BIS 2A Vocab Flashcards
1
Q
Paradigm
A
Dominant way of thinking
2
Q
Dogma
A
Set of principles that is inconvertibly true
3
Q
Great Oxygenation Event
A
Cyanobacteria starts to split water and floods atmosphere with O2
4
Q
Entropy
A
Measure of disorder and spontaneity
5
Q
Gibbs Free Energy
A
Change in energy from reactants to products
5
Q
Ionic Bond
A
Transfer of electrons
5
Q
Potential energy can reduce…
A
Local entropy
6
Q
Covalent Bond
A
Sharing of electrons
7
Q
Redox
A
Transfer of electrons. One thing is reduced while another is oxidized
8
Q
O2 is the most powerful…
A
Oxidizing agent most of the time
9
Q
Oxidizing Agent
A
Reduced
10
Q
Reducing Agent
A
Oxidized
11
Q
Electron Acceptor
A
Reduced
12
Q
Electron donor
A
Oxidized
13
Q
Reductant
A
Oxidized
14
Q
Oxidant
A
Reducer
15
Q
Rate constant
A
Probability two molecules will react depending on properties of molecules
16
Q
Reaction rate
A
of molecules reacting per unit of time
17
Q
Methanogens
A
Methane-producing bacteria
Archeans
Grow on H2 and CO2
Autotrophs
CO2 + H2 –> H2O + CH4
18
Q
Biological Standard conditions
A
7 pH, 1M, aqueous environment, 25 degrees C, 1 atm
19
Q
Activation Energy
A
Energy required for reaction to occur
20
Q
Exergonic
A
Negative delta G, favorable, releases energy
21
Q
Transition state
A
Strucutre during reaction, not stable
Intrinsic Property
22
Q
Delta G knot prime
A
Standard conditions
23
Catalysts
Provide alternate route for reaction to occur with reduced activation energy.
Not used up in reaction
Can be switched on and off
Regulate rate but not direction of reaction
24
Hydrolysis
Splitting by water
25
Glycolysis
Pathway all living things use to get energy by breaking down/oxidizing glucose
Exergonic
Occurs in cytoplasm
26
Coupling
Pairing an unfavorable reaction with a very favorable one so they both can occur
27
ATP
Adenosine triphosphate
28
ATP synthesis
Making of ATP
ADP + Pi --> ATP
Unfavorable
29
Heterotrophs
Get electrons by oxidizing fuel (eating) and from other living things
30
Glyoclysis overall reaction
Glucose + 2ADP + 2Pi + 2NAD+ --> 2 pyruvate + 2ATP + 2NADH
31
Hexokinase
Enzyme that breaks down ATP while it builds glucose 6-P
ATP is source of phosphate for G-6-P
32
-Delta G = Phosphate acceptor/donor
Donor
33
Internal electron carrier
Device that carries electrons
Can be used for:
1. Biosynthetic pathways
2. Respiration
3. Dumped or excreted during fermenation
34
NAD+/NADH
Universal all-purpose internal electron carrier
Picks up and delivers electrons and energy
Costs a lot to make
Nicotinamide adenine dinucleotide
35
Fermentation
NAD+ is regenerated by reducing pyruvate and excreting product (Lactate/ethanol)
Allows glycolysis to keep running
Occurs when there is no external electron acceptor
36
Respiration
Occurs in presene of external electron acceptor
Oxidates glucose all the way to CO2
Harvesting electrons during glycolysis, pyruvate oxidation, TCA cycle
Cash in electrons for ATP
Pumping protons
Proton diffusion
37
Degradative pathways
Take large molecules and break them down
Release energy
38
Biosyntehtic pathways
Use energy released from biosynthetic pathways
Take smaller molecules and build larger ones
Use NADP+ and NADPH
39
Substrate level phosphorylation
Taking a phosphate from a substrate to generate ATP
Ex: Oxidation of glucose to 6 CO2 to make 4 ATP
40
Oxidative phosphorylation
Phosphorylation from redox reactions
Cashing in the NADH
ETC
ATP synthase
41
Pyruvate Oxidation
Pyruvate + NAD+ + CoA --> NADH + CO2 + Acetyl CoA
Provides rest of glycolysis with NADH
Occurs in mitochondrial matrix
42
Citric Acid Cycle/Krebs Cycle/TCA
Acetyl CoA + ADP/GDP + FAD + NAD+ --> CO2 + NADH FADH2 _ ATP/GTP
Aerobic
Occurs in Mitochondrial matrix
Provides 6 more NADH, 2 FADH2, and 2 ATP per glucose
Main purpose to take oxidized electron carriers and reduce them to perform oxidative phosphorylation
Most remaining energy stored as NADH
43
Autotrophs
Perform processes from glucose made themsleves
Grab their carbon from the air(CO2)
Must have the ability to fix CO2 into organic compounds and capture high energy electrons from an inorganic source
44
Terminal electron acceptor
Final molecule to receive electron
Always O2 in aerobic organisms
45
Reduction potential
Molecule's ability to acqurie an electron
More positive reduction potential means it is more likely to accept electron
46
Delta E knot prime
How much energy will be released when a compound is reduced to a certain degree
47
Positive delta E gives...
