1. Molecular Biology; Cellular Respiration Flashcards
ExamKrackers Chapter 1
1
Q
How much of the cell’s mass is made up of water?
A
70% - 80%
2
Q
Hydrophobic
A
Water Fearing
Molecules that move away from water.
3
Q
Hydrophilic
A
Water loving
Molecules that dissolves easily in water. They’re polar molecules like water.
4
Q
Lipid
Examples?
A
hydrophobic molecule
low solubility in water
high solubility in nonpolar organic solvents
fxn: barriers separating aqueous environment
examples: fatty acids, triacylglycerols, phospholipids, glycolipids, steroids, terpenes.
5
Q
Fatty Acids
A
carbon chain, one end is carboxylic acid
come in even number of carbons. max of 24 C in humans.
most fats reach the cell in this form. oxidation provides a lot of chemical energy for a cell.
6
Q
Fatty Acids
Saturated vs. Unsaturated
A
Saturated: contains only SINGLE C-C bonds.
Unsaturated: contains DOUBLE C=C bonds.
7
Q
Triacylglycerides
A
Fats, oils.
Fxn in cell: store energy.
Fxn: thermal insulation, padding.
8
Q
Adipocytes
A
Specialized fat cells.
Cytoplasm contains A LOT of triglycerides.
9
Q
Phospholipids
A
Amphipathic (polar - phosphate end, nonpolar - fatty acid end).
Fxn: structural component of membranes.
10
Q
Steroids
A
Four ringed structure.
Component of membrane.
Fxn: regulate metabolic activities.
Examples: hormones, vitamin D, cholesterol.
11
Q
Major Functions of Lipids
- Phospholipids
- Triacyglycerols
- Steroids
- Fatty Acids (eicosanoids)
A
- Phospholipids - structural component of membranes.
- Triacyglycerols - store metabolic energy, provide termal insulation and padding.
- Steroids - regulate metabolic activities.
- Fatty Acids (eicosanoids) - local hormones.
12
Q
How are lipids transported in the blood?
A
Lipids are hydrophobic, blood is hydrophillic.
Transported via lipoproteins.
13
Q
Lipoproteins
A
Transports lipids in blood.
Has a hydrophobic core (made up of lipids) and hydrophillic shell (phospholipids and apoproteins).
14
Q
How are lipoproteins classified?
What are the major classes?
A
Classified by density.
Low density = Greater ratio of lipid to protein.
Classes:
- Chylomicrons
- VLDL (very low density lipoproteins)
- LDL
- HDL
15
Q
Define protein
A
amino acids chain linked by peptide bonds
16
Q
What makes an amino acid ‘essential’? How many are tehre?
A
‘essential’ proteins cannot be made by the body, must be ingested.
10 of 20.
17
Q
What are the four groups breakdown for the 20 common amino acids?
A
They are categorized based on R groups (side chains)
- Nonpolar
- Polar
- Acidic
- Basic
18
Q
Define protein’s ‘Primary Structure’.
A
Number and sequence of amino acids in polypeptide chain.
19
Q
Define protein’s ‘Secondary Structure’.
A
alpha-helix and beta-pleated sheets make up conformation of protein.
alpha-helix: single chain twists
beta-pleated sheets: single chain lie along side itself in parallel or antiparallel.
connected by hydrogen bonds.
20
Q
Define protein’s ‘Tertiary Structure”.
Define protein’s ‘Quaternary Structure”.
A
Tertiary: 3-D shape formed when peptide chain curls and folds.
Quaternary: Two or more polypeptide chains bind together
All proteins have primary and secondary structures, but not tertiary or quaternary.
21
Q
What are the 5 forces creating protein’s tertiary and quaternary structures?
A
- covalent disulfide bonds between 2 cysteine AA on different parts of the chain.
- electrostatic (ionic) interactions mostly between acidic and basic side chains
- hydrogen bonds
- van der Waals forces
- hydrophobic side chains pushed away from water and toward center of protein
22
Q
Define denatured protein.
Name the force the following denaturing agents disrupt.
A
protein’s conformation is disrupted.
