Bio1 Lesson 1: Biological Molecules and Enzymes Flashcards
What is the key solvent for all biochemical reactions within cells?
Water
Is water large/small and polar/nonpolar?
Small, polar
What is hydrogen bonding?
Intermolecular bonding between H, F, O, or N
What is a solvation sell?
A shell of solvent surrounding a solute
What type of reaction uses water to break molecules?
Hydrolysis reactions
In what type of reaction is water a byproduct of combining molecules?
Dehydration/condensation reactions
Are lipids polar/nonpolar and hydrophilic/hydrophobic?
Nonpolar, hydrophobic
What are the 3 major roles of lipids?
1) Energy storage, 2) Cellular organization and structure (especially in membrane), 3) Precursor for vitamins and hormones
What are the 7 major classifications of lipids?
1) Fatty Acids, 2) Triacylglycerols/Triglycerides, 3) Phospholipids, 4) Glycolipids, 5) Steroids, 6) Terpenes and Eicosanoids, 7) Waxes
What are fatty acids and what are their roles?
- Long chains of carbon truncated at one end by a carboxylic acid
- Building blocks for complex lipids
- Body fuel and components of cell membranes
Describe a saturated fatty acid and its function.
- Only single bonds
- Hang straight
- Prefer to be stored when there is excess energy
Describe an unsatured fatty acid and its function.
- One or more double/triple bonds
- Kinked structure
- Used for energy
Describe the structure and function of phospholipids.
- Glycerol attached to 2 fatty accid chains + a polar phosphate group
- Amphipathic
- Structural component of membrane
Describe the structure and function of glycolipids.
- Glycerol attached to 2 fatty acid chains + 1 or more carbohydrates (sugars)
- Amphipathic
- Found in membranes of myelinated cells
Describe the structure and function of steroids.
- 4-ringed structures
- Include some hormones, Vitamin D, cholesterol
- Metabolic activity
Which classification of lipids is cholesterol part of and what is its function?
- Steroids
- Maintains membrane stability and fluidity
- Precursor for steroid hormones
Describe the function of terpenes and eicosanoids.
- Pigments
- Paracrine signalling (communication with neighbour cells)
- Some serve as local hormones
Describe the structure and function of waxes.
- Ester linkage between a long-chain alcohol and a long-chain fatty accid
- Protects from water loss, pathogens, and parasites
Describe the strucutre and function of lipoproteins.
-Have a lipid hydrophobic core (triacylglycerols and cholesterol)
surrounded by phospholipids and apoproteins
-Used to transport lipids in blood
What are the 4 classes of lipoproteins in decreasing size and ratio of lipid:protein?
1) Chylomicrons: dietary fat
2) VLDL (sticky on arteries)
3) LDL (sticky on arteries)
4) HDL: healthy/good cholesterol
Is Glycine a polar/nonpolar amino acid?
Nonpolar
Is Alanine a polar/nonpolar amino acid?
Nonpolar
Is Valine a polar/nonpolar amino acid?
Nonpolar
Is Leucine a polar/nonpolar amino acid?
Nonpolar
Is Isoleucine a polar/nonpolar amino acid?
Nonpolar
Is Phenylalanine a polar/nonpolar amino acid?
Nonpolar
Is Tryptophan a polar/nonpolar amino acid?
Nonpolar
Is Methionine polar/nonpolar amino acid?
Nonpolar
Is Proline a polar/nonpolar amino acid?
Nonpolar
Is Serine a polar/nonpolar amino acid?
Polar
Is Cysteine a polar/nonpolar amino acid?
Polar
Is Threonine a polar/nonpolar amino acid?
Polar
Is Tyrosine a polar/nonpolar amino acid?
Polar
Is Asparagine a polar/nonpolar amino acid?
Polar
Is Glutamine a polar/nonpolar amino acid?
Polar
Is Aspartate a polar/nonpolar amino acid?
Polar
Is Glutamate a polar/nonpolar amino acid?
Polar
Is Histidine a polar/nonpolar amino acid?
Polar
Is Lysine a polar/nonpolar amino acid?
Polar
Is Arginine a polar/nonpolar amino acid?
Polar
Is Aspartate acidic/basic?
Acidic
Is Glutamate acidic/basic?
