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BIO 1111 007 > Chapter 4 Proteins and Nucleic Acids > Flashcards

Chapter 4 Proteins and Nucleic Acids Flashcards

1
Q

Out of all the macromolecules proteins have the most diverse what?

A

Range of functions

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2
Q

What is the most abundant organic molecule in living systems?

A

Proteins

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3
Q

What do all proteins have in common?

A

They are all polymers of animo acids, and they are all arranged in a linear sequence

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4
Q

What are the traits of proteins?

A

Structural, regulatory, contractile, and protective

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5
Q

Where do proteins serve?

A

Transportation, storage, and membranes

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6
Q

What are the types of proteins?

A

Enzymes or toxins

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7
Q

What are the two ways proteins vary most?

A

Structure and function

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8
Q

How many proteins can a cell in a living system contain?

A

Thousands of uniquely functioning proteins

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9
Q

What are four examples of digestive enzyme proteins?

A

Amylase, lipase, pepsin, and trypsin

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10
Q

What is the function of digestive enzyme proteins?

A

They digest food by catalyzing nutrients into monomeric units

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11
Q

What are two examples of transport proteins?

A

Hemoglobin and albumin

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12
Q

What is the function of transport proteins?

A

To carry substances in the blood or lymph nodes throughout the body

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13
Q

What are three examples of structural proteins?

A

Actin, tubulin, and keratin

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14
Q

What is the function of structural proteins?

A

To construct different structures, like cyto skeletons found inside cells

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15
Q

What are two examples of hormone proteins?

A

Insulin and thyroxine

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16
Q

What is the function of hormone proteins?

A

To coordinate the activity of different body systems

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17
Q

What is an example of a defense protein?

A

Immunoglobulin

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18
Q

What is the function of defense proteins?

A

To protect the body from foreign pathogens

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19
Q

What are two examples of contractile proteins?

A

Actin n myosin

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20
Q

What is the function of defense proteins?

A

To effect muscle contraction

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21
Q

What are two examples of storage proteins?

A

Legume storage proteins and egg white/albumin

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22
Q

What is the function of storage proteins?

A

To provide nourishment in early development of the embryo and seedling

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23
Q

Denaturation Definition/Explanation

A

A change in temperature, pH, and/or exposure to chemicals results in a permanent change in the proteins shape which causes it to lose function; a process

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24
Q

What shape is hemoglobin?

A

Globular

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25
Q

What shape is collogen?

A

Fibrous

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26
Q

How is the shape of proteins maintained?

A

Via various different chemical bonds

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27
Q

Is shape critical to protein function?

A

Yes

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28
Q

What is an amino acid?

A

A monomer that makes up proteins

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29
Q

What is the fundamental structure of all animo acids?

A

A central carbon with an attached amino group (NH2), carboxyl group (COOH), and a variable R group/sidechain

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30
Q

What is another term for side chain?

A

R group

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31
Q

Where is the name animo acid derived from?

A

The amino group and acidic carboxyl group

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32
Q

How many animo acids are essential to humans?

A

10

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33
Q

What makes an amino acid essential?

A

The body’s inability to synthesize the amino acid on its own

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34
Q

What part of an amino acid is different from other animo acids?

A

The R group/side chain

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35
Q

What are the chemical natures of amino acids?

A

Acidic (positively charged), basic (negatively charged), polar, and non-polar

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36
Q

What determines the amino acids’ nature?

A

The nature of its R group/side chain

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37
Q

What are the 9 nonpolar amino acids?

A

Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline

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38
Q

What are the 6 polar amino acids?

A

Serine, threonine, cysteine, tyrosine, asparagine, glutamine

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39
Q

What are the 2 acidic/positively charged amino acids?

A

Aspartic acid and glutamic acid

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40
Q

What are the 3 basic/negatively charged amino acids?

A

Lysine, arginine, histidine

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41
Q

What is often used as an interchangeable term for protein?

A

polypeptide

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42
Q

What is a polypeptide?

A

A polymer of amino acids where the monomers are linked in linear chains

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43
Q

What is a protein

A

Polypeptide(s) that have a distinct shape and unique function

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44
Q

What determines a protein’s shape, size, and function?

A

The sequence and number of amino acids

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45
Q

What must happen before a protein can function completely?

A

It must have gone through protein synthesis and modification

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46
Q

What are the parts of a polypeptide?

