Biochemistry Flashcards
0
Q
What has more carbon oxidation: alkane (in fats) or carbon dioxide?
A
Carbon dioxide
1
Q
What is phosphorylation and de-phosphorylation?
A
The addition or removal of PO4
2
Q
What is the final product of catabolism?
A
Carbon dioxide
3
Q
What is more reduced: alcohol or aldehyde?
A
Alcohol
4
Q
What are three biomolecules used for information storage?
A
DNA
RNA
NADH/NAD
5
Q
What is the energy currency?
A
ATP
6
Q
What do peptides and proteins consist of?
A
Amino acids
7
Q
Give three types of lipids
A
Triglycerides
Phospholipids
Steroids
8
Q
What are the two nucleic acids?
A
DNA
RNA
9
Q
Name 4 disaccharides
A
Lactose
Maltose
Sucrose
Cellobiose
10
Q
Name two polysaccharides
A
Cellulose
Glycogen
11
Q
What is the first law of thermodynamics?
A
Energy is neither created or destroyed
12
Q
What is the second law of thermodynamics?
A
When energy is converted from one form to another, some of that energy becomes unavailable to do work
13
Q
What are reactions in which the total free energy of the product is less that the total free energy of the reactant?
A
Exergonic reactions
14
Q
In an exergonic reaction, what is deltaG? and are the reactions spontaneous or not?
A
Negative and spontaneous
15
Q
What are reactions in which the total free energy of the products is more than the total free energy of the reactants?
A
Endergonic
16
Q
What is deltaG in endergonic reactions?
A
positive
17
Q
deltaG values of near zero are characteristic of what?
A
Readily reversible reactions
18
Q
What enzyme catalyses the reaction of glucose-6-phosphate to glucose-1-phosphate?
A
Phosphoglucomutase
19
Q
What are anhydride bonds?
A
High energy bonds
20
Q
What is catabolism?
A
breaking down complex molecules into smaller ones and releasing energy
21
Q
What is anabolism?
A
Synthesising complex molecules out of smaller ones in energy-consuming reactions
22
Q
Give an example for a catabolic pathway?
A
Glycolysis
23
Q
What pathway is the initial breakdown of glucose for the generation of ATP?
A
Glycolysis
24
What is the net gain of ATP molecules per glucose molecule in glycolysis?
Net gain of 2 ATP
25
Give an example of an anabolic pathway?
Gluconeogenesis
26
What pathway involves making new glucose from non-carbohydrate precursors such as pyruvate?
Gluconeogenesis
27
What are useful control points in metabolic pathways?
Reactions with large negative deltaG values are useful control points
28
Is water polar or non-polar?
Polar
29
What shape are water molecules?
Tetrahedral shape and forms a dipole
30
What are amphipathic molecules?
Both hydrophilic and hydrophobic
31
What type of molecule is sodium palmitate?
Amphipathic
32
What do peptides have at each end of their molecules?
N-terminal residue and C-terminal residue
33
What direction is the peptide chain in?
From N-terminal to C-terminal
34
State three things about peptide bonds?
Peptide bonds have a partial double bond character
Peptide bonds are planar
Peptide bonds are strong and rigid
35
What is pH?
The measurement of the amount of protons in a solutions
36
What important equation lets us calculate the properties of buffer solutions?
Henderson-Hasselbalch equation
37
State the Henderson-Hasselbalch equation
pH = pKa + log [A-]/[HA]
38
What substances tend to resist a change of pH on addition of moderate amounts of acid or base?
A buffer solution
39
What are zwitterions?
Amino acids without charged side groups exist as these in neutral solution
40
What is the pH at which a molecule has no net charge called?
The isoelectric pH
41
What can act as buffers?
Proteins e.g. haemoglobin in the blood
42
What is the primary structure of a protein?
The sequence of amino acid residues
43
What is the secondary structure of a protein?
The localised conformation of the polypeptide backbone
44
What is the tertiary structure of a protein?
The three-dimensional structure of an entire polypeptide chain, including its side chains
45
What is the quaternanry structure of a protein?
The spatial arrangement of polypeptide chains in a protein with multiple subunits
46
What two angles can polypeptides rotate around?
angle between:
The alpha-carbon and the amino group
The alpha-carbon and the carboxyl group
47
What are the three types of secondary protein structures?
