Biochem 1 Flashcards
Major (non-enzymatic) protein functions
- Recognizing proteins:
ANY PROTEIN in a cell must have been ___ for by ___
Ultimately, all proteins are ___ products
- Must have been coded for by DNA
Ultimately, ALL PROTEINS ARE
GENE PRODUCTS
Carbohydrates
- Common disaccharides
- Lactose= ___+___?
LACTOSE=
galactose + glucose (ß-linked)
Vitamins & Minerals
- Define “MINERALS”
- What are 3 things theyre used for?
- How do you GAIN them?
- Are needed in Big/Small quantities?
MINERALS
Are inorganic elements or compounds
- Are necessary for:
- Bone formation
- ion gradients
- O2 transport, etc.
They are gained through: DIET
- Are needed in very small quantities
- which makes them “macronutrients”*
Protein Folding
- Hydrophobic surface:
The majority of the R groups on the surface of a globular protein are either ___ or ___ed
either POLAR or CHARGED
Substrate-Enzyme specificity
- The Enzyme-substrate (ES) complex is formed when?
- Show what the rxn looks like
is formed when substrate is bound to active site
E+S ⇔ES ⇔ EP ⇔ E+P
Protein Folding
- How do Salt Bridges form?
Formed when acidic & basic R groups undergo a NEUTRALIZATION rxn
- resulting in a salt
AA Rxns
- Protein hydrolysis
- TRYPSIN cleaves on the ____ side of WHAT AA’s?
Cleaves proteins on the CARBOXYL side of:
- Arginine and Lysine
What effect do ENZYMES (“Catalysts”) have on:
- Keq
- Yield
- % yield
NONE!!
LIPIDS are:
“Hydro_____ __________s”
“Hydrophobic Biomolecules”
Carbohydrates
- List the “8 Common Monosaccharides”
- glyceraldehyde
- dihydroxyacetone
- ribose
- deoxyribose
- glucose
- fructose
- galactose
- mannose
Enzyme Inhibition
- Feedback Inhibition
NEGATIVE FEEDBACK
- is what kind of inhibition?
- What does it do?
- What 3 things will you see it in?
NEGATIVE FEEDBACK
A specific type of non-competitive or
allosteric inhibition
- In it, one of the PRODUCTS of the reaction LATER in the chain
- …acts as an INHIBITOR for one of the enzymes EARLIER in the chain
Seen in:
- Multi-step reactions
-
Synthetic pathways
- e.g., GLYCOLYSIS
- Cascades
Major (non-enzymatic) protein functions
Immune system
- Name the 2 (GENERAL) types of proteins
AntiGENS & AntiBODIES
3º Protein structure
6 INTERACTIONS B/T AA’s that contribute to 3º structure
-
H-bonding
- Are ___-_____ bonds between WHAT 2 THINGS?
NON-COVALENT bond between either:
-
Backbone atoms
- N-H or
- C=O
-
Side chains
- Amine groups
- Carboxyl groups
- Alcohol groups, etc.
Enzyme Inhibition/Reversible Inhibition/Competitive inhibition does what? Effect on Vmax and Km
inhibitor binds AT the active site, and inhibitor resembles substrate in shape. Can be overcome by [S]. Vmax=NO ∆. Km=INCREASES.
PEPTIDES are
WRITTEN, READ, & SYNTHESIZED
from the ___ to ___ terminus
N to C
Lipids/Triaglycerols/ Saturated vs Unsaturated. Compare. Which is healthier? Why?
Saturated=no DBs, solid @ RT, Higher MPs. Unsaturated=at least 1 DB, liquid @ RT, Lower MPs). Unsaturated is healthier b/c they generate fewer calories when metabolized.
Mechanisms of Catalysis
- What are COFACTORS?
- What 2 things qualify as Cofactors?
General term for any species that is:
- required by an enzyme to function
Coenzymes and Prosthetic groups are both cofactors
Draw a mechanism for:
SULFUR LINKAGE OF TWO CYSTEINES
Enzyme classification by rxn type
- What kind of reactions do TRANSFERASES participate in?