A

A N terminal with an amino group and a C terminal with a carboxyl group

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47
Q

What type of bonds do amino acids use?

A

Covalent bonds called peptide bonds

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48
Q

What parts of the amino acids bond?

A

The carboxyl group of one to ethe amino group of another

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49
Q

Where are additional amino acids added?

A

To the C terminus (the last carbon)

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50
Q

What is a carbon-nitrogen backbone?

A

A peptide backbone that is identical for all proteins

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51
Q

What are the four levels of protein structure?

A

Primary, secondary, tertiary, and quandary

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52
Q

What is primary structure?

A

A linear sequence of amino acids in a protein

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53
Q

What is a disulfide-bond (S – S bond)

A

The only covalent bond formed during protein folding in tertiary structures

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54
Q

What determines the primary sequence?

A

The gene encoding the protein

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55
Q

What happens if there is a change in a protein encoding gene?

A

A different amino acid may result and be added on to a peptide chain possibly resulting in ailment

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56
Q

What is secondary structure?

A

A regular structure formed by proteins by hydrogen bonding between the amino acids

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57
Q

What are the most common secondary structures?

A

a-helix and b-pleated sheet

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58
Q

What do the a-helix and b-pleated sheet have in common?

A

Both are formed by hydrogen bonds between oxygen atoms in the carbonyl group and the oxygen in the amino group four acids further in the chain

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59
Q

What is tertiary structure?

A

The three-dimensional conformation of a protein formed from interactions between amino acid side chains

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60
Q

The tertiary structure is mostly made of interaction between what part of an amino acid?

A

R-group

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61
Q

What is the interaction between to like charged R groups

A

Repulsion

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62
Q

What is the interaction between two oppositely charged R groups?

A

Attraction in the form of an ionic bond

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63
Q

What happens when protein folding happens in a watery environment?

A

Hydrophobic R groups of nonpolar amino acids lay on the interior of the protein while the hydrophilic R’s of the poplar amino acids face out

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64
Q

What type of R groups interact using van der Waals forces?

A

Hydrophobic R groups

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65
Q

What R-groups interact in disulfide bonds?

A

Cysteine R-groups

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66
Q

What happens what a protein losses its shape

A

cease function

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67
Q

What is quandary structure?

A

An association of discrete polypeptide subunits in a protein

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68
Q

What stabilizes the structure of quandary structures?

A

Weak interaction between subunits

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69
Q

Catalyst

A

A substance that helps a chemical reaction take place

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70
Q

Enzyme

A

A protein that catalyzes biochemical reactions

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71
Q

What is an enzymes task?

A

To lower the amount of energy needed to perform a certain chemical reaction

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72
Q

How do enzymes complete their task?

A

They bind to substrates and hold them in a way to speed up creation or breakage of a bond

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73
Q

Is an enzyme an organic catalyst? And what does this mean?

A

Yes, it means all enzymes increase the rate of reaction

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74
Q

Substrate

A

The chemical reactants that bind to enzymes

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75
Q

Active site

A

The special place on an enzyme where the substrate binds to

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76
Q

What is at an enzyme’s active site?

A

A unique combo of amino acids that create an environment specific to certain substrates and their chemical reactions

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77
Q

What are enzyme’s known for?

A

Specificity

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78
Q

What happens to an enzyme when it faces extreme temperatures?

A

It may become less suited for binding substrates, and at high temperature it may denature

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79
Q

What happens when enzymes face extreme pH values?

A

It may denature

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80
Q

The ranges of what affect enzymes?

A

Temperature and pH

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81
Q

Induced Fit Definition

A

A dynamic fit between an enzyme and its substrate

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82
Q

What happens in induced fit?

A

Substrates interact with an enzyme causing a mild shift in the enzyme which confirms the ideal binding arrangement maximizing ability to catalyze the reaction

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83
Q

What always happens after a reaction occurs in an enzyme?

A

It returns to its original state

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84
Q

What is an enzyme’s hallmark property relating to the completion of a chemical reaction?

A

Remains unchanged by the catalyzed reaction

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85
Q

What are products released from an enzyme?

A

After, the chemical reaction is completed

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86
Q

Free Energy

A

The usable energy, or energy that is available to do work

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87
Q

What is another term for free energy?

A

Gibbs free energy (G)

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88
Q

What does Gibbs free energy refer to specifically?

A

The energy associated with a chemical reaction after entropy is accounted for

89
Q

What is delta G?

