Final Lecture Exam (new) Flashcards
light rxns:
pigment molecules (like chlorophylls) are critical to the light reactions bc they _____
capture light energy
light rxns:
chlorophylls are contained w/in structures called ___
photosystems
light rxns:
photosystems are located in ___
thylakoid membranes
light rxns:
photon energy is captured by ___ contained in ___
chlorophylls contained in photosystems
light rxns:
photon capture (mechanism)
antenna chlorophylls (AC) capture photon energy
photon energy radiated from AC to AC
energy captured by the reaction center chlorophyll (RCC)
energy is absorbed by electrons in the RCC
energized electrons are:
1) ejected from RCC
2) captured by an electron carrier
3) enter into an electron transport chain
ejected electrons are replaced
light rxns:
where are the photosystems located?
thylakoid membrane
light rxns:
PS2 gets replacement electrons from ___
H2O
light rxns:
PS1 gets its electrons from ___
PS2
light rxns:
in both PS1 and PS2, antenna chlorophyll ___
capture photon/light energy
light rxns:
in both PS1 and PS2, photon energy is used to ___ w/in ___
energize electrons w/in reaction center chlorophylls (RCC)
light rxns:
in PS2, energized electrons enter the ___ and are transported from ___
ETC and are transported from PS2 to PS1
light rxns:
in PS2, energy from the electrons in ETC is used to ___
produce ATP
light rxns:
in PS2, ___ is used to produce ATP
energy from the electrons in ETC
light rxns:
in PS2, replacement electrons come from ___
H2O
light rxns:
in PS2, ___ enter the ETC and are transported from PS2 to PS1
energized electrons
light rxns:
in PS2, ___ come from H2O
replacement electrons
light rxns:
in PS1, replacement electrons come from ___
PS2
light rxns:
in PS1, ___ come from PS2
replacement electrons
light rxns:
in PS1, de-energized electrons from PS2 are ___ w/ ___
re-energized w/ photon energy
light rxns:
in PS1, ___ from PS2 are re-energized w/ photon energy
de-energized electrons
light rxns:
in PS1, energized electrons are transferred to ___, thereby ___ to ___
NADP+
thereby reducing it to
NADPH
light rxns:
in PS1, ___ are transferred to NADP+, thereby reducing it to NADPH
energized electrons
light rxns:
in PS2, energized electrons get ejected and enter into the ___
ETC
light rxns:
in PS2, ___ ___ get ejected and enter into the ETC
energized electrons
light rxns:
the ___ carries electrons from PS2 to PS1
ETC
light rxns:
when electrons reach PS1, they have ___ ___ ___
lost their energy
light rxns:
when electrons reach ___, they have lost their energy
PS1
light rxns:
where does lost electron energy in PS1 go?
energy stored in electrons at PS1 is used to power a H+ pump
light rxns:
what does the H+ pump do?
what are the protons doing thru the proton pump?
creates a proton gradient across the membrane
protons are flowing from stroma into inner thylakoid space via the proton pump
light rxns:
to diffuse back across the ___, H+s need a ___
membrane
channel
light rxns:
what is the channel that allows H+s to diffuse back across the membrane?
what type of molecule is it?
ATP Synthase
enzyme/transport protein
light rxns:
ATP Synthase uses the ___ to make ATP
energy of H+ flow
light rxns:
ATP Synthase uses the energy of H+ flow to ___ ___
make ATP
light rxns:
how light reactions make ATP (mechanism)
excited electrons pass from PS2 to PS1 thru the ETC
ETC powers proton pump which builds up a H+ gradient on the inner thylakoid membrane
protons flow back out into stroma thru ATP Synthase
ATP Synthase spins as protons flow thru –> generates ATP
light rxns:
how light reactions make NADPH (mechanism)
photon energy from light is used to re-energize the electrons in PS1
re-energized electrons are used to reduce NADP+ to NADPH
where do dark reactions occur?
