Lecture 1 - Molecular Biology Flashcards
What can water act as?
- solvent
- reactant
- product
Hydrogen Bonding of Water
- Allows it to maintain its liquid state in cell environment
- Provides strong cohesive forces btwn water molecules
How are macromolecules broken apart?
hydrolysis
How are macromolecules formed?
dehydration synthesis
Lipids
- Low solubility in water & high solubility in nonpolar organic solvents
- Hydrophobic = Excellent barriers separating aqueous environments
What are the major groups of lipids?
- fatty acids
- triacylglycerols
- phospholipids
- glycolipids
- steroids
- terpenes
Fatty Acids
- some can serve as local hormones
- building blocks for most complex lipids
- long chains of carbons truncated at one end by a carboxylic acid
- usually have an even # of carbons, with the max # in humans being 24
- can be saturated or unsaturated
- oxidation of them liberates large amounts of chemical energy for cell
- most fats reach cell in form of fatty acid, not triacylglycerols
Saturated Fatty Acid
- Possess only single C-C bonds
Unsaturated Fatty Acids
possess one or more C-C double bonds
Triacylglycerols
- AKA triglycerides, or simply fats & oils
- Constructed from a 3-Carbon backbone called glycerol, attached to 3 fatty acids
Functions of Triglycerides
- Store energy
- Provide thermal insulation
- Provide padding
Adipocytes
- AKA fat cells
- Specialized cells whose cytoplasm contains almost nothing but triglycerides
Phospholipids
- Built from glycerol backbone, but a polar phosphate group replaces one of fatty acids
- Amphipathic
- Serve as structural component of membranes
Amphipathicity of Phospholipids
- Phosphate group lies on opposite side of glycerol from the fatty acids, making the phospholipid polar at the phosphate end & nonpolar at the fatty acid end
- Makes them well suited as the major component of membranes
Glycolipids
- Similar to phospholipids
- Have one or more carbs attached to the glycerol backbone instead of phosphate group
- amphipathic
- found in abundance in membranes of myelinated cells in nervous system
Steroids
- four ringed structures
- regulate metabolic activities
- some hormones, vitamin D, cholesterol
Terpenes
Vitamin A - important for vision
Eicosanoids
- Another class of lipids
- 20 carbon
- Prostaglandins, thromboxanes, & leukotrienes
- Released from cell membranes as local hormones that regulate blood pressure, body temp, and smooth muscle contraction
Aspirin
Commonly used inhibitor of the synthesis of prostaglandins
Lipoproteins
- contains a lipid core surrounded by phospholipids and apoproteins
- lipids are transported in the blood via lipoproteins
- able to dissolve lipids in its hydrophobic core and then move freely through the aq. solution due to its hydrophilic shell
- classified by their density
- the greater the ratio of lipid to protein, the lower the density
Major Classes of Lipoproteins in Humans
- Chylomicrons
- Very low density lipoproteins (VLDL)
- Low density lipoproteins (LDL)
- High density lipoproteins (HDL)
Relative Mass of Molecular Components of a Living Cell
From Greatest to Least…
Water, Protein, Lipid, Carb, RNA, Inorganic, DNA, Other organic
Proteins
- Built from a chain of amino acids linked together by peptide bonds
- AKA polypeptides
- Nearly all built from the same 20 alpha-amino acids
Amino Acids
- called alpha-amino acid because amine is attached to the C in the alpha position to the carbonyl
- Each A.A. in a polypeptide chain is referred to as a residue
- A.A. differ from each other only in their side chains (R groups)
- Side chain is also attached to the alpha carbon
- Digested proteins reach the cells of the body as single A.A.
