Test 3 Flashcards
(87 cards)
1
Q
What is protein synthesis catelyzed by?
A
Ribosomes
2
Q
2 major groups of the ribosomes?
A
small unit and large unit
3
Q
When an Anhydride bond breaks it is worth how much energy?
A
~30.5 KJ
4
Q
transfer RNA (tRNA) has a codon/anticodon?
A
anticodon
5
Q
tRNA has a specific amino acid?
A
adenine
6
Q
mTRNA?
How many phosphoanhydride bonds?
Energy released?
A
amino acid + ATP——->aminoadenylate tRNA + PPi
2
61.0 KJ
7
Q
degeneracy?
A
codon usage table-64 codons- we have more than we need
8
Q
Where does protein synthesis occur?
A
in the cytoplasm
9
Q
What 2 parts make up the small unit of the ribosome?
A
P-site
A-site
10
Q
Step 1 in protein synthesis?
A
small unit of ribosome binds to mRNA
11
Q
P-site (peptidyl site)
A
growing peptide chain is here
12
Q
A-site (amino acyl site)
A
New amino acid brought here
13
Q
Step 2 in protein synthesis
A
methionine-tRNA recruited to the P-site
14
Q
Step 3 in protein synthesis?
A
larger ribosomal subunit binds
15
Q
Energy expended to move the ribosome one complete codon?
A
1 phospho anhydride bond-1 ATP
16
Q
Step 4 of protein synthesis
A
activated tRNA is recruited -uses 1 ATP ( 1 phospho anhydride bond is broken)
17
Q
Step 5 in protein synthesis?
A
Peptidyl transferase-breaks bond (cleaves ester bond between the carboxy group of growing protein( P-site) and tRNA)
18
Q
Step 6 in protein synthesis
A
Peptidyl transferase catalyzes peptide bond formation between C-terminus of growing protein + N-terminus of the ammoniacal-tRNA in the “A” site of the ribosome
19
Q
Step 7 in protein synthesis
A
tRNA in the “P” site has to leave
- “P” site is now empty
growing chain in the “A” site
20
Q
Step 8 in protein synthesis
A
ribosome moves 1 codon downstream on mRNA
* movement burns 1 GTP
growing chain is now in the “P” site
21
Q
Step 9 in protein synthesis
A
repeat steps 4-9.
* every recruitment of aminoacyl-tRNA costs
1 ATP———->1 ADP
22
Q
Step 10 in protein synthesis
A
ribosome encounters a stop codon and the whole complex falls apart
* protein is in sites along with the ribosome parts
23
Q
tRNA and rRNA are what kind of structures?
A
secondary structures
24
Q
What kind of structure does mRNA have?
A
mRNA=polyribosome-more than 1 ribosome can be bound to it at once simultaneously
linear structure not secondary
25
mRNA
Why are polyribosomes important?
Because RNA has a short 1/2 life
26
net balance for protein synthesis?
activate mRNA 2 phosphoanhydride
recruitment 1 phosphoanhydride
transfer 1 phosphoanhydride
_______________________________
total cost = 4 phosphoanhyride bonds
27
Examples of Post translational modifications?
- glycoproteins( oligosaccharide side chains)
- phosphorylation
- proteolytic activity
- addition of prosthetic groups
28
Proteolytic process?
extra amino acids are cleaved off
| *pro/presequences are cleaved off
29
Any sequence of the pre sequences will have _____in their sequence?
KDEL
30
An address label sending this to the ER 100% of the time?
pre-sequence (KDEL)
31
Pre vs Pro sequences
pre-sequences usually function as single peptides for protein targeting
pro-sequences usually play a role in the folding of proteins( prevents protein from being active)
32
2 sources from proteins
1-digests from external
| 2-synthesize them itself
33
what is endocytosis?
the contents of vesicle is engulfed into the cell
34
T/F
| Vesicles serve as the stomach for cells and when the pH gets low enough lysosomes are pumped out?
True
35
What are ligands?
degraded material
36
What releases ligands?
receptors under conformational change
37
List the process in which a cell takes in nutrients?