Denaturing Agents Forces Disrupted
Urea Hydrogen bonds
Salt/pH change Electrostatic bonds
Mercaptoethanol Disulfide bonds
Organic solvents Hydrophobic forces
Heat All forces
23
Q
How do we know AA sequence plays a key role in protein conformation?
A
After a protein denatures and the detaturing agent is removed, the protein refold to its original conformation.
24
Q
globular vs. structural proteins
A
Globular: enzymes, hormones, membrane pumps and chanels, membrane receptors, intercellular and intracellular transport and storage, osmotic regulators, immune response, etc.
Structural: maintain and add strength of cellular and matrix structure (collagen, microtubules).
25
26
-ase
ending clue for an enzyme. This means it contains nitrogen and is subject to denaturation.
27
-ose
ending clue for carbs.
28
Acetyl CoA
A coenzyme. Pyruvate is converted to acetyl CoA in a reaction that produces NADH and CO2.
29
Active Site
Position on enzyme to where the substrate binds with noncovalent bonds.
30
Adipocytes
aka fat cells. Specialized cells whose cytoplasm contains almost nothing but triglycerides.
31
Aerobic Respiration
Oxygen is used. Respiration is the energy acquiring stages (glycolysis, kreb cycle, ETC). Pyruvate and NADH (glycolosis products) will move into mitochondria matrix to continue process of making energy. Net 36 ATPs. Final electron acceptor is oxygen (why oxygen is necessary in aerobic respiration).
32
Allosteric Regulation
Binds to enzyme and cause conformational change to inhibit (allosteric inhibitors) or increase (allosteric activators) reactions. Aka negative and positive feedback.
33
alpha-helix
Single chain of primary structure twists into alpha-helix. Reinforced by hydrogen bonds between carbonyl oxygen and hydrogen on the amino group.
34
Amino Acids
Building blocks of proteins. They're alpha AA because the amine is attached to the carbon in the alpha position to the carbonyl. Basic (HAL): Histidine, Argininine, LysineAcidic: Glutamic acid, Aspartic acidPolar (CGATHS): Cysteine, Glutamine, Asparagine, Tyrosine, Threonine, SerineNon-polar: Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline
35
Amphipathic
Having polar and nonpolar characteristics. Polar at one end, nonpolar at the other end.
36
Anaerobic Respiration
Oxygen is NOT used. Respiration is the energy acquiring stages.
37
Apoenzyme
An enzyme without its cofactor and is nonfunctional.
38
ATP
A nucleotide. Source of readily available energy for the cell. Acts as cosubstrate type of coenzyme.
39
ATP Synthase
Protein on mitochondrion membrane that makes ATP as part of ETC. This is oxidative phosphorylation.
40
beta-pleated sheet
Single chain of primary structure lie along side itself forming the beta-pleated sheet. The connecting segments of the two strands of the sheet can lie in the same direction (parallel) or opposite (antiparallel). Reinforced by hydrogen bonds between carbonyl oxygen and hydrogen on the amino group.
41
Carbohydrates
aka sugars or saccharides. Made up of carbon and water, formula C(H2O).
42
Catalyst
Enzymes lower the energy of activation for a bilogical reaction and increase the rate of that reaction. Not consumed nor permanently altered by the reactions. Do not alter equilibrium of a reaction.
43
Cellular Respiration
The second and third stages where energy is acquired. Glucose + O2 --\> CO2 + H2O (combustion rxn).
44
Cellulose
Cellulose is polysaccaride of glucose formed in plants. Beta linkages. Animals do not have the enzymes to digest beta linkages. Bacteria in stomach does the digestion for an animal.
45
Citric Acid Cycle
aka Krebs cycle
46
Coenzymes
A cofactor. Divided into two types cosubstrates and prosthetic groups, both are organic molecules. Cosubstrate: substrate that binds to enzyme, transfer chemical group to the substrate reacting and reforms into original form. It is not destroyed or change, kinda like a catalyst. Example is ATP. Prostetic groups: Covalently bound to the enzyme throughout the reaction and emerge unchanged. Example is heme.
