Mid Term Review Flashcards
Ace this thing. Prove you are a good biologist. (125 cards)
1
Q
What is photosynthesis?
A
Process using sunlight to produce carbohydrate. Needs sunlight, CO2, and H2O, making O2 as a by-product.
2
Q
Briefly summarise the historical perspectives of photosynthesis. (multistep)
A
1700’s:
The belief that plant nourishment was from the air.
3
Q
Second perspective
A
1700’s:
Perhaps O2? Mouse under the glass makes air “bad”, but survives when a plant is there!
4
Q
Third perspective
A
1800’s:
OOH PLants gain weight, therefore not just CO2 and O2 released….. Mayhaps WATER?
5
Q
Fourth Perspective
A
1900’s:
Do CO2 and H2O react directly to make carbs? Fellow studying sulfur bacteria, figures out the oxygen spat out comes from H2O!
6
Q
Fifth perspective
A
1939:
H2O splitting in presence of light is called HILL REACTION
7
Q
Sixth perspective
A
1900’s
Radioactive carbon 14 used. Found that CO2 used to make sugar. We know now that reactions use ATP and NADPH made by photosynthesis.
8
Q
Seventh perspective
A
2000’s:
Crystallography and Fourier-transform spectroscopy help us understand the energy efficiency and methods of photosynthetic pathways
9
Q
What is the purpose of Photosynthesis?
A
Energy from the sun must be transformed into chemical energy for use by organisms who make it, and eat it from them.
10
Q
Where does Photosynthesis occur?
A
- In autotrophic tissue containing chlorophyll (green pigment)
- 40-50 chloroplasts per cell
- specifically, the Thylakoid, grana, and stroma
11
Q
How does photosynth occur? (Basics)
A
- Light DEPENDENT rxns produce O2 from H2O
- Calvin Cycle (Light INDEPENDENT) produces sugar from CO2
- E-s are released in the light DEP. rxns when H2O is split to form O2 gas
- E-s are transferred to NADP+, making NADPH
- Calvin Cycle uses this NADPH to make CO2
12
Q
Light-dependent reactions. Overview
A
Photosystem II, then photosystem I. Linked by the Z-scheme
13
Q
What is phosphorylation?
A
The capture of light energy by PS II to make ATP.
Essentially tossing on a Phosphate
14
Q
What is the order of the Photosystems?
A
II then I
15
Q
Why have two PS’s
A
Together, they capture red and far-red light to more than double the efficiency of the processes. (Called an ENHANCEMENT EFFECT)
16
Q
What is a photosystem?
A
A complex of chlorophyll molecules working together in groups.
17
Q
Where does photosystem 2 take place?
A
In the thylakoid membrane.
18
Q
A photon hits chlorophyll in PS2. What happens next?
A
Chlorophyll is oxidized, electron leaves the chlorophyll and goes to pheophytin where an ETC begins to unfold.
19
Q
Where does E- go after Pheophytin?
A
Plastiquinone then cytochrome complex
20
Q
What happens in the ETC
A
The E- is passed through a series of redox rxns, stepping down its energy bit-by-bit
21
Q
What do the Redox rxns in PS2 do?
A
They pump protons into the thyllakoid lumen. Increase the concentration 1000 fold.
22
Q
Where does the electron for the electron transport chain come from?
A
WATER
23
Q
What is oxygenic photosynthesis?
A
When PS II “Splits water” to replace its lost electrons, and produces O2 in the process.
24
Q
What is proton motive force and why is it important?
A
In PS II, the increased electronegativity in the thylakoid lumen is balanced by the diffusion of protons across the membrane to equalise concentrations. This force is harnessed by ATP synthase to phosphorylate ADP. Ultimately called photophosphorylation.
25
How are PS I and II linked?
Cytochrome complex passes the electron of PS II to plastocyanin, which carries it to P700 chlorophyll.
26
What happens after PS II and I are linked?
The P700 chlorophyll is excited by another photon to another ETC. More H2O is oxidized to replace the E-s lost from P700
27
What happens in the ETC of PS 1
P700 passes two E-s to ferredoxin, which oxidizes NADP+ to NADPH for the Calvin cycle.
28
Basic input/output of Calvin cycle.
OUT:
TWO 3C molecules
IN:
ONE Carbon Dioxide molecule
29
Where does the Calvin Cycle occur?
