Mcat Biology Lecture 1

Front 1

Major function of lipids:

Back 1

1. Structural component of membranes (phospholipids)
2. store metabolic energy and pr ovide padding (triacylglycerols)
3. Regulate metabolic activities (steroids)
4. Local hormones (eicosanoids)

Front 2

Structural Proteins

Back 2

Made from long polymers

Maintain and add strength to cellular and matrix structure (collagen, globular tubulin)

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Residue

Back 3

an amino acid in a polypeptide chain

Front 4

Glycoproteins

Back 4

Proteins with carbohydrate groups attached

Components of cellular plasma membranes

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Proteoglycans

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Mixture of proteins and carbohydrates

Consist of more than 50% carbohydrates

Major component of extracellular matrix

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Cytochromes

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Proteins which require a prosthetic (nonproteinaceous) heme group in order to function

Add color to cell

Examples:
Hemoglobin
Cytochromes of electron transport chain in inner-membrane of mitochondria

Front 7

Conjugated Proteins

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Proteins containing other nonproteinaceous components

Front 8

Carbohydrates

Back 8

Sugars or saccharides (-ose)

Empirical formula = C(H2O)

Are ketones/aldehydes, water can be break the glycoside linkages of carbohydrates

Front 9

Anomeric Carbon

Back 9

Cyclization of a carbohydrate causes the formation of 2 new diasteriomers. They differ in the position of the attachment of a certain group to the new stereocenter. The new stereocenter is referred to as the
anomeric carbon.

To find it, locate lone oxygen on ring, then find alpha carbon with OH (anomeric carbon), not CH2-OH.

Front 10

Glucose

Back 10

6-C carbohydrate

Account for 80% of carbohydrates absorbed by humans

All digested carbohydrates reach cells as glucose

Forms ring over chain form in aqueous solutions

Front 11

The 2 glucose anomers:

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Ring form

Alpha-glucose: hydroxyl group on anomeric C (C #1) and methoxy group (C #6) are on opposite sides of ring

Beta-glucose: hydroxyl group and methoxy group are on same side of ring

Front 12

Glycogen

Back 12

alpha 1,6 (branch) and alpha 1,4 linkages

If sufficient ATP, glucose is polymerized to a polysaccharide (glycogen) or converted to fat

Found in all animal cells, large amounts in liver and muscle cells

Front 13

Starch

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2 forms:
1. Amylose (isomer of cellulose, alpha 1,4 linkages)
2. Amylopectin (resembles glycogen, different branching structure)

Plants form starch from glucose

Front 14

Cellulose

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Beta 1,4 linkages

Plants form cellulose from glucose

Animals do not have enzymes to digest beta-linkages (bacteria inside animals do)

Front 15

3 components of Nucleotides

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1. 5-C sugar (pentose)
2. Nitrogenous base
3. Phosphate group

Front 16

Nucleotides form polymers to create:

Back 16

1. Nucleic acids
2. DNA (double stranded)
3. RNA (single stranded)

Front 17

Phosphodiester bonds

Back 17

strong covalent bonds between a phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds.

In DNA and RNA, the phosphodiester bond is the linkage between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another, deoxyribose in DNA and ribose in RNA.

Front 18

Cyclic AMP

Back 18

Nucleotide: Component in many second messenger systems

Front 19

NADH & FADH2

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Nucleotides: Coenzymes involved in Krebs cycle

Front 20

Minerals

Back 20

Dissolved inorganic ions inside and outside cell

By creating electrochemical gradients across membranes, they assist in transport of substances entering and exiting cells

Can combine and solidify to give strength to a matrix (hydroxyapatite in bone)

Act as cofactors assisting enzyme or protein function (iron in heme, prosthetic group of cytochromes)

Front 21

Enzymes

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Globular proteins

Act as a catalyst = lowering activation energy for biological reactions and increasing reaction rates

Not consumed or permanently altered by reactions

Do not alter equilibrium of reaction

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Substrate

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Reactant upon which an enzyme works

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Active site

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Position on enzyme to which subtrate binds with numerous covalent bonds

Front 24

Lock & Key Theory

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Example of enzyme specificity

Active site of enzyme has specific shape (lock) that only fits a specific substrate (key)

Model does not explain all enzymes

Front 25

Induced Fit Model

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Shape of both enzyme and substrate are altered upon binding

Alteration helps reaction proceed and increases specificity

Front 26

Saturation Kinetics

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As relative concentration of substrate increases, rate of reaction also increases, but to a lesser degree until a maximum rate (Vmax) is achieved

More substrate is added and therefore must wait in line for free enzyme

Vmax is proportional to substrate concentration

Front 27

What affects enzyme reactions?

