Midterm Flashcards
how does the cell membrane maintain life
uses selective permeability to maintain gradients and inequilibrium
metabolism (catabolism vs anabolism)
all chem reactions that maintain cell life.
catabolism: breakdown of molecules to obtain energy
anabolism: synthesis of all compounds need by cell
attributes of all living organisms (7)
cell membrane, metabolic processes facilitated by enzymes, spend energy, react to stimuli, reproduction, mutability, non-equilib (selective permeability)
stereoisomer, chiral center, enantiomer
stereoisomer: 2 molecules w same formula and f.g. but cannot be superimposed
chiral center: center of asymmetry
enantiomer: mirror image
end of monosacharride
carbon of aldehyde or ketone (lowest number convention)
reaction of monosaccharide
- reaction with aldehyde or ketone (hemiacetal/hemiketal product)
- linear to ring structure forms
glycosidic bond
- dehydration synthesis reaction
- join monosacc/longer sugar chains
forms di,oligo,polysaccharides - in acidic environment
central dogma of molecular biology
DNA-(transcription)->RNA-(translation)->protein (amino acid)
nucleotide vs nucleoside
nucleotide: sugar ribose+base+phosphate
nucleoside: sugar ribose+base
nitrogenous bases (5)
pyrimidine: C, T (DNA), U (RNA)
purine: A, G
define deoxy-ribo-nucleic-acid
deoxy: without oxygen on 2’ carbon of ribose
ribo: ribose sugar
nucleic acid: nucleotide
acid: acidic phosphate group
why does DNA have double helix?
- strands oriented is opposite direction
- complementary base pairs
- H bond bw bp
- VDW bw stacked bases
heterochromatin vs euchromatin
hetero: when cells not dividing (interphase), chromosones are more packed
euchro: less condensed (in prokaryotes)
denaturation, annealing, melting
denat: DNA strand seperation, w/ or w/out T chnage
annealing: upon cooling, some/all complementary strands re establish
melting: seperation above given T
DNA melting curve, DNA melting temperature
- dna absorbs more light when it denatures
- T as which slope of absorbance is steepest
result of RNA annealing
- forms double helical and complex 3D structure
- tRNA (transfer)
- rRNA (ribosome)
tRNA vs rRNA
tRNA: 3D cloverleaf created by local annealing of nucleotides
rRNA: 3D in ribosome, part of catalytic rxn to make protein (active site of ribosome)
interactions that stabilize DNA (4)
- hydrophobic effect
- H bond bw bp
- base stacking
- ionic int bw neg phosphate backbone and ions in solution
peptide bond
- between carboxyl and amino group
- condensation/dehydration synthesis
pKa and acidity
pKa incr, Ka decr, acidity decr
pH>pKa vs pH
pH>pKa (basic): fg deprot ie acts as acid
pH
buffer selection
- capacity highest when pH=pKa
- low slope regions: low pH changes
isoelectric point
pH at which the average charge of a solution containing the amino acid is neutral
secondary structure
- h bond within backbone of one strand
- alpha helix
- beta sheet (parallel vs antiparallel)
tertiary structure
organisations of series of secondary structure elements (h bond, hydrophobic, polypetide backbone, disulfide bridge, ionic bond)
disulfide bond
- 2 cyteines in close proximity form covalent bond
- stabilizes tertiary structure
quaternary structure
each peptide chain is a protein subunit
motif
- small regions of 3D structure/AA sequence shared among proteins
- conserved
- unique function
fold
orientations of motifs within tertiary protein structure
domain
- conserved sequence pattern
- independent functional and structural unit
- longer than motifs
classes of proteins (3)
- globular (transport)
- fibrillar (structure)
- integral (receptor)
glycosylation
- protein-saccharide link
- covalent
- takes place in ER and golgi
- can change protein half life
types of glycosylation
- N-link: occurs on side chain of Asn
2. O-link: occurs on side chain of Ser or Thr
triacylglcerols (triglycerides)
- fat
- acid, hydrocarbon, alc
- high energy
glycerophospholipids (phosphoglycerides)
- one of hydroxyl groups of glycerol is occupied by phosphodiatic head
- amphiphilic: molecule w/ polar and non polar regions
glycerophospholipids (phosphoglycerides)
- one of hydroxyl groups of glycerol is occupied by phosphodiatic head
- amphiphilic: molecule w/ polar and non polar regions
sphingo-lipids
- phosphate group can be switched w/ OH
- glycerol backbone is bound by amine or amide
saponification
triglyceride+NaOH=
glycerol+soap molecule
steroids
- slightly amphiphilic due to OH
- rigid ring structure provides rigidity to membrane
diffusion (2 types)
transverse: flip flop, slow
lateral: fast
transition temperature
- from solid to liquid of phosphlipid bilayer
- gel like solid: T below Tt
- liquid crystal: T above Tt
factors affecting transition temp
- chain length
2. number of double bond
liposomes
- phospholipid as drug delivery vehicle
- entry routes of liposome into cell: receptor specific endocytosis, adsorption
gram positive vs negative bacteria
- peptidoglycan: thick in (+)
- membrane structure: (-) have 2 membranes (inner, outer)
- lipopolysaccharides: (-)
LPS
- outer membrane bacteria (-)
- lipids with polysaccharide chain
- trigger immune reactions in animals against pathogenic bacteria
enzymes
- large proteins that catalyze rxn
- do not change G, but change time needed for rxn
enzyme anatomy
- scaffold to support and position active site
- binding site: bind and orient substrate
- catalytic site: reduce Ea
theories of enzyme binding (2)
- lock and key
2. induced fit
cofactors and coenzymes
- used by enzymes to complete met. rxn
cofactor: inorganic ions (metals)
coenzyme: organic molecules
enzyme functions (5)
- acid base catalysis
- covalent catalysis
- metal ion catalysis
- electrostatic catlysis
- proximity and orientation effects
Km
substrate concentration that provides a reaction velocity that is half the max velocity under saturating substrate conditions
turnover number (kcat)
- measure if catalytic act
- # substrate molecules converted to product/enzyme molecule/time
- if MM: k2=kcat=Vmax/Et
catalytic efficiency (kcat/Km)
- estimate of how perfect enzyme is
- measures enzyme performance when S is low
Lineweaver-Burk diagram
double reciprocal plot of 1/[S] vs 1/V
- slope=Km/Vmax
- yint=1/Vmax
enzyme inhibition
- regulatory mechanism
cells: change enzyme concentration, regulate activity of enzymes
types of inhibition (3)
- competitive: Km incr
- uncompetitive: Km, Vmax decr
- mixed inhibition: Vmax reduced
specific activity of pure enzyme
units: micromoles/min/mg of enzyme
