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MCAT Biology EK > Molecular Bio And Cellular Respiration > Flashcards

Molecular Bio And Cellular Respiration Flashcards

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0
Q

Fatty Acids *

A
  • Lipid
  • Building blocks of complex lipids
  • Long chains of carbon (usually even #, max 24) truncated by carboxylic acid
  • Saturated or Unsaturated
  • Most fats reach the cell in this form
  • **Includes eicosanoids, which serve as local hormones
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1
Q

Six Major Groups of Lipids *

A
  • fatty acids
  • triacylglycerols
  • phospholipids
  • glycolipids
  • steroids
  • terpenes
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2
Q

Triacylglycerols *

A
  • Lipid
  • aka triglycerides aka fats or oils
  • three carbon backbone, glycerol, attached to three FAs
  • **store energy in the cell
  • **provide padding and thermal insulation
  • found in the cytoplasm of adipocytes
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3
Q

Phospholipids *

A
  • Lipid
  • also contain glycerol backbone, but contain phosphate group instead of one FA
  • amphipathic molecules
  • **component of cell membranes
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4
Q

Glycolipids

A
  • Lipid
  • glycerol backbone with a sugar molecule attached
  • amphipathic molecules
  • present in myelinated cells of the nervous system
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5
Q

Steroids *

A
  • lipid
  • four ringed structures
  • component of hormones, vitamin D, cholesterol
  • **regulate metabolic activities
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6
Q

Terpenes

A
  • Lipid

- examples include vitamin A (important for vision)

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7
Q

Eicosanoids

A
  • Lipid, often listed as FA
  • 20 carbons
  • include prostaglandins, thromboxanes, leukotrienes
  • local hormones secreted to regulate blood pressure, body temperature, and smooth muscle contraction
  • aspirin often used to inhibit prostaglandin synthesis
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8
Q

Lipoproteins (definition and composition)

A
  • transport hydrophobic lipid molecules in the blood
  • lipid core surrounded by phospholipids and apoproteins
  • classified by density: the greater the ratio of lipid to protein, the LOWER the density
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9
Q

Main Lipoproteins

A

Chylomicrons
Very low density lipoproteins (VLDL)
Low density lipoproteins (LDL)
High density lipoproteins (HDL)

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10
Q

Protein Composition **

A
  • when you see nitrogen on the MCAT, think protein!!
  • Built from chains of AAs linked by peptide bonds - proteins are sometimes called polypeptides
  • Almost all built from alpha AAs, meaning the amine is attached to the alpha position to the carbonyl
  • Digested proteins reach the cell as single AAs
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11
Q

Essential Amino Acids **

A
  • In humans, 10 of the 20 AAs are essential

- The body cannot manufacture these 10 so they must be ingested directly

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12
Q

Primary, Secondary, Tertiary, and Quaternary Structure of a Protein **

A 
1* = AA sequence 
2* = single chain twisted into alpha helix or beta pleated sheet (conformation)
3* = three dimensional shape from twists and turns
4* = multiple polypeptides bonded together
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13
Q

Alpha helices **

A
  • reinforced by hydrogen bonds between the carbonyl oxygen and the hydrogen on the amino group
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14
Q

Beta pleated sheets **

A
  • reinforced by hydrogen bonds between the carbonyl carbon and hydrogen on amino group
  • connected segments of the two strands can be parallel (lie in the same direction) or antiparallel (lie in opposite directions)
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15
Q

Tertiary Structure of a Protein **

Five forces

A
  • three dimensional shape
  • five forces:
    1) covalent disulfide bonds between two cysteine AAs
    2) electrostatic/ionic interactions between acidic and basic side chains
    3) hydrogen bonds
    4) Van der waals forces
    5) hydrophobic interactions of side chains away from water and toward the center of the protein
  • proline introduces turns
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16
Q

Quaternary Structure

A
  • same five forces as tertiary - interaction of multiple polypeptides
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17
Q

