Molecular Biology Flashcards
(106 cards)
1
Q
Hydrophilic?
A
Water loving Polar compounds Dissolve in water
2
Q
Hyrdophobic?
A
Water repelling Nonpolar Compounds Aggregate away from water
3
Q
Solvant Shell
A
Shell of solvent surrounding a solute If water is the solvent, called hydration shell
4
Q
Amphipathic lipids
A
Molecules with hydrophilic polar head groups and hydrophobic non-polar tail groups i.e. phospholipids
5
Q
Hyrdolysis reaction?
A
Water is used to break apart macromolecules
6
Q
Dehyrdation reaction?
A
Water is a product of macromolecular synthesis
7
Q
Relative amount of water compared to other molecular components in a cell is?
A
75%
8
Q
Lipids?
A
Hydrophobic Energy storage function Structural fuction
9
Q
Types of lipids:
A
- Triglycerides 2. Fatty acids (including eicosanoids) 3. Phospholipids 4. Glycolipids 5. Steroids 6. Terpenes
10
Q
Fatty acids:
A
Buliding blocks Energy produced when oxidized
11
Q
Saturated fatty acids vs. unsaturated?
A
Saturated = no double or triple bonds Unsaturated = double or triple bonds (evident b/c kink in structure)
12
Q
Phospholipids:
A
Part of cell membranes! i.e. Plasma membrane, micelles etc.
13
Q
Gycolipids:
A
Carbohydrate heads and nonpolar tails Energy source and cell surface markers (used for cell recognition)
14
Q
Steroids
A
Cell membrane -> Cholesterol Steroids also used for hormone synthesis i.e. androgens and corticosteroids Al
15
Q
Terpenes:
A
Contain ringed structure with tail, both have double bonds (unsaturated hydrocarbon chain) i.e. Vitamin A
16
Q
Eicosanoids:
A
Unsaturated hydrocarbon chain paracrine signalling: prostaglandins, thromboxanes and leukotrienes
17
Q
Lipoproteins:
A
Transporters of lipids (b/c insoluble in blood) lipid hydrophobic core (triacylglycerols and cholesterol) surrounded by phospholipids and apoproteins
18
Q
Triglycerides:
A
Store energy and thermal insulation/padding for organism
19
Q
Four classes of lipoproteins:
A
- Chylomicrons 2. Very low density lipoproteins 3. Low density lipoproteins (Lousy cholesterol (lower protein than fat)) 4. High density lipoproteins (Healthy cholesterol (higher protein than fat))
20
Q
Proteins are made from:
A
Amino acids
21
Q
Central alpha-carbon is linked to:
A
- Hydrogen 2. Carboylic group (COOH) 3. Amino acid (NH2) 4. -R group
22
Q
Four classes of amino acids:
A
- Acidic 2. Basic 3. Polar 4. Nonpolar
23
Q
Acidic:
A
R has a carboxylic acids group deprotonated at pH of 7 or less, amino acid has net neg charge
24
Q
Basic:
A
R has an amino group Protonated at pH of 7, amino acid has a net postivie charge
25
Polar:
R = polar and no charge
26
Nonpolar:
R = nonpolar and hydrophobic
27
Glycine
H3N+ - CH - COOH | H
28
Alanine
H3N+ - CH - COOH | CH3
29
Proline
Ringed structure, will add a Kink in the secondary structure
30
Cysteine
Forms disulfide bonds
31
Primary Structure of a protein:
Sequence of amino acids connected in a polypeptides - peptide bond formed b/c amino group and carboxylic group via dehyrdation
32
Secondary Strucutre of a protein:
Localized folding, Alpha helix and Beta pleated
33
Teritary Structure of a protein:
Folding from R-group interactions
34
R-group interactions that affect Tertiary structure:
1. Hydrophobic interactions 2. Disulfide bond b/w cysteine 3. Electrostatic interactions 4. H bonds 5. Van der Waals
35
Denaturation affects:
Teritary structure, NOT primary structure
36
What denatures a teritary structure:
1. Heat 2. Salt 3. pH change 4. Urea 5. Mercaptoethanol 6. Organic Solvents
37
Heat denatures:
Everything
38
Salt denatures:
Electrostatic bonds
39
pH change
Electrostatic bnds
40
Urea
H bonds
41
Mercaptoethanol
disulfides
42
Organic solvents
hydrophobic interactions
43
Quaternary structure:
More then one polypeptide chain, each chain is a subunit! Same bonds as involved in teritary structures
44
Homodimer
Two identical subunits
45
Heterodimer
Two non-identical subunits
46
Glycoproteins:
Carbohydrate group attached to protein (component of Plasma membrane)
47
Proteoglycans:
More than 50% carbohydrate w/ some protein component of extracellular matrix
48
Cytochromes:
Covalently attached prosthetic group necessary for functions i.e. Hb and cytochromes of electron transport chain
49
Enzymes:
- proteins that function to increase the rate of biological processes
- alternate pathway for biological interaction that reduced activation energy
- not consumed in reaction -not altered during the reaction
- globular proteins
50
51
- delta G = ?
