Ch. 9-10, 16 Flashcards
Cellular respiration, photosynthesis, and DNA replication
carbon cycle
organisms need a constant influx of organic molecules to do the work necessary for life
producers
use the energy from sunlight to turn CO2 into carbohydrates and O2
consumers
must continually eat to transform organic compounds into ATP and CO2
cellular respiration
is the catabolic pathways of aerobic and anaerobic respiration, which break down organic molecules and use an electron transport chain for the production of ATP
aerobic respiration
-is a catabolic pathway for organic molecules, using oxygen (O2) as the final electron acceptor in an electron transport chain and ultimately producing ATP
-is the most efficient pathway
-is carried out in more eukaryotic cells and most prokaryotic cells
-couples the breakdown of organic molecules (carbs, fats, proteins) into CO2 and H2O with the production of ATP
anaerobic respiration
-is a catabolic pathway in which inorganic molecules other than oxygen accept electrons in an electron transport chain
-oxygen is an excellent electron acceptor, so organisms that use other electron acceptors (like sulfate or nitrate) are less efficient in producing ATP during respiration
-live in poor oxygen rich environments like mud flats or deep-sea vents
potential energy
-complex molecules are a source of potential energy
-electronegative atoms like O hold onto electrons more tightly than C or H atoms
redox reactions
-the combination of an oxidation and a reduction
oxidation
losing electrons; the complete or partial loss of electrons from a substance in a redox reaction
reduction
gaining electrons; the complete or partial addition of electrons to a substance in a redox reduction (adding electrons reduces the amount of positive charge)
“LEO the lion says GER”
Loss
Electrons
Oxidation
Gain
Electrons
Reduction
Red/ox
Reduction=gain electrons (+ H+)
Oxidation=lose electrons (- H+)
electron donor
is the reducing agent - loses an electron
electron acceptor
is the oxidizing agent - gains an electron
why is oxygen a great oxidizing agent?
-oxygen is very electronegative
-electrons that are shared between carbon and hydrogen, which share the electrons equally, are farther away from the nucleus and have more potential energy
using glucose for respiration
the breakdown of glucose into CO2 and H2O is a redox reaction
C6H12O6 + 6O2 —> 6CO2 + 6H2O + energy
-oxygen is the oxidizing agent, it gains electrons (the electrons are closer to the nucleus), and becomes reduced (less positive charge)
-glucose is the reducing agent, it loses electrons (electrons are farther from the nucleus)
controlled reactions
-you can burn glucose and quickly release all of the energy stored in its covalent bonds, but you can’t capture energy from that reaction for work
-cellular respiration is a very ordered process, with many steps, that gradually reduces glucose to CO2 and H2O by transferring electrons from one molecule to another
>allows for more energy to be converted to work
>electrons can be donated from one molecule to another, which releases a proton into the surroundings (aka a H+ ion)
NAD+
-is an electron carrier
-Nicotinamide adenine dinucleotide (NAD)
-when it is oxidized it has a positive charge (NAD+)
-when it is reduced it gains a hydrogen atom and loses its positive charge (NADH)
-produced from the vitamin niacin (Vitamin B3)
NADH
-think ATP
-through a series of reactions the electrons being carried by NADH will be transferred to O2 forming water, and ATP will be produced
electron transport chain
is a sequence of electron carrier molecules (membrane proteins) that shuttle down a series of redox reactions that release energy used to make ATP
3 parts of aerobic cellular respiration
- glycolysis
- citric acid cycle (prep-step & CAC)
- oxidative phosphorylation (electron transport chain and chemiosmosis)