- Describe and give an example
transfer of an R group
Example: Kinases, aminotransferases
Carbohydrates/Carbohydrate Rxns/ Hydrolysis of Glycoside linkage
Polymer (n) + H2O–>Polymer (n-1)+monomer
Protein Separation Techniques/Electrophoresis: describe the experiment.
Used to separate by size. Proteins denatured by SDS, are given a uniform (-) charge. Gives protein uniform q/m ratio. Bigger proteins are found at the top of the gel, and smaller proteins move further towards the bottom.
Michaelis-Menten Kinetics/Lineweaver-Burke Plots/y-intercept=?
y-intercept= 1/Vmax
Protein structure/2º/alpha sheets: H-bonding b/t ___ and ___ that are exactly ___ residues apart. What else is involved in H bonding? Where are R groups directed?
b/t carbonyl O’s and amide H’s that are exactly 4 residues apart. ONLY every 4th residue is involved in H bonding.R groups directed towards outside of cynlinder.
Mechanisms of Catalysis/Simple proteins. If an enzyme is a simple protein, what can it also be called?
are proteins that contains only AAs and NO non-protein cofactors or prosthetic groups. If a simple protein is an enzyme, it’s called an “apoenzyme”
What important thing should you remember about ZWITTERIONS?
HINT: WHAT IS THE CONNECTION B/T ZWITTERIONS, AA’S AND pH?
ALL of the amino acids exist as
- Zwitterions at a pH of 7.4*
- With the EXCEPTION of amino acids that have charged –R groups (Asp, Glu, Lys, Arg, His)
This can be very confusing because textbooks NEVER draw them this way!
- Most texts draw them in their “non-ionized” form
- with –COOH and –NH2 groups
That combination DOES NOT EXIST!
at physiological pH
…or at ANY pH!
Below a pH of about 9 the amine group will get protonated:
- -NH3+
Above a pH of 9 the amine group will be –NH2
- (as is shown in most texts)
- …But at that very high pH (>9) the carboxyl group will have LONG AGO been deprotonated!*
- would be -COO- at a pH ~ 2
Carbohydrates/Carbohydrate Rxns/ Keto-enol tautomerization is an equilibrium b/t what two things? What are tautomers of e/o?
equilib b/t a keto form (a ketone or an aldehyde) and an enol (alcohol). Enol and Keto are tautomers of e/o.
What is a ZWITTERION?
- Give an example
a DIPOLAR VERSION of an AA
- wherein positively and negatively charged R groups CANCEL EACH OTHER OUT!
- Results in a NEUTRAL ion
Example:
- Isoleucine
- Draw a Fischer projection of the amino acid alanine in both its L- and D- forms*
- Which of the two forms is predominant in nature?*
- D – and L- amino acids are MIRROR IMAGES of one another*
- but they are NOT IDENTICAL compounds*
Think of your left and right hands
- They are mirror images
- but you cannot superimpose one upon the other
- because they are arranged in a fundamentally different way
- but you cannot superimpose one upon the other
L – amino acids
are predominant in nature
Although a few D – amino acids are used by some bacteria
Draw a mechanism for:
HYDROLYSIS OF A PEPTIDE BOND BETWEEN GLYCINE AND ALANINE
How can you tell if a substrate will bind in an active site?
- Depends on:
- the complementary charges on R groups and/or
- hydrophil/phobicity of the R groups
Carbohydrates/what are the 2 types? What MFs to they have?
1) Monosaccharides (CH2)n.2) Disaccharides Cn(H2O)x.
Carbohydrates/Carbohydrate Rxns/ Polymerization: ___+___=?
monosaccharides + disaccharides=polysaccharides
Protein structure/3º: List the 6 molecular interactions that contribute to 3º structure?
1) H-bonding. 2) DSB’s. 3) Hydrophobic/philic interxns. 4) Ionic interxns. 5) VDWs. 6) Proline turns.
Protein structure/2º/Beta sheets: H-bonding b/t what? Where are the R groups located? What shape do beta sheets have? What does this serve?
