BIO 93 Midterm pt 2 Flashcards
(194 cards)
1
Q
The bonding of molecules requires:
A
the release of a water molecule
2
Q
What is a dehydration reaction?
A
water molecule is released when bonding molecules
3
Q
What is a hydrolysis reaction?
A
adding water to a large molecule to break it into smaller molecules
4
Q
What are the two groups ALWAYS present in an animo acid?
A
amino group and carboxyl group
5
Q
What is a polymer?
A
a long molecule built from similar subunits (monomers) linked by covalent bonds
6
Q
What are monomers?
A
subunits to polymers
7
Q
Which of the following are polymers?
Carbohydrates, proteins, nucleic acids, lipids
A
carbohydrates, proteins, nucleic acids
8
Q
What are amino acids?
A
monomers, combine to form polymers
9
Q
What is a polypeptide?
A
polymer of AAs in a specific sequence
10
Q
What is a protein?
A
one or more polypeptides with specific 3-D conformation
11
Q
Form follows ______
A
function
12
Q
Function of enzymatic proteins?
A
selective acceleration of chemical reactions (i.e. digestive enzymes catalyze the hydrolysis of bonds in food molecules)
13
Q
Function of defensive proteins?
A
protection against disease (i.e. antibodies inactivate and help destroy viruses and bacteria)
14
Q
Function of storage proteins?
A
storage of amino acids (i.e. casein (milk), seeds, ovalbumin (egg white))
15
Q
Function of transport proteins?
A
transport of substances
16
Q
Function of hormonal proteins?
A
coordination of an organism’s activities (i.e. insulin)
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)
18
Q
Function of contractile and motor proteins?
A
movement (i.e. cilia, flagella)
19
Q
Function of structural proteins?
A
support (i.e. keratin (hair), collagen (skin/tissue))
20
Q
Proteins are all constructed from the same set of _______ amino acids.
A
20
21
Q
What is a R group?
A
variable side chain
22
Q
Effect of nonpolar R group?
A
hydrophobic (9/20 groups)
23
Q
Effect of polar R group?
A
hydrophilic (6/20)
24
Q
Effect on ionized R group? (charged at cellular pH)
A
acids and bases ; hydrophilic
25
What is the name of the carbon in the middle of an amino acid?
α (alpha) carbon
26
When is a carboxyl group considered an acid?
when the H+ isn't present
27
Nonpolar molecules are ______
hydrophobic
28
Polar molecules are _______
hydrophilic
29
What is required for a dehydration reaction to occur?
an enzyme
30
What is the amino end of a polypeptide?
N terminus ; area with the amino group
31
What is the carboxyl end of a polypeptide?
C terminus ; area with the carboxyl group
32
What type of bond is a peptide bond?
covalent bond
33
What are the 3/4 protein structures?
primary, secondary, tertiary, quaternary
34
What is a requirement for a protein to have a quaternary structure?
2+ polypeptides (oligomer)
35
Primary structure is determined by ____________
AA sequence
36
What MUST happen for proteins to function properly?
fold properly
37
What are the two forms of secondary structure?
alpha helix (coils)
beta pleated sheets (folds)
38
Where is the H-bonding in alpha helices?
between the coils (intramolecular), every 4th amino acid
39
Where is the H-bonding in beta pleated sheets?
between parts of the two parallel segments (intermolecular)
40
Which ends are beta sheets shown folded towards (when shown as a flat arrow)?
carboxyl end
41
What creates the polypeptide backbone?
the H-bonding by atoms in the secondary structure
42
What is the tertiary structure a result of?
R group interactions
43
What is a disulfide bridge?
an R group interacting between 2 sulfhydryl groups (covalent bond)
44
What are the weak R group interactions?
h-bonds, ionic bonds, hydrophobic, van der waals interactions
45
What are the strong R group interactions?
only disulfide bridge :)
46
What is the quaternary structure?
structure resulting from combined polypeptides (2+)
stabilized by R group interactions (between the polypeptides)
47
The effect of a single change in primary structure can have ___________ ________________.
pleiotropic consequences
48
Sickle cell anemia is caused by?
single base change in DNA --> singe base change in mRNA --> single AA change in protein
49
What is sickle cell anemia?
disorder that affects hemoglobin (decreased capacity to carry oxygen)
50
What are the two groups associated with the mutation in sickle cell anemia?
substitution of valine for glutamic acid
51
Protein conformation is influenced by?
pH, high salt concentration, temperature
52
What are chaperone proteins?
proteins that promote proper folding and refolding by providing the appropriate environment
53
What is the main effect of a denatured protein?
changes in the protein's function
54
What happens to damaged or misfolded proteins?
tagged with ubiquitin --> delivered to proteasomes --> are recycled
55
What is ubiquitin?
chemical used to tag damaged proteins, "kiss of death"
56
What are proteasomes?