Negative delta G
48
Electron Transport Chain
Series of electorn carriers and redox reactions
Located in the membrane
O2 is the external electron acceptor
These complexes carry NADH and FADH2 electrons to O2
Mechanically coupled to proton pumping (Complexes 1,3,4)
Protons pumped out of cytosol
49
Proton pumping
Occurs during ETC
Protons pumped from mitochondrial matrix to intermembrane space
Proton gradient is formed
50
ATP synthase
Includes a turbine that crosses shaft of proton resistant membrane
Protons diffuse from gradient into cell through the turbine
ATP is generated
51
Protein co-factors
Carry electrons (wires)
52
Chemiosmosis
Proton transport due to high concentration
53
Carboxylic Acid
COOH
Double bond on one O
Single bond with OH
54
Amine
NH2
55
Methyl
CH3
56
Alcohol
OH
57
Amide
OCNH2
Double bond with O
NH2 single bonded
58
Pronation
Addition of H+ to atom or molecule
59
De-Pronation
Removal of H+ to an atom or molecule
60
Carbohydrates
Always consist of C,H,O
Contain -OH
Usually rings with O
61
Nucleic Acids
C,H,O,N,P
Made of nucleotides
5 carbon ribose or deoxyribose sugar
Nitrogenous base
Phosphate group
62
Lipids
Always contain C and H
Multiple C-C and C-H bonds
Polar and non polar heads
Less C-O bonds than carbohydrates
63
Proteins
C,H,O,N
N-C-C backbone
Caboxyl group
Amine group
Specific polymer of amino acids
64
Decarboxylation reaction
Reaction where CO2 is a product
65
Reducing Energy
Source of high energy electrons and energy
Take form of NADH, NAPDH, or ATP
Needed for cell growth and survival
66
Photosynthesis
Creating recuding energy and energy using light
67
Catabolism
Gradually oxidizing fuel to form NADH and ATP
68
Anabolism
Using ATP, NADH/NADPH to drive biosynthesis
Opposite of catabolism
69
Light reactions
Get electrons to ETC without strong electron donor
Depend on light
Products are NADPH and ATP
70
Dark reactions
Using ATP and NADH to reduce CO2 and generate glucose
71
Steps of light reactions
1. Energy from sun is captured to excite electrons
2. Electrons travel through ETC to pump protons, making ATP
3. High energy electrons transferred to NADP+
4. Lower energy electrons replaced from external electron source
72
Dark reaction steps
1. CO2 fixed onto organic molecules and reduced with high energy electrons from light reactions
2. Also reduced by energy from ATP hydrolysis, forming a storable form of fuel
73
Pigments
Molecules that absorb specific wavelengths in the visible range
74
Reaction center
Specific chlorophyll capable of transferring an electron to ETC
75
P840
Pigment involved in green sulur bacteria light reactions
Strong reducing agent when excited. Strong oxidizing agent after it loses its electron
76
Cyclic Photosynthesis
Electron ends up where it started back in chlorophyll
77
Periplasmic space
Between two membranes
78
Cytosol
Between two membranes
79
Steps of cyclic photosynthesis (Green sulfur bacteria)
Light energy extracted from electrons via ETC
Protons are pumped into gradient
ATP synthase forms ATP from proton gradient
Electron goes back to bacteriochlorophyll
80
Non-Cyclic Photosynthesis
Electron from P840 doesn't return to P840ox, but is picked up by NADP instead
81
Non-Cyclic Photosynthesis steps (Green sulfur bacteria)
P840 is excited and gives electrons to NADP+
P840ox is a strong oxidizing agent. Strong enough to strip H2S of electrons
H2S --> S + 2e- + 2H+
82
What is special about green sulfur bacteria?
