Bio Chapter 1 Flashcards
Atom
The smallest unit of an element that retains all the properties of the element.
Proton, Neutron, Electron
Molecule
Two or more atoms chemically linked.
Matter
Anything that occupies space and has a mass.
Trace elements
Mo, Zn, Cu
Main Bio elements
C, H, O, N P, S
Mass of atoms
Neutron>Proton>Electron
Nucleons
Protons and Neutrons
Neutron # =
Mass # - Atomic #
H2O Universal Solvent
High boiling, melting, delta H vaporization, dipole
Bent molecule, 105 degrees, and polar molecule capable of forming 4 H bonds
H bond
F,O,N
Intra and intermolecular
Nonpolar covalent bond
Molecules share electrons equally.
Polar bond
Unequal sharing of electrons.
Ionic bonds
Electrons transferred between a metal and non metal.
N+ is a sign of an ionic bond.
Ionic compounds
NaCl, MgBr2, NH4Cl
Most polar molecules and ionic compounds are water soluble.
Why can’t hydrocarbons dissolve in water?
Water molecules have extensive H bonds that would have to break to make room for hydrophobic solute. Not spontaneous.
Surface of proteins charges
Charges are hydrophilic. H20 is very polar and shields the charges from each other. Interior of the protein charges interact strongly.
H20 electrostatic interactions
H20 diminishes the charge by forming solvent shell which produces an electric field which opposes ion fields.
ΔG Free Energy
ΔG = ΔH - TΔS
Endergonic: +ΔH, +ΔG
Exergonic: -ΔH, -ΔG
Guanranteed Spontaneous ΔG
-ΔH and +ΔS will be spontaneous at all temperatures.
K= Products/ Reactants
No solids or pure liquids
K»1 favors products, K«1 favors reactants
ΔG= -2.303RTLogK or ΔG=-RTlnK
pH equations
pH= -log[H3O+]
pOH= -log[OH-]
pH= pH + pOH
Large Ka = small pKa
Henderson Hasselback Equation
Buffers
pH = pKa + Log [Base/Acid]
Energy Main categories
Kinetic and Potential
Other types: Gravitation, Electrical, Thermal, Nuclear, Mechanical, Magnetic
Temperature
Average kinetic energy measured
F= 1.8C + 23
K= C+273
1st Law Thermodynamics
Normal conditions, energy can not be created nor destroyed. Only transferred or changed.
2nd Law Thermodynamics
Entropy of the universe is always increasing. No heat transfer is 100% efficient.
3rd Law Thermodynamics
As temperature approaches absolute zero, entropy is at a minimum.
Systems of Heat
Open system: mass and energy can exchange
E.g. H20 in open container
Closed: allows energy to transfer, no mass
E.g. H20 in a flask
Isolated: neither energy nor mass can transfer
E.g. H20 in a flask in a vacuum.
S->L
Melting (+ΔH)
Heat of fusion
L->S
Freezing (-ΔH)
L->G
Vaporization (boiling) (+ΔH)
G->L
Condensing (-ΔH)
S->G
Sublimation (+ΔH)
G->S
Deposition (-ΔH)
ATP and Cell metabolism
Phosphoandride bond, Phosphate transfer by (-ΔG) cellular work, biosynthesis to ADP. Condensation reaction through Glycolysis, TCA cycle, oxidation phosphorylation, or photosynthesis back to ATP.
ATP bottom line
Allows endergonic reactions to become exergonic
ATP reaction
ATP + H2O ->
ATP has a high phosphoryl group transfer potential
At pH 7, ATP is very negatively charged. It carries 4 negative charges which strongly repel each other. When hydrolyzed, this decreases repulsion.
ADP and Pi are resonance stabilized than ATP alone.
ATP and strenuous exercise
Vertebrate muscles contain creatine phosphate which easily transfer its phosphoryl group to form a high conc. of ATP.