- Vesicle contents lower in pH
- vesicle----->lysosome ="stomach of the cell"
- receptors from cell undergo conformational change--release ligands
- vesicle uptakes bud from lysosome
- bud is recycled to plasma membrane
- receptors release more ligands
- process repeats
- recognizes foreign form itself
38
Endogenous protein?
degradation-(this is targeted) not random
39
What types of proteins are targeted?
- old
- mis-folded
- not needed anymore
40
How are targeted proteins tagged for destruction?
Ubiquitin ( attached covalently
41
What is Ubiquitin?
Ubiquitin is a small petite 76 amino acids long that tags targeted proteins for destruction
*flag for protein destruction
42
What is ubiquitin covalently attached to?
covalently attached to lysine on the targeted protein
43
What are polyubiquitins?
multiple ubiquitins-only the 1st is covalently attached to protein
44
What is the 26s Proteasome?
degrades proteins that are tagged with ubiquitin
45
What is happening when a protein is being sucked through the barrel like structure of the 26s proteasome?
it is removing the secondary(2),tertiary(3), and quaternary(4) structure of the protein
46
What is required(energy) for the 26s proteasome?
1 ATP per amino acid is needed to get rid of it
47
What is a metabolite?
small molecules that are intermediates of metabolism
- metabolites
- enzymes
48
T/F
| Metabolic pathways are both divergent and convergent?
True
49
What is a metabolon?
multiple related enzymes in a pathway that are physically connected to one another. (one enzyme shuttles to another-all are physically connected)
50
What is an advantage of metabolons?
not limited by rate of diffusion-very fast pathway
51
2 types of metabolism
1-catabolism-releases energy
| 2-anabolism-consumes energy
52
How are both catabolism and anabolism linked?
via energy-phosphoanhydride bonds
53
6 main types of reactions?
```
1-redox
2-group transfer
3-hydrolysis
4-non-hydrolytic bond cleavage
5-isomerizations
6-bond formation using ATP as energy
```
54
3 important take aways from metabolism?
1-metabolic pathways are all connected (convergent and non-convergent)
2-pathway activity is regulated (inhibited or stimulated)
3-Not every cell carries out every pathway
55
Gibbs free energy equation?
ΔG = ΔH - TΔS
H=heat KJ/mole T=temp in K
56
```
ΔG= (-)
ΔG= (+)
```
(-) = spontaneous-reaction will proceed in forward direction
(+) = not spontaneous-reaction will proceed in reverse direction
57
Rxn 1 in Glycolysis?
```
1-aka-
2-enzyme used?
3-ΔG
4-what direction will this reaction proceed?
5-coupled with ATP?
```
conversion of glucose to glucose-6-phosphate
1-hexokinase rxn
2-hexokinase
3-ΔG=~-16 kJ/mol
4-will proceed in forward only-(unidirectional)
5-yes
58
Reaction # 2 glycolysis?
```
1-aka
2-enzyme used?
3-ΔG
4-what direction will this reaction proceed?
5-coupled with ATP?
```
conversion of glucose-6-phosphate to fructose-6-phosphate
```
1-phosphoglucoisomerase rxn
2-phosphoglucoisomerase
3-ΔG=~0
4-bi-directional can go both ways
5- this rxn is not linked to ATP
```
59
Reaction #3 in glycolysis?
```
1-aka
2-enzyme used?
3-ΔG
4-what direction will this reaction proceed?
5-coupled with ATP?
```
conversion of fructose-6-phosphate to fructose-1,6 biphosphate
```
1-phosphofructokinase rxn
2-phosphofructokinase
3-ΔG= (-)
4-only proceeds in the forward direction (unidirectional)
5- coupled with ATP
```
60
Reaction # 4 in glycolysis?
```
1-aka
2-enzyme used?
3-ΔG
4-what direction will this reaction proceed?
5-coupled with ATP?
```
breaks fructose 1-6 biphosphate up into DHAP and GAP
```
1-adolase reaction
2-adolase
3-ΔG=~ 0
4-bidirectional enzyme
5-no
```
61
Reaction # 5 glycolysis?
```
1-aka
2-enzyme used?
3-ΔG
4-what direction will the reaction proceed?
5-coupled with ATP?
```
conversion of Dihydroxyacetonephosphate to Glyceraldehyde-3-phosphate
```
1-triose-phosphate isomerase reaction
2-triose-phospahte isomerase
3-ΔG=~0
4-bi-directional
5-no
```
62
Reaction #6?