-technically, cellular respiration only includes the citric acid cycle and the electron transport chain; glycolysis also occurs in cells during fermentation when no oxygen is present
3 types of ATP synthase
-substrate level phosphorylation
-oxidative phosphorylation
-photophosphorylation
glycolysis
-(splitting of sugar) is a series of reactions that splits glucose into pyruvate
-occurs in cytoplasm of both prokaryotes and eukaryotes
part 1 of glycolysis
energy investment phase
part 2 of glycolysis
energy payoff phase
INs and OUTs of glycolysis
6-C glucose –(oxi.)–> 2 x 3-C pyruvate
2 ATP –(SLP)–> 4 ATP (kinase) [net 2 ATP]
2 NAD+ –(red.)–> 2 NADH
prep step (pyruvate oxidation)
-pyruvate is transported from the cytosol into the mitochondria
-pyruvate is oxidized
>split off one carbon and form CO2
>transfer an electron and a hydrogen to NAD+ to form NADH
>add coenzyme A to form acetyl coenzyme A (Acetyl CoA)
INs and OUTs of prep step
2 x 3-C pyruvate –(oxi.)–> 2 x 2C acetyl-coA + 2 CO2
2 NAD+ –(red.)–> 2 NADH
Citric Acid Cycle (CAC)
-Acetyl CoA (2 carbons) enters the citric acid cycle and forms a 6-C molecule, citrate, by making a covalent bond with a 4-C molecule (CoA is recycled)
-after changing citrate into a structural isomer, a 6-C molecule is oxidized forming one NADH and releasing CO2, producing a 4-C molecule with CoA attached
-The 4-C CoA molecule substitutes a phosphate for the CoA, which is recycled
-by substrate-level phosphorylation an ATP is produced and the phosphate removed from the 4-C molecule
- 2 hydrogen atoms are stripped from the 4-C molecule, producing one FADH2
-A final 4-C molecule loses a hydrogen atom and an electron forming one NADH. The original 4-C molecule from the beginning of the cycle is reformed
INs and OUTs of the citric acid cycle
2 x 2-C acetyle CoA –(oxi)–> 4 x CO2
6 NAD+ –(red)–> 6 NADH [2x3=6]
2 FAD –(red)–> 2 FADH2 [2x1=2]
2 ADP –(SLP)–> 2 ATP [2x1=2]
INs and OUTs of fermentation
2 NADH –(oxi)–> 2 NAD+
3_C pyruvate –(red)–> fermentation products [ex: lactic acid, alcohols like ethanol +CO3]
chemiosmosis
the process of ions moving across a semipermeable membrane from an area of high concentration to an area of low concentration
oxidative phosphorylation
the production of ATP using energy derived from the redox reactions of an electron transport chain
INs and OUTs of electron transport chain
10 NADH –(oxi)–> 10 NAD+ H+
2 FADH2 –(oxi)–> 2 FAD + H+
6 O2 –(red)–> 6 H2O
photosynthesis
-the conversion of light energy to chemical energy that is stored in sugars or other organic compounds
-occurs in plants, algae, and certain prokaryotes
-is the basis for almost all life on earth
autotrophs
self-feeders, organisms that utilize photosynthesis
heterotrophs
other feeders, feed on other organisms
chloroplasts
organelle with a double membrane
stroma
-space inside the double membrane
-site of Calvin Cycle (pt 2 of photosynthesis)
-contains ribosomes and DNA
thylakoids
-are a third membrane system suspended in the stroma
-contain chlorophyll embedded in the membrane
-site of the light reactions (pt 1 of photosynthesis)
thylakoid space
inside the thylakoid
granum
a stack of thylakoids
carbon fixation
-the process by which living organisms, primarily plants through photosynthesis, convert inorganic carbon dioxide from the atmosphere into organic compounds
-“fixing” carbon into a usable form for life
(inorganic—>organic)
major site of photosynthesis
any green part of a plant, but especially the leaves
mesophyll
the middle layer of a leaf
stomata
a microscopic pore surrounded by guard cells in the epidermis of leaves and stems
absorption spectrum
-a graph plotting a pigment’s light absorption vs. wavelength
-plants have multiple pigments that absorb light of different wavelengths
spectrophotometer
a machine that passes individual wavelengths of light through a solution and measures the amount of light transmitted
pigments
substances that absorb visible light
What happens when light strikes an object?
