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Ethans Flashcards > BIS 2A Vocab > Flashcards

BIS 2A Vocab Flashcards

1
Q

Paradigm

A

Dominant way of thinking

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2
Q

Dogma

A

Set of principles that is inconvertibly true

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3
Q

Great Oxygenation Event

A

Cyanobacteria starts to split water and floods atmosphere with O2

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4
Q

Entropy

A

Measure of disorder and spontaneity

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5
Q

Gibbs Free Energy

A

Change in energy from reactants to products

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5
Q

Ionic Bond

A

Transfer of electrons

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5
Q

Potential energy can reduce…

A

Local entropy

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6
Q

Covalent Bond

A

Sharing of electrons

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7
Q

Redox

A

Transfer of electrons. One thing is reduced while another is oxidized

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8
Q

O2 is the most powerful…

A

Oxidizing agent most of the time

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9
Q

Oxidizing Agent

A

Reduced

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10
Q

Reducing Agent

A

Oxidized

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11
Q

Electron Acceptor

A

Reduced

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12
Q

Electron donor

A

Oxidized

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13
Q

Reductant

A

Oxidized

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14
Q

Oxidant

A

Reducer

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15
Q

Rate constant

A

Probability two molecules will react depending on properties of molecules

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16
Q

Reaction rate

A

of molecules reacting per unit of time

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17
Q

Methanogens

A

Methane-producing bacteria
Archeans
Grow on H2 and CO2
Autotrophs
CO2 + H2 –> H2O + CH4

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18
Q

Biological Standard conditions

A

7 pH, 1M, aqueous environment, 25 degrees C, 1 atm

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19
Q

Activation Energy

A

Energy required for reaction to occur

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20
Q

Exergonic

A

Negative delta G, favorable, releases energy

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21
Q

Transition state

A

Strucutre during reaction, not stable
Intrinsic Property

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22
Q

Delta G knot prime

A

Standard conditions

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23
Q

Catalysts

A

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

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24
Q

Hydrolysis

A

Splitting by water

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25
Q

Glycolysis

A

Pathway all living things use to get energy by breaking down/oxidizing glucose
Exergonic
Occurs in cytoplasm

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26
Q

Coupling

A

Pairing an unfavorable reaction with a very favorable one so they both can occur

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27
Q

ATP

A

Adenosine triphosphate

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28
Q

ATP synthesis

A

Making of ATP
ADP + Pi –> ATP
Unfavorable

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29
Q

Heterotrophs

A

Get electrons by oxidizing fuel (eating) and from other living things

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30
Q

Glyoclysis overall reaction

A

Glucose + 2ADP + 2Pi + 2NAD+ –> 2 pyruvate + 2ATP + 2NADH

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31
Q

Hexokinase

A

Enzyme that breaks down ATP while it builds glucose 6-P
ATP is source of phosphate for G-6-P

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32
Q

-Delta G = Phosphate acceptor/donor

A

Donor

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33
Q

Internal electron carrier

A

Device that carries electrons
Can be used for:
1. Biosynthetic pathways
2. Respiration
3. Dumped or excreted during fermenation

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34
Q

NAD+/NADH

A

Universal all-purpose internal electron carrier
Picks up and delivers electrons and energy
Costs a lot to make
Nicotinamide adenine dinucleotide

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35
Q

Fermentation

A

NAD+ is regenerated by reducing pyruvate and excreting product (Lactate/ethanol)
Allows glycolysis to keep running
Occurs when there is no external electron acceptor

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36
Q

Respiration

A

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

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37
Q

Degradative pathways

A

Take large molecules and break them down
Release energy

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38
Q

Biosyntehtic pathways

A

Use energy released from biosynthetic pathways
Take smaller molecules and build larger ones
Use NADP+ and NADPH

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39
Q

Substrate level phosphorylation

A

Taking a phosphate from a substrate to generate ATP
Ex: Oxidation of glucose to 6 CO2 to make 4 ATP

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40
Q

Oxidative phosphorylation

A

Phosphorylation from redox reactions
Cashing in the NADH
ETC
ATP synthase

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41
Q

Pyruvate Oxidation

A

Pyruvate + NAD+ + CoA –> NADH + CO2 + Acetyl CoA
Provides rest of glycolysis with NADH
Occurs in mitochondrial matrix

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42
Q

Citric Acid Cycle/Krebs Cycle/TCA

A

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

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43
Q

Autotrophs

A

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

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44
Q

Terminal electron acceptor

A

Final molecule to receive electron
Always O2 in aerobic organisms

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45
Q

Reduction potential

A

Molecule’s ability to acqurie an electron
More positive reduction potential means it is more likely to accept electron