They can use electrons and light to make proton motive force and ATP OR make NADPH
83
Phosphoanhydride bond
Hydride bond between two phosphate groups
84
Photophosphorylation
Phosphorylation that includes excitement of photons
85
Cristae
Rdiges on inner membrane of mitochondria
86
Bacteriochlorophyll
Photosynthetic pigments found in bacteria
87
Carbon fixation
Reduction of CO2 to build fuel
Combining RUBP(5 carbon sugar) and CO2. 6 cycles will allow us to build one glucose molecule
88
Ways to fix carbon
Reverse TCA cycle (Green sulfur bacteria)
Calvin cycle (cyanobacteria, green plants)
89
Reverse TCA cycle
Prodcued Acetyl CoA with 2 CO2
2CO2 + 2NADPH + FADH2 + Fdred + 2 ATP + coA --> acetyl CoA + 2NAD+ + FAD + Fdox + 2ADP + 2Pi
90
Ferredoxin
Electron carrier from the light reactions
Also small proteins containing iron and sulfur
H2S + Fdox --> S + Fdred
91
P680
Pigment that is able to oxidize water located in PSII
92
P700
Pigment that is able to reduce NADP located in PSI
93
Z scheme
Cyclic and non-cyclic process in oxygenic photosynthesis combined (The light reactions)
94
Rubisco
World's most abundant protein
Catalyzes first step of Calvin Cycle
Can bind to CO2 better than O2
O2 is an inhibitor
It is slow and inefficient
95
Chemoautotroph
Synthesize food using chemical energy
96
Organotroph
Organsim that obtains hydrogen or electrons from organic substrates
97
Chloroplast anatomy
Stroma is big area. There are granum, and each one is called a thylakoid. Inide is the thylakoid membrane and the lumen which is the innermost compartment
98
Calvin Cycle
6CO2 + 18ATP + 12 NADPH --> 2G3P
99
Cytochrome B6F
Ability to pump protons from stroma of chloroplast to lumen of thylakoid
100
Peptide bonds
Hold amino acids together between the carboxyl and amine group
One molecule of H2O is formed when a peptide bond is formed
101
Photorespiration
Error by rubisco. Can unfix CO2
102
Lysozyme
Breaks down bacterial cell walls
103
Protein Primary structure
Chain of amino acids
104
R groups
20 unique amino acids. Charged or polar groups are hydrophilic. Nonpolar and uncharged groups are hydrophobic and are involved in hydrophobic interactions
105
Protein Secondary Structures
Beta sheets and alpha helices
Stabilized by hydrogen bonds between N-H and C--O groups
106
Hydrogen bond
Weak ionic bond
Become really strong when added up
107
Protein tertiary structures
3-D shape of folded protein
Determined by R groups
Stabilized by hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bridge
108
Disulfide bridge
Bond between S-S
Can only be made by cysteine
109
Quaternary structure
2+ tertiary structures coming together
Same bonds as tertiary structures
110
Renaturation
Synthesizing a protein
111
Denatured
Unfolded protein
Proteins that can be denatured are usually small
Stabilized by disulfide bonds
112
Cofactor
Regenerated during catalytic cycle. Not used up. Help power enzymes
Can drastically modify reduction potentials
113
Feedback Inhibition
Product of long pathway inhibits enzyme that catalyzes the first dedicated step of pathway
114
Enzyme regulation
Cells manipulate the accessibility of active site to switch enzymes on or off
115
Allosteric activator
Binds to enzyme, allowing substrate to bind to it and a reaction occurs
116
Allosteric inhibitor
Binds to enzyme, preventing substrate from binding to it
117
Competitive inhibitor
Fights with the substrate for the binding site
To get rid of inhibitor, either get rid of it or add more substrate
118
Noncompetitive inhibitor
Substrate and inhibitor bind to different sites
Product can only be formed when only the substrate binds to the enzyme
119
Irreversible inhibition
