Final Exam Flashcards
(131 cards)
1
Q
What is signal transduction?
A
one cell sends out a signal and it has to be received by another cell
2
Q
In signal transduction what receives the signal?
A
receptors
3
Q
What does the receptor have to do in order to receive the signal?
A
the receptor has to physically bind to the signal molecule
4
Q
What type of fit does the signal cell and the receptor cell have?
A
induced fit
5
Q
What happens when the signal cell and the receptor bind with an induced fit?
A
conformational change
6
Q
T/F
The conformational change from the induced fit of the signal cell and the receptor cell is information that can be passed on to other proteins?
A
True
7
Q
General features of signal transduction?
A
- always a receptor
- always a signal (ligand)
- always a non-covalent
8
Q
Ligand?
A
the signal cell
9
Q
R + L R*L
where R=receptor L=ligand
A
Kd=[R][L]
——–
[R*L]
10
Q
If Kd is really low?
A
tight Receptor*Ligand (high affinity for Ligand)
11
Q
If Kd is really high?
A
the R*L complex concentration is much higher than the bare [R] and [L]
12
Q
The point where 1/2 of all the receptors are bound to ligand and 1/2 are free?
A
[ligand] = Kd
13
Q
GTP-binding Proteins (G-protein) coupled Receptors?
G-Protein?
A
G-protein is a protein that can bind GTP or GDP
14
Q
receptor for GTP/GDP?
A
GPCR
15
Q
GPCR-is an _________ protein
A
integral membrane protein
16
Q
How many different types of GPCR’s are there?
A
~800
17
Q
T/F One ligand (signal) can result in 10,000k-millions of signals inside a cell?
A
True
18
Q
What is amplification?
A
One ligand (signal) can result in 10,000k-millions of signals inside a cell.
19
Q
GTP-binding Proteins have ____ transmembrane spanning ________ linked via loops, bends and other secondary structures.
A
- 7 (highly conserved) but the rest of the protein is diverse
- alpha-helices
20
Q
3 distinct domains of the 7 transmembrane proteins spanning alpha- helices?
A
1-Extracellular
2-membrane
3-Intracellular
21
Q
The ligand is where?
A
extracellular
22
Q
The G-protein is where?
A
Intracellular
23
Q
The signal travels from ______the cell to ________ the cell?
A
inside
outside
24
Q
What has to physically touch the receptor?
A
The G-proteins
25
What happens when the G-protein physically touches the receptor?
A conformational change in the G-protein
26
G-proteins are?
heterotrimeric- G alpha, G beta, G gamma
27
What portion of the G-protein binds GTP and/or GDP?
G alpha binds GTP and/or GDP
28
When is G-alpha inactive?
When it is bound to GDP
29
When is G-alpha active?
When it is bound to GTP
30
T/F
| G-alpha is a lipid linked protein
True
* have fatty acids covalently linked to them
can only diffuse in 2 dimensions
31
Where must the G-alpha protein stay?
on the cytoplasmic face of the membrane
32
G-alpha diassociates from ______ and _________.
receptor
G-beta G-gamma
*will re-associate with the receptor and G-beta and G-gamma
33
Signal transduction pathway #2?
cAMP-cyclic AMP
| *phosphate is bound to Carbon 5 and 3-this is why it is cyclic
34
cAMP is considered a _______ messenger
2nd
35
Is cAMP soluble?
yes in the cytoplasm
| *can go anywhere in the cytoplasm
36
What does cAMP do?
activates intracellular kinase and phosphatase
37
1-inactive cAMP
| 2-active cAMP
1-RR 2-RR + C + C
| CC
38
(PKA) protein kinase is activated by what?
increase in cAMP
39
4 covalent interactions?
1-H bonds
2-Van der waals forces (london dispersion)
3-Hydrophobic interactions
4-Ionic interactions
40
not static?
break and reform very rapidly
41
If each of the covalent interactions are individually weak then why are they so important?
the effect of these interactions are cumulative
| * they sum up to make a big impact
42
1-donors?
| 2-acceptors?
1-will always be an H bonded to something more electronegative
2-will always be a (-) atom... O,N
43
H-bonds are the strongest when?
when the donor and acceptor are linear
| *linear forces structure on both donors and acceptors
44
The more donors + acceptors it has means it's more likely to?
enter into solution
45
Amphipathic?