stroma of chloroplast
dark reactions require…
NADPH (produced by light rxns)
ATP (produced by light rxns)
CO2
dark reactions occur in 3 steps
- carbon fixation
- reduction of PGA
- regeneration of RuBP
carbon fixation (general)
___ step of the dark rxns
converts an ___ form of carbon (specify) into an ___ form (specify)
1st step of dark rxns
converts an inorganic form of carbon (CO2) into an organic form (PGA)
reduction of PGA (general)
___ step of the dark rxns
electrons are transferred to ___ from ___
2nd step of dark rxns
electrons are transferred to PGA from NADPH
regeneration of RuBP (general)
___ step in dark rxns
3rd step of dark rxns
RuBP is a molecule required for the carbon fixation step
carbon fixation (detailed mechanism)
begins w/ RuBP and CO2
RuBP & CO2 form a covalent bond:
1 RuBP + 1 CO2 –> 6-C molecule
this rxn is catalyzed by enzyme Rubicso
Next:
6-C molecule spontaneously breaks down into two, 3-C molecules (PGA):
one, 6-C molecule –> two, 3-C PGA molecules
RuBP (what is it)
5-C sugar known as the “carbon acceptor”
rubisco (definition)
enzyme that catalyzes the addition of CO2 to RuBP
reduction of PGA uses
NADPH as electron source
ATP as energy source
reduction of PGA (overview)
PGA is reduced and converted: PGA –> G3P
G3P has 2 functions
used to make glucose
used to regenerate RuBP for carbon fixation
carbon fixation ends in the production of ___ PGA molecules
2
carbon fixation ends in the production of 2 ___
PGA molecules
___ ___ ends in the production of 2 PGA molecules
carbon fixation
summary: dark rxns
carbon fixation
5-C (carbon) RuBP + CO2 –(Rubisco enzyme)–> 6-C intermediate that breaks down into 2, 3-C molecules (PGA)
summary: dark rxns
reduction of PGA
3-C molecules (PGA)
Using energy from ATP and electrons from NADPH:
2, 3-C PGA molecules –> G3P molecules
summary: dark rxns
RuBP regeneration
using G3P molecules:
some G3P used to make more RuBP
some G3P used to make glucose
*glucose is not only molecule made by dark rxns
dark rxns and metabolism:
the DRs feed into many different ___ pathways
synthesis
dark rxns and metabolism:
DRs feed into many different synthesis pathways:
other sugars
amino acids
lipids
nucleic acids
glucose as fuel:
glucose contains lots of ___
energy
glucose as fuel:
glucose ∆G = ___
ATP Hydrolysis = ___
- 686 kcal/mol
- 7.3 kcal/mol
how do organisms extract the energy from glucose?
thru the oxidation of glucose
oxidation of glucose has 2 phases
glycolysis and cellular respiration
oxidation of glucose (2 phases):
phase 1 is ___
glycolysis
oxidation of glucose (2 phases):
phase 1, glycolysis:
occurs in the ___
glucose is converted into ___
cytoplasm of cells
pyruvate
oxidation of glucose (2 phases):
phase 2 is ___
cellular respiration
oxidation of glucose (2 phases):
phase 2, cellular respiration:
occurs in ___
mitochondria of cells
oxidation of glucose (2 phases):
phase 2, cellular respiration:
CR has 3 stages:
oxidation of pyruvate
citric acid cycle (TCA, Krebs cycle)
electron transport chain
oxidation of glucose (2 phases):
these stepwise processes allow for a controlled, regulated release of energy from ___
glucose
oxidation of glucose (2 phases):
these stepwise processes allow for a controlled, regulated release of ___ from glucose
energy
oxidation of glucose (2 phases):
these stepwise processes allow for a ___, ___ release of energy from glucose
controlled, regulated
oxidation of glucose (2 phases):
these ___ ___ allow for a controlled, regulated release of energy from glucose
stepwise processes
ATP production:
during Glycolysis and cellular respiration, ATP can be generated in how many ways?
