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BME 501 > Section 1 - Cells and Genomes > Flashcards

Section 1 - Cells and Genomes Flashcards

1
Q

How much diversity is there with species on Earth?

A

Lots. Between 10-100 million species have been identified

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2
Q

How are the characteristics of offspring determined?

A

Parent organism provides genetic material to (partially) determine characteristics

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3
Q

What hereditary information does the cell contain?

A

Generate machinery to gather raw materials for life, and form new cells (to survive!)

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4
Q

True or false: single cells are very similar

A

True: cells have many similarities

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5
Q

True or false: matured organisms are very similar

A

False: matured organisms are very different

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6
Q

True or false: different matured organisms come from different single cells

A

False: even though the matured organisms are different, the single cells are fairly similar

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7
Q

How do living cells store hereditary information?

A

DNA

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8
Q

What is DNA comprised of?

A

A, T, C, and G

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9
Q

What makes DNA different than engineered data storage methods?

A

DNA can be read and used by any cell type

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10
Q

How is DNA replicated?

A

From a template strand (semi-conservative)

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11
Q

What is the central dogma?

A

DNA -> RNA -> Protein

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12
Q

What is the most fundamental information in BME 501?

A

The central dogma

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13
Q

What does the central dogma describe?

A

How information flows in molecular biology

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14
Q

What is the process to turn DNA -> DNA?

A

DNA synthesis / replication

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15
Q

What does DNA synthesis do?

A

DNA -> DNA

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16
Q

What is the process to turn DNA -> RNA?

A

Transcription

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17
Q

What does transcription do?

A

DNA -> RNA

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18
Q

What is the process to turn RNA -> protein?

A

Translation

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19
Q

What does translation do?

A

RNA -> protein

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20
Q

Is DNA disposable or reusable?

A

Reusable (stable molecule)

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21
Q

Is RNA disposable or reusable?

A

Disposable (rapidly created and degraded)

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22
Q

Are proteins disposable or resuable?

A

Somewhat disposable (depends on the protein)

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23
Q

What is the intermediate of the central dogma?

A

RNA

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24
Q

What is a codon?

A

A group of 3 nucleotides

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25
Q

How controlled is gene expression?

A

Tightly controlled (feedback, protection, etc.)

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26
Q

Why is gene expression so tightly controlled?

A

Don’t want to waste energy making proteins randomly

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27
Q

How much free energy is needed for DNA replication?

A

A large amount

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28
Q

Why is a lot of energy needed for DNA replication?

A

DNA is a very stable molecule (high energy)

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29
Q

What are on/off processes?

A

Protein machinery binding / dissociating for useful work

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30
Q

Do on/off processes require energy?

A

Yes, binding and work of proteins requires energy

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31
Q

True or false: All cells use the same basic building blocks

A

True: all cells use nucleotides, amino acids, simple sugars, and ATP

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32
Q

True or false: Since all cells use the same basic building blocks, they all have the same function

A

False: just because all cells have the same tools does not mean that they have the same function

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33
Q

What structure are all cells enclosed in?

A

Plasma membrane

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34
Q

What are the two basic functions of the cell membrane?

A
  1. Differentiate between inside and outside

2. Be selective with materials that enter or exit the cell

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35
Q

Chemically, what are the vast majority of cellular molecules based on?

A

Carbon compounds

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36
Q

What environment do cellular reactions take place in?

A

Aqueous environments

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37
Q

What are some advantages of doing reactions in aqueous environments?

A

Use water binding in some cell processes

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38
Q

What are some disadvantages of doing reactions in aqueous environments?

A

Water can bind to polar molecules, expend energy to move water out of the way

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39
Q

What are atoms composed of?

A

Neutrons, protons, and electrons

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40
Q

What is the atomic weight?

A

Sum of the protons and neutrons (weight of the atom)

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41
Q

What electrons determine binding?

A

Valence (outermost electrons)

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42
Q

What is the size of an atom dependent on ?

A

Orbital paths of the electrons

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43
Q

What are the 4 most common elements in living organisms?

A

Carbon, nitrogen, hydrogen, and oxygen (HONC)

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44
Q

True or false: The most common elements in living organisms is the same as the most common elements in Earth’s crust

A

False: the two have largely different makeups

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45
Q

True or false: The environment organisms live in is different than their biological environment

A

True: the compositions are different

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46
Q

True or false: The only elements living organisms need is hydrogen, oxygen, nitrogen, and carbon

A

False: trace elements (such as Zinc) are also needed

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47
Q

If an element is reactive, what can you say about its electron shell?