H-bonding b/t ALL carbonyl O’s and the amide H’s in the adjacent row. R groups are perpendicular to the plane of the beta sheet, on both sides.Beta sheets have PLEATED conformation. THis lines carboxyl & amide regions up so that each residue is participating in 2 H bonds.
Two theories of enzyme specificity/Lock & Key model
enzyme to substrate is an EXACT FIT (not favored by scientists)
Enzyme Inhibition/Irreversible Inhibition: how does the inhibitor bind? What effect does this have?
Inhibitor binds COVALENTLY to enzyme and/or the active site, disabling the enzyme for either a long time or permanently
Michaelis-Menten Kinetics/MM constant (Km)= relative measure of what? What is Km equal to?
measure of an enzyme affinity for its substrate. Km=[S] at 1/2 Vmax
Michaelis-Menten Kinetics/MM equation=? Shows relationship b/t?
v=Vmax[S]/(Km+[S]). Shows relationship b/t rxn velocity, Km, and [S].
What does it mean when pH is lower than pI?
it means the molecule has a (+) pI value
Mechanisms of Catalysis/Conjugated proteins. Define & give an example. If an enzyme is a conjugated protein, what is it called?
=a protein that is associated with its cofactors, either covalently or via IMFs. Ex: Hb (which has its NP Heme group). If its a conjugated protein thats an enzyme, its called a “holoenzyme”
Carbohydrates
Glucose Polysaccharides
- What is STARCH?
- What is it found in, and what is it used for?
branched, α-linked (“alpha-site” side)
- glucose polymer*
- used for energy storage in PLANTS
Protein Folding
- Entropy & Protein Folding:
Transition from solvation of ___-_____regions to solvation of ___ or ___ed globular protein surface results _______ed ENTROPY
- Transition from solvation of NONPOLAR regions to*
- solvation of POLAR or CHARGED globular protein*
- surfaces results in INCREASED entropy*
- Even when water interacts with a dissolved polar solute, this interaction is less entropically favorable that those same water molecules interacting with only other water molecules
- However, the driving thermodynamic force that favors protein folding results from the fact that non-polar regions require a much GREATER ordering of water molecules to accomplish solvation
- Therefore, transitioning from solvation of non-polar regions to solvation of a mostly polar or charged globular protein surface represents a net increase in entropy*
- In fact, it is enough to overcome the decreased entropy associated with the protein being in a folded rather than an unfolded state
This favorable increase in entropy is a major contributor to the overall conformational stability of the folded protein
- Each AA has a minimum of __ acidic protons, which are?
- Do ALL AAs have this many?
2 acidic protons
-COOH and -NH3+
- 7 AA’s have acidic R groups
- So they have 3 acidic protons in total
Feedback Inhibition
-
Phosphorylation:
- ….Is the addition of what?
- What puts it there?
Ph group added to a molecule
- by a KINASE (Which is a type of TRANSFERASE)
Draw a mechanism for:
STRECKER SYNTHESIS OF ALANINE
Protein Folding
-
Electrostatic Interxns:
- Are interactions between WHAT?
- What 2 things do these interactions do?
are interactions between CHARGED R GROUPS
Functions:
- Encourage the ACT of folding
- STABILIZE the protein once it IS folded
Carbohydrate Rxns
- What happens during “RING CLOSING?”
INTRAmolecular Nucleophilic substitution
(aka is all happening within the same ring-containing molecule)
Here, the -OH group
- (of the chiral C that is FURTHEST from the carbonyl C)
- acts as a NUCLEOPHILE–
- Attacking the (ELECTROPHILIC) carbonyl C
- Carbonyl Oxygen is then protonated to form a -OH group
- Attacking the (ELECTROPHILIC) carbonyl C
Protein Folding/ Protein denaturing: name the 4 protein denaturing agents.
1) Heat. 2) Acid. 3) Urea. 4) Mercaptoethanol.
Carbohydrates
Glucose Polysaccharides
- Describe GLYCOGEN
- What organisms use it, and what for?