Denaturation of a Protein

A
  • Loss of secondary, tertiary, quaternary structure
  • Very often will reassemble when denaturing agent is removed (meaning the AA sequence must play role in protein conformation)
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18
Q

Common Denaturing Agents

A
  • Urea (hydrogen bonds)
  • Salt or pH change (electrostatic bonds)
  • Mercaptoethanol (disulfide bonds)
  • Organic solvents (hydrophobic forces)
  • Heat (all forces)
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19
Q

Two Types of Proteins

A
  • globular and structural
  • GLOBULAR proteins function as:
    • enzymes (ex pepsin)
    • hormones (ex insulin)
    • membrane pumps (ex Na+/K+ pump and voltage-gated sodium channels)
    • membrane receptors
    • intracellular and intercellular transport and storage (ex hemoglobin and myoglobin)
    • osmotic regulators (ex albumin)
    • antibodies, and more
  • STRUCTURAL proteins
    • long polymers
    • add strength to matrix
    • ex Collagen, adds strength to skin, tendons, ligaments and bone
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20
Q

Glycoproteins

A
  • proteins with carbohydrate groups attached

- component of plasma membranes

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21
Q

Proteoglycans

A
  • Mixture of protein and carbohydrates (usually >50% carb)

- Major component of extracellular matrix

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22
Q

Cytochromes

A
  • Proteins requiring a prosthetic heme group in order to function
  • get their name from the color they add to the cell
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23
Q

Carbohydrate Composition **

A
  • carbon and water

- five and six (pentoses and hexoses) are most common in nature

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24
Q

Glucose ** (in animals)

A
  • six carbon carbohydrate
  • accounts for nearly 80% of carbohydrates absorbed by humans
  • essentially all ingested carbohydrates are converted to glucose by the liver or enterocytes
  • ring form had two anomers: alpha glucose (anomeric OH points down) and beta glucose (anomeric OH points up)
  • oxidized to produce ATP
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25
Q

Glycogen **

A
  • polymerized form of glucose, formed when the body as adequate ATP
  • alpha linkages
  • in all animal cells, particularly in the liver and muscle
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26
Q

Cellular Absorption of Glucose

A
  • only the liver can reform glucose from glycogen to release back into the bloodstream
  • certain cells in the digestive tract and proximal tubule of the kidney can absorb glucose against the concentration gradient of sodium
  • all other cells absorb glucose via facilitated diffusion
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27
Q

Insulin **

A
  • hormone composed of globular protein
  • increases facilitated diffusion of glucose into cells
  • in absence of insulin, only neural and hepatic cells can continue to intake glucose via facilitated diffusion
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28
Q

Glucose ** (in plants)

A
  • plants use glucose to form starch and cellulose
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29
Q

Starch **

A
  • Two forms: amylose and amylopectin
  • Amylose is an isomer of cellulose, branched or unbranched, with alpha linkages
  • Amylopectin resembles glycogen with different branching structure
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30
Q

Cellulose **

A
  • isomer of amylose (starch)
  • beta linkages
  • most animals can digest alpha linkages but not the beta linkages found in cellulose (though some animals release enzymes to digest them, like cows and termites)
31
Q

Nucleotides - Three Parts **

A

1) pentose
2) nitrogenous base (adenine, guanine, cytosine, thymine, uracil)
3) phosphate group

32
Q

Nucleic Acids **

A
  • DNA and RNA
  • nucleotides joined by phosphodiester bonds between phosphate of one and 3rd carbon of the other
  • Nucleotide strands are written in the 5’–>3’ direction
  • DNA consists of two strands joined by hydrogen bonds to form a double helix (A and T form two, C and G form three)
33
Q

Important Nucleotides in Biochemistry **

A
  • ATP (adenosine triphosphate)
  • cyclic AMP (important in second messenger systems)
  • NADH and FADH2 (coenzymes in the Krebs cycle)
34
Q

Minerals **

A
  • Dissolved inorganic ions inside and outside the cell that create electrochemical gradients across membranes to assist in the transport of substances entering and editing the cell.
  • They can also solidify to give strength to a matrix or act as cofactors to assist enzyme/protein function (such as iron in heme groups)
35
Q

