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BIOB 160 > Test 2 > Flashcards

Test 2 Flashcards

1
Q

Metabolism

A

Is the totality of an organism’s chemical reactions

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2
Q

catabolic pathways

A

break down complex molecules into simpler compounds

release energy

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3
Q

anabolic pathways

A

build complicated molecules from simpler ones

consume energy

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4
Q

kinetic energy

A

associated with motion

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5
Q

potential energy

A

stored in the location of the matter

includes chem energy stored in molecular structure

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6
Q

thermodynamics

A

the study of energy transformations

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7
Q

1st law of thermodynamics

A

Energy can be transferred and transformed but it cannot be created nor destroyed

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8
Q

2nd Law of Thermodynamics

A

Spontaneous changes that do not require outside energy increase the entropy, or disorder, or the universe

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9
Q

Biological order and disorder

A

living systems

  • increase the entropy of the universe
  • use energy to maintain order
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10
Q

Free Energy Change

A

(Delta G)
Tells us whether the reaction occurs spontaneously
Directly related to the enthalpy change and the change in entropy (Delta G=Delta H-TDeltaS)

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11
Q

Free energy- living system

A

The energy that can do work under cellular conditions

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12
Q

Entropy

A

(Delta S)

Disorder of the system

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13
Q

Enthalpy

A

(Delta H)

Heat of the reaction

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14
Q

During a spontaneous change…

A

Free energy decreases and the stability increases

(Delta G

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15
Q

During a non-spontaneous change…

A

Free energy has to be added and the stability decreases

Delta G>0

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16
Q

Exergonic

A

Spontaneous

Net release of free energy

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17
Q

Endergonic

A

Non-spontaneous

Net absorption of free energy

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18
Q

3 kinds of work in a cell

A

Mechanical
Transport
Chemical

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19
Q

Cellular work powered by?

A

Hydrolysis of ATP

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20
Q

How is ATP used to store energy?

A
  • Energy coupling is key
  • ATP hydrolysis is exergonic
  • Phosphate bonds in ATP are normal “high energy” bonds (difference is in free energies of compounds before and after ATP hydrolysis)
  • Crowding of (-) charged phosphates contributes to “high energy” of ATP
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21
Q

ATP

A

Adenosine triphosphate

-cells energy shuttle, provides energy for cellular functions

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22
Q

When is energy released from ATP?

What’s produced?

A

When the terminal phosphate is broken

-Produces, inorganic phosphate, adenosine diphosphate(ADP) and energy

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23
Q

ATP as “molecular spring”

A

Phosphate groups are negative and are repulsed by one another. It takes energy to bring the three phosphate groups together and like a compressed spring, that invested energy will be returned when it releases

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24
Q

How does ATP perform work?

A

It drives endergonic reactions by phophorylation (transferring a phosphate to other molecules)
by causing conformational changes in molecules
by making unstable rxn intermediates that turn ender into exergonic

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25
Q

What is a catalyst?

A

a chemical agent that speeds up a reaction w/o being consumed by the reaction

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26
Q

What is an enzyme?

A

a catalytic protein

-speeds up metabolic reactions by lowering energy barriers

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27
Q

Why do reactions need catalysts?

A

Every chemical reaction b/w molecules involves both bond breaking and bond forming

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28
Q

What is Activation Energy?

A

The initial amount of energy needed to start a chemical reaction
-often supplied in the form of heat from the surroundings in a system

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29
Q

What is a substrate?

A

The reactant an enzyme acts on

  • The enyzme binds to its substrate, forming an enzyme-substrate complex
  • substrate specificity of enzymes varies, they sometimes catalyze chemically similar reactions
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30
Q

Where do substrates bind?

A

The active site

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31
Q

What is induced fit of a substrate?

A

Brings the chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction

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32
Q

How can active sites lower the activation energy barrier?

A
  • orienting substrates correctly
  • straining substrate bonds
  • providing a favorable microenvironment
  • covalently bonding to the substrate
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33
Q

Local conditions of enzyme activity?

A

Each enzyme has an optimal temp, pH in which it can function

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34
Q

What are cofactors?

A

Non protein enzyme helpers

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35
Q

What are coenzymes?

A

Organic cofactors

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36
Q

What are enzyme inhibitors?