Essential Amino Acids
- 10 of the 20 amino acids are essential
- Body can’t manufacture these 10, must be ingested directly
Primary Structure of a Protein
- The # & sequence of amino acids in a polypeptide
- all proteins have a primary structure
- once primary structure is formed, the single chain can twist or lie along itself to form the secondary structure
Secondary Structure of a Protein
- alpha-helix or Beta-pleated sheets
- Contribute to the conformation of the protein
- beta-pleated sheets can be parallel or anti-parallel
- reinforced by H-bonds between the carbonyl oxygen and the H on the amino group
- most proteins have a secondary structure
- a single protein usually contains both structures at various locations along its chain
Tertiary Structure of a Protein
- the 3-D shape formed when the peptide chain curls & folds
- Five forces create the tertiary structure
5 Forces That Create the Tertiary and Quaternary Structure
- Covalent disulfide bonds between cysteine amino acids on different parts of the chain
- Electrostatic (Ionic) interactions mostly btwn acidic and basic side chains
- H-bonds
- Van der Waals Forces
- Hydrophobic side chains pushed away from water, toward center of protein
Quaternary Structure of a Protein
- When 2 or more polypeptide chains bind together
- 5 forces create the quaternary structure
Denaturation of a Protein
- When protein conformation is disrupted
- Loses most of its secondary, tertiary, and quaternary structure
- Once denaturing agent is removed, very often, the protein will spontaneously refold to its original conformation… This suggests the A.A. sequence plays a key role in conformation
Two Different Types of Proteins
- globular and structural
- more types of globular than structural
Globular Proteins
- Function as enzymes, hormones, membrane pumps and channels, membrane receptors, intercellular and intracellular transport and storage, osmotic regulators
Structural Proteins
- Made from long polymers
- Maintain and add strength to cellular and matrix structure
- Collagen: most abundant protein in the body
- Microtubules
Glycoproteins
Don’t need to know
- Proteins with carb groups attached
- Component of cellular plasma membranes
Proteoglycans
Don’t need to know
- Mix of proteins and carbs, consist of more than 50% carbs
- Major component of extracellular matrix
Cytochromes
Don’t need to know
- Proteins which require a prosthetic heme group in order to function
- Hemoglobin
Conjugated Proteins
Don’t need to know
Proteins containing nonproteinaceous components
General Structure of A.A.
R
H2N-C-COOH
H
When you see nitrogen…
THINK PROTEIN!!
Denaturing Agent and Forces Disrupted
Urea = H-bonds Salt or Change in pH = Electrostatic Bonds Mercaptoethanol = Disulfide bonds Organic Solvents = Hydrophobic Forces Heat = All forces
Carbohydrates
- Made from carbon and water
- AKA sugars or saccharides
- Have empirical formula C(H2O)
- Pentoses and hexoses are most common in nature
- Glucose is most commonly occurring 6-C carb
Glucose
- Accounts for 80% of carbs absorbed by humans
- Digested carbs reaching body cells have been converted to glucose by liver or enterocytes
- Exists in aq. solution in an unequal equilibrium heavily favoring the ring form over the chain form
- Animals eat alpha linkages, but only bacteria break beta linkages
Oxidation of Glucose
- Cell can oxidize glucose transferring chemical energy to a more readily usable form, ATP
- If cell has sufficient ATP, glucose is polymerized to polysaccharide, glycogen or converted to fat.
Anomers of Glucose
The ring form of glucose has two anomers - alpha and beta glucose
Alpha-Glucose
- Hydroxyl group on the anomeric C (#1 C) and the methoxy group (C-6) are on opposite sides of the C-ring
Beta Glucose
Hydroxyl group and methoxy group are on same side of the C-ring
Glycogen
- Branched glucose polymer with alpha linkages
- Found in all animal cells
- Large amounts in muscle and liver cells
Liver Cells
Liver regulates blood glucose level, so liver cells are one of few capable of reforming glucose from glycogen and releasing it back into bloodstream
Insulin
Increases the rate of facilitated diffusion for glucose and other monosaccharides
Absence of Insulin
In absence of insulin, only neural and hepatic cells are capable of absorbing sufficient amounts of glucose via the facilitated transport system
Starch
- Plants form starch from glucose
- Two forms: amylose and amylopectin
Amylose
Isomer of cellulose that may be branched or unbranched and has same alpha linkages as glycogen
Amylopectin
Resembles glycogen but has different branching structure
Cellulose
- Plants form cellulose from glucose
- Has beta linkages
- Animals have enzymes to digest alpha linkages of starch and glycogen but not beta linkages of cellulose
- Some animals like cows and termites have bacteria in digestive systems that release an enzyme to digest the beta linkages in cellulose
Composition of Nucleotides
- Five carbon sugar
- Nitrogenous base
- Phosphate group
Most Common Nitrogenous Bases
- Adenine
- Guanine
- Cytosine
- Thymine
- Uracil
What do nucleotides form?
Polymers to create the nucleic acids, DNA & RNA
Nucleic Acids
Nucleotides joined together by phosphodiester bonds btwn the phosphate group of one nucleotide and the 3rd C of the pentose of the other nucleotide, forming long strands
How is a strand of nucleotides written?
As a list of their nitrogenous bases, 5’ to 3’
DNA
- Two strands are joined by H-bonds to make a double helix
- A & T form 2 H-bonds
- G & C form 3 H-bonds
- Top strand runs 5’ to 3’ and bottom runs 3’ to 5’
RNA
- 1 strand, no helix
- uracil replaces thymine
Other Nucleotides
- ATP: Adenosine Triphosphate: energy source for cell
- Cyclic AMP: component in many 2nd messenger systems
- NADH & FADH2: coenzymes in Kreb’s cycle
What are minerals?