Enzymes **

A
  • Globular proteins that act as catalysts, lowering the activation energy for a biological reaction and increasing the rate of reaction
  • Neither consumed nor altered by reactions
  • Do not affect the equilibrium of reactions
36
Q

Substrates **

A
  • Reactant(s) acted upon by enzymes in a reaction - typically smaller than the enzyme
  • Substrate binds to the active site of the enzyme via numerous noncovalent bonds, forming the enzyme-substrate complex
37
Q

Enzyme Specificity **

  • Lock and key theory
  • Induced fit model
A
  • Enzymes are typically designed to work only with a specific substrate or group of closely related substrates
  • The lock and key theory states that the active site of an enzyme is like a lock that fits only a certain key (substrate)
  • The induced fit model states that the enzyme and substrate change shape upon binding to further the reaction and coordinate multiple substrates
38
Q

Saturation Kinetics **

A
  • This is a trait exhibited by enzymes that involves reaction rate increasing with substrate concentration steadily until all available enzymes are bonded to substrates (Vmax)
  • The turnover rate is the # of substrate molecules an enzyme can convert to product at Vmax for a given unit of time
39
Q

Michaelis Constant

A

The Michaelis constant (Km) is the point where [substrate] = 1/2 Vmax

40
Q

Effect of Temperature and pH on Enzymatic Reactions

A

TEMP

  • while heat initially increases the rate of reaction, too much heat will begin to denature enzymes
  • most enzymes operate at 37*C

pH
- All enzymes have an optimal pH range (ex pepsin in the stomach prefers below 2 while trypsin in the small intestine prefers 6-7)

41
Q

Cofactors for Enzymes **

A
  • In order to operate efficiently, many enzymes require non-protein cofactors
  • These cofactors may be metal ions or coenzymes
  • Coenzymes can be further divided into two groups of organic molecules:
    1) prosthetic groups
    2) cosubstrates (reversibly bind to an enzyme to transfer a chemical group to a substrate then convert back to original form rather than made into product) – ex ATP
  • *many coenzymes are vitamins and their derivatives
42
Q

Vitamins **

A
  • Often serve as coenzymes

- Essential (must be ingested)

43
Q

Heme

A

A prosthetic group (type of coenzyme) that binds with catalase in peroxisomes to degrade hydrogen peroxide

44
Q

Apoenzyme versus Holoenzyme

A

Apoenzyme = enzyme without it’s cofactor; nonfunctional

Holoenzyme = enzyme with it’s cofactor

45
Q

Three Mechanisms of Enzyme Inhibition

A

1) Irreversible inhibitors
2) Competitive inhibitors
3) Noncompetitive inhibitors

46
Q

Irreversible Enzyme Inhibitors **

A
  • Bind covalently to enzymes to disrupt their function (some do bind noncovalently)
  • Tend to be highly toxic
  • Ex Penicillin that blocks bacterial enzymes that aid in the production of peptidoglycan cell walls
47
Q

Competitive Enzyme Inhibitors **

A
  • Compete with the substrate by noncovalently binding to the active site of an enzyme
  • Because substrates can also block these inhibitors, the Km is affected but Vmax is not; the original Vmax can be obtained by raising the [substrate]
  • Competitive inhibitors often resemble the substrate
  • Ex Sulfanilamide is an antibiotic that blocks enzymes that produce folic acid, required for bacterial cell walls (humans use folic acid but produce it through a different pathway)
48
Q

Noncompetitive Enzyme Inhibitors **

A
  • Change the conformation of an enzyme by noncovalently binding onto a location other than the active site
  • Lower Vmax - cannot be overcome by adding more substrate
  • Km unchanged as they do not affect enzyme affinity for substrate
49
Q

Four Forms of Enzyme Regulation

A

1) Proteolytic cleavage (Irreversible Covalent Modification)
- zymogens/proenzymes (inactive form of enzymes) are cleaved at peptide bonds by other enzymes or by environmental changes