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1. Substrate concentration
2. pH (optimal pH)
3. Temperature (as temperature increases, reaction rate increases until enzyme denatures)

Front 28

Cofactor

Back 28

Non-protein component that helps enzymes reach their optimal activity

Can be coenzymes or metal ions

Front 29

Coenzymes

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2 groups:
1. Cosubstrates
2. Prosthetic groups

Organic molecules

Front 30

Cosubstrates

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Category of cofactor

Reversibly bind to a specific enzyme and transfer some chemical group to another substrate

Reverted to original form by another enzymatic reaction (distinguishing it from a normal substrate)

Example: ATP

Front 31

Prosthetic groups

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Remain covalently bound to enzyme throughout reaction

Emerge from reaction unchanged

Example: Heme & metal ions (can act alone or with prosthetic group)

Front 32

Vitamins

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Can be coenzymes

Are essential organic molecules: cannot be produced by body

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Apoenzyme

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Enzyme without cofactor

Completely nonfunctional

Front 34

Holoenzyme

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Enzyme with cofactor

Front 35

3 mechanisms of enzyme inhibition

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1. Irreversible inhibition
2. Competitive inhibition
3. Noncompetitive inhibition

Front 36

Irreversible Inhibitors

Back 36

Agents which bind covalently to enzymes and disrupt their function

Highly toxic (penicillin)

Front 37

Competitive Inhibitors

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Compete with substrate by binding reversibly with noncovalent bonds to active site

Can overcome inhibition by increasing concentration of substrate

Resemble substrate

Front 38

Noncompetitive Inhibitors

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Bind noncovalently to enzyme at spot other than active site and change conformation of enzyme

Do not prevent substrate from binding

Do not resemble substrate

Act on more than one enzyme

Cannot be overcome by excess substrate

Do not lower enzyme affinity for substrate

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4 mechanisms by which enzymes are regulated:

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1. Proteolytic cleavage (irreversible covalent modification)
2. Reversible covalent modification (AMP, phosphorylation, or hydrolysis)
3. Control proteins (activate or inhibit activity)
4. Allosteric interactions (modification of enzyme)

Front 40

Zymogen (proenzyme)

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Inactive form of enzyme

Specific cleavage of peptide bonds irreversibly activates enzyme

Activation may be instigated by other enzymes

Example: pepsinogen (pepsin)

Front 41

Allosteric Interactions

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Modification of enzyme conformation resulting from binding of activator or inhibitor at specific binding site on enzyme

Can be allosteric activators or allosteric inhibitors of an enzyme, competitive or noncompetitive

Front 42

Negative feedback (feedback inhibition)

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Product of downstream reaction inhibits enzymatic activity in upstream reaction

Provides shut-down mechanism for series of enzymatic reactions when it has produced sufficient amount of product

Do not resemble substrate of enzymes that they inhibit - bind to enzyme and cause conformational change (allosteric regulation)

Front 43

Positive feedback

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Product activates enzyme

Front 44

Positive cooperativity

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1st substrate changes shape of enzyme allowing other substrates to bind more easily

Front 45

Negative cooperativity

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1st substrate changes shape of enzyme, inhibiting substrate binding

Front 46

Enzyme Nomenclature

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Suffix "ase" is added to end of substrate upon which enzyme acts

(acetylcholinesterase acts upon the ester group in acetylcholine)

Front 47

Lyase (an enzyme classification)

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(aka synthase) Catalyzes addition of 1 substrate to a double bond of a 2nd substrate

Example: ATP synthase

Front 48

Ligase (an enzyme classification)

Back 48

(synthetase) Governs an addition reaction

Requires energy from ATP or other nucleotide

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Kinase

Back 49

Enzyme which phosphorylates something

Front 50

Phosphatase

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Enzyme which dephosphorylates something

Front 51

Products and reactants for respiration? What kind of reaction is it?