A

The change in free energy

90
Q

What is the equation that calculates delta G?

A

ΔG = ΔH − T ΔS

91
Q

How is delta G denoted in an equation?

A

ΔG 

92
Q

What does ΔH symbolize in the delta G formula?

A

The total energy change of the system

93
Q

What does ΔS symbolize in the delta G formula?

A

The amount of energy lost to entropy

94
Q

What does T symbolize in the delta G formula?

A

Absolute temperature in Kelvin

95
Q

In what units is the standard free energy change expressed when under standard pH, temperature, and pressure change?

A

Kilojoules per mole (kJ/mol) or kilocalories per mole (kcal/mole)

96
Q

What are considered the standard conditions for free energy change?

A

A pH of 7 at 25 degrees Celsius under 1 atm of pressure

97
Q

What is a reaction where the reactants have more free energy than the products?

A

Exergonic reaction

98
Q

What is the reaction when the delta G equation is negative?

A

Exergonic

99
Q

Enthalpy

A

The total energy of a system

100
Q

What is a reaction where the product has more free energy than the reactants?

A

Endergonic Reaction

101
Q

What is the reaction when the delta G equation is positive?

A

Endergonic

102
Q

What reaction is referred to as a spontaneous reaction? And why?

A

Exergonic, because they occur without additional energy

103
Q

What are two terms for a reaction that requires additional energy to occur?

A

Endergonic and non-spontaneous

104
Q

Out of exergonic and endergonic reactions which releases energy, and which requires energy?

A

Exergonic releases energy and endogenic requires energy

105
Q

Does a reaction be spontaneous mean that the reaction occurs immediately or Fastly?

A

No

106
Q

What is activation energy (E(subscript)A)?

A

The energy necessary for a chemical reaction to occur

107
Q

How much activation energy is needed in exergonic reactions?

A

Very little

108
Q

Do enzymes affect the output of free energy?

A

No

109
Q

Why do exergonic reactions still need energy to occur?

A

Due to the breakage and formation of bonds

110
Q

What state must a molecule be in to break a bond?

A

transition state

111
Q

Transition state

A

The high energy, unstable state of a molecule

112
Q

What determines whether the products exit with higher or lower energy than the reactions?

A

Whether they are exergonic or endergonic

113
Q

The transition state always exists what in comparison to reactants?

A

At a higher energy state

114
Q

What is typically the source of activation energy?

A

Heat energy from the surroundings

115
Q

What does heat energy do?

A

It speeds up the motion of molecules increasing collisions and moves atoms and bonds helping a molecule reach the transition state

116
Q

The rate at which a chemical reaction will occur is determined by its what?

A

Activation energy requirements

117
Q

Which reaction is slower, a high activation energy reaction or a low activation energy reaction?

A

The high activation energy reaction

118
Q

Most of the chemical reactions found in cells require too much of what to make them efficient?

A

Activation Energy

119
Q

Why can’t enzymes be in a 100% ideal scenario?

A

Cellular needs vary from cell to cell and may change in individual cells over time

120
Q

What happens during competitive inhibition?

A

An inhibitor molecule attaches to the activation site to prevent substrate-enzyme bonding

121
Q

What happens in allosteric inhibition?

A

An inhibitor molecule attaches to an area that is not the activation site of an enzyme, and alters the shape of the activation site preventing substrate-enzyme bonding

122
Q

What is the site where something attaches to an enzyme that isn’t the activation site?

A

Allosteric site

123
Q

What is an allosteric activator?

A

An activator that binds to an allosteric site and increases the compatibility of an enzyme and its substrate(s)

124
Q

Do many enzymes work optimally on their own?

A

No

125
Q

What is needed to make many enzymes work and work optimally?

A

A specific non-protein helper molecule

126
Q

What are two types of helper molecules?

A

Cofactors and coenzymes

127
Q

What are cofactors?

A

Inorganic ions that bind to enzymes to promote optimal conformation and function

128
Q

What are the most common sources of coenzymes?

A

Dietary vitamins

129
Q

Which dietary enzymes are coenzymes or precursors of coenzymes?

A

Vitamin A, Folic Acid, Vitamin B1, Vitamin B2, Vitamin B6 (pyridoxine), Vitamin C, Vitamin D2 (calciferol), and Vitamin E (alpha – tocopherol)

130
Q

Is enzyme function partially regulated by coenzymes and cofactors?

