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BIO 93 midterm pt 2 > BIO 93 Midterm pt 2 > Flashcards

BIO 93 Midterm pt 2 Flashcards

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1
Q

The bonding of molecules requires:

A

the release of a water molecule

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2
Q

What is a dehydration reaction?

A

water molecule is released when bonding molecules

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3
Q

What is a hydrolysis reaction?

A

adding water to a large molecule to break it into smaller molecules

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4
Q

What are the two groups ALWAYS present in an animo acid?

A

amino group and carboxyl group

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5
Q

What is a polymer?

A

a long molecule built from similar subunits (monomers) linked by covalent bonds

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6
Q

What are monomers?

A

subunits to polymers

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7
Q

Which of the following are polymers?

Carbohydrates, proteins, nucleic acids, lipids

A

carbohydrates, proteins, nucleic acids

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8
Q

What are amino acids?

A

monomers, combine to form polymers

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9
Q

What is a polypeptide?

A

polymer of AAs in a specific sequence

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10
Q

What is a protein?

A

one or more polypeptides with specific 3-D conformation

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11
Q

Form follows ______

A

function

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12
Q

Function of enzymatic proteins?

A

selective acceleration of chemical reactions (i.e. digestive enzymes catalyze the hydrolysis of bonds in food molecules)

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13
Q

Function of defensive proteins?

A

protection against disease (i.e. antibodies inactivate and help destroy viruses and bacteria)

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14
Q

Function of storage proteins?

A

storage of amino acids (i.e. casein (milk), seeds, ovalbumin (egg white))

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15
Q

Function of transport proteins?

A

transport of substances

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16
Q

Function of hormonal proteins?

A

coordination of an organism’s activities (i.e. insulin)

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17
Q

Function of receptor proteins?

A

response of cell to chemical stimuli (i.e. receptors built into the membrane to detect specific signal molecules)

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18
Q

Function of contractile and motor proteins?

A

movement (i.e. cilia, flagella)

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19
Q

Function of structural proteins?

A

support (i.e. keratin (hair), collagen (skin/tissue))

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20
Q

Proteins are all constructed from the same set of _______ amino acids.

A

20

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21
Q

What is a R group?

A

variable side chain

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22
Q

Effect of nonpolar R group?

A

hydrophobic (9/20 groups)

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23
Q

Effect of polar R group?

A

hydrophilic (6/20)

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24
Q

Effect on ionized R group? (charged at cellular pH)

A

acids and bases ; hydrophilic

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25
Q

What is the name of the carbon in the middle of an amino acid?

A

α (alpha) carbon

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26
Q

When is a carboxyl group considered an acid?

A

when the H+ isn’t present

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27
Q

Nonpolar molecules are ______

A

hydrophobic

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28
Q

Polar molecules are _______

A

hydrophilic

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29
Q

What is required for a dehydration reaction to occur?

A

an enzyme

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30
Q

What is the amino end of a polypeptide?

A

N terminus ; area with the amino group

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31
Q

What is the carboxyl end of a polypeptide?

A

C terminus ; area with the carboxyl group

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32
Q

What type of bond is a peptide bond?

A

covalent bond

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33
Q

What are the 3/4 protein structures?

A

primary, secondary, tertiary, quaternary

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34
Q

What is a requirement for a protein to have a quaternary structure?

A

2+ polypeptides (oligomer)

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35
Q

Primary structure is determined by ____________

A

AA sequence

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36
Q

What MUST happen for proteins to function properly?

A

fold properly

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37
Q

What are the two forms of secondary structure?

A

alpha helix (coils)
beta pleated sheets (folds)

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38
Q

Where is the H-bonding in alpha helices?

A

between the coils (intramolecular), every 4th amino acid

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39
Q

Where is the H-bonding in beta pleated sheets?

A

between parts of the two parallel segments (intermolecular)

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40
Q

Which ends are beta sheets shown folded towards (when shown as a flat arrow)?

A

carboxyl end

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41
Q

What creates the polypeptide backbone?