Acidic
Is Histidine acidic/basic?
Basic
Is Lysine acidic/basic?
Basic
Is Arginine acid acidic/basic?
Basic
Name the acidic amino acids.
- Aspartic acid
- Glutamic acid
Name the basic amino acids.
- Histidine
- Lysine
- Arginine
What are carbohydrates made from?
Carbon and water
What is the empirical formula of a carbohydrate?
CH2O
What is glucose?
A 6 carbon carbohydrate that can exist in one of two ring from anomers: alpha or beta
What is glycogen?
Glucose polymerized for storage
Describe the structure and function of glycogen.
- Branched glucose polymer that consists of alpha (trans) linkages in alpha (1-4) and (1-6) pattern
- Used in animal storage
What do plants store glucose in?
Starch or cellulose
Describe the two forms of starch.
- Amylose: alpha (1-4) – only straight chain
- Amylopectin: alpha (1-4) with some (1-6) – minimal branches
Describe cellulose
Beta linkages with no branching
___ eat alpha linkages. ___ break beta linkages.
Animals, bacteria
Describe the structue of a protein.
Built from a chain of amino acid residues linked together by a peptide bond
How many total amino acids are there and how many are essential?
20, 9
Describe the structure of an amino acid.
Each amino acid has a central-alpha carbon linked to a:
1) Amino group (NH3+/NH2)
2) Carboxyl group (COOH/COO-)
3) Hydrogen
4) Sidegroup (R)
How does pH affect the charge of an amino acid?
- Lower pH (Higher acidity) : + charged amino acid
- Higher pH (Lower acidity): - charged area
What is the primary structure of proteins?
The amino acid sequence
What is the secondary structure of proteins?
Folding in polypeptide chain resulting from H-bonds
- R group NOT involved
- a-helix or B-pleated sheets
What is the tertiary structure of proteins?
3D shape resulting from R-group interactions:
1) H-bonds
2) Ionic/electrostatic interactions (+/- charges)
3) Vanderwaals force: london dispersion, dipole-dipole
5) Covalent bond: disulfide bonds (can link two amino acids that are far apart from each other to form a stable bridge)
What is the quaternary structure of proteins?
Proteins made up of more than 1 polypeptide chain
- Homodimer: protein with 2 identical subunits
- Heterodimer: protein with 2 non-identical subunits
Describe the two types of proteins.
1) Globular
- Enzymes
- Hormones
- Membrane pumps and channels
- Membrane receptors
- Inter/intracellular transport and storage
- Osmotic regulation
- In the immune response
2) Structural
- Maintain and add strength to cellular and matrix structure
Name all denaturing agents of proteins and what kinds of forces they disrupt.
- Heat – disrupts all forces
- Salt/change in pH – disrupts ionic/electrostatic bonds
- Organic solvents – disrupt hydrophobic interactions
- Urea – disrupts hydrogen bonds
- Mercaptoethanol – disrupts disulfide bonds
Name and describe the 3 protein complexes.
1) Glycoproteins:
- More than 50% protein
- In plasma membrane
2) Proteoglycans:
- More than 50% carbs and some protein
- Extracellular matrix
3) Cytochromes:
- Protein + prosthetic (covalently bonded) attached heme group
- Enzymes in liver
- Electron transport chain
Describe non-enzyme proteins and the 4 types.
Can bind to their targets but do NOT catalyze reactions
1) Membrane channels and receptors
- In membrane and bind target/ligand
2) Transport proteins
- Facilitate transfer of small molecules with or between cells
3) Antibodies
- Specific to immune system
- Bind and eliminate antigens
4) Motor proteins
- Generate force for cellular movement
What are enzymes?
Catalyst proteins that increase the rate of biological processes by “lowering” the activation energy (Ea)
What is the susbtrate?
The reactant upon which an enzyme works
-Substrates are smaller than enzymes and bind non-covalently to its active site
What is the lock and key theory?
- Aka the active site model
- Substrate fits exactly into the active site
What is the induce fit model?
Active site of enzyme changes shape as the substrate binds
What are cofactors and coenzymes?
Non-protein components required for the enzyme to function as a catalyst
What are the types of cofactors?
1) Organic molecules (coenzymes)
2) Inorganic moldecules (metal ions)
What is a prosthetic group?