- The dissolved inorganic ions inside and outside the body
- can combine & solidify to give strength to a matrix
- act as cofactors assisting protein or enzyme function
What do minerals assist in the transport of substances?
Assist in the transport of substances entering and exiting the cell by creating electrochemical gradients across membranes
Enzymes
- govern all biological rxns
- typically globular proteins
- not consumed or altered by rxns
- do not alter equilibrium of rxn
- only small amount required for rxn
What is the function of an enzyme?
Catalyst: Lowers the energy of activation and increases rate of rxn
Substrate
- Reactants upon which an enzyme works
- generally smaller than the enzyme
Active Site
Position on enzyme where the substrate binds, usually w/ numerous non-covalent bonds
Enzyme-Substrate Complex
Enzyme bound to the substrate
Enzyme Specificity
Enzymes work only on specific substrate or group of closely related substrates
Lock & Key Theory
Example of enzyme specificity
Induced Fit Model
- Shape of both the enzyme and substrate are altered upon binding
- The alteration increases specificity & helps reaction to proceed
Saturation Kinetics
- Enzymes exhibit this
- As relative [ ] of substrate increases, the rate of rxn increases, but to a lesser and lesser degree until a max rate is achieved (Vmax).
- Vmax is proportional to enzyme [ ].
Turnover Number
Don’t need to know
Number of substrate molecules one enzyme active site can convert to product in a given unit of time when an enzyme solution is saturated with substrate
Km
Don’t need to know
- the substrate [ ] at which the rxn rate = 1/2 Vmax
- Doesn’t vary when enzyme [ ] is changed
- good indicator of enzyme’s affinity for its substrate
Effect of Temperature on Reaction Rate
- As temp increases, reaction rate increases
- But at some point, enzyme denatures & the rxn rate drops off
What is the optimal temp for enzymes in the human body?
37 degrees Celsius
Effect of pH on Reaction Rate
- optimal pH depends
- Pepsin - in stomach - prefers a pH < 2
- Trypsin - active in S.I.- prefers pH btwn 6 & 7
Cofactor
- Non-protein component many enzymes require to reach their optimal activity
- can be coenzymes or metal ions (minerals)
Coenzymes
- Many are vitamins or their derivatives
- two types: cosubstrates (ATP) and prosthetic groups (Heme)
- both organic molecules
Cosubstrate
Don’t need to know
Reversibly bind to specific enzyme and transfer some chemical group to another substrate, then reverted to its original form by another enzymatic rxn.
Apoenzyme
Enzyme without its cofactor (completely nonfunctional)
Holoenzyme
Enzyme with its cofactor
KNOW REACTION RATE GRAPHS
Rxn Rate vs. pH
Rxn Rate vs. Temp
Rxn Rate vs. Substrate [ ]
Enzyme Inhibitors
- Irreversible Inhibitors
- Competitive Inhibitors
- Noncompetitive Inhibitors
Irreversible Inhibitors
- Agents that bind covalently to enzymes and disrupt their function
- Highly toxic
- Ex: penicillin
Competitive Inhibitors
Compete with substrate by binding reversibly w/ noncovalent bonds to the active site
Noncompetitive Inhibitors
Bind noncovalently to the enzyme at a spot other than the active site and change the conformation of the enzyme
What are enzymes regulated by?
- Proteolytic Cleavage (irreversible covalent modification)
- Reversible Covalent Modification
- Control Proteins
- Allosteric Interactions
Zygomen or Proenzyme
Inactive form of an enzyme
Proteolytic Cleavage
- Specific peptide bonds on zygomens are cleaved, they become irreversibly activated
- can be instigated by other enzymes or change in the environment
Reversible Covalent Modification
Activate/deactivate enzymes by phosphorylation or addition of some other modifier like AMP
Control Proteins
Protein subunits that activate or inhibit enzyme activity
Allosteric Interactions
Modification of enzyme configuration from the binding of an activator or inhibitor at a specific binding site on the enzyme
Negative Feedback
- AKA feedback inhibition
- One of the products downstream in a rxn series comes back and inhibits the enzymatic activity in an early rxn.
Positive Feedback
- Product returns like in negative feedback but to activate the enzyme
Allosteric Regulation
- Don’t resemble substrate of enzyme they inhibit
- They bind to enzyme and cause a conformational change
Positive Cooperativity
- At low substrate [ ], small increases in substrate [ ]’s increase enzyme efficiency and rxn rate.