Spontaneous Reaction
52
+ delta G = ?
Nonspontaneous reaction
53
Models for enzyme-substrate complex?
1. Lock and Key Theory
2. Induced Fit theory
54
Lock and Key Theory
Substrate fits exactly into the active site of the enzyme
55
Induced fit theory
Active site of the enzyme changes shape as the substrate binds
(High specificty of the substrate, for enzymes that bind to more than one substrate)
56
What are Cofactors?
Nonprotein componenets that allow many enzymes to reach their optimal activity
57
Types of cofactors:
Inorganic metal ions (Fe-S, Mg2+, Cu+ and Mn2+)
organic coenzymes (vitamins and their derivatives)
58
Holoenzyme
Complete, catalytically active enzyme together with its bound coenzyme and/or metal ion
59
Apoenzyme
Protein part of an enzyme
60
What affects enzyme reaction rate?
pH, Temperature and substrate concentration
61
Optimal range of temperature and pH for most human enzymes:
Temperature: 37°C
pH range: 6 - 8
62
Competitive Inhibitors
Reversibly bind to a portion of the active site, blocking substrate from binding
Vmax is the same but Km decreases (lower affinity for substrate)
63
Noncompetitive Inhibitors
Bind to portion of enzyme that is not the active site and changing the conformation of the acitve site.
Decrease Vmax but Km is the same
64
What is Vmax?
The maximum initial velocity or rate of a reaction. Achieved when all the active sites are bound with substrate.
65
What is Km?
Km is the concentration of substrate that leads to half-maximal velocity. Km = 1/2 Vmax
66
How can the rate of reaction for a competitively inhibited enzyme be increased?
Overcome by increasing substrate concentration
67
How can the rate of reaction for a noncompetitively inhibited enzyme be increased?
Can't be increased!
68
What is negative feedback?
Regulation of enzymes that occurs when one of the products downstream in a reaction series comes back and inhibits the enzymatic activity of an earlier step.
69
What is positive feedback?
Regulation of enzymes that occurs when one of the products downstream in a reaction comes back and increases the enzymatic activity of an earlier step
70
What is proteolytic cleavage?
Inactive enzymes are irreversibly activated by proteolytic cleavage
71
Zymogens
Inactive enzymes
72
Reversible covalent Modification
Enzyme activation often via a modifer (i.e. phosphorylation)
73
Control Proteins
Control protein(s) subunits assocaite with enzyme to activate or inhibit their activity (removal or addition)
74
Allosteric Interactions
Allosteric regulators modify enzyme configuration and activity by binding to specific sites on the enzyme
Both allosteric inhibitors and allosteric activators can exist for same enzyme!
75
Carbohydrates
Made from carbon and water and have the empirical formula C(H2O)
76
Anomers
Stereoisomers of cyclic saccharides that differ in their configuration at the anomeric carbon
(desginated Alpha and beta)
77
alpha - D - glucopyranose
78
beta - D - glucopyranose
79
What is a glycosidic linkage?
A type of covalent bond that joins a carbohydrate(sugar) molecule to another group, which may or may not be another carbohydrate
80
Storage of glucose in plants are primarily which compounds?
Starch and Cellulose
81
Cellulose contains which linkages?
Beta Linkages (i.e. ß- 1,4) (without any branching)
82
Glycogen contains which linkage?
Alpha linkages (with branch)
83
Starch contains which linkage?