some wavelengths are absorbed, while others are reflected
What results in the perceived color of an object?
reflected light
light absorption
-when atoms absorb energy from the environment, electrons move from an electron shell with low to high potential energy [ground to excited state]
-electrons don’t stay in the excited state, but return to the ground state, releasing energy (heat and light)
carotenoids
pigments in chloroplasts that broaden the spectrum of absorbed light
-appear yellow and orange
-may act as photoprotection
photoprotection
the biochemical process that helps organisms cope with molecular damage caused by sunlight
Van Niel’s Stable O-isotope experiment
confirmed that the oxygen released during photosynthesis by plants comes from the splitting of water molecules, not from carbon dioxide
photosynthesis as a redox
-carbon dioxide is reduced and water is oxidized
-process splits water into hydrogen and oxygen
-consumes 12 water molecules and generates 6 new water molecules
-an endergonic reaction
-is a net consumer of water
endergonic reaction
requires an input of energy to drive the reaction
linear electron flow
the light reactions produce ATP and NADPH that will provide chemical energy and reducing power to synthesize carbohydrates during the Calvin Cycle
light reactions
-are the steps of photosynthesis that convert solar energy to chemical energy
-produce ATP and NADH that supplies the energy for the second step of photosynthesis
-occurs in the thylakoids
Calvin Cycle
-uses the energy produced in the light reactions to incorporate carbon from Co2 into organic molecules
-carbon fixation
-occurs in the stroma
carbon fixation
is the initial incorporation of carbon from CO2 into an organic compound by an autotrophic organism
photosystem
light-capturing units consisting of a reaction-center
complex surrounded by numerous light-harvesting
complexes
(photosynthesis depends on this)
reaction-center complex
a complex of proteins associated with a special pair of
chlorophyll a molecules (P680 in PSII and P700 in PSI) and a primary electron acceptor. Located centrally in a photosystem this complex triggers the light reactions of photosynthesis. Excited by light energy, the pair of chlorophylls donates an electron to the primary electron acceptor, which passes an electron to an electron transport chain.
light-harvesting complex
a complex of proteins associated with pigment molecules (including chlorophyll a and b and carotenoids) that captures light energy and transfers it to reaction-center pigments in a photosystem
2 types of photosystem (I and II)
-Photosystem II (PS II) is the first component and absorbs light at 680 nm
-Photosystem I (PS I) functions after photosystem II and absorbs light at 700 nm
-Both use chlorophyll a in the reaction center, but the proteins that the chlorophyll associates with are different in the two complexes. The different proteins cause the light to be absorbed at slightly different wavelengths
making glucose
-G3P is an intermediate step of glycolysis
-running the reactions backwards turns G3P into fructose or glucose
-fructose and glucose together make sucrose
-or turn glucose into starch or cellulose
3 steps of Calvin Cycle
- carbon fixation
- reduction
- regeneration
INs and OUTs of Calvin Cycle
3 CO2 –(red)–> 1 x 3-C G3P [6-C]
9 ATP –(SLP)–> 9 ADP + P
6 NADPH –(oxi)–> NADP+
carbon fixation
-one CO2 is added to a 5-carbon molecule (Ribulose bis-phosphate or RuBP) to produce a 6-carbon intermediate molecule
>3 CO2 enter the cycle and are added to 3 RuBP
>catalyzed by an enzyme named rubisco
-the 6-carbon intermediate quickly breaks into two molecules of a 3-carbon molecule (3-phosphoglycerate)
reduction
-one ATP is used to phosphorylate each 3-phosphorglycerate forming 1, 3-biphosphoglycerate [6 total ATP are converted to ADP]
-one NADPH donates two electrons to 1, 3-biphosphoglycerate, one of two phosphate groups is lost, forming Glyceraldehyde 3-Phosphate (G3P) [6 total NADPH are used to form 6 G3P]
-one of the 6 G3P can leave the cycle to form glucose, the rest are recycled
rubisco
is an enzyme crucial for photosynthesis primarily responsible for carbon fixation, considered the most abundant protein on Earth
kinase
an enzyme that attaches phosphate groups to other molecules, such as proteins, lipids, or nucleotides
isomerase
a general class of enzymes that convert a molecule from one isomer to another