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46
Q

Delta E knot prime

A

How much energy will be released when a compound is reduced to a certain degree

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47
Q

Positive delta E gives…

A

Negative delta G

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48
Q

Electron Transport Chain

A

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

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49
Q

Proton pumping

A

Occurs during ETC
Protons pumped from mitochondrial matrix to intermembrane space
Proton gradient is formed

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50
Q

ATP synthase

A

Includes a turbine that crosses shaft of proton resistant membrane
Protons diffuse from gradient into cell through the turbine
ATP is generated

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51
Q

Protein co-factors

A

Carry electrons (wires)

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52
Q

Chemiosmosis

A

Proton transport due to high concentration

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53
Q

Carboxylic Acid

A

COOH
Double bond on one O
Single bond with OH

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54
Q

Amine

A

NH2

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55
Q

Methyl

A

CH3

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56
Q

Alcohol

A

OH

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57
Q

Amide

A

OCNH2
Double bond with O
NH2 single bonded

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58
Q

Pronation

A

Addition of H+ to atom or molecule

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59
Q

De-Pronation

A

Removal of H+ to an atom or molecule

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60
Q

Carbohydrates

A

Always consist of C,H,O
Contain -OH
Usually rings with O

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61
Q

Nucleic Acids

A

C,H,O,N,P
Made of nucleotides
5 carbon ribose or deoxyribose sugar
Nitrogenous base
Phosphate group

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62
Q

Lipids

A

Always contain C and H
Multiple C-C and C-H bonds
Polar and non polar heads
Less C-O bonds than carbohydrates

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63
Q

Proteins

A

C,H,O,N
N-C-C backbone
Caboxyl group
Amine group
Specific polymer of amino acids

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64
Q

Decarboxylation reaction

A

Reaction where CO2 is a product

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65
Q

Reducing Energy

A

Source of high energy electrons and energy
Take form of NADH, NAPDH, or ATP
Needed for cell growth and survival

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66
Q

Photosynthesis

A

Creating recuding energy and energy using light

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67
Q

Catabolism

A

Gradually oxidizing fuel to form NADH and ATP

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68
Q

Anabolism

A

Using ATP, NADH/NADPH to drive biosynthesis
Opposite of catabolism

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69
Q

Light reactions

A

Get electrons to ETC without strong electron donor
Depend on light
Products are NADPH and ATP

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70
Q

Dark reactions

A

Using ATP and NADH to reduce CO2 and generate glucose

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71
Q

Steps of light reactions

A
  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
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72
Q

Dark reaction steps

A
  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
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73
Q

Pigments

A

Molecules that absorb specific wavelengths in the visible range

74
Q

Reaction center

A

Specific chlorophyll capable of transferring an electron to ETC

75
Q

P840

A

Pigment involved in green sulur bacteria light reactions
Strong reducing agent when excited. Strong oxidizing agent after it loses its electron

76
Q

Cyclic Photosynthesis

A

Electron ends up where it started back in chlorophyll

77
Q

Periplasmic space

A

Between two membranes

78
Q

Cytosol

A

Between two membranes

79
Q

Steps of cyclic photosynthesis (Green sulfur bacteria)

A

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
Q

Non-Cyclic Photosynthesis

A

Electron from P840 doesn’t return to P840ox, but is picked up by NADP instead

81
Q

Non-Cyclic Photosynthesis steps (Green sulfur bacteria)

A

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
Q

What is special about green sulfur bacteria?

A

They can use electrons and light to make proton motive force and ATP OR make NADPH

83
Q

Phosphoanhydride bond

A

Hydride bond between two phosphate groups

84
Q

Photophosphorylation

A

Phosphorylation that includes excitement of photons

85
Q

Cristae

A

Rdiges on inner membrane of mitochondria

86
Q

Bacteriochlorophyll

A

Photosynthetic pigments found in bacteria

87
Q

Carbon fixation

A

Reduction of CO2 to build fuel
Combining RUBP(5 carbon sugar) and CO2. 6 cycles will allow us to build one glucose molecule

88
Q

Ways to fix carbon

A

Reverse TCA cycle (Green sulfur bacteria)
Calvin cycle (cyanobacteria, green plants)

89
Q

Reverse TCA cycle

A

Prodcued Acetyl CoA with 2 CO2
2CO2 + 2NADPH + FADH2 + Fdred + 2 ATP + coA –> acetyl CoA + 2NAD+ + FAD + Fdox + 2ADP + 2Pi