Chemotrophs
Derive free energy from the oxidation of fuel molecules
NADH and FADH2
Major electron carriers
Biotin
Carrier molecule, CO2
S-Adenosylmethionine (SAM)
Carrier molecule, CH3 groups
Carbohydrates
Sugars and starches, polyhydroxy aldehydes and polyhydroxy ketones
Glucose
An aldohexose, most common simple sugar
D sugars
Sugar Chemistry
If OH is on the right = R configuration
If OH is on the left = S configuration.
Dissaccharides are made
By linking monosaccharides though dehydration synthesis.
Chitin
Derivative of glucose. Component of cell walls of fungi and part of the exoskeleton of arthropods: crustaceans and insects.
Glycogen
Animal starch. We store glucose as glycogen. Found mainly in the liver and skeletal muscles. Largely branched molecule. Stored in granules.
Lipids functions
1) Used for energy
2) Components of nerve cells
3) Protection
4) Membrane components
Steroids, Prostaglandins, Triglycerides, Waxes, Terpenes
Prostaglandin
Produced by most cells, involved with processes such as inflammation, blood clotting and labor.
Triglyceride
Glycerol and 3 fatty acids, can be saturated or unsatured. Always cis
Terpenes
Produced mainly by plants. Used in spices, perfumes, and medicine.
Waxes
Esters of fatty acids and long chain alcohols
Phospholipids
Cell membrane
3 C alkanes + 2 COOR + Phosphate group
Phospholipid examples
Certain animals have been found to have more flexible and fluid like membranes in extreme temperatures.
If too hot: increase % of saturated fatty acids
If too cold increase % of unsaturated fatty acids
Steroid structure
3, 6 membered rings and 1, 5 membered ring
Estrogen, Cholesterol, Progesterone, and Testosterone
Cholesterol
Unsaturated steroid alcohol which makes up a significant part of membranes. Works with prostaglandins and hormones.
1) Help regulate blood flow
2) Effect nerve transmission
Prostaglandins and Inflammation
Aspirin can inhibit the work of an enzyme needed in the synthesis of prostaglandins.
Protein Main Elements
C,H,O,N, S
Lipids and Carbohydrates don’t have S
Protein Function
Widest array of functions: Enzymes, Hormones, Protective, Storage, Receptors, Transport, Structure, and Motor Movement.
Protein structure
Collagen, Keratin, and Elastin are fibrous proteins contributing to the structural integrity of the organism.
Protein Motor Movement
Dynein is a motor protein, actin and myosin are also proteins
Amino acid hydrophobicity
AA with Hydrophobic R group contain only C and H
AA with hydrophilic R groups contain O or N
Amino acid peptide bond
40% double bond character. Rigid, not allowing free rotation. Flat sp2 structure. Steric hinderance causes the trans conformation to be more stable.
Protein Chirality
Proteins use L-amino acids. All L- amino acids have the S configuration except cysteine (S containing aa)
Primary Structure
Sequence of amino acids, held by covalent bonds including disulfide bonds
Secondary structure
3D conformation of localized regions. (e.g. helix of beta pleated sheets held by H bonds).
Tertiatery structure
3D shape of the entire molecule held by H bonds, disulfide bonds, salt bridges (electrostatic) and VDW (hydrophobic).
Quaternary structure
How one polypeptide chain interacts with another. Same four interactions as 3prime.
Protein digestion
Breaking of the amide (or peptide bond), losing primary structure.
Protein Denaturation
Primary is not changed but all others structures are
Denaturing agents
Heat/Radiation/Urea: Disrupts H bonds
Detergents, Strong acids/bases: Affects salt bridges and H bonds
Salts of heavy metals (Ag+, Hg++, Pb++): combine with SH and form precipitates and acidic aa.
Nucleotide
Monomers of nucleic acids. Hydrolysable into:
Sugar, phosphate, and N base.
Pyrimidines
C,U,T
1 ring structurally
Purines
A, G
2 rings structurally
H bonds nucleotides
A=T, two H bonds
C=_G, 3 H bonds
Nucleoside
Sugar + N base
Structural framework of DNA/RNA
Sugar phosphate backbone
Phosphodiester link
3’ OH sugar join with 5’ OH another sugar