A

Competitive inhibitors- bind to the active site of an enzyme, competing w/ the substrate
Noncompetitive inhibitors- bind to another part o the enzyme, changing the function

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37
Q

What is allosteric regulation?

A

The term used to describe any case in which a protein’s function at one site is affected by binding of a regulatory molecule at another site

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38
Q

What is cooperativity?

A

a form of allosteric regulation that can amplify enzyme activity

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39
Q

Where are enzymes in the cell?

A
  • grouped into complexes
  • incorporated into membranes
  • contained inside organelles
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40
Q

How do catabolic pathways yield energy?

A
  • by oxidizing organic fuels

- due to transfer of electrons

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41
Q

Is the breakdown of organic molecules exergonic or endergonic?

A

exergonic

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42
Q

What is fermentation?

A

A catabolic process- a partial degradation of sugars that occurs w/o oxygen

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43
Q

What is cellular respiration?

A

The most prevalent and efficient catabolic pathway

  • consumes oxygen and organic molecules such as glucose
  • yields to ATP
  • to keep working, cells must regenerate ATP
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44
Q

Redox reactions

A

-transfer electrons from one reactant to another by oxidation and reduction

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45
Q

Oxidation

A

A substance loses electrons (is oxidized)

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46
Q

Reduction

A

A substance gains electrons (is reduced)

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47
Q

Oxidation of organic molecules during cellular respiration

A
  • Glucose is oxidized and oxygen is reduced

- Happens in a series of steps involving NAD+ and the e- transport chain

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48
Q

What is NAD+?

A

A coenzyme

-electrons from organic compounds are usually transferred to NAD+ first

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49
Q

What is NADH?

A

The reduced form of NAD+

-passes the electrons to the electron transport chain

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50
Q

Why do electron transfer reactions occur in small steps?

A

-if not stepwise a large release of energy occurs (probs explosion)

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51
Q

What does the electron transport chain do?

A

Passes electrons in a series of steps instead of in one explosive reaction
-uses the energy from the electron transfer to form ATP

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52
Q

What are the stages of cellular respiration?

A

Glycolysis
The citric acid cycle
Oxidative phosphorylation

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53
Q

What does glycolysis do?

A

Harvests energy by oxidizing (breaking down) glucose into two molecules of pyruvate

  • Means “splitting sugar”
  • Occurs in the cytoplasm of the cell
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54
Q

What does the citric acid cycle do?

A

Completes the energy-yielding oxidation (breakdown) of organic molecules (glucose)
-takes place in the matrix of the mitochondrion

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55
Q

What does oxidative phosphorylation do?

A

Generates ATP

-is driven by the electron transport chain

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56
Q

How do gylcolysis and the citric acid cylce generate ATP?

A

Substrate-level phosphorylation

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57
Q

Two main phases or gylcolysis?

A

Energy investment phase

Energy payoff phase

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58
Q

Enzymes in energy investment phase of glycolysis?

A 
Hexokinase
Phosphoglucoisomerase
Phosphofructokinase
Aldolase
Isomerase
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59
Q

Ensymes in the energy payoff phase of glycolysis?

A 
Triose phosphate dehydrogenase
Phosphoglycerokinase
Phosphoglyceromutase
Enolase
Pyruvate kinase
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60
Q

How many ATP are invested verses produced in glycolysis?

A

2 ATP invested, 4 gained

Net=2

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61
Q

Before the citric acid cycle can begin what must occur?

A

Pyruvate must be converted to acetyl CoA, which links the cycle to glycolysis

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62
Q

Ribosomes

A

Complexes that synthesis proteins
Made of ribosomal DNA
decipher codons and interpret info in DNA

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63
Q

Cytosol

A

Semi-fluid, jellylike substance in all cells

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64
Q

Golgi apparatus

A
  • Organelle active in synthesis, modification, sorting and secretion of cell products
  • Warehouse for receiving, sorting, shipping some manufacturing
  • receives many of the transport vesicles produced in rough ER
  • consists of flattened membranous sacs called cisternae
  • trans side: shipping
  • cis side: receiving
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65
Q

Lysosome

A

membranous sac of hydrolytic enzymes

-can digest all kinds of macromolecules

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66
Q

Chloroplast

A

Photosynthetic organelle, converts energy of sunlight to chemical energy stored in sugar molecules