```
1-aka
2-enzyme used?
3-ΔG
4-what direction will the reaction proceed?
5-coupled with ATP?
```
conversion of Glyceraldehyde-3-phosphate to 1,3-bi-phosphoglycerate
1-glyceraldehyde-3-phosphate dehydrogenase reaction
2-glyceraldehyde-3-phosphate dehydrogenase
3-ΔG~0
4-bi-directional
5-no
63
Reaction 6 of glycolysis gives off what?
1-NADH and 1 is given off as proton
64
Reaction # 7 of glycolysis?
```
1-aka
2-enzyme used?
3-ΔG
4-what direction will the reaction proceed?
5-coupled with ATP?
```
conversion of 1,3-bisphosphoglycerate to 3-phosphoglycerate
```
1-phosphoglycerate kinase reaction
2-phosphoglycerate kinase
3-ΔG=~0
4-bi-directional
5-no
```
65
Reaction # 8 of glycolysis?
```
1-aka
2-enzyme used?
3-ΔG
4-what direction will the reaction will proceed?
5-coupled with ATP?
```
conversion of 3-phosphoglycerate to 2-phosphoglycerate
```
1-phosphoglycerate mutase reaction
2-phosphoglycerate mutase
3-ΔG~0
4-bi-directional
5-isomerization rxn
```
* isomerization rxn
66
Reaction # 9 of glycolysis?
```
1-aka
2-enzyme used?
3-ΔG
4-what direction will the reaction proceed?
5-coupled with ATP?
```
conversion of 2-phosphoglycerate to phosphoenolpyruvate
```
1-enolase reaction
2-enolase
3-ΔG=~0
4-bi-directional
5-no
```
67
Reaction # 10 of glycolysis?
```
1-aka
2-enzyme used?
3-ΔG
4-what direction will the reaction proceed?
5-coupled with ATP?
```
conversion of phosphoenolpyruvate to pyruvate
```
1-pyruvate kinase reaction
2-pyruvate kinase
3-ΔG= (-)
4-unidirectional
5-yes
```
68
Net reaction for glycolysis?
Glucose + 2 NAD +2ADP + 2 Pi-------->
| 2 Pyruvate + 2 NADA + 2H + 2ATP
69
What is substrate level phosphorylation?
transfer of phosphate from a metabolite to ADP to form ATP
70
What 3 reactions in glycolysis produce ATP?
Reactions 1,3,10
71
How do we get glucose out of storage?
glycogen phosphorylase breaks down alpha 1-4 bonds of glucose
72
What is amylase used for?
dietary starch
73
Which is more oxidized?
pyruvate or glucose
pyruvate
74
Pyruvate is toxic and cannot be allowed to build up. What is it converted to?
lactic acid
75
what is gluconeogenesis?
the production of glucose from pyruvate and other small molecules
76
Which enzymes in glycolysis are also used in gluconeogenesis?
the bidirectional ones
77
Where does gluconeogenesis take place
cytosol
78
For every 1 glucose molecule the gluconeogenesis cycle needs to be repeated how many times?
2X
79
What happens if the glucose levels are low in gluconeogenesis?
the pathways will go back towards glucose
80
net reaction for gluconeogenesis?
2 pyruvate + 4 ATP+ 2 GTP + 2 NADH + 6 H2O--------->Glucose = 2 NAD + 4 ADP + 2 GDP + 6 Pi
81
negative energy (-)
oxidation of NADH + FADH2 by O2
82
positive energy (+)
coupled to formation of ATP from ADP + Pi
83
Where does each take place?
1-glycolysis?
2-Krebs?
3-oxidative phosphorylation (electron transport chain)?
1-cytoplasm
2-matrix
3-innermembrane of mitochondria space
84
Oxidation=
| Reduction=
Ox-Loss of e-
| Red-gain of e-
85
How many ATP's for every NADH?
~3 ATP's
86
Enzyme for krebs cycle in mitochondrial matrix (2)?
1-outer-very poris-free flowing
| 2-inner-excedingly good barrier-non-poris. if anything gets transported-by a specific protein
87
Glycolsis
unidirectional enzymes (3)
1-hexokinase
2-phosphofructokinase
3-pyruvate kinase