1. Alpha helix
2. Beta strands and sheets
3. Triple helix
48
How many polypeptide chains does an alpha helix have?
One
49
What residues break alpha helixes?
Proline residues
50
What two directions could betasheets be in?
Parallel or antiparallel
51
What are the turns between strands on beta sheets?
Glycine and proline
52
Give an example of a triple helix?
Collagen triple helix
53
What type of protein structure is the component of bone and conective tissues?
Collagen triple helix (secondary)
54
In what protein structure does this occur: three left handed helical chains twisted around each other form a right-handed superhelix?
Collagen triple helix
55
What 2 types of bonds do collagen triple helixes have?
Inter-chain H-bonds - involving hydroxylysine and hydroxyproline
Covalent inter- and intra-molecular bonds
56
What type of protein structure are fibrous proteins and globular proteins?
Tertiary structures
57
What type of proteins contain polypeptide chains organised approximately parallel along a single axis?
Fibrous proteins
58
Give two examples of fibrous protein?
1. Keratin of hair and wool
| 2. Collagen of connective tissue of animals including cartilage, bones, teeth, skin and blood vessels
59
What proteins are folded into more or less spherical shapes?
Globular proteins
60
Which are soluble in water: Globular proteins or Fibrous protiens?
Globular protiens
61
Give two examples of globular proteins?
Myoglobin
| Haemoglobin
62
What 5 forces stabilise tertiary protein structures?
1. Covalent disulphide bonds
2. Electrostatic interactions = salt bridges
3. Hydrophobic interactions
4. Hydrogen bonds: back bone, side chain
5. Complex formation with metal ions
63
Where are charged (polar) side groups normally located?
On the outside of proteins
64
Where do amino acids with hydrophobic side-chains tend to cluster?
In the centre of globular proteins
65
In sickle cell anaemia - what is the single nucleotide sequence change?
In coding region of the beta-chain of haemoglobin A
66
What does the single nucleotide sequence change in sickle cell anaemia result in?
Valine instead of glutamic acid
67
What happens to haemoglobin under low oxygen conditions?
Haemoglobin polymerises which results in rigid, sickle shape cells
68
Give 2 examples of disease caused by malfunctions with folding polypeptide chains
Alzheimers
| Parkinsons
69
What are prion proteins?
Normal components of teh brain
70
Where are disease-causing forms of prion proteins?
Enriched in beta-sheets (aggregates into multimeric complexes, resistant to degradation)
71
What do Thiol agents and reducing agents do to disulphide bonds?
Reduce and therby disrupt disulphide bonds
72
In myoglobin - what does the haem group contain?
An iron ion (Fe II) and a prosthetic group
73
How many subunits does haemoglobin have?
4 - two alpha and two beta chains
74
How many oxygen molecules can each sub unit of haemoglobin bind?
ONE
75
What is nucleotide to nucleotide?
Transcription
76
What is nucleotide to amino acid?
Translation
77
What is a nucleoside?
A base and sugar
78
What is a nucleotide?
A nucleoside and a phosphate group
79
What does ribose have attached to carbon 2?
OH
80
What does 2-deoxyribose have attached to its carbon 2?
H
81
What are the purines?
Adenine and Guanine
82
What are the pyrimidines?
Uracil, Thymine and Cytosine
83
What is a phosphodiester bond formed between?
A free 3' OH group and a 5' triphosphate group
84
What end of the DNA strand are new nucleotides added to?
3'
85
What drug is used to suppress HIV?
Retrovir
86
How many hydrogen bonds are between A and T?
2
87
How many hydrogen bonds are between C and G?
3
88
What type of replication is semi-conservative?
DNA replication
89
What is DNA replication catalysed by?
DNA polymerase
90
What is required to start DNA replication?
An RNA primer
91
What are the fragments called on a lagging strand?
Okazaki fragments
92
What unwinds the double helix?
DNA helicase
93
What are the 4 building blocks of DNA replication?
dATP
dTTP
dCTP
dGTP
94
During DNA replication one phosphate group froms phosphodiester bond, what do the other two leave as?
Pyrophosphate - energy supply
95
What strand is the leading strand?