A

the H-bonding by atoms in the secondary structure

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42
Q

What is the tertiary structure a result of?

A

R group interactions

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43
Q

What is a disulfide bridge?

A

an R group interacting between 2 sulfhydryl groups (covalent bond)

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44
Q

What are the weak R group interactions?

A

h-bonds, ionic bonds, hydrophobic, van der waals interactions

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45
Q

What are the strong R group interactions?

A

only disulfide bridge :)

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46
Q

What is the quaternary structure?

A

structure resulting from combined polypeptides (2+)

stabilized by R group interactions (between the polypeptides)

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47
Q

The effect of a single change in primary structure can have ___________ ________________.

A

pleiotropic consequences

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48
Q

Sickle cell anemia is caused by?

A

single base change in DNA –> singe base change in mRNA –> single AA change in protein

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49
Q

What is sickle cell anemia?

A

disorder that affects hemoglobin (decreased capacity to carry oxygen)

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50
Q

What are the two groups associated with the mutation in sickle cell anemia?

A

substitution of valine for glutamic acid

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51
Q

Protein conformation is influenced by?

A

pH, high salt concentration, temperature

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52
Q

What are chaperone proteins?

A

proteins that promote proper folding and refolding by providing the appropriate environment

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53
Q

What is the main effect of a denatured protein?

A

changes in the protein’s function

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54
Q

What happens to damaged or misfolded proteins?

A

tagged with ubiquitin –> delivered to proteasomes –> are recycled

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55
Q

What is ubiquitin?

A

chemical used to tag damaged proteins, “kiss of death”

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56
Q

What are proteasomes?

A

“garbage disposal” for damaged proteins, regulated degradation of proteins

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57
Q

What is the function of nucleic acids?

A

store and transmit hereditary information

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58
Q

What are the two types of nucleic acids?

A

deoxyribonucleic acid (DNA), ribonucleic acid (RNA)

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59
Q

What are nucleotide monomers made of?

A

pentose sugar, nitrogen base, phosphate group

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60
Q

What is the shape of DNA?

A

double stranded, double helix

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61
Q

What is the shape of RNA?

A

single stranded

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62
Q

What are the nitrogen bases of DNA?

A

C G A T

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63
Q

What are the nitrogen bases for RNA?

A

C G A U

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64
Q

What nitrogen bases pair up together? (hint: 2 pairs)

A

C and G

A and T/U

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65
Q

What are DNA nucleotide monomers made of?

A

*deoxyribose sugar, phosphate group, nitrogen bases

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66
Q

What are RNA nucleotide monomers made of?

A

*ribose sugar, phosphate group, nitrogen bases

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67
Q

(in a polynucleotide) Sugar is connected to the ______________ of the adjacent nucleotide by a ____________ linkage.

A

phosphate group

phosphodiester linkage

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68
Q

What part of the polynucleotide is considered as the “backbone”?

A

the sugar-phosphate units

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69
Q

What are the side chains in a polynucleotide? What are the different types?

A

nitrogen bases

  1. purines (two ring)
  2. pyrimidines (one ring)
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70
Q

What are purines?

A

two carbon-nitrogen rings bases (fused together)

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71
Q

What are pyrimidines?

A

one carbon-nitrogen ring base

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72
Q

What are the two ends of a DNA strand?

A

5’ and 3’

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73
Q

Which end of DNA is the 5’?

A

phosphate group is attached to 5’ carbon

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74
Q

Which end of DNA is the 3’?

A

hydroxyl group is attached to 3’ carbon

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75
Q

What do you call the orientation of the two strands of DNA?

A

anti-parallel

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76
Q

What determines the orientation of the protein in the membrane?

A

the way in which a newly synthesized protein is inserted into the ER membrane

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77
Q

What is the structure of the nucleus?

A

nuclear membrane (has nuclear pores), nucleoplasm (has chromatin), nucleolus

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78
Q

What is chromatin?

A

DNA and associated proteins

79
Q

What does chromatin synthesize?

A

messenger RNA (mRNA)

80
Q

What does nucleolus synthesize?