2
ATP production:
what are the 2 ways ATP can be produced during glycolysis and cellular respiration?
chemiosmosis
substrate-level phosphorylation
ATP production:
chemiosmosis (definition)
flow of protons thru ATP synthase
ATP production:
substrate-level phosphorylation (steps)
an enzyme:
1) takes a phosphate from 1 molecule
2) adds a phosphate to ADP:
ADP –> ATP
glycolysis occurs in the ___
cytoplasm
___ occurs in the cytoplasm
glycolysis
in glycolysis, glucose is converted to ___
pyruvate
in ___, glucose is converted to pyruvate
glycolysis
in glycolysis, ___ is converted to pyruvate
glucose
glycolysis is a ___-step process
10
inputs of glycolysis
1 glucose (6-C)
2 NAD+
2 ADP
outputs of glycolysis
2 NADH (reduction of NAD+) 2 ATP (substrate-level phos.) 2 pyruvate (3C)
what happens next to the pyruvate produced during glycolysis?
depends on oxygen availability:
either aerobic (cellular reps.) or anaerobic respiration (fermentation) can occur
the fate of pyruvate:
thru glycolysis, glucose –> ___
pyruvate
the fate of pyruvate:
thru glycolysis, ___ –> pyruvate
glucose
the fate of pyruvate:
thru ___, glucose –> pyruvate
glycolysis
the fate of pyruvate:
if oxygen available:
aerobic respiration (in mitochondria)
cellular respiration
the fate of pyruvate:
if oxygen not available
anaerobic respiration (in cytoplasm)
fermentation
the fate of pyruvate:
aerobic respiration is…
cellular respiration
the fate of pyruvate:
aerobic respiration occurs in the ___
mitochondria
the fate of pyruvate:
aerobic respiration/cellular respiration occurs when…
oxygen is present
characteristics of cellular respiration:
complete oxidation
produces CO2 and H2O
can make 36 ATP (max)
~38% efficiency (max)
the fate of pyruvate:
anaerobic respiration is…
fermentation
the fate of pyruvate:
anaerobic respiration occurs in the ___
cytoplasm
the fate of pyruvate:
anaerobic respiration/fermentation occurs when…
oxygen is not present
characteristics of fermentation:
incomplete oxidation produces organic products produces NAD+ 2 ATP (from glycolysis) ~2% efficiency
glycolysis + anaerobic respiration (yeast):
glycolysis rxns occur in the ___
inputs:
outputs:
cytoplasm
inputs:
1 glucose
2 NAD+
2 ADP
outputs:
2 NADH (reduction of NAD+)
2 ATP (substrate-level phos.)
2 pyruvates
glycolysis + anaerobic respiration (yeast):
anaerobic resp. in yeast cells occur in the ___
inputs:
outputs:
cytoplasm
inputs:
2 pyruvates
2 NADH
outputs:
2 NAD+ (back to glycolysis)
2 ethanol (fermentation)
2 CO2
purpose of anaerobic respiration/fermentation in yeast cells:
regenerate NAD+ to keep glycolysis going
fermentation total yield and % efficiency in yeast cells:
2 ATPs/glucose
2% efficiency
glycolysis + anaerobic respiration (muscle cells):
anaerobic respiration in muscle cells occur in the ___
inputs:
outputs:
cytoplasm
inputs:
2 pyruvates
2 NADH
outputs:
2 NAD+ (back to glycolysis)
2 lactate (fermentation)
purpose of anaerobic respiration in muscle cells:
regenerate NAD+ to keep glycolysis going
total yield and % efficiency of anaerobic resp. in muscle cells:
2 ATPs/glucose
2% efficiency
glycolysis + anaerobic resp. (muscle cells)
lactate:
1) can be converted back into pyruvate (in cells)
2) can be converted back to glucose (by the liver)
anaerobic respiration in muscle cells is also known as…
lactic acid fermentation
during lactic acid fermentation in muscle cells, pyruvate is converted into ___
lactate
during lactic acid fermentation in muscle cells, ___ is converted into lactate
pyruvate
after pyruvate is produced from glycolysis:
if there is sufficient oxygen:
1) pyruvate will enter the mitochondria
2) cellular respiration will begin
the oxidation of pyruvate occurs in the ___ of the ___
matrix of the mitochondria
oxidation of pyruvate:
equation:
1 pyruvate (3C) + Coenzyme A (CoA) –> Acetyl-CoA
citric acid cycle overview:
completes the oxidation of the ___
acetyl group
citric acid cycle overview:
completes the ___ of the acetyl group
oxidation
citric acid cycle overview:
___ the oxidation of the acetyl group
completes
citric acid cycle overview:
occurs in the ___ of the ___
matrix of the mitochondria
citric acid cycle overview:
___ reactions in ___ phases
1)
2)
3)
9 reactions in 3 phases
1) (2C) Acetyl + (4C) oxaloacetate (the Acetyl acceptor) –> (6C) citrate (citric acid)
2) the oxidation of the acetyl group is completed