aldolase
(breaking molecule) a protein enzyme that breaks down sugars to produce energy
enzymes involved in the energy investment phase of glycolysis
kinase, isomerase, aldolase
dehydrogenase
an enzyme that catalyzes the removal of hydrogen atoms/ions from biological compounds
pyruvate
-is a three-carbon organic molecule that serves as a key intermediate in cellular metabolism
-produced as the final product of glycolysis (the breakdown of glucose)
-used as a starting point for further energy production within the citric acid cycle when oxygen is present, or converted to lactate during anaerobic conditions (fermentation)
most to least efficient respiration
-aerobic respiration (oxygen)
-anaerobic respiration (nitrate, sulfate)
-fermentation (no oxygen)
Griffith Experiment (1928)
-observed that mixing a heat-killed pathogenic strain of bacteria (smooth) with a living nonpathogenic strain (rough) can convert some of the living cells into the pathogenic form
-identified that something in a cell was transformative
Horizontal Gene Transfer (HGT)
-aka lateral transfer
-the process by which genetic material is exchanged between organisms that are not related by parent and offspring
viruses
consist of DNA surrounded by a protein coat; they force cells to make more viruses
Alfred Hershey and Martha Chase (1952)
-were able to label the viral protein coat with radioactive sulfur (DNA does not contain sulfur) or the DNA with radioactive phosphorus (very little phosphorus in protein)
-identified that DNA is the genetic material of viruses
bacteriophage
viruses that infect and replicate only in bacterial cells
Chargaff’s rules
- the base composition of DNA varies between species
- within a species, the number of A and T bases are equal and the number of G and C are equal
Franklin’s contribution
-she produced the best image available of DNA
-the image suggests that DNA consists of a double helix
-her X-ray crystallography shows a molecule with a consistent width
Watson and Crick
-from Franklin’s data they knew that DNA adopted a double helical shape
-also learned that the sugar and phosphates were on the outside of the helix
-knew Chargaff’s rules
-worked out that the hydrogen bonds between the bases and that the two strands were antiparallel
-their semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand
Matthew Meselson and Frank Stahl’s experiment (1958)
-devised an experiment to test various models of DNA replication
-grew bacteria in a culture with a heavy isotope of nitrogen (15N)
-move the bacteria into media with a lighter isotope of nitrogen (14N)
-separate the DNA based on density with a centrifuge
-confirmed DNA replication happened in a semiconservative manner, rather than conservative or dispersive
3 models of DNA replication
- Conservative model
- Semiconservative model
- Dispersive model
origins of replication
-replication occurs at a specific site with a specific sequence of nucleotides
-proteins attach to the origin of replication and separate the two strands of DNA, forming a bubble
-
replication fork
the site at each end of the bubble where DNA strands are being unwound and separated
eukaryotic vs prokaryotic chromosomes
-eukaryotes have multiple chromosomes that are larger than bacterial chromosomes
-eukaryotic chromosomes are linear
-eukaryotes have multiple sites where replication begins, instead of just one
helicase
the protein that untwists the double helix at the replication fork
primase
is an enzyme that creates an RNA molecule that is complementary to the template DNA strand
topoisomerase
is a protein that breaks, swivels, and rejoins the parental DNA ahead of the replication fork, relieving the strain caused by unwinding
DNA Polymerase (III)
is the enzyme that catalyzes the synthesis of new DNA by adding nucleotides to a preexisting chain
DNA Polymerase I
removes the primer and replaces it with new DNA nucleotides
polynucleotides
dehydration reactions between the phosphate group on one nucleotide and the hydroxyl on the 3’ carbon of a second nucleotide link monomers together in a phosphodiester bond
DNA ligase
catalyzes the covalent bond between the two Okazaki fragments (links them together)
Single-stranded binding proteins
bind to the newly separated DNA strands and prevent them from re-pairing
Why are origins of replication enriched in adenines and thymines?