In the stroma of the chloroplast (the space) (like cytoplasm)
30
What are the three phases of the Calvin Cycle?
1) Fixation of CO2 to 3-PhosphoGlycerate by RuBP
2) 3-PGA is phosphorylated by ATP and reduced by NADPH to form G3P
3) Remaining G3P not used for glucose goes to regenerating RuBP
31
What is Rubisco and what's its problem?
It's an enzyme used to catalyze one of the parts of CO2 fixation. It's the most prevalent protein in the world!
It is a slow enzyme, only catalyzing a few rxns/sec as opposed to thousands.
32
What is photorespiration?
When plants take up Oxygen for substrate of Rubisco .
33
Why is photorespiration a real bummer for plants?
Because in order to take in the O, a C is lost, which can't go towards sugar. To fix it, another ATP and CO2 must be used.
34
Where does CO2 fixation occur?
In the mesophyll cells of plants.
35
What's the difference between STOMA and STROMA?
A stoma is the singular of STOMATA, which are the guard cells of plants guarding the pores of plants where CO2 and water exchange take place, and stroma are the spaces between chloroplast membrane and thylakoid.
36
When are stomata open? Closed?
Typically open during the night, or when CO2 concentration is depleted in photosynthesis and closed in the day to prevent water loss.
37
What is the problem with the Calvin cycle?
When C3 plants are in hot and dry conditions, they must keep their stomata closed to prevent water loss, which stops photosynthesis.
38
What is the solution to the water loss problem of C3 plants?
C4 plants! Carbon fixation and the Calvin Cycle occur in different types of cells. Spatial partioning.
39
How does C4 photosynthesis work? Best advantage?
C4 makes CO2 into 4-C molecules, not G3P
These travel to bundle-sheath cells, release a CO2, used by Rubsico to make 3-PGA, start Calvin Cycle.
Reduces the damaging effects of photorespiration.
40
How does CAM photosynth differ from C4 photosynthesis?
Temporal partitioning as opposed to spatial.
41
How does CAM photosynth work?
Open stomata in the nighttime , close in the day. Still uses C4 acids, just during the day.
42
First organisms to perform photosynthesis?
Ancient Cyanobacteria.
43
Why is photosynthesis so inefficient?
It is a robust system. Works across a broad range of environments, and has solutions to make it work in the more difficult environments. It is a robust system.
44
Why is biorefinery process so difficult?
We are limited by the efficiency of the organisms.
45
What are battery molecules?
Molecules with easily breakable bonds for energy storage and retrieval. Glucose is an example.
46
What is cellular respiration?
The input of glucose (chemical energy), resulting in the output of ATP (usable energy) and NADPH (also usable energy)
47
Where does cellular respiration take place?
Glycolysis in the cytoplasm of the cell. Citric acid cycle in the mitochondria (POWERHOUSE).
48
Give an overview of glucose processing:
- Glycolysis
- Pyruvate processing
- Krebs (citric acid) cycle
- ETC
49
What is fermentation?
An alternate pathway to continue performing glycolysis when no electron acceptor exists and the ETC is shut down.
50
Summarise step one of glucose processing:
Glycolysis breaks glucose into two 3C pyruvate molecules.
| Pyruvate is used to phosphorylate ADP to ATP, and NAD+ is oxidized to NADH
51
Summarise step two of glucose processing:
Pyruvate is changed to acetyl- Coenzyme A. During this process, another molecule of NADH is produced.
One of the carbon atoms is used to produce CO2
52
How is glycolysis regulated?
A negative feedback loop: High levels of ATP prevents the function of enzyme phosphofructokinase, whose product is vital to glycolysis. ATP binds where its supposed to (active site) and regulatory site, changing the enzymes conformation and dropping its efficiency.
53
Summarise step three of glucose processing:
Acetyl Co-A is oxidized to two molecules of Co2. The energy released is used to:
- Reduce NAD+ to NADH
- Reduce FAD+ to FADH2
- Phosphorylate ADP to make ATP
54
Where does pyruvate processing occur?
Mitochondrial matrix
55
What controls the rate of pyruvate processing?
Both positive and negative feedback.
56
Summarise step four of glucose processing:
Electron transport chain:
The electrons carried in NADH and FADH2 are gradually reduced through a series of redox rxns. The proteins performing these rxns make ETC. Pumps protons across membrane of mitochondria, makes strong electrochemical gradient. When protons flow through ATP synthase, oxidative phosphoryllation occurs. Oxygen is the final electron acceptor, making H2O
57
What regulates the Krebs cycle?