A

ribosomal RNA (rRNA)

formation of ribosomal subunits with accessory proteins

81
Q

The nucleus is enclosed by a ___________ ___________

A

double membrane

82
Q

What are nuclear pores composed of?

A

nucleoproteins

83
Q

What is the function of nuclear pores?

A

mediate transport in and out of the nucleus

84
Q

What do substances that travel through the pores have to have in order to pass?

A

nuclear localization signals

85
Q

What two things CAN’T DIFFUSE through nucleoproteins?

A

proteins and mRNA

86
Q

What is STORM?

A

microscopy with resolution on the order of fractions of a nanometer

87
Q

How are items of interests tagged so they can be viewed under STORM?

A

anti-body binds to interest, tags with florescent tag

88
Q

What do ribosomes do?

A

synthesize proteins

89
Q

What are ribosomes composed of?

A

rRNA combined with cytosolic proteins

2 subunits, one large and one small

90
Q

What do free ribosomes synthesize?

A

cytosolic proteins

91
Q

What do bound ribosomes synthesize?

A

integral membrane proteins and secreted proteins

92
Q

Where are bound ribosomes embedded in?

A

rER

93
Q

What is a part of the endomembrane system?

A

nuclear envelope, lysosomes, vesicles, the ER, Golgi apparatus, plasma membrane

94
Q

What is the main structural difference between the smooth ER and rough ER?

A

sER: ribosome free

rER: ribosome attached

95
Q

Where are free ribosomes located?

A

cytosol, but not in the cell nucleus and other organelles

96
Q

The ER is continuous with the ___________ _____________

A

nuclear envelope

97
Q

What is the ER made of?

A

membranous tubules and cisternae

98
Q

What are cisternae?

A

internal membrane stacks found in the ER and in the golgi apparatus

99
Q

What is the ER lumen?

A

the area enclosed by the ER’s membrane

100
Q

Specialized cells have large proportions of _____

A

sER

101
Q

The sER is rich in ___________ ____________

A

metabolic enzymes

102
Q

What are the four main functions of the sER?

A

synthesis of lipids and hormones

metabolism of carbohydrates

detoxification of drugs and poisons

calcium sequestration

103
Q

What specifically does the sER synthesize?

A

lipids (e.g. new phospholipids)

in the gonads: steroid hormones (sex hormones)

104
Q

What’s an example of the sER metabolizing carbohydrates?

A

in the liver: breakdown of glycogen

105
Q

What’s an example of the sER detoxifying drugs and poisons?

A

in the liver: metabolization of toxic substances

106
Q

How does drug tolerance happen?

A

increase in drugs induce the increase of sER & its drug enzymes –> increase rate of detoxification

107
Q

What are two examples of sER calcium sequestration?

A

muscle cells: regulation of Ca stores that mediate muscle contraction

secretory cells: Ca regulated vesicle secretion

108
Q

What is a gonad?

A

(sex gland, reproductive gland) mixed gland that produces the gametes (sex cells) and sex hormones in an organism

female: egg cells
male: sperm

109
Q

What is the main function of the rER?

A

processing of proteins synthesized by ER-bound ribosomes

110
Q

How does the rER process secreted proteins?

A

secreted proteins enter luminal space (through special pores)

protein folding, processing (glycoproteins)

transported in lumen

111
Q

How does the rER process membrane proteins?

A

synthesized and inserted into ER membrane

folding and processing

transported in membrane

112
Q

The rER is also a _______ ____________

A

membrane factory

113
Q

Other than making secretory proteins, what else can the rER synthesize?

A

phospholipids from precursors in the cytosol

114
Q

How does the rER grow?

A

it grows in place by adding membrane proteins and phospholipids to its own membrane

115
Q

What happens when the rER grows/expands?

A

portions of it are transferred in the form of transport vesicles to other organelles or cell membrane

116
Q

During modification, proteins travel from the _____ face of the golgi apparatus to the ________ face.

A

cis to trans face

117
Q

Which face of the golgi apparatus is the receiving side? How is the material received?

