Chapter 1 Flashcards
Atom
Made up of neutron, protons and electrons.
Molecules
Group of 2 or more atoms joined via chemical bond. Chemical bonds are due to electron interaction.
Electronegativity
The ability of an atom to attract electrons.
Ionic and Covalent bonds are ____________________? Whereas hydrogen bonds are__________________?
Intramolecular/ Intermolecular
Ionic Bond
Complete Transfer of electrons from one atom to another.
Covalent Bond
Electrons are shared between atoms.
Nonpolar Covalent Bond
Equal sharing of electrons between atoms.
Polar Covalent Bond
Unequal sharing of electrons between atoms.(Forms Dipoles).
Hydrogen Bond
Weak intermolecular bond between molecules that results when a hydrogen attaching to highly electronegative atoms is attracted to a negative charge on another molecule. ( F, O or N atom).
What do organic molecules consist of?
Carbon atoms.
What do macromolecules form?
Monomers (Single unit) Mono- = One
When monomers are combined what is formed?
Polymers (Repeating monomers) Poly- = Multiple
- Monosaccharides
Single sugar molecules.
Ex. glucose, fructose, galactose
Alpha vs Beta….. The ‘OH’ will be on the bottom for alpha whereas the ‘OH’ will be on top for the beta.
Disaccharides
Two sugar molecules joined together by glycosidic linkage other wise known as dehydration.
Ex. Sucrose (glucose + fructose)
Lactose (glucose + galactose)
Maltose (glucose + glucose)
Polysaccharides
series of connected monosaccharides.
Ex. Polymer
bonded together by dehydration synthesis and broken down with hydrolysis.
What are the alpha-glucose polymer carbohydrates?
Starch and Glycogen.
What are the beta-glucose polymer carbohydrates?
Cellulose and chitin.
Starch
Function to store energy in plant cells. Consists of amylose and amylopectin.
Glycogen
Functions to store energy in animal cells Differs from starch in its polymer branching.
Cellulose
Functions as a structural molecule for the walls of plant cells and wood.
Chitin
Functions as the structural molecule in fungal cell walls and arthropod exoskeletons. Structure similar to cellulose but with nitrogen groups attached the beta-glucose ring.
What are polymers of amino acids joined by?
Peptide Bonds
Amino acid Strucures
Consist of an alpha-carbon bonded to H, NH2, COOH and a variable R.
How can proteins be classified?
Structural or composition.
Structural- Based on the structure of the protein
- Fibrous
- Globular
- Intermediate
Structural
- Fibrous- Insoluble, long polymer
- Ex. Collagen
- Globular-Soluble, folded tightly
- Ex. Albumin
- Intermediate-Soluble, fiber shaped
- Ex. Fibrinogen
Composition- Based on the composition of the protein
- Simple
- Conjugated
Composition
- Simple- only amino acids
- Ex. Albumin
- Conjugated- Amino acids and non-protein components
- Ex. Glycoprotein (Mucin), Metalloprotein (hemoglobin), Lipoprotein ( HDL/LDL)
Primary structure of a protein?
Amino acid sequence.
Secondary structure of a protein?
- The 3D shape that causes the hydrogen bonding between amino and carboxyl groups of an adjacent amino acid.
- The secondary Strucutre includes the alpha helix and beta sheet.
Tertiary Strucutre of a protein?
3D structure due to non-covalent interaction between R-groups and amino acids.
- Ex. -Hydrogen bonds
- Ionic bonds
- Hydrophobic effect (R-groups are pushed away from the water center
- Disulfide bonds
- Van der waals forces
Quaternary Structure
Protein in a 3D structure from the grouping of two or more separate peptide chains.
What type of structures do large proteins have?
Large proteins have tertiary and quaternary structure but all proteins have primary and most have secondary.
What happens to the structure during protein denaturation?
Any secondary, tertiary and quaternary structures are removed and the primary structure stays intact.
What cause protein denaturation?
Excess temperature, chemical stress, pH variance, heavy metal salts and radiation. The 3D structure usually loses it functions and shape when denatured.
Storage
Biological reserves of amino acids.
Ex. Ovalbumin (egg whites), casein (milk), plant seeds
Transport
movement of substances with and between cells.
Ex. Hemoglobin (transport oxygen), cytochromes (carry electrons).
Hormones
Signaling molecules that throughout the body to regulate organs.
Ex. Growth hormones
Receptors
Membrane proteins that bind ions and signaling molecules, causing changes on a cellular level.
Ex. Insulin Receptors, ligand-gated ion channels.
Motion
movement on a cellular level or an entire organism.
Ex. tublin (flagella-cell), actin and myosin ( Skeletal Muscles).
Structure
Strengthen and support tissues.
Ex. Collagen (connective tissue), keratin (nails).
Immune Defense
prevent and protect against pathogen attack.
Ex. Antibodies
Enzymes
Globular proteins that act as catalyst, lowering the activation energy and accelerating the rate of reaction.
Ex. Amylase
Enzymes Part 2
- Enzymes can catalyze reactions in both forward and reverse directions depending on the substrate concentration.
- Enzymes remain chemically unchanged throughout a reaction but go through conformational changes.
- Not all enzymes are proteins. some can be RNA like ribozymes.
Enzymes Part 3
- Enzyme efficiency depends on temperature and pH.
- Enzymes cannot change the spontaneity of a reaction.
- Enzymes bind at the active site via Induced fit (enzyme that binds to a specific structure).