3) regeneration of oxaloacetate
citric acid cycle summary:
inputs:
___-step process
outputs:
inputs:
acetyl group
oxaloacetate
9-step process
outputs: NADH (reduction of NAD+) FADH2 (reduction of FAD) ATP (substrate level phos.) CO2
after the citric acid cycle:
___ and ___ will transport the electrons to the ETC
NADH and FADH2
after the citric acid cycle:
NADH and FADH2 will transport the ___ to the ETC
electrons
after the citric acid cycle:
NADH and FADH2 will transport the electrons to the ___
ETC
mitochondria:
glycolysis and anerobic respiration occur in the ___
cytoplasm
mitochondria:
___ and anaerobic respiration occur in the cytoplasm
glycolysis
mitochondria:
glycolysis and ___ occur in the cytoplasm
anaerobic respiration
mitochondria:
oxidation of pyruvate and the citric acid cycle occur in the ___
matrix
mitochondria:
___ and the citric acid cycle occur in the matrix
oxidation of pyruvate
mitochondria:
oxidation of pyruvate and the ___ occur in the matrix
citric acid cycle
mitochondrial structure:
how many types of proton pumps are there in the intermembrane space?
3
ETC:
___ transports electrons to proton pump 1
NADH
ETC:
NADH transports electrons to ___
proton pump 1
ETC:
NADH transports ___ to proton pump 1
electrons
ETC:
___ transports electrons to proton pump 2
FADH2
ETC:
FADH2 transports electrons to ___
proton pump 2
ETC:
FADH2 transports ___ to proton pump 2
electrons
ETC:
an ETC carries electrons to proton pumps ___ and ___
2 and 3
ETC:
an ETC carries ___ to proton pumps 2 and 3
electrons
ETC:
an ___ carries electrons to proton pumps 2 and 3
ETC
ETC:
in the ETC, oxygen is the final electron ___
acceptor
ETC:
in the ETC, oxygen is the final ___ acceptor
electron
ETC:
in the ETC, oxygen is the ___ electron acceptor
final
ETC:
in the ETC, ___ is the final electron acceptor
oxygen
proton gradient formation:
energy from the electrons powers the ___
proton pumps
proton gradient formation:
energy from the ___ powers the proton pumps
electrons
proton gradient formation:
___ from the electrons powers the proton pumps
energy
proton gradient formation:
protons (from the matrix) form a ___ in the intermembrane space
gradient
proton gradient formation:
protons (from the matrix) form a gradient in the ___
intermembrane space
proton gradient formation:
protons (from the ___) form a gradient in the intermembrane space
matrix
proton gradient formation:
___ (from the matrix) form a gradient in the intermembrane space
protons
chemiosmosis:
protons flow thru the ATP synthase and power production of ___
ATP
chemiosmosis:
protons flow thru the ___ and power production of ATP
ATP synthase
chemiosmosis:
___ flow thru the ATP synthase and power the production of ATP
protons
summary of cell. resp. (ETC and chemiosmosis)
NADH gives electrons to proton pump 1
FADH2 gives electrons to proton pump 2
ETC carries electrons to proton pumps 2 & 3
proton pumps use energy from electrons to allow protons to pass thru from the matrix into the intermembrane space
the protons form a gradient in the intermembrane space
protons flow back into the matrix from the intermembrane space thru the ATP synthase
while protons flow out of ATP synthase, ATP is generated from ADP +Pi
efficiency of respiration:
ATP yield from 1 glucose molecule and % efficiency
36 ATPs
38% efficiency, the max for eukaryotes
efficiency of respiration:
usually less than 36 ATPS are made because:
mitochondrial membrane leks, dissipating some of the proton gradient
the proton gradient is also used to drive other processes (sacrificing some ATP production)
the diversity of life is ___
vast
why we need to categorize and name organisms:
allows scientists to communicate about individual organisms or groups of organisms precisely
provides a method to show relationships b/n organisms (phylogeny)
- how closely or distantly organisms are related
relationships (phylogeny):
similar features allow us to:
group organisms together
infer common ancestry
similarities b/n organisms come in 2 types:
homology
analogy
homology (definition and example)
similarities due to common ancestry
ex. foreleg of a horse and cow
analogy (definition and example)
similarities due to a common type of solution to a survival problem
ex. wings of a bat and wings of a fly
___ is useful in building family trees, while ___ is not so useful
homology is useful in building family trees while analogy is not so useful