A

cis face

vesicles fuse, material moves through stack and is modified

118
Q

What face of the golgi apparatus is the shipping side? How is the material shipped?

A

trans face

vesicles tagged to direct location

119
Q

What is the function of cisternae in the golgi apparatus?

A

separates the golgi apparatus’ internal space from the cytosol

120
Q

(in the Golgi Apparatus) Each cisterna contains ________ __________

A

specific enzymes

121
Q

What does the golgi modify?

A

proteins and phospholipids

122
Q

What does the golgi manufacture?

A

polysaccharides

123
Q

DNA doesn’t have a _____________ ______________ _______________

A

nuclear localization signal

124
Q

What is a lysosome?

A

a digestive organelle

125
Q

Where are lysosomes synthesized, processed, and activated?

A

synthesized in the rER

processed and activated in golgi apparatus

126
Q

What do lysosomes digest?

A

vacuoles, food vacuoles (phagosomes), and damaged organelles

127
Q

What is autophagy?

A

lysosome digesting damaged organelles

128
Q

Lysosomes enzymes work best at ______ pH (~ what number)?

A

low, ~5

129
Q

How does the lysosomal membrane maintain a low internal pH?

A

proton pumps

130
Q

What do lysosome enzymes do?

A

hydrolyze proteins, fats, polysaccharides, and nucleic acids

131
Q

What are the three functions of lysosomes?

A

digestion of food particles, recycling cellular organelles, destroy bacterial invaders

132
Q

The lysosomal membrane isolates ___________ ____________ from the rest of the cell.

A

digestive enzymes

133
Q

Genetic mutations affecting the function of ___________ __________ lead to lysosomal storage disorders (LSD).

A

lysosomal enzymes

134
Q

What are lysosomal storage disorders (LSDs)?

A

autosomal recessive disorders

not enough enzymes to breakdown fats or carbohydrates –> they accumulate in lysosomes

135
Q

Cell signaling mechanisms have been highly __________

A

conserved

136
Q

Cells must communicate to __________ their ____________

A

coordinate, activities

137
Q

What are the three steps of cell signaling?

A

reception –> transduction –> cellular response

138
Q

What are some examples of cellular response?

A

changes in metabolisms, cytoplasm/cytoskeleton

generation of ATP

139
Q

What are the 4 different types of signals

A
  1. secreted signals (local)
  2. secreted signals (distant)
  3. intercellular signals
  4. cell surface signals
140
Q

What are the two different types of secreted signals that act locally?

A

paracine signaling, synaptic signaling

141
Q

What is paracrine signaling?

A

local signaling

142
Q

What is an example of paracine signaling?

A

growth factors

143
Q

What are growth factors?

A

compounds that stimulate nearby target cells to grow and divide

144
Q

What is a specific example of a growth factor?

A

release of platelet-derived growth factor (PDGF) from aggregating platelets to signal healing of wound

145
Q

What is synaptic signaling?

A

electrical signal along a nerve cell triggers the secretion of neurotransmitter molecules

146
Q

How does an electrical signal trigger the secretion of neurotransmitters?

A

electrical signal –> Ca+ go through channels –> vesticles containing NT are destroyed

…Na+ goes in to depolarize the membrane

147
Q

What blocks vesicles from forming into membrane?

A

botox

148
Q

What is a bio-marker for Alzheimer’s?

A

synapse loss proceeds memory loss

149
Q

Secreted signals that act at distance sites are ____________

A

hormones

150
Q

Where do hormones enter to travel to their target cells?

A

blood stream/circulatory system

151
Q

What is endocrine signaling?

A

hormonal signaling in animals

152
Q

What are intercellular signals?

A

gap junctions (animal) and plasmodesmata (plants)

153
Q

What protein is used for cell to cell recognition?

A

glycoproteins

154
Q

What are cell surface signals important for?

A

important during development and for immune response

155
Q

What is an example of cell surface signals?

A

FC receptors on white blood cells bind to antibodies

once bound, trigger phagocytosis

156
Q

What is a ligand?