90
Q

Ferredoxin

A

Electron carrier from the light reactions
Also small proteins containing iron and sulfur
H2S + Fdox –> S + Fdred

91
Q

P680

A

Pigment that is able to oxidize water located in PSII

92
Q

P700

A

Pigment that is able to reduce NADP located in PSI

93
Q

Z scheme

A

Cyclic and non-cyclic process in oxygenic photosynthesis combined (The light reactions)

94
Q

Rubisco

A

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
Q

Chemoautotroph

A

Synthesize food using chemical energy

96
Q

Organotroph

A

Organsim that obtains hydrogen or electrons from organic substrates

97
Q

Chloroplast anatomy

A

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
Q

Calvin Cycle

A

6CO2 + 18ATP + 12 NADPH –> 2G3P

99
Q

Cytochrome B6F

A

Ability to pump protons from stroma of chloroplast to lumen of thylakoid

100
Q

Peptide bonds

A

Hold amino acids together between the carboxyl and amine group
One molecule of H2O is formed when a peptide bond is formed

101
Q

Photorespiration

A

Error by rubisco. Can unfix CO2

102
Q

Lysozyme

A

Breaks down bacterial cell walls

103
Q

Protein Primary structure

A

Chain of amino acids

104
Q

R groups

A

20 unique amino acids. Charged or polar groups are hydrophilic. Nonpolar and uncharged groups are hydrophobic and are involved in hydrophobic interactions

105
Q

Protein Secondary Structures

A

Beta sheets and alpha helices
Stabilized by hydrogen bonds between N-H and C–O groups

106
Q

Hydrogen bond

A

Weak ionic bond
Become really strong when added up

107
Q

Protein tertiary structures

A

3-D shape of folded protein
Determined by R groups
Stabilized by hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bridge

108
Q

Disulfide bridge

A

Bond between S-S
Can only be made by cysteine

109
Q

Quaternary structure

A

2+ tertiary structures coming together
Same bonds as tertiary structures

110
Q

Renaturation

A

Synthesizing a protein

111
Q

Denatured

A

Unfolded protein
Proteins that can be denatured are usually small
Stabilized by disulfide bonds

112
Q

Cofactor

A

Regenerated during catalytic cycle. Not used up. Help power enzymes
Can drastically modify reduction potentials

113
Q

Feedback Inhibition

A

Product of long pathway inhibits enzyme that catalyzes the first dedicated step of pathway

114
Q

Enzyme regulation

A

Cells manipulate the accessibility of active site to switch enzymes on or off

115
Q

Allosteric activator

A

Binds to enzyme, allowing substrate to bind to it and a reaction occurs

116
Q

Allosteric inhibitor

A

Binds to enzyme, preventing substrate from binding to it

117
Q

Competitive inhibitor

A

Fights with the substrate for the binding site
To get rid of inhibitor, either get rid of it or add more substrate

118
Q

Noncompetitive inhibitor

A

Substrate and inhibitor bind to different sites
Product can only be formed when only the substrate binds to the enzyme

119
Q

Irreversible inhibition

A

Noncompetitive inhibitor that covalently bonds to allosteric site or active site

120
Q

Phosphofructokinase

A

Catalyzes the first dedicated step of glycolysis
Reaction is regulated allosterically by high levels of ADP
Sensitive to many metabolites

121
Q

PEP

A

Allosteric regulator of phosphofructokinase

122
Q

Signal metabolites

A

Can switch a protein on or off allosterically, affecting its affinity for the substrate

123
Q

A cell

A

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
Q

Bacteria

A

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
Q

Archaea

A

Prokaryotes
Share same qualities as bacteria

126
Q

Prokaryotes

A

Evolutionary distinct domains of life

127
Q

Microbial mats/large biofilms

A

May represent the earliest forms of life on Earth
Multi-layered sheet of microbes composed of bacteria

128
Q

Plasma membrane

A

Phospholipid membrane that defines the boundary between inside and outside of cell

129
Q

Cytoplasm

A

Where soluble reactions occur
Contains ribosomes , protein-RNA complex where proteins are synthesized
Tends to be vicscous

130
Q

Cell wall

A

Provide protection and maintain shape
Only found in plant cells
Prevent cells from exploding in water

131
Q

Amphipathic

A

Hydrophilic head, hydrophobic tail
Charged, polar head
Greasy, very non-polar head

132
Q

Viscosity

A

Measure of fluids resistance to flow

133
Q

Internal Membranes

A

Create specialized subcellular environments
Form electrochemical gradients
Provide additional surface area
Allow for sub-cellular specialization and complexity