naming and categorizing organisms distinguishes them down to a ___, leading to ___
fundamental level
hierarchical systems
naming and categorizing organisms distinguish them ___ to a fundamental level, leading to hierarchical systems
down
___ and ___ organisms distinguish them down to a fundamental level, leading to hierarchical systems
naming and categorizing
hierarchical systems:
higher order groups contain more organisms than ___ groups
lower order
hierarchical systems:
___ groups contain more organisms than lower order groups
higher order
hierarchical systems:
higher order groups contain more ___ than lower order groups
organisms
Linnaean system Hierarchical:
what are the hierarchical groups?
what happens as you go down the system to lower levels?
what were the groups based on?
Kingdoms -- largest group (ex. plants) Phylums Classes Orders Families Genera Species -- (single group of organisms)
King Phil’s Closets Often Fold Green Socks
as you go down, get to smaller, more defined groups
all groups were based on physical characterstics
modification of the Linnean system:
what was the modification?
added 3 domains of life, above level of Kingdom:
bacteria, archaea, eukarya
eukarya domain:
examples:
characteristics:
examples:
animals, plants, fungi, protists
characteristics:
all are eukaryotic
have a membrane-bound nucleus and an endomembrane system
have many types of organelles
DNA sequences of the ribosomal (r) protein & rRNA genes are unique from those of archaea and bacteria
archaea and bacteria domains:
archaea and bacteria similarities:
archaea and bacteria similarities:
both are single-celled microorganisms
both have a cell wall
both have a plasma membrane and ribosomes
both lack a nucleus and internal membranes
archaea and bacteria domains:
at one time, archaea were classified as ___
bacteria
archaea and bacteria domains:
at one time, ___ were classified as bacteria
archaea
archaea and bacteria domains:
why did archaea stop being classified as bacteria?
there are significant structural/biochemical differences b/n them
genetic sequencing has shown that they are as distantly related from each other as they are from eukaryotes
archaea domain:
characteristics:
many are found in extreme environments (extremophiles)
have a plasma membrane structure that is biochemically unique from bacteria
have a cell wall structure that is biochemically unique from bacteria
the DNA sequences of the ribosomal (r) protein & rRNA genes are unique from eukaryotes & bacteria
bacteria domain:
characteristics:
AKA “eubacteria” – ‘true’ bacteria
have standard phospholipid plasma membranes
cell walls biochemically unique from archaea
the DNA sequences of the ribosomal (r) protein & rRNA genes are unique from archaea and eukaryotes
life is divided into 3 domains:
bacteria, archaea, & eukarya
eukarya are divided into 4 kingdoms:
plant, fungi, animal, & protista
common features of animals:
all animals are metazoan: multicellular
all animal cells lack a cell wall
all animals are heterotrophs: get their carbon from organic molecules that they consume
all animals obtain energy by consuming other organisms and/or substances produced by other organisms
common features of plants:
all plants obtain energy from the sun (photosynthesis)
all plants contain photon capturing pigments such as Chlorophylls
all plants are autotrophic: carbon source is CO2
all plants have cel walls made of cellulose
common features of fungi:
extract & absorb energy/carbon from their surroundings by secreting digestive enzymes
have cell walls containing chitin
reproduce by releasing spores
genetic analysis has shown that fungi are more closely related to animals than to plants
chitin
a structural polysaccharide made from chains of modified glucose
spores
reproductive cells capable of giving rise to an adult organism
common feature of protists:
being eukaryotic is the only unifying feature among protists
protists don’t fit neatly into other kingdoms:
- plant “like” protists: ex. algae, giant kelp
- animal “like” protists: ex. amoebas, paramecium
- fungi “like” protists: ex. slime & water molds
they can be unicellular or multicellular, microscopic or large in size
display a range of nutritional strategies:
- mixotrophs
mixotrophs
use a mix of different sources to obtain energy and carbon
what is a species?