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67
Q

Endomembrane system

A

Nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles and vacuoles, plasma membrane
Synthesizes proteins, transports proteins into membranes of organelles or out of cell, metabolism and movement of lipids, detox of poisons

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68
Q

Endoplasmic reticulum

A

Network of membranous tubules and sacs called cisternae

accounts for more than half the total membrane in many eukaryotic cells (continuous w/ nuclear envelope)

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69
Q

Phagocytosis

A

Lysosome digesting food (intracellular)

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70
Q

Autophagy

A

Lysosome breaking down damaged organelles

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71
Q

Mitochondrion

A

Organelle where cellular respiration occurs and most ATP is generated
-found in nearly all eukaryotic cells

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72
Q

Citric Acid Cycle

A
  1. Acetyl group added to oxaloacetate and CoA is regererated
  2. Isomerization (water, no energy required)
  3. Citrate loses CO2, NAD+ is reduced to NADH
  4. Substrate-level phosphoyrlation makes GTP, and converts it to ATP
  5. Last two H transfered to FADH2 (More EN than NADH)
  6. Substrates are rearranged and oxidized, another NADH is made and oxaloacetate is regenerated
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73
Q

Oxidative phosphorylation

A

Chemiosmosis couples electron transport to ATP synthesis

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74
Q

NADH oxidation

A

Exergonic (-53kcal/mol)

-energy released in small steps as opposed to one inefficient burst

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75
Q

Role of NADH and FADH2 in electron transport chain

A

both donate electrons to the electron transport chain, which powers ATP synthesis via oxidative phosphorylation
-electrons from both lose energy in several steps

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76
Q

What happens at the end of the electron transport chain?

A

e- are passed to oxygen, forming water

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77
Q

ATP synthase

A

the enzyme that actually makes ATP

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78
Q

ATP synthase and e- transport chain

A

At certain steps in the chain:

  • exergonic transfer of e- causes protein complexes to pump H+ from mitochondria to intermembrane space
  • H+ wants to move back to mitochondria, and ATP synthase complexes are the only sites on the membrane to allow that
  • This H+ gradient stores energy, drives chemiosmosis, is proton motive force
79
Q

Chemiosmosis

A

an energy-coupling mechanism that uses energy in the form of a H+ gradient across a membrane to drive cellular work

80
Q

How much H+ and ATP does NADH pump?

A

10 H+

3 ATPs

81
Q

How much H+ and ATP does FADH2?

A

6 H+

2 ATPs

82
Q

What percentage of energy in a glucose molecule is transferred to ATP during cellular respiration?

A

40%
-686 kcal/mol (energy in glucose molecule)
total 36-38 ATPs produced

83
Q

Fermentation vs. respiration

A
  • Glycolysis can produce ATP w/ or w/o O2
  • No oxygen- cells still produce ATP through fermentation; NAD+ must be regenerated or glycolysis will shut down
  • Oxygen- cellular respiration produces ATP
84
Q

Fermentation consists of

A

Glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis

85
Q

Types of fermentation

A

Alcohol

Lactic acid

86
Q

Alcohol fermentation

A

Pyruvate is converted to ethanol in two steps, one of which releases CO2
Baking and brewing (CO2 rises dough)

87
Q

Lactic acid fermentation

A

Pyruvate is reduced directly to NADH to form lactate as a waste product
(dairy industry, muscles)

88
Q

Does fermentation or cellular respiration produce more ATP?

A

respiration

89
Q

When did gylcolysis evolve?

A

In ancient prokarylotes (3.5 billion years ago) before there was O2 (2.7 billion years ago)
-important for energy production even when oxygen supply is scarce

90
Q

Light microscopes

A

LMs
pass visible light through a specimen
magnify cellular structures with lenses

91
Q

Scanning electron microscopes

A

SEM
focus a beam of electrons onto a specimen surface
-provides for a detailed study of the surface of a specimen

92
Q

Transmission electron microscopes

A

TEM
focus a beam of electrons through a specimen
-provides for detailed study of the internal ultrastructure of cells