134
Q

Cytoskeleton

A

Protein polymers
Functions: Roads for intracellular transport
- Shape of cell
- Mechanical strength
- Cellular locomotion
Subunits held longitudinally and laterally by non-covalent interactions

135
Q

3 Types of cytoskeleton

A

Intermiediate filaments
Microtubules
Actin

136
Q

Unsaturated Phospholipids

A

At least one double bond
Causes kink at increased permeability

137
Q

Cell placed in hypotonic solution

A

Hypotonic solution: Low solute concentration
outside the cell compared to inside. Water enters and cells explodes

138
Q

Cell placed in hypertonic solution

A

Hypertonic solution: High solute concentration outisde cell compared to inside. Water escapes and cell shrivels up and dies

139
Q

Cell placed in isotonic solution

A

No net movement of water. Equal osmolarity

140
Q

Turgor

A

Normal, strong rigid shape

141
Q

Flaccid

A

Limp

142
Q

Plasmolyzed

A

Lack of water

143
Q

Cell wall

A

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
Q

Chloroplast

A

Descended from symbiotic cyanobacteria, which were acquired by single-celled eukaryote about 580 million years ago
Contained in plant cells only

145
Q

Amphipathic proteins

A

Can integrate into lipid bilayers

146
Q

Integral Proteins

A

Embedded within/across the plane of the membrane

147
Q

Peripheral Proteins

A

Attached to inner or outer surface of membraner

148
Q

Passive Transport

A

High to low concentration
- Simple diffusion
- Facilitated diffusion

149
Q

Simple diffusion

A

High to low concentration with no protein help

150
Q

Facilitated diffusion

A

High to low concentration with help of transport protein

151
Q

Active transport

A

Low to high-concentration, with help of transport protein
Has +deltaG
Couples with favorable reaction to occur

152
Q

Uniport

A

One thing, one direction

153
Q

Simport

A

2 things, one direction

154
Q

Antiport

A

2 things, 2 directions

155
Q

Intermediate filaments

A

Mechanical strength and resistance to shear stress
Rope-like proteins
Mainly cell specific

156
Q

Microtubules

A

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
Q

Actin

A

Asymmetric
Transport, cell shape, cell locomotion
Subunits assemble head to head
Monomers
Binds and hydrolyzes ATP
Road for myosin
Polymerization induces ATP hydrolysis

158
Q

Microtubule dynamic instability

A

Microtubules growing and shrinking at the same tubulin concentration
Crucial for microtubule function
Highly regulated

159
Q

Actin treadmilling

A

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
Q

Motor proteins commonalities

A

Enzymes
Powered by conformational changes driven by ATP hydrolysis
Generate force by coupling ATP hydrolysis and conformational changes

161
Q

Binary fission

A

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
Q

Checkpoints in Cell Cycle

A

Trigger arrest until problems are solved

163
Q

Cell Cycle phases

A

G1, S, G2, M phase

164
Q

G1-S checkpoint

A

Commit to DNA replication and cell division
Makes sure the environment is favorable

165
Q

S checkpoint

A

Makes sure all DNA is replicated properly

166
Q

G2-M checkpoint

A

Check if there’s any DNA damage that needs ton be repaired

167
Q

Spindle assembly checkpoint

A

Make sure that all chromosomes are all attached to the spindles
Prevents opening of cohesins at centromere

168
Q

CDKs

A

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
Q

Cyclin

A

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
Q

Replication (S-Phase)

A

Triggered by S-CDK and cyclin

171
Q

Viscosity

A

Measure of fluids resistance to flow

172
Q

Compartmentalization

A

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
Q

Endosymbiosis

A

One cell engulfing another to ensure they both stay alive

174
Q

Diploid

A

Two sets of chromosomes

175
Q

Haploid

A

One set of chromosomes

176
Q

Cohesins

A

Ring like proteins that hold sister chromatids together
Resist pull from motors
Opening allows for start of anaphase

177
Q

M-phase steps

A

Prophase, prometaphase, metaphase, anaphase, telophase, cytokinesis

178
Q

Somatic cells

A

Diploid

179
Q

Gamete cells

A

Haploid, sex cells

180
Q

Centromere

A

Specialized regions where microtubules attach via kinetochores

181
Q

Kinetochores

A

Multi-protein structure that fully assembles onto centromeres during prophase
Provides attachment site for microtubules
Allows for sister chromatids to separate

182
Q

Mitosis

A

Produce identical cells

183
Q

Meiosis

A

Produce genetically different cells (gametes)
Use haploid cells

184
Q
A

Ethans Flashcards (11 decks)

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