Chapter 2: Biochemistry Flashcards
subatomic particles
protons, neutrons, and electrons
ground state
electrons are in the lowest available energy levels
excited state
electrons are in higher energy levels
isotopes
vary in number of neutrons
half-life
amount of time for half of an isoptope to decay
tracer
used to trace the path of specified molecule in metabolic pathway
hydrophobic
water hating
hydrophillic
water loving
properties of water
highly polar, hydrogen bonding, high specific heat, high heat of vaporization, universal solvent, strong cohesion, capillary action, surface tension
transpirational-pull cohesion tension
as one molecule of water is lost from a leaf by transpiration, another molecule is drawn up from roots
ice being less dense than water leads to…
- ice freezes: insulation of bodies of water
- ice melts: sinks to bottome of lake, bringing oxygen to depths and nutrients released by bacteria during winter to the surfce
a. spring overturn: cycling of nutrients through a lake
buffer
regulates the pH of biological systems by resisting change to pH
isomers
same molecular fromula but different structure
structural isomers
differ in the arrangement of atoms
cis-trans isomers
differ in arrangement around double bonds
entaniomers
molecules that are mirror images of each other
important in the pharmaceutical industry
left-handed: L-version
right-handed: D-version
carbohydrates
fuel for body and building materials C,H,O hydrogen to oxygen ratio-- 2:1 monomer: monosaccharide polymer: polysaccharide, disaccharide
dehydration synthesis
joining of molecules by releasing a molecule of water
hydrolysis
breakdown of compound by adding water
structural polysaccharides
plants: cellulose
animals: chitin
storage polysaccharides
plants: starch
animals: glycogen
lipids
- hydrophobic compound that consists of 1 glycerol (alcohol) and 3 fatty acids (hydrocarbon chain with a carboxyl group at the end)
- includes fats, oils, waxes, and steroids
- C,H,O,N
saturated lipid
- maximum number of H
- no double bonds between C
- solid at room temperature (butter)
unsaturated lipid
- doesn’t have maximum number of H
- double bonds between C
- liquid at room temperature (olive oil)
steroids
- lipids consisting of four fused rings
- cholesterol, testosterone, estradiol
function of lipids
- energy storage
- structural: phospholipids (glycerol, 2 fatty acids, 1 phosphate group), cholesterol in plasma membrane
- endocrine: some steroids are hormones
phospholipids
hydrophobic tail, hydrophilic head, forms plasma membrane
proteins
- growth and repair
- signaling from one cell to another
- regulation through hormones
- enzymatic activity
- movement (actin and myosin protein fibers in muscle contractions)
- C,H,O,N,P,S
- monomer: amino acid
- polymer: polypeptide (amino acids joined by peptide bonds), dipeptide
- carboxyl, amine , R group
protein conformation
shape of protein
primary stucture
linear sequence of amino acids
secondary structure
- polypeptide coils or folds into alpha helix or beta pleated sheet due to hydrogen bonding within molecule
- proteins with secondary structure are fibrous proteins
tertiary structure
- intricate 3-D shape that determines the molecules specificity
- caused by hydrogen bonding, van der waals forces, disulfide bonds between amino acids, ionic bonding hydrophobic interactions
quaternary structure
- proteins with more than one polypeptide chain
- hemoglobin
denaturation
a protein’s loss of shape due to high pH, high temperature, and high concentration of salt
chaperonins (chaperone proteins)
assist in the folding of other proteins
prions
- misfolded proteins
- can cause Mad Cow Disease, Alzheimer’s, and Parkinson’s
X-ray crystallography
- scientific method of determining the precise positions/arrangements of atoms in a crystal where beams of X-ray strikes a crystal and causes the beam of light to diffract
- technique for structure determination of proteins and biological macromolecules
bioinformatics
- uses computers and math to integrate data from amino acid sequence
- technique for structure determination of proteins and biological macromolecules
nucleic acids
-polymer for DNA and RNA (encode hereditary info)
nucleotide
- RNA and DNA monomer
- phosphate, 5-carbon sugar (deoxyribose or ribose), nitrogenous base (adenine, thymine, guanine, cytosine, uracil)
- C,H,O,N,P
exergonic
energy is released
endergonic
energy is absorbed
metabolism
sum of chemical reactions that take place in cells
catabolism
break down molecules
anabolism
build up molecules
pathways
- series of metabolic reactions with a specific function
- controlled by enzymes, allowing for efficiency
enzymes
- catalytic proteins that speed up reactions by lowering activation energy required
- don’t provide energy for a reaction or cause a reaction
transition state
reactive (unstable) condition of substrate after sufficient energy has been absorbed to initiate the reaction
characteristics of enzymes
- globular (spherical) proteins with tertiary structure
- substrate-specific
- induced-fit model: wen substrate enters the active site, it causes the enzyme to change its shape to fit substrate better
- enzyme binds to substrate, causing enzyme-substrate complex
- enzymes are not destroyed, but reused
- enzyme name: substrate followed by “–ase”
- catalyze reactions in both directions
- assisted by cofactors (inorganic) or coenzymes (vitamins)
control of enzymatic activity
- switch on/off genes that code for enzymes
- noncompetitive and competitive inhibition
competitive inhibition
- competitive inhibitors mimic substrate molecules and compete for the active site, therefore reducing productivity of enzyme
- overcome by increasing the concentration of substrate
- can be reversible or non-reversible
noncompetitive inhibition
noncompetitive inhibitors, or allosteric regulators, bind to an alternate site distinct from the active site of an enzyme, inhibiting enzyme from catalyzing substrate into product
allosteric
- change in shape alters efficiency
- allosteric enzymes switch between active shape and inactive shape
feedback inhibition
end product of the pathway is the allosteric inhibitor for an enzyme that catalyzed an earlier step in the pathway
cooperativity
- type of allosteric activation
- binding of one substrate molecule to the active site of one subunit of the enzyme causes a change in the whole molecule that locks all subunits into active position