A

Yes

131
Q

How do eukaryote cells typically organize molecules like enzymes?

A

Into different organelles

132
Q

How can eukaryotic cells better regulate enzymes for more efficient reactions?

A

Housing the enzymes for certain cellular processes and their substrates separately

133
Q

How many chemicals reactions can occur in a single cell at any given time?

A

Thousands

134
Q

How do cells simplify the regulation of reactions?

A

The organize reactions into pathways

135
Q

What is a metabolic pathway?

A

A series of interconnected biochemical reactions that convert a substrate molecule(s) through a series of metabolic intermediates to produce a product

136
Q

A metabolic pathway can be equated to what metaphorically?

A

An assembly line

137
Q

What are anabolic pathways?

A

Pathways that make larger products from smaller substrates

138
Q

What are catabolic pathways?

A

Pathways that make smaller products from larger substrates

139
Q

Of anabolic pathways and catabolic pathways, which requires energy and which produces energy?

A

Anabolic pathways use energy and catabolic pathways produce energy

140
Q

What is feedback inhibition?

A

A form of reaction regulation; it occurs when the product of a pathway inhibits the activity of the first enzyme in the pathway

141
Q

What allows a cell to maintain homeostasis of a product?

A

Feedback inhibition

142
Q

What does feedback inhibition mean what there are high levels of product and low levels of products?

A

High levels of products means that a pathway reduces product production and low levels of products means that a pathway increases product production

143
Q

Nucleic Acid

A

A biological macromolecule that carries the genetic blueprint of a cell

144
Q

What is the most important macromolecule for the continuation of life?

A

Nucleic Acids

145
Q

What are the two main types of nucleic acids?

A

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

146
Q

DNA

A

The nucleic acid that contains the hereditary information of a being and carries the codes to make protein

147
Q

RNA

A

A nucleic acid involved with protein synthesis

148
Q

Nucleic acid

A

The linear chains of monomers that make up nucleic acids

149
Q

What are the components of a nucleotide?

A

A pentose sugar, nitrogenous base (contains nitrogen), and one or more phosphate group(s)

150
Q

What are the carbons of a nucleotide’s pentose sugar called?

A

One prime, two prime, etc. or 1’, 2’, etc

151
Q

The nucleotide’s nitrogenous base is attached to which carbon in its pentose sugar?

A

One prime or 1’

152
Q

The nucleotide’s phosphate group(s) are attached to which carbon(s) in its pentose sugar?

A

Five prime or 5’

153
Q

What is always attached to the 3rd carbon in a nucleotide’s pentose sugar?

A

hydroxyl group

154
Q

What are the two pentose sugars of nucleic acids?

A

Deoxyribose and ribose

155
Q

How are deoxyribose and ribose different?

A

Deoxyribose is found in DNA and lacks a hydroxyl group in its 3’ carbon (means it has a hydrogen there instead); ribose is found in RNA and has a hydroxyl group in its 3’ carbon

156
Q

What are the nitrogenous bases of nucleotides?

A

Organic molecules containing nitrogen

157
Q

Why are the nitrogenous bases of nucleotides bases?

A

Because they have an amino group that can bind to an extra hydrogen

158
Q

What are the 4 possible nitrogenous bases of DNA?

A

Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)

159
Q

What are the 4 possible nitrogenous bases of RNA?

A

Adenine (A), Guanine (G), Cytosine (C), and Uracil (U)

160
Q

What are the 3 shared nitrogenous bases between DNA and RNA?

A

Adenine (A), Guanine (G), and Cytosine (C)

161
Q

How are nitrogenous bases classified?

A

As either purines or pyrimidines

162
Q

What makes a nitrogenous base a purine?

A

Having two carbon-nitrogen rings

163
Q

What makes a nitrogenous base a pyrimidine?

A

Having a single carbon-nitrogen ring

164
Q

What nitrogenous bases are purines?

A

Cytosine, Thymine, and Uracil

165
Q

What nitrogenous bases are pyrimidines?

A

Adenine and Guanine

166
Q

What are phosphodiester linkages/bonds?

A

Covalent bonds between nucleotides

167
Q

What are phosphodiester linkages/bonds?

A

Covalent bonds between nucleotides

168
Q

What is the nucleic acid directionality?

A

The first nucleotide has a free (unbonded) phosphate at 5’ and the last nucleotide has a free hydroxyl group at 3’

169
Q

What is the structure of DNA?