(3' - 5')
96
What strand is the lagging strand?
(5' - 3")
97
What is the RNA primer synthesised by?
Primase
98
What are the 3 main classes of RNA?
1. Ribosomal RNA (rRNA) - combines with proteins to form ribosomes where protein synthesis takes place
2. transfer RNA (tRNA) - carries the amino acids to be incorporated into the protein
3. messenger RNA (mRNA) - carries the genetic information for protein synthesis
99
What are the two stable types of RNA?
Ribosomal RNA and Tranfer RNA
100
How many types of RNA polymerases do prokaryotic cells have?
One
101
How many types of RNA polymerase fo eukaryotic cells have?
Pol I, Pol II and Pol III (3 types)
102
How can Pol I, Pol II and Pol II be distinguished?
By their sensitivity to toxins like alpha-amanitin
103
What does Pol II synthesise?
All mRNA
104
What are the five steps of transcription?
```
RNA polymerase binding
DNA chain seperation
Transcription initiation
Elongation
Termination
```
105
What does RNA polymerase binding require?
Transcription factors
106
What are initiation sites on DNA called?
Promoters
107
Where is the TATA box found?
In a promoter
108
What does a TATA box binding protein do first?
Recognises TATA box
109
What is TFIID?
a general transcription factor
110
What is TFIID required for?
All Pol II transcribed genes
111
What two steps occur after TATA box binding protein has recognised a TATA box?
1. Introduces a kink into DNA - determines transcriptional start and direction
2. Provides a landing platform for further transcription factors and for RNA polymerase
112
What do Pol II and TFIID do on their own?
Extend transcript
113
What kind of structure does newly synthesised RNA make?
A stem loop structure
114
Specific regulation of transcription requires 'specific' transcription factors - what are they?
DNA-binding proteins
115
What do DNA-binding proteins do?
Bind to specific DNA sequences in the vicinity of a promotor
| Regulate transcription postively or negatively
116
Name a family of transcription factors
Steroid receptors
117
What 3 domains do steroid receptors have?
Transactivation domain
DNA-binding domain
Ligand-binding domain
118
What can be said about the DNA-binding and ligand-binding domains on a steroid receptor?
They are highly conservative
119
Where are steroid receptors located?
In the cell cytoplasm (inactive)
120
What do steroid receptors do once they have binded to a ligand?
Move to nucleus and bind to DNA at steroid-response elements
121
In eukaryotic genes what are the coding regions (exons) interrupted by?
Non-coding regions (introns)
122
What has to be removed before translation into a protein?
Introns (splicing)
123
When processing the ends of mRNAs, what two things are added?
1. Addition of poly(A) TAIL
| 2. Addition of 5' cap
124
During translation, anticodons of tRNA molecules form base pairs with what?
Codons on mRNA
125
What are the 7 components of translation?
1. Amino acids
2. tRNAs
3. Aminoacyl-tRNA synthetases
4. Set of protein factor for initiation of protein synthesis, elongation of polypeptide chain and translocation and termination
5. ATP and GTP as sources of energy
6. Ribosomes
7. mRNA
126
What binds amino acids to their corresponding tRNA molecules?
Aminoacyl-tRNA synthetase
127
How many rRNA molecules do ribosomes contain?
4
128
What are the 3 tRNA binding sites on ribosomes?
```
E = exit
P = Peptidyl
A = aminoacyl
```
129
What does inititation require?
Initiation factors
130
What gives the energy required for initiation?
GTP is hydrolysed to provide energy for inititation
131
What is AUG?
Start codon
132
What base pairs with the start codon?
Special 'initiator' tRNA with UAC anticodon base pairs
133
During elongation: what brings the next aminoacyl-tRNA to the A site?
An elongation factor (EF-1alpha)
134
What regenerates EF1alpha to pick up the next aminoacyl-tRNA?
A second elongation factor (EFbetagamma)
135
What does peptidyl transferase catalyse?
Peptide bond formation between amino acids in the P and A sites
136
What moves the ribosome along the mRNA?
Elongation factor EF-2
137
When does termination of protein synthesis occur?
When the A site of the ribosome encounters a stop codon
138
What does release factor RF do in termination of protein synthesis?
Binds to stop codon - GTP hydrolysis
139
What is a point mutation?