2) Reversible Covalent Modification
- ex. phosphorylation by a protein kinase

3) Control proteins
- subunits that associate with certain enzymes (ex. Calmodulin or G-proteins)

4) Allosteric Interactions
- binding of an Allosteric activator or inhibitor

** Other proteins also undergo these forms of regulation

50
Q

Negative Feedback/Feedback Inhibition **

A

This occurs when one of the products downstream in a series of enzymatic reactions returns to inhibit an enzyme in an earlier reaction when the series has produced a sufficient amount of product

  • Allosteric inhibitors bind to an enzyme to cause a conformational change
51
Q

Positive Feedback **

A

A product in a series of reactions returns to further stimulate an enzyme (not as common as negative feedback)

52
Q

Allosteric Regulation **

A

In negative and positive feedback mechanisms, allosteric inhibitors or activators bind to an enzyme to create a conformational change

  • these are different from noncompetitive inhibitors because they change Km without altering Vmax
53
Q

Positive Cooperativity **

A

A first substrate binds to an enzyme, changing the enzyme shape to make it easier for subsequent substrates to bind

  • Negative Cooperativity occurs as well (ex Allosteric inhibitor 2,3BPG gives O2 dissociation curve of hemoglobin its sigmoidal shape)
54
Q

Lyases versus Ligases

A
  • Synthase = a lyase that catalyzes addition of one substrate to the double bond of another (ex. ATP synthase)
  • Synthetase = a ligase that governs an addition reaction but requires energy from ATP or some other nucleotide
55
Q

Kinases versus Phosphatases

A

Kinase = phosphorylates
Ex. Hexokinase phosphorylates glucose as soon as it enters the cell

Phosphatases = dephosphorylates

56
Q

Three Basic Stages of Cellular Metabolism **

A

1) Macromolecules (polysaccharides, proteins, lipids) are broken down into their components (monosaccharides, amino acids, FAs and glycerol) - releases little or no energy

RESPIRATION
2) Components are oxidized to acetyl-CoA, pyruvate, or other metabolites to form ATP, NADH, FADH2

3) If O2 is available, the metabolites go on to the TCA cycle and oxidative phosphorylation to form large amounts of ATP, NADH, FADH2
- If no O2 is available, NAD+ and other byproducts are recycled or expelled as waste

57
Q

Aerobic versus Anaerobic Respiration **

A
  • Steps 2 and 3 of metabolism
  • Aerobic = O2 used
  • Anaerobic = O2 not used
58
Q

Glycolysis **

A
  • first stage of anaerobic AND aerobic respiration (requires no O2)
  • occurs in the cytosol
  • glycolysis is a series of reactions that breaks a 6-carbon glucose molecule to produce:
    • two 3C molecules of pyruvate
    • 2 molecules of ATP
    • phosphate and water
    • 2 molecules NADH
59
Q

Isozyme

A

Enzymes with the same function

(ex. In the first step of glycolysis, the liver and pancreas use an enzyme called glucokinase to phosphorylate glucose rather than hexokinase)

60
Q

Steps of Glycolysis

A

1) Hexokinase phosphorylates glucose with a P from ATP to form glucose 6-phosphate (the liver and kidney contain glucose 6-phosphatase that reforms glucose)
* ATP used, irreversible*

2) G6P –> Fructose 6-phosphate

3) F6P –> F-1,6-BP
* ATP used, irreversible*

4) F-1,6-BP –> Glyceraldehyde 3-phosphate (PGAL) and Dihydroxyacetone phosphate
(Dihydroxyacetone phosphate –> more PGAL)

5) PGAL –> 1,3-Biphosphoglycerate
* *2 NADH GENERATED

6) 1,3-BPG –> 3-PG
* 2 ATP GENERATED*

7) 3-PG –> 2-PG
8) 2-PG –> Phosphoenolpyruvate

9) Phosphoenolpyruvate –> Pyruvate
* * 2 ATP GENERATED**

NET:

  • 2 ATP
  • 2 pyruvate
  • 2 NADH
61
Q

Substrate Level Phosphorylation **

A

The formation of ATP from ADP and inorganic phosphate using the energy released from the decay of high-energy phosphorylated compounds

  • As opposed to using energy from diffusion
62
Q

Fructose and Galactose in Glycolysis

A

These monosaccharides are often converted to glucose in the liver by enterocytes

Fructose can also enter glycolysis as F6P or Glyceraldehyde-3-phosphate

Galactose can be converted to G6P

63
Q

Simple Table Sugar Components

A

Disaccharide of glucose and fructose

64
Q

Lactose Composition

A

A disaccharide found in milk consisting of glucose and galactose

65
Q

Fermentation **

A
  • Anaerobic respiration
  • Includes glycolysis, but does not have O2 to proceed so pyruvate is converted to ethanol (yeast, other microorganisms) or lactic acid (humans) and NADH is converted back to NAD+ to be used again as a coenzyme in glycolysis
  • Lactic acid (or ethanol) is expelled from the cell as waste along with CO2
66
Q

Aerobic Respiration **

A
  • Glycolysis, Kreb’s Cycle, ETC
  • When O2 is present, the products of glycolysis proceed to the matrix of the mitochondrion
  • The outer membrane of the mitochondrion is permeable to small molecules, so NADH and pyruvate enter via facilitated diffusion through a membrane protein called porin
  • The inner mitochondrial membrane is less permeable, and while pyruvate enters by facilitated diffusion, NADH may or not not use ATP hydrolysis to cross
  • Once in the mitochondrial matrix, pyruvate is converted to acetyl-CoA
  • *Produces NADH and CO2**
  • IN SUM:*
  • 36 NET ATP (w glycolysis)
67
Q

Kreb’s Cycle **

A
  • Acetyl CoA produced from aerobic respiration produces OAA to begin the Kreb’s Cycle
  • *NET IN TWO TURNs (1 glucose = 2 turns)
  • 2 ATP
  • 6 NADH
  • 2 FADH2
  • ATP produced through substrate-level phosphorylation
  • Two carbons lost as CO2, OAA reproduced to begin cycle over again
68
Q

Triglycerides and the Kreb’s Cycle

A

FAs are converted to acyl-CoA along the outer mitochondrial membrane at the expense of 1 ATP

  • Then brought into matrix to be cleaved to form acetyl-CoA, forming NADH and FADH2 for every 2C from the FA
  • Glycerol backbone converted to PGAL
69
Q

Amino Acids and the Kreb’s Cycle

A

AAs are deaminated in the liver to enter the Kreb’s Cycle at various stages, depending on the AA

  • usually pyruvic acid or acetyl CoA
70
Q

NADH and FADH2 –> ATP Yield in Aerobic Respiration

A

1 NADH = 2-3 ATP

1 FADH2 = 2 ATP

71
Q

Electron Transport Chain **

A
  • A series of proteins (including cytochromes with heme) lining the inner membrane of the mitochondria
  • First protein oxidizes NADH to accept high-energy electrons which are then passed along the chain and ultimately accepted by oxygen to form water (2-3 ATP per NADH)
  • FADH2 reduces a protein further down the chain, producing 2 ATP per FADH2

O2 is the final electron acceptor

72
Q

Proton Motive Force of the ETC **

A
  • As electrons are transported along the ETC, a proton gradient is established by protons being pumped into the intermembrane space with each NADH
  • *Note the intermembrane space of the mitochondria had a lower pH than the matrix
  • Protons are propelled through ATP Synthase to form ATP
73
Q

Oxidative Phosphorylation **

A

Production of ATP via the ETC by protons being pumped through ATP synthase by the proton motive force

74
Q

Reactants and Products for Aerobic Respiration **

A

Glucose + O2 —> CO2 + H2O

This is a combustion reaction

MCAT Biology EK (1 decks)

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