1 part hydrophilic and 1 part hydrophobic
| * hydrophobic will surround hydrophobic
46
What is a micelle?
the only possible shape that can form from amphipathic cells.
47
Amphipathic cells will spontaneously form what?
micelle (sphere shape)
48
interior of micelle will contain what?
100% hydrophilic heads
49
What does the Ka measure?
the strength of an acid
50
larger the Ka the _______ the acid
stronger the acid
51
smaller the Ka the ________ the acid
weaker the acid
52
Smaller the pKa the ________ the acid
stronger the acid
53
What is pH=pKa?
the point when parent is in equilibrium w/ conjugate base
54
What is a buffer?
The point acid/conjugate base pair resist pH change
55
Le Chatlea's Principle?
this is why acid/conjugate base pairs work as buffers
| *we can shift the direction by adding one or the other to offset the balance
56
Buffers are only effective around what range?
+/- 1 pH unit from the pKa
57
What is the parent acid?
the one with more H+ ions that can disassociate
| * whichever one has less= base
58
All amino acids have 4 things?
1-alpha C
2-amine group
3-side chain
4-are chiral molecules
59
Individual amino acids exist as what?
Zwitter ions
| * are both + and - (has no net charge)
60
What links amino acids together?
peptide bonds
61
peptide=string of amino acids > than 100
| protein = string of amino acids > than 100
peptide=< than 100
| protein=> than 100
62
Each amino acid is called a _____ in a string of amino acids where the far left will always have _______ and the far right will always have_________.
residue
have a free amine group=N terminus
have a free carboy group=C terminus
63
Insulin is connected by what?
2 disulfide bonds
64
The 2 basic amino acids?
1-Arginine (Arg)
| 2-Lysine (Lys)
65
The 2 acidic amino acids?
1-Aspartate(Asp)
| 2-Glutamate(Glu)
66
Shapes of proteins
```
1-1 chain
2-multiple poly peptide chains
3-made of just amino acids
4-round
5-non-amino acids in their structure
```
1-monomeric proteins
2-multimeric proteins
3-simple proteins
4-Globular-exterior ( contact with H2O) and interior (shielded from H2O)
5-conjugated proteins
* most of the proteins we talk about are globular
67
What is inside the middle of a globular protein?
nothing but the amino acid
68
Why do proteins have a particular shape?
intermolecular forces give proteins they shape
69
native conformation
normal active shape
70
denatured state?
not active- destroyed native conformation
71
how is an amino acid sequence linked?
via covalent peptide bonds
72
What is unique about proline?
due to its structure it puts an end to beta sheets and alpha helices
73
What is the most important interaction in tertiary structure?
hydrophobic interactions
74
monomeric proteins have how many levels of protein structure?
3
75
T/F
| Native structure is the lowest energy state
True
| *protein assumes it's final structure because it is the lowest energy state
76
What are Chaperone proteins?
protein that catalyze correct protein folding when the protein is endangered of being denatured from heat
* aka heat shock protein
77
Cooperative binding?
each molecule that binds, binds the previous molecule tighter.
*O2 in hemoglobin physically touch each other and binds the previous more tightly
last O2 binds 100X more tighter than the first
78
Allosteric effect=___________________
conformational change
79
substrate binding site
1-substrate
2-active site
3-binding site
4-ligand
1-reactants
2-binds substrate and catalyzes reaction
3-binds a ligand
4-somehting bound by a protein(not a substrate)
80
substrate binding is?
non-covalent interactions
81
The state in which the energy is the highest and it is bound more tightly that the substrate or the product
transition state
82
3 types of enzyme inhibition
1-competitive inhibition
2-non-competitive inhibition
3-un-competitive inhibition
83
competitive inhibition?
substrate and inhibitor competing for the same site
| *Vmax stays the same in competitive inhibition
84
non-competitive inhibition?
inhibitor binds to the enzyme at a site that is not the active site
Km doesn't change but Vmax decreases
(allosteric effect = conformational change
85
un-competitive inhibition
substrate has to change conformation of the enzyme in order for the inhibitor to bind
Km increases and Vmax decreases
86
enzymes can be regulated by the ability of what?