"garbage disposal" for damaged proteins, regulated degradation of proteins
57
What is the function of nucleic acids?
store and transmit hereditary information
58
What are the two types of nucleic acids?
deoxyribonucleic acid (DNA), ribonucleic acid (RNA)
59
What are nucleotide monomers made of?
pentose sugar, nitrogen base, phosphate group
60
What is the shape of DNA?
double stranded, double helix
61
What is the shape of RNA?
single stranded
62
What are the nitrogen bases of DNA?
C G A T
63
What are the nitrogen bases for RNA?
C G A U
64
What nitrogen bases pair up together? (hint: 2 pairs)
C and G
A and T/U
65
What are DNA nucleotide monomers made of?
*deoxyribose sugar, phosphate group, nitrogen bases
66
What are RNA nucleotide monomers made of?
*ribose sugar, phosphate group, nitrogen bases
67
(in a polynucleotide) Sugar is connected to the ______________ of the adjacent nucleotide by a ____________ linkage.
phosphate group
phosphodiester linkage
68
What part of the polynucleotide is considered as the "backbone"?
the sugar-phosphate units
69
What are the side chains in a polynucleotide? What are the different types?
nitrogen bases
1. purines (two ring)
2. pyrimidines (one ring)
70
What are purines?
two carbon-nitrogen rings bases (fused together)
71
What are pyrimidines?
one carbon-nitrogen ring base
72
What are the two ends of a DNA strand?
5' and 3'
73
Which end of DNA is the 5'?
phosphate group is attached to 5' carbon
74
Which end of DNA is the 3'?
hydroxyl group is attached to 3' carbon
75
What do you call the orientation of the two strands of DNA?
anti-parallel
76
What determines the orientation of the protein in the membrane?
the way in which a newly synthesized protein is inserted into the ER membrane
77
What is the structure of the nucleus?
nuclear membrane (has nuclear pores), nucleoplasm (has chromatin), nucleolus
78
What is chromatin?
DNA and associated proteins
79
What does chromatin synthesize?
messenger RNA (mRNA)
80
What does nucleolus synthesize?
ribosomal RNA (rRNA)
formation of ribosomal subunits with accessory proteins
81
The nucleus is enclosed by a ___________ ___________
double membrane
82
What are nuclear pores composed of?
nucleoproteins
83
What is the function of nuclear pores?
mediate transport in and out of the nucleus
84
What do substances that travel through the pores have to have in order to pass?
nuclear localization signals
85
What two things CAN'T DIFFUSE through nucleoproteins?
proteins and mRNA
86
What is STORM?
microscopy with resolution on the order of fractions of a nanometer
87
How are items of interests tagged so they can be viewed under STORM?
anti-body binds to interest, tags with florescent tag
88
What do ribosomes do?
synthesize proteins
89
What are ribosomes composed of?
rRNA combined with cytosolic proteins
2 subunits, one large and one small
90
What do free ribosomes synthesize?
cytosolic proteins
91
What do bound ribosomes synthesize?
integral membrane proteins and secreted proteins
92
Where are bound ribosomes embedded in?
rER
93
What is a part of the endomembrane system?
nuclear envelope, lysosomes, vesicles, the ER, Golgi apparatus, plasma membrane
94
What is the main structural difference between the smooth ER and rough ER?
sER: ribosome free
rER: ribosome attached
95
Where are free ribosomes located?
cytosol, but not in the cell nucleus and other organelles
96
The ER is continuous with the ___________ _____________
nuclear envelope
97
What is the ER made of?
membranous tubules and cisternae
98
What are cisternae?
internal membrane stacks found in the ER and in the golgi apparatus
99
What is the ER lumen?
the area enclosed by the ER's membrane
100
Specialized cells have large proportions of _____
sER
101
The sER is rich in ___________ ____________
metabolic enzymes
102
What are the four main functions of the sER?