A change in a single base in DNA
140
What is a missense mutation?
Results in a change of amino acid sequence
| Can change protein function e.g. altered haemoglobin in sickle cell anaemia
141
What mutation creates a new termination codon and changes the length of protein due to premature stop of translation?
Nonsense mutation
142
What mutation is due to degeneracy of the genetic code, has no effect on protein function and has no change of amino acid sequence?
Silent mutation
143
What is a frameshift mutation?
Addition or deletion of a single base
144
What are the 4 chromosomal mutations?
1. Deletions
2. Duplications
3. Inversions
4. Translocations
145
What do free ribosomes in the cytosol make proteins destined for?
Cytosol
Nucleus
Mitochondria
Translocated post-trranslationally
146
Where do bound ribosomes on the rough endoplasmic reticulum make proteins destined for?
```
Plasma membrane
ER
Golgi apparatus
Secretion
Translocated co-translationally
```
147
What is glycosylation?
The addition and processing of carbohydrates in the ER and the Golgi
148
Give three examples of post-translational modifications?
1. Proteolysis
2. Glycosylation
3. Phosphorlyation
149
What is I-cell disease?
Inherited recessive disorder of protein targeting
Proteins normally destined for lysosomes are not properly sorted in the Golgi
End up secreted from cell
Lysosomes cannot properly digest material and become clogged
150
What do enzymes do to the activation energy?
Reduce it by providing alternative reaction pathways
151
What does catalytic activity of many enzymes depend on the presence of?
Cofactors
152
What are the two types of cofactors?
1. Metal ions
| 2. Organic molecules - also called coenzymes
153
What are tightly bound coenzymes called?
Prosthetic goup
154
What is an enzyme without a cofactor called?
Apoenzyme
155
What is an enzyme with cofactor called?
Holoenzyme
156
What are NAD+ and FAD?
Coenzymes
157
What does CoA (coenzyme A) do?
Transfers acetyl groups
158
Three pancreatic serine proteases contain reactive serine residue and they catalyse hydrolysis of peptides at specific sites. What are the three proteases and how do they work?
1. Chymotrypsin: hydrophobic pocket binds aromatic amino acids
2. Trypsin: negatively charged Asp interacts with positively charged Lys or Arg
3. Elastase: active site partially blocked, only amino acids with small or no side chains can bind
159
Would trypsin active site be affected by a small change in pH?
Yes
160
What are isozymes?
They are isoforms of enzymes that catalyse the same reaction but have different properties and structure
161
What isozyme is involved in developmental variation?
Haaemoglobin
162
Give an example of a tissue specific isoform?
Lactate Dehydrogenase (LDH)
163
Where are the two types of subunit in LDH present?
One predominantly in the heart
| One predominantly in skeletal muscle
164
What does an increase in LDH in blood suggest?
Tissue damage
165
What is Creatine Kinase (CK)?
A dimeric protein which binds to the muscle sacromere
166
Where is the M form of CK produced?
In the muscle
167
Where is the B form of CK produced?
In the brain
168
What are phosphorylation reactions carried out by?
Protein kinases
169
What are zymogens?
Inactive precursors of an enzyme - are irreversibly transformed into active enzymes by cleavage of a covalent bond
170
In the pancreas: what two zymogens are formed?
1. Trypsinogen
| 2. Chymotrypsinogen
171
What is the formation of the enzyme-substrate complex (ES) described by?
KM - The Michaelis constant - a combination of all rate constants in the reaction
172
What is Vmax?
The maximal rate of reaction at unlimited substrate concentration
173
How is the initial rate of an enzyme reaction is measured?
The tangent at the curve at time 0
174
What is the Michaelis constant KM equivalent to?
The substrate concentration where the intitial reaction rate is half-maximal
175
KM = [S] at?
at 0.5 Vmax
176
What does a low KM mean?
That an enzyme only needs a little substrate to work at half-maximal velocity
177
What does a high KM mean?
That an enzyme needs a lot of substrate to work at half-maximal velocity
178
What describes the rate of catalysis as a function of substrate concentration?
The Michaelis-Menton equation
179
On a Lineweaver-Burk plot how can Vmax be determined?