A

It is unfilled

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48
Q

If an element is nonreactive, what can you say about its electron shell?

A

It is filled

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49
Q

What is an ionic bond?

A

Exchange of electrons to create of bond

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50
Q

What is a covalent bond?

A

Sharing of electrons to create a bond

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51
Q

When is a covalent bond in equilibrium?

A

When the repulsive and attractive forces are equal

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52
Q

What happens to the bond when it is in equilibrium?

A

There is a particular bond strength, length, and angle

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53
Q

What is the importance of bond strength?

A

Tells you how much energy is needed to break it

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54
Q

True or false: you can tell the bond strength by the elements in a covalent bond

A

True: covalent bonds have a particular bond strength in equilibrium

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55
Q

True or false: you can tell the bond strength by the elements in an ionic bond

A

False: ionic bonds do not follow a particular bond strength

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56
Q

What is a polar covalent bond?

A

Unequal sharing of electrons, leading to dipoles

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57
Q

Which side of water is electronegative?

A

Oxygen

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58
Q

Which side of water is electropostivie?

A

Hydrogen

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59
Q

What are single bonds?

A

Sharing of two electrons

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60
Q

How much movement is possible with single bonds?

A

Complete rotation around the bond

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61
Q

What are double bonds?

A

Sharing of four electrons

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62
Q

How much movement is possible with double bonds?

A

No rotation around the bond

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63
Q

What is a hydrogen bond?

A

An attraction between hydrogens on polar atoms / molecules

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64
Q

What can be said about the direction and strength of hydrogen bonds?

A

The bond is fairly weak (weaker than covalent bonds) and directional

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65
Q

What are Van der Waals forces?

A

Transient forces between changes in electron density

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66
Q

What are hydrophobic forces?

A

Interactions between nonpolar molecules to move away from environments with lots of hydrogen bonding

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67
Q

How do energetics dictate binding?

A

Specific binding has specific energies that are optimized for specific substrates

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68
Q

What is the primary function of sugars?

A

Energy source for cells

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69
Q

What form (chemically) do monosaccharides follow?

A

(CH2O)n

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70
Q

True or false: Since the formula for monosaccharides is simple, there are relatively few sugars

A

False: different arrangements and handiness increase the amount of sugars

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71
Q

How are polysaccharides formed?

A

Through condensation reactions

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72
Q

In cell biology, what are the primary form of sugars?

A

Monosaccharides (with some disaccharides)

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73
Q

What are the functions of fatty acids?

A

Secondary energy storage, and the cell membrane

74
Q

What is the structure of a fatty acid?

A

Long hydrocarbon tail, and carboxyl group

75
Q

What are the properties of a long hydrocarbon tail?

A

Hydrophobic and not very reactive

76
Q

What are the properties of a carboxyl group?

A

Hydrophilic and reactive

77
Q

What are some properties and characteristics of saturated fatty acids?

A

Only single bonds, increases packing density and strength, straight chained, usually solid

78
Q

What are some properties and characteristics of unsaturated fatty acids?

A

Double or triple bonds, decreased packing density and strength, kinked chained, usually liquid

79
Q

What is a chemical model of a molecule?

A

Writing out the chemical formula

80
Q

What is the advantage of a chemical model?

A

Can clearly see what atoms make up the molecule

81
Q

What is a wire model of a molecule?

A

Showing the bonds between atoms

82
Q

What is the advantage of a wire model?

A

Can clearly see how the bonding occurs between the elements

83
Q

What is a space filling model of a molecule?

A

Showing the space that an atom takes up in a molecule

84
Q

What is the advantage of a space filling molecule?

A

Can see where the molecule can get attacked (based on structure) (reactivity)

85
Q

How are fatty acids normally stored in cells?

A

In triacylglycerols

86
Q

What is a triacylglycerol?

A

3 fatty acids chains connected to a glycerol molecule

87
Q

What is the structure of a phospholipid?

A

Two fatty acid tails and one polar head group, connected by glycerol

88
Q

What is the primary function of phospholipids?

A

Cell membrane

89
Q

What does it mean to be amphipathic?

A

A molecule that has both hydrophilic and hydrophobic parts

90
Q

What is an example of an amphipathic molecule?

A

A phospholipid (hydrophilic head, hydrophobic tails)

91
Q

How many amino acids are in living cells?

A

20

92
Q

What is the function of amino acids?