synthesis of lipids and hormones
metabolism of carbohydrates
detoxification of drugs and poisons
calcium sequestration
103
What specifically does the sER synthesize?
lipids (e.g. new phospholipids)
in the gonads: steroid hormones (sex hormones)
104
What's an example of the sER metabolizing carbohydrates?
in the liver: breakdown of glycogen
105
What's an example of the sER detoxifying drugs and poisons?
in the liver: metabolization of toxic substances
106
How does drug tolerance happen?
increase in drugs induce the increase of sER & its drug enzymes --> increase rate of detoxification
107
What are two examples of sER calcium sequestration?
muscle cells: regulation of Ca stores that mediate muscle contraction
secretory cells: Ca regulated vesicle secretion
108
What is a gonad?
(sex gland, reproductive gland) mixed gland that produces the gametes (sex cells) and sex hormones in an organism
female: egg cells
male: sperm
109
What is the main function of the rER?
processing of proteins synthesized by ER-bound ribosomes
110
How does the rER process secreted proteins?
secreted proteins enter luminal space (through special pores)
protein folding, processing (glycoproteins)
transported in lumen
111
How does the rER process membrane proteins?
synthesized and inserted into ER membrane
folding and processing
transported in membrane
112
The rER is also a _______ ____________
membrane factory
113
Other than making secretory proteins, what else can the rER synthesize?
phospholipids from precursors in the cytosol
114
How does the rER grow?
it grows in place by adding membrane proteins and phospholipids to its own membrane
115
What happens when the rER grows/expands?
portions of it are transferred in the form of transport vesicles to other organelles or cell membrane
116
During modification, proteins travel from the _____ face of the golgi apparatus to the ________ face.
cis to trans face
117
Which face of the golgi apparatus is the receiving side? How is the material received?
cis face
vesicles fuse, material moves through stack and is modified
118
What face of the golgi apparatus is the shipping side? How is the material shipped?
trans face
vesicles tagged to direct location
119
What is the function of cisternae in the golgi apparatus?
separates the golgi apparatus' internal space from the cytosol
120
(in the Golgi Apparatus) Each cisterna contains ________ __________
specific enzymes
121
What does the golgi modify?
proteins and phospholipids
122
What does the golgi manufacture?
polysaccharides
123
DNA doesn't have a _____________ ______________ _______________
nuclear localization signal
124
What is a lysosome?
a digestive organelle
125
Where are lysosomes synthesized, processed, and activated?
synthesized in the rER
processed and activated in golgi apparatus
126
What do lysosomes digest?
vacuoles, food vacuoles (phagosomes), and damaged organelles
127
What is autophagy?
lysosome digesting damaged organelles
128
Lysosomes enzymes work best at ______ pH (~ what number)?
low, ~5
129
How does the lysosomal membrane maintain a low internal pH?
proton pumps
130
What do lysosome enzymes do?
hydrolyze proteins, fats, polysaccharides, and nucleic acids
131
What are the three functions of lysosomes?
digestion of food particles, recycling cellular organelles, destroy bacterial invaders
132
The lysosomal membrane isolates ___________ ____________ from the rest of the cell.
digestive enzymes
133
Genetic mutations affecting the function of ___________ __________ lead to lysosomal storage disorders (LSD).
lysosomal enzymes
134
What are lysosomal storage disorders (LSDs)?
autosomal recessive disorders
not enough enzymes to breakdown fats or carbohydrates --> they accumulate in lysosomes
135
Cell signaling mechanisms have been highly __________
conserved
136
Cells must communicate to __________ their ____________
coordinate, activities
137
What are the three steps of cell signaling?
reception --> transduction --> cellular response
138
What are some examples of cellular response?
changes in metabolisms, cytoplasm/cytoskeleton
generation of ATP
139
What are the 4 different types of signals
1. secreted signals (local)
2. secreted signals (distant)
3. intercellular signals
4. cell surface signals
140
What are the two different types of secreted signals that act locally?
paracine signaling, synaptic signaling
141
What is paracrine signaling?
local signaling
142
What is an example of paracine signaling?
growth factors
143
What are growth factors?
compounds that stimulate nearby target cells to grow and divide
144
What is a specific example of a growth factor?
release of platelet-derived growth factor (PDGF) from aggregating platelets to signal healing of wound
145
What is synaptic signaling?
electrical signal along a nerve cell triggers the secretion of neurotransmitter molecules
146
How does an electrical signal trigger the secretion of neurotransmitters?
