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Biochem > Quiz 1: Reading Info > Flashcards

Quiz 1: Reading Info Flashcards

1
Q

Cytoplasm

A

aqueous internal solution and suspended particles

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2
Q

Cytosol

A

just aqueous solution

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3
Q

Metabolite

A

intermediated in biosynthetic and degradation pathways

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4
Q

What limits cellular dimensions?

A

lower limit of size set by minimum number of biomolecules required by the cell

upper limit of size is set by the rate of diffusion: need a high surface-to-volume ratio for diffusion to occur

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5
Q

Are eukaryotes more closely related to bacteria or archaea?

A

Archaea

Share closer common ancestor

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6
Q

Types of single cell organisms

A

Archaea- extreme environments

Bacteria- soils, surface waters, tissues of other organisms

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7
Q

What organelles do all cells have?

A

cytoplasm, plasma membrane, ribosomes

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8
Q

What types of cells have a nucleoid?

A

Bacterial cell

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9
Q

Do bacteria cells have membrane bound organelles?

A

No

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10
Q

Cell envelope

A

the plasma membrane and the layers outside of it

differ in bacteria cells (gram+, gram-, etc.)

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11
Q

Gram positive bacteria

A

have a thick layer of peptidoglycan outside their plasma membrane but lack an outer membrane

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12
Q

Gram negative bacteria

A

have an outer membrane composed of a lipid bilayer

the cell wall is wedged between 2 membranes

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13
Q

What is in the outer membrane of gram negative bacteria?

A

1) porins: provide transmembrane channels for low molecular weight compounds and ions to diffuse
2) lipopolysacchrides

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14
Q

Do archaea have cell walls?

A

yes, normally made of peptidoglycan or hard protein

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15
Q

plasmids

A

small circular segments of DNA in the cytoplasm of bacteria

outside of the main DNA in the nucleoid

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16
Q

What gave the first hints that bacteria and archaea constitute different domains?

A

ribosomal differences

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17
Q

Size difference between eukaryotic cells and bacteria/archaea cells

A

5-100µm for eukaryotic cells

2µm for prokaryotic cells (less stuff to contain)

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18
Q

Mitochondria

A

site of most of the energy extracting reactions of the cell

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19
Q

Golgi complex

A

postmaster of the cell

processes, packages, and targets proteins to other organelles for export

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20
Q

Rough endoplasmic reticulum

A

site of much protein synthesis

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21
Q

Smooth endoplasmic reticulum

A

site of lipid synthesis and drug metabolism

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22
Q

Peroxisomes

A

oxidize fatty acids (breakdown fatty acids)

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23
Q

Lysosomes

A

filled with digestive enzymes to degrade unneeded cellular debris

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24
Q

vacuoles

A

store large quantities of organic acids

*large central vacuole found in plant cells

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25
Q

chloroplasts

A

sunlight drives the synthesis of ATP in the process of photosynthesis

*found in plant cells

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26
Q

Do plant cells have mitochondria?

A

Yes

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27
Q

Are plant cells or animal cells larger?

A

Plant cells

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28
Q

Thylakoids

A

site of light-driven ATP synthesis

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29
Q

Plasmodesma

A

provides path between two plant cells

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30
Q

How can you determine the function of the different organelles?

A

gently rupture the plasma membrane by physical shear

then centifuge the organelles

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31
Q

Cytoskeleton

A

protein filaments that crisscross the eukaryotic cell, forming an interlocking 3D meshwork

provide structure, shape and organization to the cell

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32
Q

3 types of cytoplasmic filaments

A

1) actin filaments
2) microtubules
3) intermediate filaments

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33
Q

Are cytoplasmic filaments set in place?

A

No! They constantly change locations and break down into protein subunits

Controlled by regulatory proteins when to move

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34
Q

Endomembrane system

A

segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur

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35
Q

Exocytosis and endocytosis

A

mechanisms of transport that involve membrane fusion and fission, provide paths between the cytoplasm and surrounding medium

allowing for secretion of substances produced in the cell and uptake of extracellular materials

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36
Q

How big are ribosomes?

A

20 nm

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37
Q

How big are amino acids?

A

0.5 nm

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38
Q

How big is the mitochondria?

A

1000 nm

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39
Q

What makes carbon so crucial to life?

A

Its ability to make 4 stable single bonds and its bonding versatility

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40
Q

What are the central metabolites?

A

small organic molecules that are the building blocks of life

these molecules may be polar or charged and are soluble in water: this traps them in the cell

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41
Q

Can polar molecules diffuse across the cell membrane?

A

Most cannot, unless very small

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42
Q

Metabolomics

A

the systematic characterization of the metabolome under very specific conditions, such as following the administration of a drug

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43
Q

Macromolecules

A

polymers with molecular weights above ~5000 that are assembled from relatively simple precursors

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44
Q

Oligomers

A

shorter polymers

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45
Q

What may macromolecules be assembled into?