From the intersection of the straight line with the Y axis
180
On a Lineweaver-Burk plot, how can KM be determined?
From the intersection with the X axis
181
What is glucokinase?
An isozyme in liver and pancreas
182
Where is hexokinase I found?
In red blood cells
183
What is caused by mutations in pancreatic glucokinase which affect KM or Vmax?
MODY - Maturity-Onset Diabetes of the Young
184
What is a reversible inhibitor?
A substance that binds to an enzyme to inhibit it, but which can be reversed
185
What is an irreversible inhibitor?
A substance that causes inhibition that cannot be reversed
186
How can the competetive inhibitor of an enzyme be 'out-competed'?
By the addition of lots of substrate
187
How can a non-competitive inhibitor be 'out-competed'?
It cannot
188
What are the 5 methods of enzyme control?
1. Allosteric control
2. Regulation of traanscription - varies rate of protein synthesis
3. Reversible covalent modification - we have seen phosphorylation as one mechanism
4. Irreversible covalent modification - we have seen proteolytic cleavage
5. Degradation
189
Inhibition of rate limiting enzymes by end products is a common mechanism of what?
Allosteric control
190
What type of enzymes do not follow Michaelis-Menten kinetics?
Allosteric enzymes
191
Give an important example for allosteric regulation
Binding of oxygen to haemoglobin
192
What is the binding of oxygen to haemoglobin controlled by?
H+
CO2
2,3 bisphosphoglycerate (side product of glycolysis)
193
In the absence of substrate - what are most enzyme subunits in?
The inactive from (tight form)
194
The binding of a substrate induces a conformational change from which forms?
T form to R form
195
What do allosteric activators or inhibitors do to the binding of a substrate?
Lock subunits in the T or R form
196
Where is fat stored?
In adipose tissue
197
Where are ketone bodies formed?
In liver mitochondria
198
What type of process is catabolism?
Oxidative, endergonic
199
What type of process is anabolism?
Reductive, endergonic
200
What are proteins broken down into?
Amino acids
201
What are polysaccharides broken down into?
Simple sugars
202
What are lipids broken down into?
Fatty acids and glycerol
203
During catabolism: small molecules from the degradation of macromolecules enter cells and are converted into a small number of very simple molecules, what are they?
2- carbon acetyl-CoA
| some ATP is produced
204
What group of acetly-CoA enters the Krebs cycle?
Acetyl group
205
What happens to the acetyl group one it has entered the Krebs cycle?
It is completely degraded to CO2 and water
206
What allows glucose to transport into cells?
Na+/glucose symporters, via passive facilitated diffusion glucose transporters
207
Where is GLUT 1 transporter present?
In teh brain
208
Where is GLUT 2 transporter present?
In the liver
| Beta-cells
209
Where is GLUT 3 transporter present?
In the brain
210
Where are GLUT 4 transporters present?
In muscle and adipose tissue
211
Where are GLUT 5 transporters present?
In teh gut
212
What is the initial pathway for the conversion of glucose to pyruvate?
Glycolysis
213
What is hexokinase involved in?
The conversion of glucose to glucose-6-phosphate
214
What is phosphofructokinase involved in?
The conversion of fructose 6-phosphate to fructose 1,6-biphosphate
215
What controls the conversion of phosphoenolpyruvate to pyruvate?
Pyruvate kinase
216
What is the key enzyme in the control of glycolysis?
Phosphofructokinase
217
What are the 3 negative modulators of phosphofructokinase?
1. ATP
2. Citrate
3. H+ - prevents the excessive formation of lactic acid
218
What are the 2 positive modulators of phosphofructokinase?
AMP
| fructose 2,6-bisphosphate
219
The ATP/AMP ratio is called the energy charge: if all adenylate nucleotides are in the shape of ATP what is the cell said to be in?
A fully charged state
220
What does glycolysis reduce NAD+ to?
NADH + H+
221
What must happen to NADH for glycolysis to continue?
It must be re-oxidised
222
What are the 2 fates of pyruvate anaerobically?
1. Alcohol fermentation - yeast can form ethanol from pyruvate
2. Lactic acid fermentation - some microorganisms can convert pyruvate to lactate
223
What is the fate of pyruvate in aerobic conditions?