ATP and NADH abundance produce negative feedback in multiple parts of the cycle.
58
What is oxidative phosphorylation?
The synthesis of ATP from ADP as proton motive force is used by ATP synthase. This step produces 26 of the 30 total ATP from cell. resp.
59
Difference between aerobic and anaerobic respiration?
Aerobic: O2 is final E- acceptor
Anaerobic: Pyruvate accepts E- from NADH
60
Explain the two mechanisms of fermentation.
Lactic acid: Lactate and NAD+ are produced
| Alcohol: Ethanol and NAD+ are produced.
61
Why is fermentation a bummer for the cell?
Requires a lot more ATP to continue the process. Less efficient.
(just 2ATP per glucose as opposed to 30)
62
What molecular tools are necessary to manipulate?
Cutting Tools
Pasting/Sealing tools
Amplification tools
Conversion tools
63
What do Restriction Enzymes do?
They recognize short, palindromic sequences in DNA and cut at specific sites within that short sequence.
64
Give an example of pasting/sealing tools.
DNA ligase
65
Give an example of amplification tools.
Cloning Vectors, cDNA libraries, PCR (polymerase chain rxn)
66
Give an example of Conversion tools
Reverse transcriptase, cDNA synthesis
67
How can a gene be cloned?
Restriction enzyme recognizes sequence. Put that sequence on either end of desired gene. Stick modified gene into plasmid by DNA ligase. Put recombinant plasmid into cloning vector. Make lots of it, em. Boom, tons of genes.
68
Difference between cDNA and gDNA libraries? First, what are they?
Both are amplification tools to do the actual cloning. cDNA is synthesized from mRNA in a rxn catalyzed by reverse transcriptase and DNA polymerase. The cDNA recombinated plasmids are then put into E.coli cells to be replicated. gDNA are isolated directly from chromosomes/nucleus.
69
What is a cloning vector?
Basically a modified plasmid with the gene we want in it.
70
How does reverse transcription work?
Enzyme- reverse transcriptase recognises a primer (Oligo dT). Starts cDNA synthesis from mRNA from 5' to 3'.
71
What is PCR? What are the requirements?
Polymerase Chain Reaction is a mechanism by which mass amoounts of cDNA or gDNA can be replicated. You need a solution with template DNA, lots of G-C-A-T (dNTPs), and primers that set the scene for the gene sequence.
72
What are the steps for PCR?
1) A solution with DNA template, primers, dNTPs.
2) Denaturation of the DNA template, two strands separate
3) Primers anneal on both sides of the DNA by complementary base pairs
4) Taq polymerase clips onto the primer and synthesizes the rest of the DNA
5) Repeat those steps to double the number of strands
6) Do it a bunch of times, get MILLIONS
73
How do you screen a cDNA library to find the gene you want?
Place a filter on the colonies, remove, and get less of the colonies. Treat the filter with a chemical that breaks open the cells and splits DNA into single strands. Put a DNA probe in with a short sequence from the desired gene. Look for the labelled probe, and locate the colony(ies) on the original plate, and analyze.
74
What is genetic engineering?
Inserting Genes (or manipulating DNA) into Cells and Organism.
75
What are the three examples of genetic engineering?
1) Using a retrovirus to infect cells
2) Making transgenic plants
3) Making transgenic animals
76
How does one genetically engineer something by a retrovirus?
A virus containing recombinant RNA of desired human genes within viral RNA and reverse transcriptase is inserted into the body. Viral enzymes then produce double-stranded DNA versions of the recombinant RNA. These are then incorporated into the chromosome and ultimately transcribed.
77
What is golden rice?
Genetically engineered rice which synthesizes beta-carotene, the precursor of vitamin A!
78
How do they do it?
A plasmid with a tumour-inducing gene is used. The tumour-inducing gene is replaced with one which code for enzymes triggering biosynthesis of beta-carotene. The plasmid is then put into rice plants.
79
How are transgenic animals produced?
A fertilized egg is removed from a female. The embryo is injected with foreign DNA, and replaced into a pseudopregnant female. The offspring are tested for the transgene, and those with it are bred to produce mice homozygous for the gene.
80
What is genome editing?