- The 1st substrate changes the shape of the enzyme allowing other substrates to bind more easily
Six Categories of Enzymes
Don’t need to know
- Oxidoreductases
- Transferases
- Hydrolases
- Lyases
- Isomerases
- Ligases
Lyase
Catalyzes addition of one substrate to a double bond of a second substrate - called a synthase
Ligase
Also governs an addition rxn, but requires energy from ATP or other nucleotide - called a synthetase
Kinase
Enzyme which phosphorylates something
Phosphatase
Enzyme which dephosphorylates something
What is metabolism?
- All cellular chemical rxns
- Anabolism + catabolism
Anabolism
Molecular synthesis
Catabolism
Molecular degradation
1st stage of Metabolism
Macromolecules are broken down into their constituent parts, releasing little or no energy
2nd Stage of Metabolism
Constituent parts are oxidized to acetyl CoA, pyruvate, or other metabolites forming some ATP and reduced coenzymes (NADH & FADH2) in a process that doesn’t directly utilize oxygen
3rd Stage of Metabolism
If oxygen is available and the cell is capable of using oxygen, these metabolites go into the citric acid cycle and oxidative phosphorylation to form large amounts of energy.
Otherwise, the coenzyme NAD+ and other byproducts are recycled or expelled as waste
Respiration
2nd and 3rd stages of metabolism - energy acquiring
Glycolysis
- Anaerobic respiration
- 1st stage of anaerobic and aerobic respiration
- Series of rxns that breaks a 6-C glucose molecule into 3-C molecules of pyruvate
- operates in presence and absence of oxygen
- occurs in cytosol of cells
- all living cells and organisms are capable of breaking down glucose to pyruvate
Products of Glycolysis
- 2 NADH (from reduction of NAD+)
- Total 4 ATP, Net 2 ATP
- 2 pyruvate
- inorganic phosphate
- water
Pyruvate
Conjugate base of pyruvic acid
2 Stages of Glycolysis
- Six Carbon Stage: Expends 2 ATPs to phosphorylate the molecule
- Three Carbon Stage: Synthesizes 2 ATP with each 3-C molecule
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 the energy from diffusion
Fermentation
- Anaerobic respiration
- Includes glycolysis, the reduction of pyruvate to ethanol or lactic acid, and the oxidation of NADH back to NAD+
- NAD+ is restored for use in its role in glycolysis as a coenzyme
- Lactic acid and ethanol are expelled as waste product with CO2
- Produces 2 ATP
When does fermentation take place?
When cell is unable to assimilate the energy from NADH and pyruvate, or has no oxygen available
What organisms go through fermentation?
- Yeast and some microorganisms produce ethanol
- Human muscle cells and other microorganisms produce lactic acid
Aerobic Respiration
- Requires oxygen
- If oxygen is present, the products of glycolysis (pyruvate & NADH) will move into the matrix of a mitochondria by facilitated diffusion through large membrane protein - porin
- Once inside the matrix, pyruvate is converted to acetyl CoA in a rxn that produces NADH and carbon dioxide
Kreb’s Cycle
- AKA citric acid cycle
- Acetyl CoA is coenzyme that transfers 2 C’s to the 4-C oxaloacetic acid to begin the cycle
- Two C’s are lost as carbon dioxide, and oxaloacetic acid is reproduced to begin the cycle over again
- Fatty acids and amino acids can be converted into acetyl CoA and enter the cycle
What is the production of ATP in the Kreb’s cycle called?
Substrate level phosphorylation
What does each turn of the Kreb’s cycle produce?
- 1 ATP
- 3 NADH
- 1 FADH2
How many turns of the Kreb’s cycle does one molecule of glucose produce?
2 turns
Electron Transport Chain
- Series of proteins in the inner membrane of mitochondria
- The 1st protein complex oxidizes NADH, then electrons are passed down and accepted by oxygen to form water.
- As electrons are passed along, protons are pumped into the intermembrane space for each NADH, which establishes a proton gradient.
What is the production of ATP in the ETC called?
Oxidative phosphorylation
What is the proton gradient in the ETC called? What does it do?
Proton-motive force - propels protons through ATP synthase to manufacture ATP
How many ATPs are manufactured for each NADH in the ETC?
2 to 3 ATPs
How many ATPs are manufactured for each FADH2 in the ETC?
2 ATPs
How many net ATPs does aerobic respiration produce?
36 net ATPs
pH of Intermembrane Space vs. Matrix
Intermembrane space has lower pH than matrix
Overall Reaction of Respiration
Glucose + O2 –> CO2 + H2O (Combustion Rxn)