Cofactors
Are non-protein molecules that assist enzymes usually by donating or accepting some part of the reaction like electrons.
Coenzymes
Organic cofactors.
Ex. Vitamins
What are some inorganic cofactors?
Usually metal ions like Fe2+ and Mg2+
Prosthetic group
Cofactors that bind tightly/covalently to an enzyme
Apoenzyme
Enzyme without cofactor
Holoenzyme
Enzyme with cofactor
During enzyme regulation, what has both an active site and a allosteric site?
Allosteric Enzymes
Active Site is used for what?
Substrate binding
Allosteric Site is used for what?
Binding of an allosteric effector- can be used as an activator or inhibitor.
Competitive inhibition
Occurs when a substance mimics the substrate and it binds at active site.
- Competitive inhibition can be overcome by increasing substrate concentration.
- Km is raised but Vmax remains the same.
Noncompetitive inhibition
Occurs when a substance inhibits an enzyme by binding at a location other than the active site
-Km remains the same but Vmax is lowered.
Enzyme that is cooperatively?
It allows the enzyme to become increasingly receptive to addition substrate molecules after a substrate molecule has been attached to the active site.
Ex. Hemoglobin binding additional oxygen (although hemoglobin is not an enzyme).
What is Km?
Michaelis constant.
- Represent substrate concentration at which the rate of reaction is half of Vmax.
- A small Km means an enzyme requires only a small amount of substrate to become saturated.
- A large Km means an enzyme requires high amounts of substrate to get Vmax.
- High Km= worse substrate binding, Low Km= better substrate binding
Enzyme that is specificity constant ?
Measures how efficiently an enzyme converts a substrate to product.
- High specificity constant= high enzyme efficiency and substrate affinity.
- High specificity constant= high rate of reaction until molecule is fully saturated.
What are lipids?
Hydrophobic molecules with multiple factors: Insulation, energy storage, structure, endocrine.
Triglycerides (Lipid)
three fatty acid chain attached to a glycerol backbone
What is saturated?
No double bonds
Ex. Bad for health. Saturated = straight chains which stacks densely and form fat plaques.
What is unsaturated?
Double bonds exist.
Ex. Better for health. Unsaturated= double bonds causing branching= stack less densely.
Phospholipids (Lipid)
Two fatty acids and a phosphate group (+R) attached to a glycerol.
Amphipathic
Both hydrophilic and hydrophobic
Hydrophilic
water loving
Hydrophobic
water resistant
Steroids (Lipid)
4 ring structure consisting of three 6-membered rings and one 5-membered ring.
Ex. Used for hormones and structural component of membranes ( Cholesterol).
What are other forms of lipids?
Waxes, Carotenoids, Porphyrins
Adipocytes
Specialized fat cells
-White fat cells contain large lipid droplets made up of triglycerides with a small layer of cytoplasm around it.
-Brown fat cells contain large amount of cytoplasm with smaller amount of lipid droplets throughout the cell.
Glycolipids
Like phospholipids but with a carbohydrate group rather than a phosphate group.
Lipoproteins
A lipid core surrounded by phospholipids and apolipoproteins.
E.g Lipids are insoluble and must be transported in the blood via lipoproteins.
High unsaturated fatty acid = High membrane fluidity
-Unsaturated fatty acids tails have double bonds that promote bending in the molecule which prevents packing or stacking. Even when cold temperature it still is fluid.
High saturated fatty acid = Low membrane fluidity
Saturated fatty acid tails lack double bonds and are straight chains that pack close together and have less movement which mean less fluidity. In warm temperature high saturated fatty acids increase rigidity and avoid more fluidity.
What is cholesterol?
In the plasma membrane of animals and also influences fluidity
- High temperatures, phospholipids are prevented from excess movements which prevents excess fluidity.
- Low temperatures, phospholipids are prevented from packing together too closely preventing excess rigidity.
Sterols
Similar functions as cholesterol but in plant cells instead of animal cells. Also hopanoids are used instead of cholesterol in the plasma membranes.
What is the polymer of nucleotides?
DNA
What is contained in DNA nucleotides?
A nitrogen base, five carbon sugar deoxyribose and a phosphate group.
What are the categories of nucleotides are there depending on the nitrogen base?
Purines and Pyrimidines
Purines
Adenine and guanine and have 2 rings.
-Adenin and thymine are connected via 2 hydrogen bonds
Pyrimidines
Thymine and cytosine and have 1 ring.
-Cytosine and guanine are connected via 3 hydrogen bonds
Nucleosides contain what?
nitrogen base and a five carbon sugar
What is the backbone of DNA held together by?
Phosphodiester bonds
What type of formation does DNA form?
Two antiparallel strands that are double helix running from 5’ to 3’ in opposite directions.
RNA
- Polymer of nucleotides that contain ribose sugar instead of deoxyribose.
- Thymine is not seen in RNA and is replaced with uracil which is paired with adenine with 2 hydrogen bonds.
- RNA is usually single stranded were DNA is double stranded.
- RNA is less stable than DNA because of the extra hydroxyl group which is more likely to go through a chemical reaction.
Properties of water
- High heat capacity
- Cohesion/Surface tension
- Adhesion
- Unique solid density
- Strong solvent
Central dogma of genetics
DNA -> RNA -> proteins.
-biological information can not be transferred backwards
RNA world hypothesis
RNA can store genetic information like DNA
RNA can catalyze chemical reactions similar to enzymes