A

a molecule that specifically binds to another molecule

157
Q

(in cell communication) What happens in reception?

A

ligand binds to receptor

induces change in location/shape in the receptor

158
Q

(in cell communication) What happens in transduction?

A

amplification, converts signal into form that can be read to activate cellular response

159
Q

What is a signal transduction pathway?

A

a sequence of changes in a series of different molecules

160
Q

Reception occurs most of the time at the ____ _____

A

cell surface

161
Q

What are the properties of ligands that bind to plasma membrane proteins?

A

secreted, hydrophilic, water soluble, membrane bound

162
Q

What are the properties of ligands that bind to cytoplasmic or nuclear proteins?

A

hydrophobic, lipid soluble

163
Q

___% of all proteins encoded by the human genome are cell-surface receptors!

A

30

164
Q

What is a G-protein-coupled receptor (GPCR)?

A

plasma membrane (or cell surface) receptor

165
Q

What are the ligands for GPCRs?

A

hormones, neurotransmitters

166
Q

What are GPCR’s main function?

A

sensory reception (i.e. vision, smell, taste, etc.)

167
Q

More than ________ GPCRs have been characterized in humans

A

1000

168
Q

__% of current medicines target GPCR pathways.

A

60

169
Q

What are the two toxins that interfere with GPCR function?

A

botulin toxin and cholera toxins

170
Q

What does GPCRs break down? What does it turn into?

A

breakdown GTP into GDP

171
Q

What does GTP stand for?

A

guanosine triphosphate

172
Q

What are tyrosine kinase receptors (TKRs)?

A

plasma membrane receptors characterized by having enzymatic activity

173
Q

What are the ligands for TKRs?

A

growth factors

174
Q

What are kinases?

A

enzymes that catalyze transfer of phosphate groups

175
Q

What is the major difference between GPCRs and TKRs?

A

GPCRs can only activate a single transduction pathway
…while TKRs can activate MULTIPLE

176
Q

What do TKRs regulate?

A

cell growth and reproduction

177
Q

What is abnormal TKRs associated with?

A

cancer

178
Q

What’s being used to treat different types of cancer? (hint: TKRs)

A

antibodies that block TKRs and drugs that block their action

179
Q

What are ligand-gated ion channels?

A

type of membrane channel receptor containing a region that can act as a “gate”

opens and closes from ligand

180
Q

What are the ligands for ligand-gated ion channels?

A

neurotransmitters

181
Q

What are the two common ions that pass through ligand-gated ion channels? Where do they flow?

A

Na+ and Ca+, flow in or out of cell (follows electrochem. gradient)

182
Q

What are ligand-gated ion channels important for?

A

communication between nerve cells

183
Q

Where are some ligand-gated ion channels present?

A

membrane of organelles, such as sER

184
Q

What are voltage-gated ion channels?

A

gated ion channels that are activated by electric signals

185
Q

What are stretch-activated ion channels?

A

gated ion channels that are activated by a mechanical change in the cell membrane

186
Q

Where are intracellular receptors (proteins) located?

A

in the cytoplasm or the nucleus of target cell

187
Q

What are the ligands that bind to intracellular receptors?

A

steroid, hormones, thyroid hormones, nitric oxide (NO)

188
Q

How do ligands reach intracellular receptors?

A

directly cross the membrane bilayer

189
Q

(in intracellular receptors) Hormone-receptor complex acts as a ___________ __________

A

transcription factor

190
Q

What are the two common mechanisms of transduction?

A

protein phosphorylation cascades, second messengers

191
Q

What are some examples of second messengers?

A

calcium**, IP3, cAMP

192
Q

Many GFs/NTs/hormones signal via modulating _____ ____. (hint: second word is an ion)

A

cytolic Ca2+

193
Q

Cells use ___ as a 2nd messenger in pathways trigger by GPCRs and TKRs.

A

Ca

194
Q

In GCPRs, using IP3 and Ca as 2nd messengers triggers __ different possible _______.

A

2, pathways

BIO 93 midterm pt 2 (1 decks)

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