week 1&2 - lectures 1,2 and part of 3 Flashcards
name the 4 features of functional groups
- # and type of carbon bonds: single bonds, double bonds, triple bonds
- branching, rings
- isomers: are compounds that have same molecular formula but different structural formulas
- functional groups attached to the carbon backbone
what are functional groups
- impart diverse properties to organic compounds that are the characteristics of life
- determine the kind of reactions in which the compounds participate
what is metabolism
- total sum of chemical reactions that occur in the cell
- describes the transformation of substances into energy or materials that the cell can use or store
- sum of chemical cellular reactions
describe dehydration synthesis and give an ex
- link monomers to form polymers
- aka condensation
- anabolism
- water is released
- ex: protein synthesis
describe hydrolysis and give an ex
- molecules are broken down to monomers
- catabolism
- protein digestion
- water is used to break bond (needed)
describe proteins
- built of 20 amino acids
- CHNOS
- different side chain R
name the 3 classifications of amino acids
non polar
polar
charged
describe non polar
hydrophobic
ex: glycine, alanine, valine, leucine etc
CH rich
describe polar
hydrophilic
ex: serine, threonine, cysteine
functional groups OH, amide CO - NH2, SH
describe charged
hydrophilic
ex: aspartic acid, glutamic acid - acidic, lysine, arginine, histidine - basic
what does cysteine mean
disulfide bonds
need 2 S
describe linkage between amino acids
dehydration synthesis - covalent linkage between amino acids - peptide bonds
where is the side chain attached to
the central carbon
what is physiological pH
7.3-7.4
which side of amino acid is positive and which is negative
NH3 +
COO -
describe zwitterion
a molecule or ion having separately positively and negatively charged groups
at low pH - coo accepts h bc extreme pH level
at high pH NHH acts as an acid
describe protein functions
- buffers - albumin in blood
- enzymes catalyzing chemical reactions; increase the rate of reaction
- cell transport, channels and pumps
- regulation of processes and signalling
- maintaining homeostasis, hormones and receptors
- defenses against diseases (immunoglobulins-antibodies)
describe main steps of protein structure formation
right after protein synthesis - primary structure
FOLD
secondary structure
FOLD - lots of bonds forming
tertiary structure - 3d shape
FORMS complex - sometimes
quaternary structure
describe primary structure
peptide bonds form backbone
carboxyl ends
aa sequence
ONLY affected by mutations or when aa chain is disrupted
boiling wont affect primary structure but will denature protein
describe secondary structure
beta sheets/strands - stretched
alpha helix - more twisted
H bonds of backbone
antiparallel
describe tertiary structure
r side chain interactions
functional (native) protein
1 polypeptide, 1 chain
disulfide bonds
describe quaternary structure
protein complex
2 or more polypeptides/chains
what are anfisens conclusions
folding of proteins depends on the primary structure
folding into native structure is spontaneous deltaG < 0
name the factors that affect protein structure
causes denaturation and loss of function
- mutations
- temp
- pH
- reducing/oxidizing agents
describe how temp affects protein structure
affects secondary and above structures
describe how mutations affects protein structure
affects primary and above structures, beyond denaturation
describe how pH affects protein structure
affects ionic bonds
mainly tertiary and quaternary structures
describe how reducing/oxidizing agents affects protein structure
affect disulfide bonds
tertiary and above structures
name and describe side chain interactions for tertiary and quaternary structures
covalent - disulfide - 2 cysteines
ionic - 2 charged - salt bridges
H bonds - 2 polar aa or charge & polar aa
hydrophobic - 2 nonpolar aa
T or F energy flows and cycles
F the first and second law explain why energy flows but does not cycle
describe entropy
G=0, equilibrium
∆G>0, unfavourable, endergonic
∆G<0, favourable, exergonic
describe exergonic reactions/processes
exergonic reaction reactants free energy > products free energy; free energy is released
describe endergonic reactions/processes
endergonic reaction reactants free energy < products free energy; free energy is required
describe catabolic reactions
breakdown of molecules and macromolecules - exergonic
no energy input required
releases free energy for work
name and describe processes that need work
chemical anabolic reactions - DNA replication, gene expression
transport - exocytosis, endocytosis, active transport
mechanical - muscle contraction, movement of cells (beating of cilia)
describe anabolic reactions and name an ex
synthesis of molecules and macromolecules - endergonic
input of energy needed
ATP hydrolysis provides free energy
describe atp hydrolysis
ATP + H2O –> ADP + Pi + energy
describe phosphorylation
- covalent linkage of phosphate on to a molecule/chemical reactant/enzyme/protein
- energizes molecule, more reactive
- release of phosphate group
- overall = change in the conformation of the molecule useful for doing work
describe atp cycle
ATP + H20 - exergonic catabolic, hydrolysis, free energy released to power work —> ADP + Pi - dehydration, anabolic, endergonic, ATP synthesis, input of free energy
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what are enzymes
proteins, highly specific for the reactions they catalyze
biological catalysts that accelerate the rate of a chemical reaction by lowering the activation energy and facilitate transition state formation
what cant enzymes do
- change ∆G
- change equilibrium concentrations of reactants (substrates) and products
- catalyse overall endergonic reactions
describe graph of free energy for enzymes
E+S = not yet reacted
old bonds broken in substrate and new bonds formed - E-S
then E+P
what is the active site
pocket with key amino acid side chains (functional groups) located within the enzyme to which the substrate binds
what is induced fit
conformational/shape change of E when bound with substrate that favours the transition state formation
what is the transition state
high energy state where reactants break and reform covalent bonds in order to become products
T or F enzymes can only be used once
F they are also reused many times in the same reaction until denatured or inactivated
what is velocity for enzymes
rate of product formation
rate of substrate disappearing
what is Vmax for enzymes
reached when the concentration of substrate is in excess and all enzyme molecules are bound with substrate at vmax, enzyme is saturated
what is Km for enzymes
Km is the concentration of substrate at which the rate is Vmax/2 and can be considered a measure of enzyme affinity for the substrate
describe rate of product formation graph
Vmax is limited by the active sites - parking lot
once they are all filled up/saturated = caps off into a horizontal line
0 enzymes = horizontal line at 0
what are cofactors
help the enzyme function
are not amino acids
are not regulatory molecules
are additional molecules
name the two cofactors
organic cofactors and inorganic cofactors
describe organic cofactors
also called coenzymes
in humans - some of them can only be made by vitamins in diet
describe inorganic cofactors
metal ions
describe enzymes at below optimal temperature
substrate molecules do not have enough kinetic energy and the number of collisions is low
describe enzymes at above optimal temperature
denaturation - secondary tertiary and quaternary structures are disrupted
describe enzymes at too high or low pH
changes in charges of r groups affect their ionic interactions and therefore the 3D structures of enzymes
T or F denaturing agents and boiling affects the primary structure of enzymes
F, NOOO, not primary, but enzymes/proteins lose activity (active site doesnt work as efficiently or at all) and sometimes aggregate (form clumps)
describe metabolic pathways and enzymes
can be linear, branched, circular, anabolic or catabolic
-are found in the same cellular component
- function together to form a common product
- like workers in a factory assembly line: product of one is substrate for next
- wont ever reach equilibrium
- not all are on at same time
- tightly regulated
describe regulation of enzymatic activity
- reversible inhibition and activation
- small modifying molecules = modification by activators (Pi or ADP) increase the activity of enzymes, inhibitors (ATP or end products of metabolic pathways) decrease activity of enzymes
- reversible inhibition and activation (enzyme resumes its shape and function once inhibitor or activator is removed
