glycolysis
2 ATP and 2 NADH
per molecule of glucose
pre-Krebs Cycle process and why this occurs
Pyruvate cannot enter Krebs
thus pyruvate oxidation occurs
2 Pyruvate ------>2 acetyle CoA + 2CO2
2NAD->2NADH+H+
Krebs cycle location
mitochondrial matrix
krebs cycle inputs and outputs
Inputs Outputs
Acetyl CoA -> CO2 (x6)
ADP + Pi -> ATP (x2)
NAD+ -> NADH
FAD+ -> FADH2
ATP and coenzyme yeild in Krebs cycle
2 ATP
NADH
FADH2
Electron transport Chain inputs and outputs
Inputs Outputs
O2 -> H2O
ADP + Pi -> ATP
NADH -> NAD+
FADH2 -> FAD+
location of ETC
inner membrane in mitochondria
Process of Electron Transport Chain
1.NADH and FADH2 drop off e- and H+
2.e- pass through each complex
3.provides energy to pump proteins into intermembrane space
-thus H+ gradient created
4.H+ flows down gradient through ATP synthase
-provides energy for ATP
goal of Krebs cycle
load as many coenzymes and produce as much ATP for the ETC
How much ATP is produced by the Electron Transport Chain
26-28 ATP
Why is ATP synthase involved in ETC
H+ cannot naturally pass through the membrane as it is not permeable
thus an enzyme must be used
what are the factors that affect rate of celular respiration
temp (same as temp for enzyme graph)
glucose conc (substrate graph)
oxygen conc (also substrate graph)
glucose and oxygen both increase rate until other limiting factors prevent their increase in rate
What and why is anaerobic fermentation
when organisms live in oxygen-deficient enviro and neep ATP (do this or anaerobic respiration
net ATP of 2
why Anaerobic respiration in humans
when supply of O2 to cells by aerobic cellular respiration cannot keep up w/ATP demand
intense athletic performances
can only last a few minutes in humans
How long can anaerobic fermentation last in yeast/bacteria
indefinetely without interruption
in humans only a few mins
diff between anaerobic fermentation and respiration
for us they are effectively the same thing
Where does anaerobic fermentation occur
cytosol
anaerobic conditions
what are the common pathways of anaerobic fermentation
lactic acid fermentation (animals)
alcohol (ethanol) fermentation (yeast)