Noncompetitive inhibitor that covalently bonds to allosteric site or active site
120
Phosphofructokinase
Catalyzes the first dedicated step of glycolysis
Reaction is regulated allosterically by high levels of ADP
Sensitive to many metabolites
121
PEP
Allosteric regulator of phosphofructokinase
122
Signal metabolites
Can switch a protein on or off allosterically, affecting its affinity for the substrate
123
A cell
Highly organized compartment
- Bound by thin, flexible membrane
- Contains concentrated chemicals dissolved in aqueous solution
- Requires transporters to get across membrane
Capable of metabolism (capturing and using energy to build things)
Capable of autonomous replication
Smallest unit with all these characteristics of life
124
Bacteria
Prokaryotes
- Lack nucleus
- Usually lack other membrane-bound organelles
- Most have cell walls
- All membrane-bound reactions happen at cytoplasmic membrane (ETC, ATP synthase, photosynthesis)
125
Archaea
Prokaryotes
Share same qualities as bacteria
126
Prokaryotes
Evolutionary distinct domains of life
127
Microbial mats/large biofilms
May represent the earliest forms of life on Earth
Multi-layered sheet of microbes composed of bacteria
128
Plasma membrane
Phospholipid membrane that defines the boundary between inside and outside of cell
129
Cytoplasm
Where soluble reactions occur
Contains ribosomes , protein-RNA complex where proteins are synthesized
Tends to be vicscous
130
Cell wall
Provide protection and maintain shape
Only found in plant cells
Prevent cells from exploding in water
131
Amphipathic
Hydrophilic head, hydrophobic tail
Charged, polar head
Greasy, very non-polar head
132
Viscosity
Measure of fluids resistance to flow
133
Internal Membranes
Create specialized subcellular environments
Form electrochemical gradients
Provide additional surface area
Allow for sub-cellular specialization and complexity
134
Cytoskeleton
Protein polymers
Functions: Roads for intracellular transport
- Shape of cell
- Mechanical strength
- Cellular locomotion
Subunits held longitudinally and laterally by non-covalent interactions
135
3 Types of cytoskeleton
Intermiediate filaments
Microtubules
Actin
136
Unsaturated Phospholipids
At least one double bond
Causes kink at increased permeability
137
Cell placed in hypotonic solution
Hypotonic solution: Low solute concentration
outside the cell compared to inside. Water enters and cells explodes
138
Cell placed in hypertonic solution
Hypertonic solution: High solute concentration outisde cell compared to inside. Water escapes and cell shrivels up and dies
139
Cell placed in isotonic solution
No net movement of water. Equal osmolarity
140
Turgor
Normal, strong rigid shape
141
Flaccid
Limp
142
Plasmolyzed
Lack of water
143
Cell wall
Solves osmolarity problems. Stops cell from exploding
Mesh of polysaccharides and/or proteins loose enough to allow many kinds of molecules to drift through
Exist in plants and prokaryotes
Small molecules can easily diffuse through
144
Chloroplast
Descended from symbiotic cyanobacteria, which were acquired by single-celled eukaryote about 580 million years ago
Contained in plant cells only
145
Amphipathic proteins
Can integrate into lipid bilayers
146
Integral Proteins
Embedded within/across the plane of the membrane
147
Peripheral Proteins
Attached to inner or outer surface of membraner
148
Passive Transport
High to low concentration
- Simple diffusion
- Facilitated diffusion
149
Simple diffusion
High to low concentration with no protein help
150
Facilitated diffusion
High to low concentration with help of transport protein
151
Active transport
Low to high-concentration, with help of transport protein