93
Q

Cell fractionation

A

Tissue Cells
Homogenate
Pellet rich in nuclei and cellular debris
Pellet rich in mitochondria (and chloroplasts if plant)
Pellet rich in “microsomes” (pieces of plasma membranes and cells’ internal membranes)
Pellet rich in ribosomes

94
Q

All cells have…

A 
semifluid substance called cytosol
chromosomes
ribosomes
DNA
bound by plasma membrane
95
Q

Prokayotic cells -DNA

A

no nucleus

DNA located in region-nulceoid

96
Q

Eukaryotic cells-DNA

A

true nucleus, bounded by a membranous nuclear envelope

generally bigger than prokaryotic cells

97
Q

Size of cells

A

A smaller cell has a higher surface area to volume ratio, which facilitates the exchange of materials in and out of the cell

98
Q

Smooth ER

A

lacks ribosomes

  • synthesizes lipids
  • metabolizes carbs
  • stores calcium
  • detoxifies poision
99
Q

Rough ER

A

has bound ribosomes

-produces proteins and membranes, which are distributed by transport vesicles

100
Q

Vacuoles

A

diverse maintenance compartments

-a plant of fungal cell may have one or several

101
Q

types of vacuoles

A

food
contractile
central

102
Q

food vacuoles

A

formed by phagocytosis

103
Q

contractile vacuoles

A

pump excess water out of protist cells

104
Q

central vacuoles

A

found in plant cells

-hold reserves of important organic compounds and water

105
Q

Chloroplasts

A
  • found only in plants, leaves and other green organs and algae!
  • site of photosynthesis
  • contain chlorophyll
  • specialized member of family closely related to plant organelles called plastids
106
Q

Two mitochondria membranes

A

smooth outer

inner folded into cristae

107
Q

Chloroplast structure includes

A
  • Thylakoids, membranous sacs

- Stroma, the internal fluid

108
Q

Peroxisomes

A

produce hydrogen peroxide and convert it to water

109
Q

Cytoskeleton

A

network of fibers (extending throughout the cytoplasm) that organizes structures and activities in the cell and gives mechanical support to the cell

110
Q

Three fibers of cytoskeleton

A

Microtubules
Microfilaments
Intemediate Filaments

111
Q

Microtubules

A 
(Tubulin Polymers)
Hollow tubes
Tubulin
-Maintenence of cell shape
-Cell motility
-Chromosome movement in cell division
-organelle movements
112
Q

Microfilaments

A 
(Actin Filaments)
Two intertwined strands
Actin
-Maintenence of cell shape
-Changes in cell shape
-Muscle contraction
-Cytoplasmic streaming
-Cell motility
-Cell division
113
Q

Intermediate Filaments

A

Fibrous proteins supercelled into thicker cells
One of several different proteins of the keratin family
-Maintenance of cell shape
-Anchorage of nucleus and certain other organelles
-formation of nuclear lamina

114
Q

Centrosome

A
  • a “microtubule-organizing center”

- contains a pair of centrioles

115
Q

Cilia and flagella

A
  • contain specialized arrangements of microtubules
  • are locomotor appendages to some cells
  • share common ultrastructure
116
Q

dynein

A

protein responsible for the bending movement of cilia and flagella

117
Q

Where are microfilaments found?

A

microvilli

118
Q

Myosin

A

protein in microfilaments that function in cellular motility (in addition to actin)

119
Q

cellular membranes

A

are fluid mosaics of lipids and proteins

120
Q

phospholipids

A
  • the most abundant lipid in plasma membrane

- amphipathic, contain both hydrophobic and hydrophilic regions

121
Q

Davson-Danielli sandwich model

A

membrane made up of a phospholipid bilayer sandwiched between two protein layers
supported by electron microscope pics

122
Q

Singer and Nelson model

A

proposed that membrane proteins are dispersed and individually inserted into phospholipid bilayer

123
Q

Freeze-Fracture

A

-supported fluid mosaic model of membrane structure

124
Q

Lateral movement w/in bilayer

A

10^7 times per second

125
Q

Flip flop movement w/in bilayer

A

once a month

126
Q

protein movement w/in plasma membrane

A

can drift w/in the bilayer

127
Q

fluid vs. viscous

A

unsaturated hydrocarbon tails with kinks vs. saturated hydrocarbon tails

128
Q

Cholesterol and membrane fluiditity

A

The steroid cholesterol has different effects on membrane fluidity at different temperature; helps retain the fluidity at low temps