electrical signal --> Ca+ go through channels --> vesticles containing NT are destroyed
...Na+ goes in to depolarize the membrane
147
What blocks vesicles from forming into membrane?
botox
148
What is a bio-marker for Alzheimer's?
synapse loss proceeds memory loss
149
Secreted signals that act at distance sites are ____________
hormones
150
Where do hormones enter to travel to their target cells?
blood stream/circulatory system
151
What is endocrine signaling?
hormonal signaling in animals
152
What are intercellular signals?
gap junctions (animal) and plasmodesmata (plants)
153
What protein is used for cell to cell recognition?
glycoproteins
154
What are cell surface signals important for?
important during development and for immune response
155
What is an example of cell surface signals?
FC receptors on white blood cells bind to antibodies
once bound, trigger phagocytosis
156
What is a ligand?
a molecule that specifically binds to another molecule
157
(in cell communication) What happens in reception?
ligand binds to receptor
induces change in location/shape in the receptor
158
(in cell communication) What happens in transduction?
amplification, converts signal into form that can be read to activate cellular response
159
What is a signal transduction pathway?
a sequence of changes in a series of different molecules
160
Reception occurs most of the time at the ____ _____
cell surface
161
What are the properties of ligands that bind to plasma membrane proteins?
secreted, hydrophilic, water soluble, membrane bound
162
What are the properties of ligands that bind to cytoplasmic or nuclear proteins?
hydrophobic, lipid soluble
163
___% of all proteins encoded by the human genome are cell-surface receptors!
30
164
What is a G-protein-coupled receptor (GPCR)?
plasma membrane (or cell surface) receptor
165
What are the ligands for GPCRs?
hormones, neurotransmitters
166
What are GPCR's main function?
sensory reception (i.e. vision, smell, taste, etc.)
167
More than ________ GPCRs have been characterized in humans
1000
168
__% of current medicines target GPCR pathways.
60
169
What are the two toxins that interfere with GPCR function?
botulin toxin and cholera toxins
170
What does GPCRs break down? What does it turn into?
breakdown GTP into GDP
171
What does GTP stand for?
guanosine triphosphate
172
What are tyrosine kinase receptors (TKRs)?
plasma membrane receptors characterized by having enzymatic activity
173
What are the ligands for TKRs?
growth factors
174
What are kinases?
enzymes that catalyze transfer of phosphate groups
175
What is the major difference between GPCRs and TKRs?
GPCRs can only activate a single transduction pathway
...while TKRs can activate MULTIPLE
176
What do TKRs regulate?
cell growth and reproduction
177
What is abnormal TKRs associated with?
cancer
178
What's being used to treat different types of cancer? (hint: TKRs)
antibodies that block TKRs and drugs that block their action
179
What are ligand-gated ion channels?
type of membrane channel receptor containing a region that can act as a "gate"
opens and closes from ligand
180
What are the ligands for ligand-gated ion channels?
neurotransmitters
181
What are the two common ions that pass through ligand-gated ion channels? Where do they flow?
Na+ and Ca+, flow in or out of cell (follows electrochem. gradient)
182
What are ligand-gated ion channels important for?
communication between nerve cells
183
Where are some ligand-gated ion channels present?
membrane of organelles, such as sER
184
What are voltage-gated ion channels?
gated ion channels that are activated by electric signals
185
What are stretch-activated ion channels?
gated ion channels that are activated by a mechanical change in the cell membrane
186
Where are intracellular receptors (proteins) located?
in the cytoplasm or the nucleus of target cell
187
What are the ligands that bind to intracellular receptors?
steroid, hormones, thyroid hormones, nitric oxide (NO)
188
How do ligands reach intracellular receptors?
directly cross the membrane bilayer
189
(in intracellular receptors) Hormone-receptor complex acts as a ___________ __________
transcription factor
190
What are the two common mechanisms of transduction?
protein phosphorylation cascades, second messengers
191
What are some examples of second messengers?
calcium****, IP3, cAMP
192
Many GFs/NTs/hormones signal via modulating _____ ____. (hint: second word is an ion)
cytolic Ca2+
193
Cells use ___ as a 2nd messenger in pathways trigger by GPCRs and TKRs.
Ca
194
In GCPRs, using IP3 and Ca as 2nd messengers triggers __ different possible _______.
2, pathways
