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68 Cards in this Set

  • Front
  • Back
Structural Proteins
Made from long polymers

Maintain and add strength to cellular and matrix structure (collagen, globular tubulin)
Glycoproteins
Proteins with carbohydrate groups attached

Components of cellular plasma membranes
Proteoglycans
Mixture of proteins and carbohydrates

Consist of more than 50% carbohydrates

Major component of extracellular matrix
Cytochromes
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
Conjugated Proteins
Proteins containing nonproteinaceous components
Carbohydrates
Sugars or saccharides

Made from carbon and water

Empirical formula = C(H2O)
Glucose
6-C carbohydrate

Most commonly occurring

Account for 80% of carbohydrates absorbed by humans

All digested carbohydrates reach cells as glucose

Forms ring over chain form in aqueous solutions
Glucose anomers
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
Glycogen
Glucose is oxidized to form ATP

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

Plants make starch from glucose
Cellulose
Contains beta-linkages

Plants form cellulose from glucose

Animals do not have enzymes to digest beta-linkages (bacteria inside animals do)
3 components of Nucleotides
1. 5-C sugar
2. Nitrogenous base
3. Phosphate group
5 common nitrogenous bases in nucleotides:
1. Adenine (A)
2. Guanine (G)
3. Cytosine (C)
4. Thymine (T)
5. Uracil (U - replaces T in RNA)
A & T form 2 H-bonds
C &G form 3 H-bonds
Nucleotides form:
Polymers to create:
1. Nucleic acids
2. DNA (double stranded)
3. RNA (single stranded)

Written 5' to 3'
Phosphodiester bonds
In nucleic acids, nucleotides join together by phosphodiester bonds between phosphate group and 1 nucleotide and 3rd C of pentose of other nucleotide
Double helix
In DNA, 2 strands are joined by hydrogen bonds to make this structure

Top strand runs 5' - 3'
Bottom strand runs 3' - 5'
Adenosine Triphosphate (ATP)
Nucleotide

Source of readily available energy for the cell
Cyclic AMP
Component in many second messenger systems
NADH & FADH2
Coenzymes involved in Krebs cycle
Minerals
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)
Enzymes
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
Substrate
Reactant upon which an enzyme works

Smaller than enzymes
Active site
Position on enzyme to which subtrate binds with numerous covalent bonds
Enzyme-substrate complex
Enzyme bound to substrate
Enzyme specificity
Enzymes are designed to work only on a specific substrate or group of closely related substrates
Lock & Key Theory
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
Induced Fit Model
Shape of both enzyme and substrate are altered upon binding

Alteration helps reaction proceed and increases specificity
Saturation Kinetics
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 wait in line for free enzyme

Vmax is proportional to substrate concentration
What affects enzyme reactions?
1. Substrate concentration
2. pH (optimal pH)
3. Temperature (as temperature increases, reaction rate increases until enzyme denatures)
Cofactor
Non-protein component that helps enzymes reach their optimal activity

Can be coenzymes or metal ions
Coenzymes
1. Cosubstrates
2. Prosthetic groups

Organic molecules
Cosubstrates
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
Prosthetic groups
Remain covalently bound to enzyme throughout reaction

Emerge from reaction unchanged

Example: Heme & metal ions (can act alone or with prosthetic group)
Vitamins
Can be coenzymes

Are essential organic molecules: cannot be produced by body
Apoenzyme
Enzyme without cofactor

Completely nonfunctional
Holoenzyme
Enzyme with cofactor
3 mechanisms of enzyme inhibition
1. Irreversible inhibition
2. Competitive inhibition
3. Noncompetitive inhibition
Irreversible Inhibitors
Agents which bind covalently to enzymes and disrupt their function

Highly toxic (penicillin)
Competitive Inhibitors
Compete with substrate by binding reversibly with noncovalent bonds to active site

Can overcome inhibition by increasing concentration of substrate

Resemble substrate
Noncompetitive Inhibitors
Bind noncovalently to enzyme at spot other than active site and change conformation of enzyme