A-T have two hydrogen bonds, which is easier to break than G-C with three hydrogen bonds
leading strands
the long continuous complementary strand that forms as the replication fork progresses, initiated by only one RNA primer on one template strand
lagging strands
the strand that forms when DNA polymerase moves away from the replication fork in the 5’ to 3’ direction, done in order to synthesize a new complementary strand on the other template strand
Okazaki fragments
-a series of short DNA segments generated on the lagging strand
-each Okazaki fragment needs a new RNA primer
-it’s synthesis is delayed compared to the leading strand
where does cellular respiration occur for a typical prokaryote?
cytoplasm, plasma/cell membrane, periplasm
where does cellular respiration occur for a typical eukaryote?
mitochondrial matrix, intermembrane space, cristae
how many ATP are formed per NADH in prokaryotes?
3 ATP
how many ATP are formed per NADH in eukaryotes?
2.5 ATP
how many ATP are formed per FADH2 in prokaryotes?
2 ATP
how many ATP are formed per FADH2 in eukaryotes?
1.5 ATP
proofreading mechanism
DNA polymerases at the replication fork can “back up” and remove a nucleotide that is incorrectly paired
mismatch repair
-when enzymes detect mismatches that occur in newly synthesized DNA, cut out the mismatched nucleotides and fill in the gap with the correct nucleotides
-can also make repairs in DNA that occur through environmental damage in addition to mistakes that occur in replication
nucleotide excision repair
the process in which multiple proteins scan the DNA for damage, a nuclease cuts out the damaged DNA, and a DNA polymerase fills in the gap, and DNA ligase completes the process
nuclease
cuts out the damaged DNA
mutations
-when a replication error or DNA damage is not repaired and replication occurs, then a permanent change results
-are the original source for variation in a population, leading to the production of new alleles
-most are deleterious, but some are beneficial
chromatin
the complex of DNA and proteins
histone
-a small protein with a high proportion of positively charged amino acids that binds to the negatively charged DNA and plays a key role in chromatin structure
nucleosome
the DNA and histone complex
linker DNA
DNA between the nucleosomes
First level of packaging
-histones organize the first level
-the DNA wraps around each histone complex twice to form a 10 nm structure
-a strand of chromatin at this first level of packaging looks like “beads on a string”
second level of chromatin packaging
-the linker DNA and nucleosomes organize into a thicker 30-nm fiber
-much of the chromatin in an interphase nucleus is organized into 30-nm fibers
third level of chromatin packaging
-scaffold proteins are necessary
-the 30-nm fibers form large loops that attach to scaffold proteins in the center of a 300-nm fiber
scaffold proteins
molecules that bind to other proteins to regulate signaling pathways and cell responses to signals
M phase chromosomes
-the highest level of chromatin packaging (not fully understood) that involves the coiling and folding of the 300-nm fibers
-highest level of chromatin packaging
-only observed as the chromosomes condense during M phase
-a chromatid in a condensed chromosome is 700 nm wide
chromatin varies in its degree of packaging during interphase
different regions of each chromosome have different degrees of packaging during interphase
heterochromatin
-regions that are more tightly packed
euchromatin
-regions that are more dispersed
-generally has more transcriptional activity than heterochromatin (RNA is more likely to be made from euchromatin than heterochromatin)
INs and OUTs of light reactions
H20 –(oxi)–> O2 + H+
NADP+ + H+ –(red)–> NADPH
ADP + P –(P.P)–> ATP