co-factors
87
saturated fats
- no double bonds
- straight
- less fluid
- maximum interactions with neighbors-bound tight
88
unsaturated fats
- has 1 or more double bonds (kinked)
- cis confirmation
- more fluid at room temperature
* tail with bend takes up more room so they are both tightly bound to neighbors therefore less hydrophobic interactions
89
polar lipids?
diacylglycerides with a polar head
- phosphate head
- 2 acyl chains-tail (fatty acids)
* forms the lipid bilayer
90
The only 2 molecules that can easily make it through the lipid membrane
O2 and CO2
91
Lateral diffusion
rapid-happens on same side
92
Transverse diffusion
(flip-flop) outside to inside
- very slow
* flipases
93
what is cholesterol and where is it found?
found in the membrane and makes bilayers less fluid
94
3 classes of proteins
1-integral-can only be removed by detergent (soap)
2-peripheral-ionic interaction w/ integral proteins
3-lipid linked proteins-lipid covalently linked (post translational modification)
95
RAS
| -main function?
cell division
| *causes cancer if it can't be turned off
96
2 types of transport
1-passive
| 2-active
97
ATP energy cost?
30.5 kJ/mol
98
aquaporin
water channel
99
(MDR)-multi -drug resistance protein
transporter found in plasma membrane-binds to organic molecules and pumps them outside cell
*if cancer cell- starts over expressing MDR-protein pumps it out but not fast enough
100
autocyclisize?
a molecule will form equilibrium between the linear form and the cyclic form w/out the help of enzymes or outside help
101
alpha position?
| beta position?
O in the down position
| O in the up position
102
mutarotation?
the breaking of the cyclic structure rotation of the carbonyl group and re-crystallization
*free rotation between 1 & 2 carbon going from linear to cyclic
103
glycogen is linked via?
alpha 1-4 and alpha 1-6 linkages
104
why is cellulose so much stronger than glycogen?
- cellulose is linked with beta 1-4 linkages
- monomers line up
- glucose-glucose H-bonds
105
Glycoproteins?
| linked?
-glycoproteins are oligosaccharide chains liked to proteins
-linked 2 ways
1-oxygen-Ser,Thr
2-Nitrogen-always linked through "N" on asparagine (Asn)
106
only 3 amino acids with free hydroxyl group
1-serine (Ser)
2-threanine (The)
3-tyrosine (Tyr)
107
2 ways to loose contact inhibition?
1-neighboring cells cannot display olgiosaccharides
| 2-neighboring cells don't have right cells to bind
108
Lectins?
proteins that bind oligosaccharide side chains
| *lectins are in charge of contact inhibition
109
3 parts of nucleic acids?
1-nitrogen base
2-5 carbon sugar
3-phosphate group
110
Phosphoester bond vs phosphoanhydride bond
phosphoester bond= not as high in energy ~6.9 kJ/mol
| phosphoanhydride bond=~30.5 kJ per mole (used as an energy source)
111
1-A=T-how many bonds?
| 2-G=C-how many bonds?
1-2 "H" bonds
| 2-3 "H" bonds
112
which type of the RNA has the anticodon?
tRNA
113
which type of RNA has the codon?
mRNA
114
exonucleases
cleave chain end nucleotides
115
endonucleases
cleave interior chain nucleotides
| *has restriction enzymes
116
name a restriction enzyme?
EcoR1
| *restriction enzymes commonly recognize palindromes
117
How does EchoR1 work?
can located and identify specific places-codons
118
palindromes?
reads the same way forward as it does backwards
119
sticky ends?
EchoR1 cleaves so that each side has 4 nucleotides with no complimentary "H" bonding
120
3 things needed for DNA polymerase
1-Free nucleotide
2-template strand
3-primer w/ free OH group
121
helicase
unzips DNA (breaks complimentary bonding)
122
DNA gyrase
helps unwind ( a topoisomerase)
123
SSB protein
stabilizes single stranded DNA
124
Primase
makes primer
125
DNA 1
removes RNA primers and replaces w/ DNA
126
DNA 3
DNA polymerase
127
DNA ligase
fixes nics
128
energy needed to move helices 1 nucleotide down
1 phosphoanhydride bond
129
okazaki fragments
short fragments made in the bottom lagging strand in DNA polymerase III
130
3 mutations
1-one base is substituted for another base
2-nucleotide can be added
3-nucleotide can be subtracted
131
example of a silent mutation?
wobble