47
Cofactor
A non-protein component that helps enzyme reach their optimal activity. Can be coenzymes or metal ions.
48
Competitive Inhibitors
Bind noncovalently to enzyme, compete with substrate. Increase substrate concentration is classic solution. Example: Sulfanilamide inhibits making of folic acid and so kills bacterial cells. Raise Km, Vmax remains the same.
49
Cooperativity
There's positive and negative cooperactivity. The first substrate changes the shape of the enzyme allowing other substrates to bind MORE easily (positive) or LESS easily (negative).
50
Cyclic AMP
A neucleotide. Important component in many 2nd messenger systems.
51
Dehydration
Water is product, macromolecules are formed. (aka condensation reaction)
52
Denatured
Protein conformation is disrupted (lost most of 1, 2, 3, 4 structures). Often, once the denaturing agent is removed, protein spontaneously refolds - this suggests AA sequence plays a key role in the protein conformation. Denaturing agents - Forces disrupted Urea - Hydrogen bonds Salt or change in pH - Electrostatic bonds Mercaptoethanol - Disulfide bonds Organic solvents - Hydrophobic forces Heat - All forces
53
Disulfide Bonds
COVALENT bond made between two sulfides. In this lecture, it's the bond created between two cysteine AA on different parts of the chain, holding together the tertiary structure.
54
DNA
Made up of nucleotides. Double helix
55
Double Helix
Two strands joined by hydrogen bonds form DNA. A=T (2) and C---G (3)
56
Electron Transport Chain (ETC)
Series of proteins, including cytochromes with heme, in the inner membrane of the mitochondion. Electrons are pass down, ultimately producing water. NADH = 2 to 3 ATPs. FADH2 = 2 ATPs. Final electron acceptor is oxygen (why oxygen is necessary in aerobic respiration).
57
Enzyme Specificity
Enzymes are designed to work only on a specific substrate or group of closely related substrates.
58
Enzyme-Substrate Complex
Enzyme bound to the substrate.
59
Enzymes
Globular proteins. Act as a catalyst.
60
Essential Amino Acid
Body cannot manufacture, it just be ingested directly. There are 10 essential AA.
61
FADH2
A neucleotide. NADH and FADH2 are coenzymes involved in the Krebs cycle.
62
Fats
aka triacylglycerols (energy, thermal insulation, padding)
63
Fatty Acids
A lipid. Building blocks for most complex lipds. Usually comes as even number of carbons, max in humans is 24-carbon chain. Oxidation liberates large amounts of chemical energy for a cell. Most fats reach the cell in this form (not as triacylglycerols). Some fatty acids (eicosanoids) even serve as local hormones
64
Feedback Inhibition
aka Negative Feedback
65
Fermentation
Anaerobic respiration. Glycolosis, reduction of pyruvate to ethanol (yeast) or lactic acid (animals) and oxidizing NADH to NAD+. Important to know fermentation recycles NADH to NAD+ to be coenzyme to go again in glycolosis. Ethanol/lactic acid expelled as waste products. Fermentation happens because cell could not get energy from NADH and pyruvate since no oxygen. NADH recyles to NAD+ to go through glycolosis again hoping there's oxygen this time to go further to get more net ATP.
66
Glucose
cells use to generate ATP for energy. 6 carbons. Accounts for 80% of carbs absorbed by humans. Liver or Enterocytes have converted digested carbs into glucose form for the cells to use. Favors the ring form over the chair form. 2 ANOMERS: - alpha-glucose (OH down) - OH of anomeric carbon and methoxy group on opposite sides. - beta-glucose (OH up) - OH and methoxy group on same side of ring. http://triton.iqfr.csic.es/guide/eNMR/sugar/gif/gluco.GIF
67
Glycerol
Backbone of triglycerides. It can be converted to PGAL to further process to pyruvate to enter Krebs cycle.
68
Glycogen
Polysaccharide of glucose with alpha linkages. Cells form glycogen when there's a surplus of glucose/ATP. Large amounts in muscle and liver cells.
69
Glycolysis
Net 2 ATP and 2 NADH. Occurs in the presence and absence of oxygen. Occurs in the CYTOSOL.