129
Q

Integral proteins

A
  • penetrate the hydrophobic core of the lipid bilayer
  • are often transmembrane proteins, completely spanning the membrane
  • “inside out proteins”
130
Q

Peripheral proteins

A

-appendages loosely bound to the surface of the membrane

131
Q

Six major functions of membrane proteins

A 
Transport
Enzymatic activity
Signal transduction
Cell-cell recognition
Intercellular joining
Attachment to the cytoskeleton and extracelluar matrix (ECM)
132
Q

Cell-cell recognition

A
  • a cells ability to distinguish one type of neighboring cell from another
  • membrane carbs interact w/ the surface molecules of other cells, facilitating cell-cell recognition
133
Q

Crossing the lipid bilayer

A
  • hydrophobic molecules: lipid soluble and can pass through the membrane rapidly
  • polar molecules do not cross rapidly
  • transport proteins allow passage of hydrophilic substances
134
Q

Diffusion

A

passive transport

-the tendency for molecules of any substance to spread out evenly in available space

135
Q

Osmosis

A

the movement of water across a semipermeable membrane; it is affected by the concentration gradient of dissolved substances

136
Q

Tonicity

A
  • the ability of a solution to cause a cell to gain or lose water
  • great impact on cells w/o walls
  • governed by differences in solute concentrations in vs. out of cell
137
Q

Isotonic solution

A

Concentration of solutes is the same as it is inside the cell
No net movement of water

138
Q

Hypertonic solution

A

The concentration of solutes is greater than it is inside the cell
The cell will lose water

139
Q

Hypotonic solution

A

The concentration of solutes is less that it is inside of the cell
The cell will gain water

140
Q

Turgid

A

(plant cell)
It is in a hypotonic environment
Firm healthy state

141
Q

Flaccid

A

(plant cell)

In an isotonic environment

142
Q

Plasmolyzed

A

(plant cell)

In a hypertonic environment, insides shrink

143
Q

Lysed

A

Animal cell in a hypotonic solution (could burst)

144
Q

Shriveled

A

Animal cell in hypertonic solution

145
Q

Facilitated diffusion

A

Transport proteins speed the movement of molecules across the plasma membrane
channel and carrier proteins

146
Q

Channel proteins

A

Provide corridors that allow a specific molecule or ion to cross the membrane

147
Q

Carrier proteins

A

Undergo a subtle change in shape that translocates the solute-binding site across the membrane

148
Q

Active transport

A

uses energy (ATP) to move substances against their concentration gradient

149
Q

Sodium Potassium Pump

A

A type of active transport system

150
Q

Membrane potential

A

the voltage difference across a membrane

151
Q

Electrochemical gradient

A

caused by the concentration electrial gradient of ions across a membrane

152
Q

Electrogenic pump

A

a transport protein that generates the voltage across a membrane

153
Q

Cotransport

A

occurs when active transport of a specific solute indirectly drives the active transport of another solute (active transport driven by a concentration gradient)

154
Q

Exocytosis

A

(Bulk transport of large proteins)

Transport vesicles migrate to the plasma membrane, fuse with it, and release their contents

155
Q

Endocytosis

A

(Bulk transport of large proteins)

The cell takes in macromolecules by forming new vesicles from the plasma membrane

156
Q

Types of endocytosis

A

Phagocytosis
Pinocytosis
Receptor-mediated endocytosis

157
Q

Signal transduction pathways

A

convert signals on a cell’s surface into cellular responses

-are similar in microbes and mammals, suggesting early origin

158
Q

Plasmodesmata

A

junctions between plant cells that connect the cytoplasm of adjacent cells

159
Q

Gap junctions

A

junctions between animal cells that connect the cytoplasm of adjacent cells

160
Q

Local signaling

A
  • animals cells may communicate via direct contact
  • May use local regulators
  • Paracrine signaling: local regulator diffuses through extracellular fluid
  • Synaptic signaling: Nerve cell releases neurotransmitter which diffuses across synapse
161
Q

Long distance singaling

A

-Both plants and animals use hormones

162
Q

Cell signaling process (3 steps)

A

Reception
Transduction
Response

163
Q

Reception (cell signaling)