Further oxidation and more energy released
224
What enzyme is involved in the conversion of pyruvate to lactate?
Lactate dehydrogenase
225
In what cycle does further oxidation of pyruvate occur?
The citric acid cycle or Krebs cycle or TCA cycle
226
What does the matrix of the mitochondria contain?
Enzymes for the TCA cycle
227
What do the inner membranes of mitochondria contain?
Proteins for electron transport chain, ATP synthase and transport proteins
228
Once in the mitochondria what does the pyruvate dehydrogenase complex (PDC) do to pyruvate?
Catalyses the oxidative decarboxylation of pyruvate to acetyl-CoA
229
Is the reaction of pyruvate to acetyl-CoA reversible?
NO ACETYL-COA CANNOT BE CONVERTED TO PYRUVATE
230
The pyruvate dehydrogenase complex consists of 3 enzymes involved in the actual reaction - what are they?
E1, E2 and E3
231
Pyruvate dehydrogenase complex also contains 2 enzymes involved in the control of PDC - what are they?
A kinase and a phosphatase in a single polypeptide
232
Pyruvate dehydrogenase complex also contains 5 coenzymes - what are they?
Thiamine, lipoic acid, coenzyme A, FAD and NAD+
233
How many GTP is formed during the TCA cycle?
one GTP
234
What enzyme of the TCA cycle is not located in the mitochondrial matrix?
Succinate dehydrogenase - integrated in the inner mitochondrial membrane
235
What enzyme is involved in this reaction:
Succinate + FAD = fumerate + FADH2
Succinate dehydrogenase
236
What is acetyl-CoA oxidised completely to in teh TCA cycle?
Carbon dioxide
237
What does each turn of the TCA cycle involve?
The uptake of 2 carbon atoms in the form of acetyl-CoA and the release of 2 carbon atoms as carbon dioxide
238
Each turn of the TCA cycle involves the transfer of 3 pairs of electrons to NAD+ to form?
NADH + H+
239
Each turn of the TCA cycle also results in the transfer of 1 pair of electrons to reduce FAD to what?
FADH2
240
From each acetyl-CoA the TCA cycle generates what?
3 x NADH + H+
1 x FADH2
1 x GTP
2 x CO2
241
All together, the reactions of glycolysis, pyruvate dehydrogenase complex and the TCA cycle produce?
10 NADH + 10 H+
| 2 FADH2
242
In oxidative phosophorylation, the electron transfer potential of NADH+ and FADH2 is converted into what?
The phosphoryl transfer potential of ATP
243
What can phosphoryl transfer potential be measured by?
Free energy change for the hydrolysis of ATP
244
What can the electron transfer potential be measured by?
The redox potential of a compound
245
What is a measure of how readily a reduced substance donates an electron?
The standard redox potential
246
What is the driving force of oxidative phosphorylation?
The reduction of oxygen by NADH
247
What are the two stages of oxidative phosphorylation?
1. Electron transport (electrons flow from NADH tand FADH2 to oxygen, respiratory chain, energy is used to pump H+ out of the mitochondrial matrix)
2. ATP synthesis
248
During electron transport - where do electrons from NADH enter?
At complex I
249
During electron transport where do the electrons from FADH2 enter?
At complex II
250
What are proteins which contain a haem group as a functional co-factor?
Cytochromes
251
Where is the F1 subunit of ATP synthase located?
Protrudes into the mitochondrial matrix
252
Where is the F0 subunit of ATP synthase located?
As a hydrophobic complex in the inner memrbane - contains the proton channel
253
What forms stator (ATP synthase)?
a, b, alpha, beta and delta subunits form stator
254
What forms rotor (ATP synthase)?
c, gamma and (greek E) subunits form rotor
255
What turns the rotor in ATP synthase?
Flow of protons
256
What three things inhibit transfer of electrons to oxygen during oxidative phosphorylation?
Cyanide
Azide
CO
257
What does brown adipose tissue contain?
Uncoupling protein (UCP) = thermogenin
258
Where does glycolysis take place?
in the cytoplasm
259
How does NADH from the cytoplasm get into the oxidative phosphorylation pathway?
The glycerol-3-phosphate and malate shuttles overcome this
260
How much ATP does one glucose molecule yield?
30-32 ATP molecules