Alpha linkage with the minimum amount of branching
84
Why can't some animals break down cellulose?
Animals eat alpha linkages, only bacteria can break beta linkages
85
Anabolic metabolism
Molecular synthesis
86
Catabolic Metabolism
Molecular degradation
87
Substrate level phosphorylation
A type of phosphorylation in which the phosphoryl group is transferred from a donor compound (a phosphorylated reactive intermediate) to the recipient compound.
In substrate-level phosphorylation, the PO43- from a phosphorylated substrate is transferred to ADP to formATP. Phosphorylases and kinases catalyse this process.
88
Oxidative Phosphorylation
A metabolic pathway that generates ATP from ADP through phosphorylation that derives the energy from theoxidation of nutrients.
The process however involves oxidation that it produces reactive oxygen species, which contributes to the propagation of free radicals.
89
During glycose metabolism what occurs in the liver?
Liver breaks down glycogen into glycose 1- phsophate, which is then converted into glucose 6-phosphate and the hydrolyzed to glucose.
This is then exported into the blood for transport.
90
What occurs when there is a high concentration of glucose present in the blood?
Insulin binds to insulin receptors which transduces a signal to GLUT4 a membrane bound protein to increase uptake of glucose into a cell.
91
Where does glycolysis take place?
Cell cytoplasm
92
What occurs in glycolysis?
Glucose (6 Carbon) is broken down into 2 pyruvate molecules (3 Carbon each). This process occurs without O2
93
What are the important steps of glycolysis?
Look at highlighted words!
94
Where does the Electron transport chain occur?
Inner membrane of the mitochondria
95
Where does the krebs cycle occur?
The matrix of the mitochondria
96
How does pyruvate enter the mitochondria?
The outer membrane of the mitochondrion is permeable to small molecules.
Note: converted into the coenzyme acteyl CoA (reaction produces NADH and CO(2))
97
Pyruvate
98
Acetyl-CoA
99
What are the important aspects of the Krebs cycle?
(Nac Nac Ga Fa Na) x 2 (2 pyruvate)
(Nac = NADH, and CO(2))
(Ga = GTP and ATP)
(Fa = FADH(2))
(Na = NADH)
100
What are the important aspects of the electron transport chain?
Cytochromes embedded within the inner membrane of mito (IMM) are arranged in increasing electronegativity ( I → II → III → IV).
Energy is released from the transfer of electrons (NADH or FADH(2)) and this energy is used o pump protons across IMM.
Redox!
Resulting proton-motive force drives ATP synthesis!
101
What are the important differences between I → II transfer and II → III transfer in the ETC?
When I → II transfer:
* NADH is used as the conenzyme (producing NAD+ + H+)
* H+ is transfered into the intermembrane space (increasing proton-motive force)
* 3 H+ is transfered by time get to IV cytochrome
When II → III transfer:
* Succinate is used as the coenzyme (producing fumarate)
* H+ is not transfered into the intermembrane space
* Only 2 H+ are only pumped across intermemrbane space by time get to IV cytochrome
102
What is the net ATP produced from one glucose molecule through an/aeronic respirtation?
36
## Footnote
From glycolysis 6 ATP derived
From prep stage (i.e. pyrivateto acetyl CoA) 6 ATP derived
From Krebs cycle + electron transport chain 24 ATP derived
103
How many ATP's are derived from NADH?
FADH(2)?
NADH: 3 ATP unless shunted from glycolysis then require ATP to do so (so 2 ATP)
(complex I)
FADH(2): 2 ATP
(complex II)
104
What would happen to the pH difference across the inner membrane of the mitochondrion if ATP synthase was posioned?
Protons would stick in IMS, pH would decrease because of an increase in H+, eventually lead to proton saturation and shut down of the electron transport chain.
105
What would occur to the generation of ATP in a mitochondrion if proton holes were suddenly created along its inner membrane?
The electrochemical gradient would dissipate, (H could just diffuse back over) this would decrease ATPase function
(note that compounds that do this are called uncouplers)
106
What are the important aspects of fermentation?
1. It is anaerobic
2. Cell can produce some ATP but cytosolic NAD+ is depleted
3. Occurs in tired muscles (lactic acid)
4. Yeast undergoes a similar process except when oxidizes NADH, pyruvate is reduced (ethanol)