A

Building blocks of proteins

93
Q

What is the same among all amino acids?

A

An amino group and a carboxylic acid group connected by a central carbon

94
Q

What is different among all amino acids?

A

The R group (side chain)

95
Q

What type (handiness) of amino acids are used in proteins?

A

L amino acids

96
Q

What is a peptide bond?

A

Bond between amino acids in a protein

97
Q

What bond binds amino acids in a protein?

A

Peptide bond

98
Q

When are D amino acids seen in the body?

A

To monitor the age of a protein (older proteins degrade, and have more D amino acids)

99
Q

What is the structure of a nucleotide?

A

Nitrogen containing ring linked to a 5 carbon sugar, and one or more phosphate groups

100
Q

How do nitrogen bases interact with protons?

A

Nitrogen bases act as proton absorbers

101
Q

What is the structure of a pyrimidine?

A

One 6-membered ring

102
Q

Which of the bases are pyrimidines?

A

C, T, U

103
Q

What is the structure of a purine?

A

One 6-membered ring fused to one 5-membered ring

104
Q

Which of the bases are purines?

A

A, G

105
Q

What is a mneumonic to memorize pyrimidines?

A

Pyramids CUT the sky (C, T, U)

106
Q

What is a mnemonic to memorize purines?

A

Pure As Gold (A, G)

107
Q

What are the functions of nucleotides?

A

Energy (ATP) and information storage (DNA)

108
Q

What is metabolism controlled by?

A

Enzymes

109
Q

How come reactions cannot occur in the body without enzymes (think temperature)?

A

Most reactions can only occur at temperatures higher than 37 C

110
Q

Where does the extra external energy come from to power reactions?

A

Enzymes

111
Q

What do enzymes control?

A

Function and energetics of cells (rate of reactions)

112
Q

What are catabolic pathways?

A

Pathways that break down molecules, and produce energy

113
Q

What are anabolic pathways?

A

Pathways that build up molecules, and use energy

114
Q

What is meant by “engineering control theory” for cell biology?

A

Important to consider the level of control that these reactions in the cell have

115
Q

What three things do catabolic pathways create?

A

Useful forms of energy (to use in anabolic reactions), building blocks for biosynthesis, and lost heat

116
Q

What is the second law of thermodynamics?

A

The entropy (disorder) of a system must increase with time

117
Q

How does the disorder of a cell change over time?

A

Decreases disorder

118
Q

How does the disorder of the extracellular environment change over time?

A

Increases disorder

119
Q

Why does the extracellular environment change over time?

A

Heat released by the cell increases the disorder

120
Q

How does the 2nd law of thermodynamics relate to the cell system?

A

The sum of the cell losing entropy, and the extracellular environment gaining entropy, tends towards increasing disorder (and thus doesn’t break the 2LoT).

121
Q

How is energy extracted from food molecules

A

Gradual oxidation (controlled burning)

122
Q

What is the most chemically stable form of carbon in the cell?

A

CO2

123
Q

What is the most chemically stable form of hydrogen in the cell?

A

H2O

124
Q

True or false: All processes have an innate barrier based on the energy needed to break or form bonds

A

True: this activation energy is present for all reactions

125
Q

What element is useful for controlled burning?

A

Oxygen

126
Q

How do enzymes catalyze reactions?

A

By lowering the activation energy needed

127
Q

True or false: enzymes change the activation energy of a reaction

A

True: this is how enzymes catalyze reactions

128
Q

True or false: enzymes change the energy of products / reactants in a reaction

A

False: this is not changed. Only the activation energy is changed

129
Q

How do enzymes determine the end product of a reaction?

A

Through quantity and type of enzyme

130
Q

How does the quantity of enzyme determine the end product?

A

Dictates speed

131
Q

How does the type of enzyme determine the end product?

A

Dictates branching pathway to follow

132
Q

How does the type of enzyme relate to control?

A

Enzyme can control which reaction is happening to get a certain output

133
Q

How can reactions can a typical enzyme catalyze in one second?

A

A thousand

134
Q

What must the enzyme do to repeatedly catalyze reactions?

A

Bind and release substrates, and find new ones quickly

135
Q

What process dictates the probability of molecules interaction with each other?

A

Diffusion

136
Q

What parameters does diffusion depend on?

A

Temperature, media, etc.

137
Q

What is the requirement to spontaneously undergo a chemical reaction?

