Midterm 1 Flashcards
Prokaryotes
no nucleus
Eukaryotes
contains DNA containing nucleus
Four Major Families of Biomolecules
Sugar, Fatty Acids, Amino Acids, Nucleotides
Monosaccharide
simple sugar (CH2O)n with n = 3, 4, 5, 6
Disaccharides
two monosaccharides bonded covalently
Oligosaccharides
3 to 10 monosaccharide chain
Polysaccharides
greater than 10 monosaccharides (10s, 100s, more); can also be called glycans.
Bacterial Growth Phase 1
Lag Phase
Bacterial Growth Phase 2
Exponential Growth Phase
Bacterial Growth Phase 3
Stationary Phase
Bacterial Growth Phase 4
Decline Phase
General Equation for Bacterial Growth (exponential)
N = Noe^(mut)
General Equation for Bacterial Growth (doubling time)
N = No*(2^(t/td))
equation for mu
mu = ln2/td
Optimal pH Neutrophiles
6-8
Optimal pH Acidophiles
<2
Optimal pH Alkaliphiles
10
Aerobic
Requires O2 for growth/metabolism
Anaerobic
Inhibited by presence of O2
Facultative
Grow in conditions with or without O2
Heterotrophs
use of organic compounds such as carbs, lipids, or hydrocarbons as carbon and energy source.
Autotrophs
Use CO2 as a carbon source
Photoautotrophs
use CO2 as a carbon source and obtain energy from light
Chemoautotrophs
use CO2 as carbon source and obtain energy from oxidation of inorganic molecules
First Law Thermodynamics
conservation of energy ( in = out )
Second Law Thermodynamics
universal increase of entropy
Gibbs Free Energy
dG = dH - TdS
Anabolic Pathways
large molecules made from smaller ones
Catabolic Pathways
large and/or energy containing molecules are broken into smaller ones, releasing energy
Activated Carriers
small organic molecules with energy-rich covalent bond(s) or high-energy electrons, easily transferrable
Catalysis (protein)
enzymes catalyze intracellular reactions
Transport (protein)
control passage of nutrients in/out of cells
Structural (proteins)
connective tissues, hair, nails, feathers, horns
Molecular Recognition (proteins)
antibodies/immune system
Motion (proteins)
cellular transport
Primary Structure
amino acid sequence
Calculating the number of different shapes a molecule can take
of bond angles ^ number of bonds
Hydrophobic effect
The release of water molecules from the structured solvation layer
around the molecule as protein folds. Hydrophobic amino acids
usually form the “core” of a protein
Hydrogen bonds
Interaction of N−H and C=O of the peptide bond leads to local regular
structures such as α helices and β sheets.
van der Waals
Medium-range weak attraction between all atoms contributes
significantly to the stability in the interior of the protein.
Electrostatic interactions
- Long-range strong interactions between permanently charged groups
– Salt bridges, especially those buried in the hydrophobic core, strongly
stabilize the protein.
denature
Unfold, but will find its most stable fold after time. the most stable fold is lowest free energy.
chaperones
chaperone proteins help other unfolded proteins by trapping them until they are folded properly
φ (phi) angle
angle around the α carbon—amide nitrogen bond
ψ (psi) angle
angle around the α carbon—carbonyl carbon bond
Ramachandran Plot
shows favorable angles
Secondary Structure
a local spatial
arrangement of the polypeptide backbone.
alpha helix
- stabilized by hydrogen bonds between nearby residues
- right handed helix
beta sheet
- formed from H-Bonding of amines.
- the planarity of the peptide bond and tetrahedral
geometry of the α carbon can create a β strand.
random coil
irregular arrangement of polypeptide chain
strong helix breaker
pro, gly
strong helix formers
ala, leu
two types of beta sheets
parallel:
—–>
—–>
—–>
antiparallel:
—–>
<—–
—–>
Amyloid
- beta sheets stacked together into long strands
- can result from protein misfolding
- associated with neurodegenerative diseases