Editing of an organism which can result in a gene being silenced (inactivated) or added or repaired.
81
How does the CRISPR-Cas9 system work?
A guide RNA which is similar to the idea of a primer is attached to the Cas9 enzyme. Cas9 is guided to cut the DNA sequence at a specific point. The DNA is then repaired in a number of possible ways for a number of different aims.
82
What is ecology? What question does it ask?
The science of interactions. How do species interact with eachother and their environment?
83
In ecology, what does everything depend on?
SCALE
84
What's the main way we study population ecology?
Dynamics. What factors affect the growth of populations through time?
85
How do we study population dynamics?
Population growth models.
86
What types of population growth models exist?
Exponential growth
| Logarithmic growth
87
Exponential growth:
the rate of change of a population density is equal to the population density times the population growth rate per capita.
88
Logistic growth:
the rate of change of a population density is equal to the (population growth rate/capita x population density x (carrying capacity - pop density)) / carrying capacity
89
What is meta-population dynamics?
The interaction of a population through time and space!
90
What are the additional rate parameters taken into account for meta-pop dynamics?
Immigration and emigration.
91
What is a meta-population?
A larger population made up of smaller, isolated populations.
92
What is a population regulating factor?
Any parameter (intra or extra) that prevents a population from achieving exponential growth.
93
What is a community?
A community interaction, not the physical presence of organisms in a place.
94
What are the four types of inter-specific interaction?
- Competition
- Consumption
- predation, parasitism, herbivory
- Mutualism
- Commensalism
95
Competition is a blank, blank interaction.
Negative negative
96
Consumption is a blank, blank interaction.
Positive, Negative
97
Mutualism is a blank, blank interaction.
Positive, positive.
98
Another definition for competition?
A struggle for limiting resources.
99
What are the four methods of competition?
- Consumption
- Allelopathy
- Preemption
- Territoriality
100
What is consumption competition.
One species inhibits the other by consuming a common resource.
101
What is preemptive competition?
Mostly among immobile species. One species just being there makes it more difficult for another.
102
What is allelopathy?
One species inhibits another by changing the chemical composition of a shared resource.
103
What is territorial competition?
One species prevents access to a shared resource by displaying behavioural aggression.
104
What is the competitive exclusion principle?
Two species cannot use a resource in the same way and coexist.
105
What happens if interspecific competition >intraspecific competition?
One species will be competitively excluded
106
What is meant by the ghost of competition past?
A species which has been competitively excluded.
107
What is consumption?
Any interaction where the increase in pop density of one species results in the increase in pop density of another. And an increase in the one consuming results in a decrease in the density of another.
108
Classical Predation:
Organism being consumed must die!
109
Herbivory:
§ Individual is not killed, some of it is eaten though.
110
Parasitism:
Usually just decrease of overall health, sometimes organsim dies.
111
Seed predation:
Classical predation but it's the babies.
112
What does the Lotka-Volterra model show?
The rate of change of population density of a population density is = to (per capita pop growth rate)(Pop density)(Carrying capacity-pop density - (competition coefficient x pop density of other species)/ carrying capacity
113
What is the competition coefficient between two species.
Measures the competitive effect one species has on another.
114
What is a disturbance?
Any factor which contributes to the decrease in number of species in a population.
115
What are the three properties of disturbances?
- type
- abiotic or biotic
- frequency
- diurnal, annual, random
- severity
- tsunami vs tide
116
What does the intermediate disturbance hypothesis say?
The number of species is greatest at intermediate disturbance
117
What is a niche?
The space a species occupies in the community.
| The environmental requirements of a species.
118
What is the fundamental vs realised niche?
Fundamental is just N-dimensional hypervolume. Realised adds the interactions at play. Realised is a smaller subset of the fundamental.
119
What is stable coexistence?
When two species can coexist without competitive exclusion ever taking place.
120
What is unstable coexistence?
When two species can coexist with competitive exclusion eventually taking place.
121
Stable coexistence can only exist
when intra>interspecific competition.
122
What is the predator functional response?
Per capita consumption of a predator given prey population.
Based on the time needed to a) hunt for prey b) handle prey
123
What is type one predator functional response?
Linear, more time spent searching, more prey
124
What is type two predator functional response?
Second order, increasingly decreasing. Ex. too much food to eat,
125
What is type three predator functional response?
Increase exponentially, then decrease exponentially § Decreases due to satiation and handling time