Do not prevent substrate from binding

Bind to enzyme with substrate and enzyme without substrate

Do not resemble substrate

Act on more than one enzyme

Cannot be overcome by excess substrate

Do not lower enzyme affinity for substrate
4 mechanisms by which enzymes are regulated:
1. Proteolytic cleavage (irreversible covalent modification)
2. Reversible covalent modification
3. Control proteins (activate or inhibit activity)
4. Allosteric interactions (modification of enzyme)
Zymogen (proenzyme)
Inactive form of enzyme

Specific cleavage of peptide bonds, irreversibly activates enzyme

Activation may be instigated by other enzymes

Example: pepsinogen (pepsin)
Allosteric Interactions
Modification of enzyme conformation resulting from binding of activator or inhibitor at specific binding site on enzyme
Negative feedback (feedback inhibition)
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)
Positive feedback
Product activates enzyme
Positive cooperativity
1st substrate changes shape of enzyme allowing other substrates to bind more easily
Negative cooperativity
1st substrate changes shape of enzyme, inhibiting substrate binding
Enzyme Nomenclature
Suffix "ase" is added to end of substrate upon which enzyme acts
Lyase
Catalyzes addition of 1 substrate to a double bond of a 2nd substrate (synthase)

Example: ATP synthase
Ligase
Governs an addition reaction (synthetase)

Requires energy from ATP or other nucleotide
Kinase
Enzyme which phosphorylates something
Phosphotase
Enzyme which dephosphorylates something
Metabolism
Cellular chemical reactions
1. Anabolism (molecular degradation)
2. Catabolism (molecular synthesis)
3 Stages of Metabolism:
1. Breakdown of macromolecules to constituent parts (no energy release)
2. Constituents are oxidized to acetyl CoA, pyruvate - forming ATP and reduced coenzymes (NADH & FADH2) in process which does not directly use O2
3. If O2 available (or can be used) metabolites go into citric acid cycle and oxidative phosphorylation to form large amount of energy - otherwise coenzyme NAD+ and other byproducts are recycled or expelled as waster
Respiration
1st & 2nd stage - energy acquiring stages of metabolism

Glucose + O2 = CO2 + H2O (not balanced - combustion reaction)
Aerobic respiration
Oxygen is used

Produces 36x net ATP (includes glycolysis)

1x NADH = 2-3x ATP
1x FADH2 = 2x ATP
Anaerobic respiration
Oxygen is not required

1st stage: Glycolysis

Fermentation
Glycolysis
1st stage of aerobic and anaerobic respiration

Series of reactions that break 6-C glucose molecules into 2x 3-C molecules of pyruvate (conjugate of pyruvic acid)

Produces:
1. 2x ATP from ADP
2. Inorganic phosphate
3. Water
4. 2x NADH from NAD+ reduction
5. 2x pyruvate molecules from glucose

Operates in both presence and absence of oxygen

Occurs in cytosol
Substrate level phosphorylation
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
Fermentation
Anaerobic respiration

1. Glycolysis
2. Reduction of pyruvate to ethanol or lactic acid (expelled with CO2 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. Has no oxygen available
Matrix of Mitochondria
Site where products of glycolysis (pyruvate and NADH) move to
Inner mitochondrial membrane
Less permeable than outer-membrane
Acetyl CoA
Once inside matrix, pyruvate is converted to acetyl CoA in a reaction that produces NADH & CO2

Coenzyme which transfers 2-C from pyruvate to 4-C oxaloacetic acid to begin Krebs cycle
Krebs Cycle (citric acid cycle)
Each turn produces:
1. 1x ATP
2. 3x NADH
3. 1x FADH2
4. 2x C lost
5. Oxaloacetic acid regenerted to begin cycle again

Process of ATP production is substrate-level phosphorylation

1x glucose = 2x turns of Krebs cycle
Electron Transport Chain (ETC)
Series of proteins, including cytochromes with heme, in inner-membrane of mitochondria

1st protein complex oxidizes NADH by acceptin 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 intro 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)
Proton-motive force
Proton gradient established from pumping out of protons into intermembrane space, which propels protons through ATP synthse to make ATP
ATP synthase
Makes ATP by oxidative phosphorylation
Intermembrane space
Lower pH than matrix