70
Heme
A prosthetic group, which is a type of coenzyme which is a type of cofactor. Heme binds with catalase in peroxisomes to degrade hydrogen peroxide.
71
Holoenzyme
An enzyme with its cofactor. Now it's functional.
72
Hydrogen Bond
Allows water to remain in liquid state in the cellular environment. Provides strong cohesive forces between water molecules.
73
Hydrolysis
Water is reactant, breaking apart macromolecules.
74
Hydrophilic
Polar. Water loving. Easily dissolves in water (water surrounds each molecules).
75
Hydrophobic
Nonpolar. Water fearing. Does not dissolve well in water (molecule remain clumped together).
76
Induced-Fit Model
Example of enzyme specificity. Shape of both the enzyme and the substrate are altered upon binding. Alteration increases specificity and helps the reaction to proceed. In reactions with more than one substrate, the enzyme may also orient the substrates relative to each other, creating optimal conditions for a reaction to take place.
77
Inner Mitochondrial Membrane
Inner membrane is less permeable. Pyruvate still movies in via faciliated difussion. NADH may/may not require hydrolysis of ATP to get inside.
78
Irreversible Inhibitors
Agents that bind covalently to enzyme and disrupt their function. (Some do bind noncovalently too). Usually highly toxic. Example: Penicillin disrupt building of peptidoglycan cell walls.
79
Krebs Cycle
aka Citric Acid Cycle. Acetyl CoA starts cycle that produces 1 ATP, 3 NADH, 1 FADH2 AND 2Co2 and oxaloacetic acid being end result begins the cycle again.Occurs in mitochondrial matrix.
80
Lipid
Hydrophobic. Fxn as barriers separating acqueous environments. (def: any biological molecule that has low solubility in water and high solubility in nonpolar organic solvents) 6 major groups: fatty acids, triacylglycerols, phospholipids, glycolipids, steroids, terpenes
81
Lipoproteins
Amphipathic, used to transport lipds in blood. Lipoproteins are classified by their density. The greater the ratio of lipid to protein, the lower the density. (density = mass/volume). Major classes of lipoproteins: chylomicrons, VLDL, LDL, HDL
82
Lock and Key Model
Example of enzyme specificity. Active site of the enzyme has a specific shape (lock) that only fits a specific substrate (key).
83
Metabolism
Cellular chemical reactions: anabolism (molecular synthesis) and catabolism (molecular degradation).
84
Minerals
Disolved inorganic ions inside and outside the cell. Their Functions: 1) They create electrochemical gradients across membranes of cells, assist in transporting substances entering and exiting the cell. 2) Combine and solidify to give strenth to a matrix. 3) Act as cofactors assisting enzyme or protein function. Ex. Fe (iron) is mineral in heme.
85
Mitochondrial Matrix
Site of aerobic respiration. Pyruvate converted to acetyl CoA, producing NADH and CO2. Outer membrane permeable to porin, membrane protein that carries pyruvate and NADH, by facilitated diffusion.
86
NADH
A neucleotide. NADH and FADH2 are coenzymes involved in the Krebs cycle.
87
Negative Feedback
The product downstream in a reaction series comes back and inhibits the enzymatic activity of an ealier reaction. Shuts down series of reaction when sufficient amount of product has been produced. (part of allosteric regulation, a type of enzyme regulation)
88
Noncompetitive Inhibitors
Bind noncovalently to enzyme at a spot other than the active site and change conformation of the enzyme, making it imposible for substrate to bind. Can bind to enzyme that already has substrate on it. Doesn't look like substrate so can bind to multiple enzymes. Lower Vmax, Km remains the same.
89
Nucleic Acids
DNA and RNA. Chains of nucleotides. Written 5-\>3.
90
Nucleotides
Made up of 1) five carbon sugar, 2) nitrogenous base (AGCTU), 3) phosphate group.
91
Oils
aka triacylglycerols (energy, thermal insulation, padding)
92
Oxidative Phosphorylation
ATP made from energy from diffusion of ions down their concentration gradient.