A

A signal molecule (ligand) binds to a receptor protein (highly specific) causing it to change shape

164
Q

Intracellular receptors

A
  • cytoplasmic or nuclear proteins
  • small hydrophobic signal molecules use these receptors and can readily cross the membrane
  • only works if both ligands and receptors are present
165
Q

Steroid hormones

A
  • bind to intracellular receptors

- receptors are transcription factors

166
Q

Receptors in the plasma membrane

A

G-protein-coupled receptors
Tyrosine kinases
ion channel receptors

167
Q

Transduction (cell signaling)

A

Cascades of molecular interactions relay signals from receptors to target molecules in the cell
-at each step, the signal is transducted to a diffrent form, commonly a conformational change in a protein

168
Q

Protein phosphorylation and dephosphorylation

A
  • A series of protein kinases add a phosphate to the next one in line, activating it
  • Phosphatase enzymes then remove the phosphates
169
Q

Second messengers

A

(ligands are “first”)
are small, nonprotein, water-soluble molecules or ions
cyclic AMP (cAMP): made from ATP

170
Q

G-proteins

A

trigger the formation of cAMP, which then acts as a second messenger

171
Q

calcium ions

A

when released into the cytosol of a cell act as a second messenger in many different pathways

172
Q

inositol triphosphate

diacylglycerol

A

second messenger that can trigger and increase in calcium in the cytosol (IP3)

173
Q

Nuclear response

A

other pathways regulate genes by activating transcription factors that turn genes on or off

174
Q

Pathway branching

A

“cross-talk”

helps the cell coordinate incoming signals

175
Q

Scaffolding proteins

A

inrease the signal transduction efficiency

stack of protein kinases

176
Q

Phosphofructokinase is an allosteric enzyme that catalyzes the conversion of fructose-6-phosphate to fructose-1,6-bisphosphate, an early step of glycolysis. In the presence of oxygen, an increase in the amount ATP in a cell would be expected to

A

inhibit the enzyme and thus slow the rates of glycolysis and the citric acid cycle

177
Q

Which of the following statements is true concerning catabolic pathways

A

They are usually coupled with anabolic pathways to which they supply energy in the form of ATP

178
Q

If an enzyme is added to a solution where its substrates and products are in equilibrium, what would occur?

A

Nothing; the reaction would stay at equilibrium. Would speed up in both directions

179
Q

Of the following, which is probably the most common route for membrane flow in the endomembrane system?

A

rough ER → vesicles → Golgi → plasma membrane

180
Q

an animal cell that lacks the ability to produce GTP

A

It would not be able to activate and inactivate the G protein on the cytoplasmic side of the plasma membrane

181
Q

Does a nucleolus contain functional ribosomes?

A

No

182
Q

Does a chloroplast contain functional ribosomes?

A

Yes

183
Q

What is most important for the glycoproteins and glycolipids of animal cell membranes?

A

cell-cell recognitions

184
Q

organelles other than nucleus that contain dna

A

mitochondria and chloroplasts (cellular respiration and photosynthesis)

185
Q

Paracrine signaling

A

involves secreting cells acting on nearby target cells by discharging a local regulator into the extracellular fluid

186
Q

Primary role of oxygen in cellular respiration

A

act as an acceptor for electrons and hydrogen, forming water

187
Q

Molecules that can potentially be converted to intermediates of glycolysis and/or the citric acid cycle include

A 
amino acids
proteins
gylcerol and fatty acids
glucose and sucrose
starch and glycogen
188
Q

Carbon dioxide (CO2) is released during which of the following stages of cellular respiration

A

Oxidation of pyruvate to aetyl CoA and the citric acid cycle

189
Q

Membrane receptors that attach phosphates to specific animo acids in proteins are

A

called receptor tyrosine-kinases

190
Q

Second messengers

A

cAMP
calcium ions
DAG
IP3

191
Q

Adenylyl cyclase has the opposite effect of?

A

phosphodiesterase

192
Q

The activation of receptor tyrosine kinases is always characterized b

A

dimerization and phosphoylation

193
Q

An inhibitor of phosphodiesterase activity would have which of the following effects

A

prolong the effect of epinephrine by maintaining elevated cAMP levels in the cytoplasm

BIOB 160 (4 decks)

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