A

Supramolecules such as ribosomes

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46
Q

Proteins

A

long polymers of amino acids

serve as enzymes, structural elements, signal receptors, or transporters

make up the 2nd largest fraction of the cell after water

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47
Q

Nucleic acids

A

either DNA or RNA

polymers of nucleotides

store and transmit genetic information

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48
Q

Polysaccharides

A

polymers of simple sugars such as glucose

energy-rich fuel stores, structure for cell walls, extracellular recognition elements that bind to proteins

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49
Q

Lipids

A

water-insoluble hydrocarbon derivatives

serve as structural components of membranes, energy-rich fuel stores, and intracellular signals

50
Q

Types of macromolecules

A

Proteins, nucleic acids, polysaccharides, lipids

51
Q

Informational macromolecules

A

proteins and nucleic acids

52
Q

Stereoisomers have different…

A

configuration!

53
Q

What is another name for cis/trans isomers?

A

geometric isomers

54
Q

Configuration is conferred by the presence of either

A

1) double bonds around which there is little or no freedom of rotation
2) chiral centers around which substituent groups are arranged in a specific orientation

55
Q

Chiral molecule

A

rotated molecule cannot be superposed on its mirror image

56
Q

Enantiomers

A

stereoisomers that are mirror images of eachother

different R/S configuration

57
Q

Diastereomers

A

stereoisomers that are not mirror images of each other

same R/S configuration

58
Q

Racemic mixture

A

equimolar solution of two enantiomers that does not show optical rotation

enantiomers rotate plane polarized light

two different enantiomers will rotate the light in opposite directions and cancel eachother out

59
Q

Conformation

A

the spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of rotation around single bonds

60
Q

Difference between empirical and molecular formulas?

A

Empirical formula simplifies number of atoms; molecular formula lists them all out

61
Q

Is a dyanmic steady state at equilibrium?

A

not exactly

in biochemistry, something is reaching equilibrium when it is dead and decaying

instead, there is a dynamic steady state when alive. the rate of breakdown equals the rate of anabolism

62
Q

system

A

all products and reactants, the solvent that contains them and the immediate atmosohere

63
Q

universe

A

the system and its surroundings

64
Q

Isolated, closed, and open systems

A

Isolated- system shares neither matter nor energy with its surroundings

Closed- system shares energy but not matter with its surroundings

Open- system shares energy and matter with its surroundings (living organisms are open systems)

65
Q

1st law of thermodynamics

A

although the form of the energy may change, the total amount of energy in the universe remains constant

66
Q

oxidation-reduction reactions

A

almost all reactions involved in electron flow

one reactant is oxidized (loses electrons) while the other is reduced (gains electrons)

67
Q

2nd law of thermodynamics

A

the total entropy of the universe is continually increasing

this applies to biochemistry, because it requires an input of energy to order things (ex: informational macromolecules have subunits in specific order)

68
Q

What type of bond breaks in ATP?

A

phosphoanhydride

69
Q

Bioenergetics

A

the study of energy transformations in living systems

concerned with how energy is coupled

70
Q

What does the magnitude of delta G depend on?

A

how far from equilibrium the system is originally

delta G measures the change from the initial state to equilibrium

71
Q

Do thermodyanmic constants like delta G tell us anything about how fast a reaction will occur?

A

No! That’s kinematics

Thermodyanmics only tell us where the final equilibrium for a reaction lies

72
Q

What is another reason why ATP breakdown is exergonic (besides neg. charged phosphate groups)?

A

cells maintain a concentration of ATP far above equilibrium concentration

products want to be made then and breakdown ATP

73
Q

Using ATP to make reactions exergonic

A

TRANSFERRING a phosphoryl group to another molecule (not just breaking down ATP)

74
Q

Why are biological macromolecules stable?

A

they are thermodynamically unstable, but kinetically stable since it takes so long to break them down

this is where enzymes come into play

75
Q

transition state

A

a state of higher energy than either the reactants or products

76
Q

activation energy

A

the change in free energy from the initial state to the transition state (delta G double-dagger)

77
Q

How do enzymes catalyze reactions?

A

1) providing a more comfortable fit for the transition state, and consequently lowering the activation energy
2) binding two or more reactants in a sterospecific orientation that favors the reaction

78
Q

What is crucial about enzymes?

A

need to be able to use them selectively

79
Q

pathways

A

sequences of consecutive reactions

the product of one reaction becomes the reactant in the next

80
Q

metabolism

A

the overall network of enzyme-catalyzed pathways both catabolic and anabolic

81
Q

feedback inhibition

A

if an enzyme is producing too many of a molecule, this higher concentration of molecule may inhibit the enzyme from working

82
Q

What type of shape does water molecule have and corresponding bond angles?

A

Tetrahedral (two lone pairs)

104º bond angles

83
Q

BDE of H-bonds

A

23 kJ/mol compared to 348 kJ/mol for C-C bond

84
Q

How many hydrogen bonds can water make with other molecules?