A

Double helix

170
Q

What is a double helix structure?

A

A structure with two linear strands of nucleotides held together with hydrogen bonds between complementary nitrogenous bases

171
Q

What does complementary nitrogenous bases mean?

A

Each nitrogenous base only connects to one other bases

172
Q

What happens in DNA replication?

A

Each strand of the DNA is copied resulting in two daughter DNA double helixes each with one copied strand from the parent and one synthesized strand

173
Q

What form the outside of a DNA helix?

A

Sugar n phosphate(s)

174
Q

What form the inside of the DNA helix and how are they arranged?

A

The nitrogenous bases form DNA interiors and are stacked like ladder rings

175
Q

Are the two DNA strands antiparallel?

A

Yes

176
Q

How is antiparallel shown in DNA?

A

If lined up the free phosphate would be parallel to the other strands free hydroxyl

177
Q

Where is DNA in eukaryotes?

A

In their nucleus, chloroplasts, and mitochondria

178
Q

Is DNA enclosed in a prokaryote’s nucleus?

A

No

179
Q

In what order is DNA coded?

A

Order of the nucleotide in the chain

180
Q

What is a gene?

A

A segment of DNA that code for one polypeptide chain

181
Q

Do all genes code for polypeptides?

A

No

182
Q

What besides a polypeptide may a gene code for?

A

RNA products

183
Q

In cell DNA is found as?

A

Long chains of nucleotides that wrap around proteins, predominantly histones, which form chromosomes

184
Q

How many genes may a chromosome hold?

A

Tens of thousands

185
Q

What is the entire genetic content of a cell?

A

The cells Genome

186
Q

What is the structure of RNA?

A

Single stranded and 3-d

187
Q

What nitrogenous base connects to guanine?

A

Cytosine

188
Q

Which nitrogenous bases connect to adenine?

A

Uracil in RNA and Thymine in DNA

189
Q

What is the structure of RNA?

A

Three dimensional single strands

190
Q

What are the four major types of RNA?

A

Messenger RNA mRNA, ribosomal RNA rRNA, transfer RNA tRNA, and microRNA miRNA

191
Q

What does mRNA do?

A

Carries the copy of genetic code from DNA

192
Q

How is RNA read?

A

Three sets of bases known as codons

193
Q

What does a codon do?

A

Codes for a single amino acid in a protein

194
Q

What is the information flow?

A

DNA – mRNA – Protein

195
Q

What is transcription?

A

A process through which messenger RNA forms on a template of DNA

196
Q

What does DNA dictate during transcription?

A

mRNA sequence

197
Q

What is translation?

A

A process through which RNA directs the formation of protein

198
Q

What does RNA dictate in translation?

A

The structure of a protein

199
Q

What is the Central Dogma of Molecular Biology?

A

DNA contains instructions for making a protein

200
Q

mRNA

A

Messenger RNA

201
Q

tRNA

A

Transfer RNA

202
Q

rRNA

A

Ribosomal RNA

203
Q

mrRNA

A

MicroRNA

204
Q

What is the function of rRNA?

A

What is the function of rRNA?

A major constituent of ribosomes that a mRNA bind to to make a protein

205
Q

What is the function of tRNA?

A

Carries amino acids to the site of protein synthesis

206
Q

What is the function of miRNA?

A

Deals in regulation of gene expression

207
Q

What is adenosine triphosphate

A

ATP, which is the cells energy currency

208
Q

What is ATP made of?

A

An adenine and three phosphates

209
Q

How does ATP work?

A

The phosphates are negatively charged and trying to repel each other, when they do bond it is a weak unstable high-energy bond particularly between the last two phosphates which means that they release a lot of energy when that bond is broken

210
Q

What are the products of ATP hydrolysis (bond break)?

A

Adenosine diphosphate (ADP) and an inorganic phosphate group (pi)

211
Q

How much ATP does the body make a day?

A

Equivalent to the body weight

212
Q

How long do you have to use ATP?

A

little time

213
Q

How is energy released during ATP hydrolysis?

A

lost as heat

214
Q

What is energy coupling?

A

A process cells use to harness the energy release in ATP hydrolysis

215
Q

What type of reaction is ATP hydrolysis?

A

Exergonic

216
Q
A
217
Q
A
218
Q
A

BIO 1111 007 (4 decks)

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