A

The free energy change (delta G) must be negative

138
Q

True or false: An enzyme changes the equilibrium point of the reaction

A

False: it only affects the speed of the reaction

139
Q

What is meant by coupling reactions?

A

An favorable reaction can be coupled to a unfavorable one to help complete it

140
Q

What are activated carriers?

A

Molecules that store energy in an easily exchangeable form

141
Q

What are some examples of activated carriers?

A

ATP, NAD+, NADP+

142
Q

What is the purpose of activated carriers?

A

Store energy to be used for other reactions

143
Q

How is energy from food derived?

A

Breakdown of chemical bonds in food molecules

144
Q

How are sugars broken down?

A

Sugars are oxidized into CO2 and H2O

145
Q

What happens if the oxidation of glucose is done in one step?

A

Huge energy loss than cannot be harvested

146
Q

What is the disadvantage of oxidizing glucose in one step?

A

There is a lot of energy lost as heat

147
Q

What happens if the oxidation of glucose is done in a series of steps?

A

Each step can be coupled to create activated carriers

148
Q

What is the advantage of oxidizing glucose in a series of steps?

A

Can harness more energy as activated carriers

149
Q

What is the process of breaking down glucose in a series of steps called?

A

Controlled oxidation

150
Q

What is the first stage of food breakdown?

A

Digestion

151
Q

What is digestion?

A

Enzymatic breakdown of large food molecules into monomers

152
Q

In digestion, what are proteins broken down into?

A

Amino acids

153
Q

In digestion, what are lipids broken down into?

A

Fatty acids and/or glycerol

154
Q

In digestion, what are polysaccharides broken down into?

A

Simple sugars

155
Q

What is the second stage of food breakdown?

A

Glycolysis

156
Q

What occurs during glycolysis?

A

Glucose is broken down into pyruvate

157
Q

How is pyruvate used by the mitochondria?

A

Converted into CO2 by the Citric Acid Cycle for more activated carriers

158
Q

What type of molecule is acetyl CoA?

A

Activated carrier

159
Q

Where does digestion occur?

A

Stomach and intestines

160
Q

Where does glycolysis occur?

A

Cytosol of the cells

161
Q

How is acetyl CoA formed?

A

Attaching coenzyme A to an acetyl group

162
Q

What is the purpose of phosphates in glycolysis?

A

Charge the molecules, and then use them to create activated carriers

163
Q

In the absence of oxygen, what occurs after glycolysis?

A

Fermentation

164
Q

What are some possible products of fermentation?

A

Lactate and ethanol / CO2

165
Q

What is the third stage of food breakdown?

A

Oxidative phosphorylation

166
Q

Where does oxidative phosphorylation occur?

A

Mitochondria

167
Q

What happens during oxidative phosphorylation?

A

NADH is used to power the electron transport chain (ETC) to generate ATP and consume O2

168
Q

What are the waste products of oxidative phosphorylation?

A

H2O, CO2, and NH3

169
Q

True or false: oxidative phosphorylation requires excess oxygen

A

True: oxygen is needed as the final electron donor

170
Q

What is pyruvate dehydrogenase, and what is its function?

A

Enzyme complex to convert pyruvate into CO2, NADH, and acetyl CoA

171
Q

In stage 3 of food breakdown, what are fatty acids converted into?

A

acetyl CoA, NADH, and FADH2

172
Q

Why is it advantageous to have pyruvate dehydrogenase as an enzyme complex (as opposed to separated)?

A

Can efficiently couple reactions in series, since the product of one reaction can be used as a reactant of the next. Thus, substrates don’t have to diffuse to find the second enzyme

173
Q

What is the general trend of the citric acid cycle (think carbons)?

A

Add 2 carbon molecule to a 4 carbon molecule to make a 6 carbon molecule, which is oxidized (by losing carbons) to produce energy

174
Q

What are the functions of the byproducts of glycolysis and the citric acid cycle?

A

Biological building blocks for other biomolecules

175
Q

How do other foods feed into glycolysis / citrus acid cycle?

A

They all converge at different points in the food breakdown cycle

176
Q

How many ATP molecules are found in a given cell?

A

10^9 (1 billion) molecules

177
Q

How frequently is ATP consumed and replenished in a given cell?

A

Every few minutes

178
Q

What is the rate of ATP consumption?

A

10^9 ATP / every few minutes

179
Q

How is GTP similar to ATP?

A

Similar amount of energy released

180
Q

How is GTP different from ATP?

A

Different structure (may not be used in reactions), ATP is more common in the body

BME 501 (5 decks)

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