Flashcards in Bio 1 Deck (93):
Name the 9 non polar amino acids
Name the 6 polar neutral amino acids
Name the 2 polar acidic amino acids
Name the 3 polar basic amino acids
Are the polar neutral amino acids hydrophilic or hydrophobic?
are polar enough to form H bonds with water
Which amino acids are usually phosphorylated by a kinase?
What is the approximate pKa of the carboxylic acid functional group on the acidic amino acids?
What is the approximate pKa for lysine?
What is the approximate pKa for arginine?
What is the approximate pKa for histidine?
What is unique about histidine?
its side chain pKa is close to neutral so it can be protonated or unprotonated at physiological pH and thus often acts as a proton acceptor and donor
What are the 8 essential amino acids?
What are the 3 and 1 letter code for alanine?
What are the 3 and 1 letter code for arginine?
What are the 3 and 1 letter code for asparagine?
What are the 3 and 1 letter code for aspartic acid?
What are the 3 and 1 letter code for cysteine?
What are the 3 and 1 letter code of glutamic acid?
What are the 3 and 1 letter code of glutamine?
What are the 3 and 1 letter code of glycine?
What are the 3 and one letter code for histidine?
What are the 3 and 1 letter code for isoleucine?
What are the 3 and 1 letter code for leucine?
What are the 3 and 1 letter code for lysine?
What are the 3 and 1 letter code for methionine?
What are the 3 and 1 letter code phenylalanine?
What are the 3 and 1 letter code for proline?
What are the 3 and 1 letter code for serine?
What are the 3 and 1 letter code for threonine?
What are the 3 and 1 letter code for tryptophan?
What are the 3 and 1 letter code for tyrosine?
What are the 3 and 1 letter code for valine?
What are the two types of covalent bonds found in proteins?
Which end of a protein is made first during synthesis?
Is protein hydrolysis thermodynamically favourable?
yes but it is kinetically slow
What is proteolysis/proteolytic cleavage?
hydrolysis of a protein by another protein
Which amino acid residue can form disulphide bonds? Which level of structure is this?
In what environment do disulphide bonds form?
oxidizing i.e. only in extracellular peptides
What are the 2 main secondary structure motifs?
alpha helix and beta pleated sheet
Describe an alpha helix
5 angstroms in width
each sub sequent AA rising 1.5 angstroms
alpha carboxyl oxygen of one AA H-bonded to the alpha amino proton of another AA 3 residues away
What makes sucrose?
glucose (alpha 1, 2) fructose
What make lactose?
galactose (beta 1,4) glucose
What makes maltose?
glucose (alpha 1, 4) glucose
What makes cellubiose?
glucose (beta 1,4) glucose
What makes glycogen?
glucose polymer with alpha 1,4 linkages and alpha 1, 6 branches
What is cellulose made of?
polymer of cellubiose (blu beta 1, 4 blu)
What is starch made of?
alpha 1,4 glucose polymer like glycogen, but the branching is a bit different
Is the hydrolysis of polysaccharides into monosaccharides favoured thermodynamically?
What are the 3 physiological roles of lipids?
triglycerides store energy in adipoctyes
phospholipids in cell membranes
cholesterol has many roles including making steroid hormones
What configuration are naturally occurring double bonds in unsaturated fatty acids?
What do fatty acids form in aqueous solutions?
What is saponification?
base-catalyzed hydrolysis of triglycerides into fatty acid salts (soaps)
What are lipases?
enzymes that hydrolyze fats
How does the oxidation/reduction of fats compare to that of carbs?
fats are much more reduced and thus store a lot more energy
What molecules make detergents?
How do phospholipids influence the fluidity of a membrane?
increasing unsaturation increases fluidity
increasing length decreases fluidity (i.e. shorter=more fluid)
How does cholesterol influence membrane fluidity?
at low temperatures it increases fluidity
at high temperatures it decreases fluidity
How many isoprene units are in a sesquiterpene?
Give an example of a terpenoid
What are steroids made of?
Is cholesterol amphipathic?
What is pyrophosphate?
two phosphates bound via an anhydride linkage
What are the 3 reasons phosphate anhydride bonds store a lot of energy?
-when bound together their negative charges repel each other
-orthophosphate (one by itself) has more resonance forms than when linked
-orthophosphate has a more favourable interaction with water than linked phosphates
What is the first law of thermodynamics?
conservation of energy
What is delta G equal to?
delta G= delta H - TdeltaS
What do exergonic reactions have?
negative delta G
What do endergonic reactions have?
positive delta G
What do exothermic reactions have?
negative delta H
What do endothermic reactions have?
positive delta H
What does ln(1) equal?
Are free energy changes additive?
yes i.e. reaction coupling
Which conformation of sugars and amino acids do our bodies use?
L amino acids and D sugars
What are cofactors? Coenzymes?
cofactors are metal ions or small molecules that aren't themselves proteins that are required for activity in many enzymes
coenzymes are cofactors that are organic molecules
Name 4 types of enzyme regulation. Are they all reversible?
association (w/other peptides)
They are all reversible except proteolytic cleavage
What is feedforward stimulation?
when an enzyme is stimulated by its substrate ( or a molecule used in the synthesis of its substrate)
Describe the relationship between Km and affinity of an enzyme for its substrate
low Km=high affinity
What kind of curve results from cooperative binding enzymes?
sigmoidal curve (S)
What is the relationship between cooperative and allosteric when referring to an enzyme?
cooperativity is a special type of allosteric interaction
Describe a competitive inhibitor and its effects
binds to the active site (often resembles transition state)
competes with substrate
doesn't change Vmax
(can be overcome by adding enough substrate)
Describe a non-competitive inhibitor and its effects
binds to an allosteric site
decreases enzyme activity
doesn't change Km
(substrate can still bind to enzyme, there just isn't any catalytic activity)
Describe an uncompetitive inhibitor and its effects
binds to the enzyme-substrate complex
decreases enzyme activity
(enzyme and substrate cannot dissociate thus it is increases the affinity)
Describe a mixed-type inhibitor and its effects
binds to the enzyme or the enzyme-substrate complex
effects of Km depend:
if inhibitor has a greater affinity for the E-S complex then Km decreases
if inhibitor has a greater affinity for the E then Km increases
if inhibitor has equal affinity for E-S and E then Km doesn't change
What are the 3 meanings of the word oxidize?
What are the 3 meanings of the word reduce?
Describe the regulation of hexokinase. What reaction does it catalyze?
catalyzes glucose to G6P
activated by glucose
inhibited by G6P
What is the committed step in glycolysis?
F6P to F16P
Describe the regulation of phosphofructokinase. What reaction does it catalyze?
catalyzes F6P to F16P
inhibited by ATP
activated by F2,6P and AMP
Describe the regulation of pyruvate kinase. What reaction does it catalyze?
catalyzes PEP to pyruvate
activated by PEP and F16P
inhibited by ATP
Describe the regulation of isocitrate dehydrogenase. What does it use and produce?
uses citrate, produces NADH and CO2
activated by ADP
inhibited by ATP and NADH
What does the Kreb's cycle net per glucose molecule?
How many protons and ATP do NADH and FADH2 net each in the electron transport chain/oxidative phosphorylation?
10 H+ / NADH = 2.5 ATP
6 H+/ FADH2 = 1.5 ATP
6 H+ / NADH from glycolysis = 1.5 ATP
(4 H+ / ATP)
How many ATP are generated per glucose molecule in cell respiration?
30 ATP for eukaryotes
32 ATP for prokaryotes