A

up to 4 due to the tetrahedral structure

on average, makes about 3.4

85
Q

Why does ice melt at room temperature and water evaporate?

A

reaction is spontaneous due to the increase in entropy

enthalpy is actually positive, so entropy drives this reactions

86
Q

When are hydrogen bonds the strongest?

A

when the hydrogen atom and the two atoms that share it are in a straight line

places a positive charge directly between two negative charges

87
Q

Why does salt dissolve in water, besides charges?

A

increase in entropy when salt leaves the ionic crystal lattice

88
Q

Why are nonpolar gases poorly soluble in water?

A

for one, they are nonpolar. for two, they go from a gas to a liquid which is a decrease in entropy

89
Q

clathrates

A

cystalline compunds of nonpolar solutes and water

90
Q

What type of molecules make micelles?

A

amphipathic

91
Q

van der Waals radius

A

every atom has an individual distance of how close the atom will allow another to approach it

92
Q

How do nonpolar interactions become strong?

A

their cumulative effects

for example, nonpolar interactions dictate protein folding

93
Q

Why are tightly bound water molecules important?

A

they allow for proton hopping to occur across them

they also can form part of binding sites

94
Q

colligative properties

A

vapor pressure, boiling point, melting point, and osmotic pressure

solutes effect all four properties

95
Q

How does water diffuse across the cell membrane?

A

aquaporins

96
Q

How do cells prevent lysis?

A

1) cell walls
2) pump water out
3) maintain extracellular environment that has same osmolarity as inside cell (blood plasma)
4) pump Na+ and other ions into extracellular environment

97
Q

What does the osmolarity of a solution depend on?

A

the number of solutes, not the mass of solutes

ex: macromolecules would have much less of an effect on osmolarity than their monomeric components

98
Q

Turgor pressure

A

pressure exerted against the cell wall of plants

99
Q

Do H+ protons exist in solution?

A

No! Hydrogen ions are immediately converted into hydronium molecules

100
Q

What gives the extent of ionization?

A

the equilibrium constant, Keq

101
Q

acidosis

A

the pH of blood is below the normal 7.4

often occurs in people with diabetes

102
Q

alkalosis

A

pH of blood is higher than normal

103
Q

Acids are

A

proton donors

104
Q

Bases are

A

proton acceptors

105
Q

What do titration curves reveal?

A

the pKa of weak acids

106
Q

What happens at the midpoint of titration curves?

A

one-half of the acid is neutralized, so [HA]=[A-]

the amount of acid is equal to the amount of conjugate base

this leaves only [H+], so pH=pKa

107
Q

How is consistency of pH primarily achieved?

A

through the use of biological buffers

108
Q

buffering zone

A

characteristic pH zone in which a weak acid is an effective buffer

109
Q

Phosphate buffer system

A

acts in the cytoplasm of all cells

maximally effective at 6.86, and thus has a pretty neutral buffering zone

110
Q

Bicarbonate system

A

buffers blood plasma

Carbonic acid (H2CO3) acts as proton donor

Bicarbonate (HCO3-) acts as proton acceptor

111
Q

How does the bicarbonate system work?

A

very little H2CO3 is in the blood plasma compared to bicarbonate (HCO3-), so you would think buffer would not work

BUT the large reserve of CO2(g) in the lungs and CO@(d) in the blood can be drawed upon to react with H2O and generate more H2CO3

112
Q

What happens to blood buffer system during exercise?

A

lactic ACID is made, so there are more H+ ions

these protons are picked up by HCO3-

and then converted to CO2 which you breath out

113
Q

Rate of respiration and the blood buffer system

A

rate of inhaling and exhaling can quickly adjust to keep the blood pH nearly constant

this is controlled by the brain stem which can detect differences in pCO2 or decreased blood pH

114
Q

What happens to individuals with diabetes?

A

lack of insulin decreases the uptake of glucose from the bloodstream

dependence on fatty acids raises the concentration of carboxylic acids in the blood

this lowers the pH of blood plasma (<7.35) and causes acidosis

this pH prevents enzymes from working at optimal pH and can have severe side effects

115
Q

Condensation reaction

A

two molecules come together and water is eliminated

endergonic reaction

116
Q

Hydrolysis reaction

A

water is added and molecule breaks apart

exergonic reaction

117
Q

hydrolases

A

catalyze hydrolysis reactions

118
Q

what does the high specific heat of water do for living organisms?

A

acts as a “heat buffer”

119
Q

what does the high heat of vaporization of water do for living organisms?

A

allows excess body heat to evaporate as sweat

120
Q

How does acidosis occur if there is too much CO2 gas in the lungs?

A

CO2 (gas) –> CO2(aqueous)
CO2 + H2O –> H2CO3
H2CO3 –> H+ + HCO3-

121
Q

What is reduced and what is oxidized in cellular respiration?

A

Oxygen is reduced
Glucose is oxidized

(makes sense when think of e values)

Biochem (20 decks)

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