A conenzyme covalently bound to enzyme
Are vitamins organic/inorganic?
Organic
Are minerals organic/inorganic?
Inorganic
Are coenzymes water-soluble?
Yes
What is a holoenzyme?
A complete catalytically active enzyme together with its bound coenzyme and/or metal ion
What is an apoenzyme?
The protein part of the enzyme
What are saturation kinetics?
As substrate concentration increases, rate of reaction also increases, but to a lesser and lesser degree until a maximum rate (Vmax) is reached
Is Vmax proportional/inversely proportional to to enzyme concentration?
Proportional
What is Km?
Substrate concentration when reaction rate is 1/2Vmax
Is Km proportional/inversely proportional to enzyme-substrate affinity?
Inversely proportional
What 3 factors is the enzymatic reaction rate closely associated with?
1) pH
2) Temperature
3) Substrate concentration
Describe enzyme inhibition and the 4 types of inhibitors (describe the binding site, the effect on Km, and the effect on Vmax).
Irreversible/reversible inhibition typically involving covalent bonds (lowering enzymatic activity)
1) Competitive inhibitors:
- Often resemble substrate and bind to enzyme’s active site
- Km increases
- Vmax is unchanged
2) Uncompetitive:
- Bind at allosteric site
- Bind to enzyme-substrate complex
- Km decreases
- Vmax decreases
3) Mixed:
- Bind at allosteric site
- Can bind to enzyme-substrate complex or enzyme alone
- Km increases/decreaes
- Vmax decreases
4) Non-competitive:
- Bind at allosteric site
- Change 3D shape
- Reaction will not occur
- Km is unchanged
- Vmax decreases
When do negative feedback loops occur?
When one of the products downstream in a reaction series comes back and inhibits enzymatic activity of an earlier step
When do positive feedback loops occur?
When one of the products downstream in a reaction series comes back and increases the enzymatic activity of an earlier step
What is anabolism?
Synthesis of molecules for energy storage
What is catabolism?
The degredation of molecules for energy expenditure
Describe the function of a “proteolytic cleavage” control mechanism for enzyme regulation.
Inactive enzymes (zymogens) are irreversibly activated
Describe the function of a “reversible covalent modification” control mechanism for enzyme regulation.
Enzyme activation often via a modifier
Describe the function of a “control protein” control mechanism for enzyme regulation.
Control proteins/protein subunits associate with enzymes to activate/inhibit activity
Describe the function of an “allosteric interaction” control mechanism for enzyme regulation.
Allosteric regulators modify enzyme congifuration and activity by binding to specific sites on an enzyme
Describe the function of kinases (a type of enzyme).
Phosphorylation of target
Define the function of a phosphotase (a type of enzyme).
Dephosphorylation of target
Cofactors tend to be organic or inorganic?
Inorganic
Coenzymes tend to be orgnaic/inorganic?
Organic
What are some water-soluble vitamins?
B vitamins, vitamin C, biotin, folate
How does pH affect the rate of reaction of an enzyme?
Rate of reaction is highest at a neutral pH of about 7. The further the pH goes from neutral, the lower the rate of reaction. Rate of reaction is lowest when pH is extremely acid or extremely basic
How does temperature affect the rate of reaction of an enzyme?
Rate of reaction increases as temperature increases, until an optimal temperature of 37 degrees is reached. Then, the rate starts to decrease as the temperature increases
How does substrate concentration affect the rate of reaction of an enzyme?
As substrate concentration increases, rate of reaction increases (but to a lesser and lesser degree) until the Vmax is reached
What is the optimal temperature for the rate of reaction of an enzyme?
37 degrees
Do negative feedback loops maintain homeostasis?
Yes
Do positive feedback loops maintain homeostasis?
No
Describe properties of polar molecules
-Share electrons unequally
-Have high electronegativities
-Hydrophilic
-Between S, N, O, P
Examples:
-Glucose
-Proteins
-DNA
-RNA
-Ions
Describe properties of nonpolar molecules
-Share electrons equally
-Organic
-Hydrophobic
-C + H bonds
Examples:
Lipids (oils, fats, steroids)
What is the side chain for Glycine?
a single H group
What is the side chain for Alanine?
A methyl group (CH3)
What is the side chain for Cysteine?
SH