93
Peptide Bonds
Links together AA that makes up proteins.
94
Phosphodiester Bonds
Join nucleotides. Phosphate group of one nucleotide and the 3rd carbon of the pentose of the other nucleotide.
95
Phospholipids
glycerol backbone + 1 polar phosphate group + 2 nonpolar fatty acids = 1 phospholipid. Amphipathic.Fxn as major component of membranes.
96
Polypeptides
aka Proteins (because many peptide bonds link AA to make up a protein).
97
Positive Feedback
The product downstream in a reaction series comes back and activate the enzymatic activity of an ealier reaction. Occurs less often then negative feedback. (part of allosteric regulation, a type of enzyme regulation)
98
Primary Structure
The number and squence of AA.
99
Proenzyme
aka Zymogen. Pro is before in greek. "Before"Enzyme
100
Proteins
Chain of amino acids linked by peptide bonds. Nearly all proteins in all species are built from the same 20 alpha-amino acids.
101
Proton-Motive Force
Proton gradient established by pumping or protons into intermembrane space of mitochondrion as electrons are passed down the ETC. The gradient propels protons through ATP synthase.
102
Pyruvate
3-carbon, two is produced per glucose.
103
Quaternary Structure
When two or more polypeptide chain binds together. Same 5 forces in the tertiary structure reinforces the quaternary structure. 1) Covalent disulfide bonds. 2) Electrostatic (ionic) interactions. 3) Hydrogen bonds. 4) Van der Waals forces. 5) Hydrophobic side chains pushed away from water.
104
RNA
Made up of nucleotides. Single stranded. Uses AUGC.
105
Saturated Fatty Acids
Only single C-C bonds.
106
Saturation Kinetics
As the relative concentration of substrate increases, the rate of the reaction also increases, but to a lesser and lesser degree until a max rate (Vmax) has been achieved. Vmax is proportional to enzyme concentration.
107
Secondary Structure
Made up of alpha-helix and beta-pleated sheets, contributing to the conformation of the protein. Contains both alpha and beta structures at various locations along its chain.
108
Side Chains
aka R group. Different on every AA, makes the identity of AA. Also attached to the alpha carbon.
109
Starch
Starch is polysaccaride of glucose formed in plants. Two forms are amylose and amylopectin. - Amylose: an isomer of cellulose that may be branched or unbranched and has same alpha linkages as glycogen. - Amylopectin: resembles glycogen but has different branching structure.
110
Steroids
Four ringed structures. Hormones (i.e. vitamin D) and Cholesterol (an important membrane component).Fxn: regulate metabolic activities
111
Substrate-Level Phosphorylation
ADP + inorganic phosphate = ATP using the energy released from the decay of high energy phosphorylated compounds. Occurs in glycolosis and Krebs cycle.
112
Substrates
This is the reactant that enzymes work upon. Smaller in size than enzymes.
113
Tertiary Structure
3D shape that formed when the peptide chain curls and folds. Only 1 polypeptide. Reinforced by 5 forces: 1) Covalent disulfide bonds between two cysteine AA on different parts of the chain. 2) Electrostatic (ionoc) interactions mostly between acids and basic side chains. 3) Hydrogen bonds. 4) Van der Waals forces. 5) Hydrophobic side chains pushed away from water (toward center of protein)
114
Triglycerides
Backbone: glycerol + 3 fatty acids = 1 Triglyceride.Aka: fats and oilsFxn: store energy in a cell. Provide thermal insulation and padding to an organism.
115
Unsaturated Fatty Acids
Contains at least one double C=C bond.
116
Vitamins
Essential to the body (body cannot produce, must be ingested). Vitamins and vitamin derivatives are the coenzymes.
117
Water
Solvent in which chemical reactions of living cells take place. Make up 70-80% cell's mass.
118
Zymogen
Enzyme inactive form that's released into environment. Enzyme is irreversibly activated by other enzymes or changes in environment when specific peptide bonds are cleaved. (a type of enzyme regulation) Example: Pepsinogen (-ogen indicate zymogen status) activated by low pH to become pepsin.