Has +deltaG
Couples with favorable reaction to occur
152
Uniport
One thing, one direction
153
Simport
2 things, one direction
154
Antiport
2 things, 2 directions
155
Intermediate filaments
Mechanical strength and resistance to shear stress
Rope-like proteins
Mainly cell specific
156
Microtubules
Intracellular transport, cell division spindle
Roads for kinesin(+ end) and dynein (- end)
Asymmetric
Bind to GTP
alpha-beta tubulin dimers
alpha-GTP/beta-GTP preferably assemble on plus end
+ end is more dynamic than - end
Subunits assemble head to tail
Beta tubulin hydrolyzes GTP
157
Actin
Asymmetric
Transport, cell shape, cell locomotion
Subunits assemble head to head
Monomers
Binds and hydrolyzes ATP
Road for myosin
Polymerization induces ATP hydrolysis
158
Microtubule dynamic instability
Microtubules growing and shrinking at the same tubulin concentration
Crucial for microtubule function
Highly regulated
159
Actin treadmilling
ATP bound monomers on the + end add at same rate as depolymerization of ADP bound actin on the - end
Actin dynamics highly regulated by actin binding proteins
Central to cell migration
160
Motor proteins commonalities
Enzymes
Powered by conformational changes driven by ATP hydrolysis
Generate force by coupling ATP hydrolysis and conformational changes
161
Binary fission
Process by which prokaryotes divide
1. DNA replication starts at origin of replication In center of cell
2. Chromosomal DNA replicated as cell grows
3. 2 Daughter molecules move apart
4. Ring forms, starting cytokinesis
5. Cytokinesis is complete
162
Checkpoints in Cell Cycle
Trigger arrest until problems are solved
163
Cell Cycle phases
G1, S, G2, M phase
164
G1-S checkpoint
Commit to DNA replication and cell division
Makes sure the environment is favorable
165
S checkpoint
Makes sure all DNA is replicated properly
166
G2-M checkpoint
Check if there's any DNA damage that needs ton be repaired
167
Spindle assembly checkpoint
Make sure that all chromosomes are all attached to the spindles
Prevents opening of cohesins at centromere
168
CDKs
Cyclin-dependent kinases
Enzymes that phosphorylate another protein to activate/inactivate it
Regulated the cell cycle
Activity rises and falls during the cell cycle
Activity regulated by abundance of cyclin
Can inhibit inhibitors or activate activators
169
Cyclin
Abundance regulates the activity of CDK
Allosterically activate CDK
Direct CDK to their substrates
Ex: Rb is a protein holds the G1/S checkpoint
Cyclin binds to CDK so that it can phosphorylate Rb for the cycle to continue
170
Replication (S-Phase)
Triggered by S-CDK and cyclin
171
Viscosity
Measure of fluids resistance to flow
172
Compartmentalization
Provides way to localize processes to smaller organelles
- Allows eukaryotes to grow
Bacteria cells cannot grow because they are held back by diffusion dependent reactions
173
Endosymbiosis
One cell engulfing another to ensure they both stay alive
174
Diploid
Two sets of chromosomes
175
Haploid
One set of chromosomes
176
Cohesins
Ring like proteins that hold sister chromatids together
Resist pull from motors
Opening allows for start of anaphase
177
M-phase steps
Prophase, prometaphase, metaphase, anaphase, telophase, cytokinesis
178
Somatic cells
Diploid
179
Gamete cells
Haploid, sex cells
180
Centromere
Specialized regions where microtubules attach via kinetochores
181
Kinetochores
Multi-protein structure that fully assembles onto centromeres during prophase
Provides attachment site for microtubules
Allows for sister chromatids to separate
182
Mitosis
Produce identical cells
183
Meiosis
Produce genetically different cells (gametes)
Use haploid cells
184