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Glucose + O2 -> CO2 + H2O

Combustion reaction

Front 52

Aerobic respiration

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Oxygen is used

Produces 32-36 ATP/glucose

Front 53

Glycolysis equation

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Glucose (6C) + 2NAD+ + 2 ADP + 2 Pi -> 2 pyruvate (3C) + 2 ATP + 2 NADH + 2 H2O

Operates in both presence and absence of oxygen, occurs in cytosol

Front 54

Substrate level phosphorylation

Back 54

Formation of ATP from ADP and Pi using the energy released from the decay of high energy phosphorylated compounds

No use of energy from diffusion

Front 55

Fermentation

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Anaerobic respiration

1. Glycolysis (glucose -> 2 pyruvate)
2. Reduction of pyruvate to ethanol or lactic acid (CO2 expelled as waste product)
3. Oxidation of NADH back to NAD+

Yeast and microorganisms produce ethanol, humans produce lactic acid

Takes place when:
1. Organism is unable to assimilate energy from NADH and pyruvate
2. Organism has no oxygen available

Front 56

Mitochondria membrane permeability

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Outer membrane: permeable to pyruvate and NADH (facilitated diffusion)
Inner membrane: permeable to pyruvate (fac. diff.) but NADH may require hydrolysis of ATP

Front 57

Once inside matrix, pyruvate is...

Back 57

converted to acetyl CoA (2C) in a reaction that produces NADH & CO2

CoenzymeA transfers 2-C from pyruvate to 4-C oxaloacetic acid to make citrate, Krebs cycle

Front 58

Krebs Cycle (citric acid cycle)

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Each turn produces:
1. 1 ATP
2. 3 NADH
3. 1 FADH2
4. 2C released as CO2
5. Oxaloacetic acid regenerted to begin cycle again

Process of ATP production is substrate-level phosphorylation

1x glucose = 2x turns of Krebs cycle

Front 59

What is the Electron Transport Chain (ETC)?

Back 59

A series of proteins, including cytochromes with heme, in inner-membrane of mitochondria

1st protein complex oxidizes NADH by accepting its high energy electrons

Electrons are passed down protein series and ultimately accepted by oxygen to form water

As electrons are passed along, protons are pumped into intermembrane space for each NADH. Establishes proton gradient which propels protons through ATP synthase to manufacture ATP (oxidative phosphorylation)

2-3x ATP made from each NADH
2x ATP made from FADH2 (reduces protein)

Front 60

Proton-motive force

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Proton gradient established from pumping out of protons into intermembrane space, which propels protons through ATP synthase to make ATP (oxidative phosphorylation!)

Front 61

ATP synthase

Back 61

Makes ATP by oxidative phosphorylation

Front 62

Acidic Alpha AAs?

Back 62

AG
Aspartic acid
Glutamic acid

Front 63

basic alpha aa's?

Back 63

HAL
Histidine
Arginine
Lysine

Front 64

Nonpolar alpha aa's?

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VIPMALT PG
Valine
Isoleucine
Proline
Methionine
Alanine
Leucine
Tryptophan
Phenylalanine
Glycine

Front 65

Polar alpha aa's?

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STAT GC
Serine
Threonine
Asparagine
Tyrosine
Glutamine
Cysteine

Front 66

Cysteine

Back 66

Has SH (sulfur) group, forms disulfide bonds

Front 67

Proline

Back 67

Creates a kink, never involved in secondary structure

Front 68

Primary Structure of Protein

Back 68

Determines ultimate configuration of protein

held together by peptide bonds

primary structure is rarely affected by denaturing agents

Front 69

Secondary structure

Back 69

Alpha helix, beta sheets

Held together by H-bonds between different AA's

Front 70

Tertiary structure

Back 70

Based on disulfide bonds, hydrophobic/philic effects, ionic bonding (between acidic and basic side chains), hydrogen bonding, and van der waals

Front 71

Quaternary structure

Back 71

Consists of multi-subunit proteins

Bonds aren't internal: bonds are made between other proteins