there are ___ ways to define a species
multiple ways
what is a species?
biological species concept:
one or more populations of individuals that:
- interbreed under natural conditions
- produce fertile offspring
what is a species?
limitations to biological species concept definition:
fossil species:
- don’t know about their breeding
asexual species:
- eg. bacteria
organisms separated by great distances:
- maybe they could interbreed but never come into contact
reproductive barriers b/n species:
interbreeding must produce ___
fertile offspring
ex. horse X donkey –> mule (infertile)
reproductive barriers b/n species:
interbreeding must occur under ___
natural circumstances
ex. wolves, dogs, etc. are different species that can interbreed and produce fertile offspring –> but pairings don’t occur in natural populations
- -> so all are still considered different species
reproductive isolation b/n species:
different species are reproductively isolated by reproductive barriers:
prezygotic barriers
postzygotic barriers
reproductive isolation b/n species:
prezygotic barriers (definition)
prevent mating or fertilization
reproductive barriers b/n species:
postzygotic barriers (definition)
mating and fertilization occur but…
- development of embryo fails… or
- offspring is sterile
reproductive isolation b/n species:
prezygotic barriers – mating (examples)
habitat (never come into contact)
behavioral isolation (incompatible mating rituals/timing/pheromones)
reproductive isolation b/n species:
prezygotic barriers – fertilization (examples)
mechanical (reproductive parts not compatible)
gametic isolation (sperm and egg can’t fuse)
reproductive isolation b/n species:
postzygotic barriers – offspring (examples)
hybrid breakdown (hybrid doesn’t develop or dies soon after birth)
sterility (hybrid lives but is infertile)
modes of speciation:
allopatric
sympatric
modes of speciation:
allopatric:
different homelands
a geographic barrier isolates 2 populations of the same species
the separated populations genetically diverge into different species
modes of speciation:
sympatric:
same homeland
no geographic isolation
a new species arises because of a sudden genetic alteration
modes of speciation:
allopatric speciation (flow-chart)
2 interbreeding populations (same species)
separated by a geographical barrier
genetic variants appear
populations diverge genetically
2 reproductively isolated species develop
modes of speciation:
types of sympatric speciation:
autopolyploidy
allopolyploidy
modes of speciation:
type of sympatric speciation:
autopolyploidy:
a new species from an old species
2 individuals from 1 species mate
an error occurs during sperm or egg formation
results in offspring w/ a different (ploidy) number of chromosome copies than the parents
AND IF:
the offspring lives and is fertile
and the offspring is reproductively isolated from the parental species
then the offspring represents a new species
*happens mostly in plants
modes of speciation:
type of sympatric speciation:
allopolyploidy:
2 different species produce a 3rd species
2 different species interbreed
an error in sperm or egg formation results in a zygote w/ a compatible # of chromosomes
AND IF:
the offspring lives and is able to reproduce
and is reproductively isolated from the 2 parent species
then the offspring represents a new species
*happens mostly in plants
population dynamics:
population (definition)
a group of individuals occupying the same area at the same time