- How does it compare to STARCH?
branched, α-linked (α 1,4/1,6)
glucose polymer
used for energy storage in ANIMALS
vs. Starch:
- Both used for energy storage
- Starch is found in PLANTS, though
- Both have same (α 1,4/1,6) linkages
- Starch is 80% amylopectin (branched) and 20% amylose (UNbranched)
Glycogen is 100% amylopectin, thus is MORE BRANCHED THAN STARCH!
Carbohydrates/Cyclic Structure & Conformation of hexoses/Hemiacetals vs Hemiketals
Hemiketal (R,R,OH,OR). Hemiacetal (R,H,OR,OH)
Major (non-enzymatic) protein functions/Structural Proteins: Name the 4 kinds, and what they are found.
1) Actin [thin filaments, microfilaments]. 2) Tubulin [MT’s]. 3) Keratin [IMFs]. 4) Elastin [collective tissue, ECM].
- All native AAs are L or D?
- Are L,D and R,S the same?
- all native AAs are L
- L,D NOT directly correlated with R,S
- Should be considered separate
- Most L AAs are S
- but some are R
- e.g. cysteine
- but some are R
Enzyme Inhibition/Reversible Inhibition/Non-competitive inhibition does what? Effect on Vmax and Km
Inhibitor binds AWAY from active site and ∆es shape of the enzyme. Inhibitor has equal affinity for both the ES complex and the enzyme. Vmax=DECREASES. Km=NO ∆.
Michaelis-Menten Kinetics/Lineweaver-Burke Plots/x-intercept=?
x-intercept= - 1/Km
WRT STEREOCHEMISTRY, what do all AAs (except for ____) have in common?
- What 4 different substituents does each AA have?
An alpha-C stereocenter:
- all AAs (except for GLYCINE ) are CHIRAL at the α-carbon
4 *DIFFERENT* substituents:
- R group
- an H
- a COOH
- an NH2
Protein Folding/ Solvation Layer: what is it and what interacts with what?
is a layer of H2O that surrounds a dissolved protein. H2O’s in the layer interact with w/o and with protein’s surface.
Protein structure/3º/6 binding forces/DSB’s
covalent bond b/t the Sulfurs (or Seleniums) of 2 Cysteine residues.
Carbohydrates/Stereochemistry/L-sugars
L sugars do NOT occur naturally in humans
Carbohydrates/Carbohydrate Rxns/ Polymerization/Glucose Polysaccharides/Cellulose
ß-linked glucose polymer, used for energy storage in plants (like starch), is INDIGESTIBLE to animals w/o some form of symbiotic bacteria
Describe FISCHER PROJECTIONS:
- What do the horizontal & vertical lines represent?
- Fischer Projections CAN be rotated ___°, but CAN’T be rotated ___° or ___°
EXPLAIN WHY YOU CAN’T ROTATE THE MOLECULE IN CERTAIN WAYS
A Fischer projection is a representation of a 3D molecule drawn in 2Ds
- A tetrahedral carbon is represented as two crossed lines
- and the groups attached to that carbon are displayed
-
The HORIZONTAL line
- is extending “OUT” of the paper
- Toward you
-
The VERTICAL line
- is BEHIND the plane of the paper
- Away from you
Because of this, Fischer projections
CAN be rotated 180°
but not 90° or 270°
180° rotation just flips the molecule over:
- the same R groups are extending forward or backward
But if you rotate the molecule just 90° in
either direction:
- you have CHANGED which R groups are above or below the plane of the paper
...which changes the stereochemistry of the molecule
Absolute configuration
- All AAs are what?
- What determines this?
Either L or D
- depending on which side the NH2 group is located in a Fischer Projection
- L=on the left
- D=on the right
Isoelectric point is similar to the ___ ___ in acid-base titration. Why?
to the equivalence point. Both are in the middle of their respective titration curves.
Carbohydrates/Stereochemistry/How are D-galactose and L-galactose related? What do the D and L represent?
They’re ENANTIOMERS (same molecule, different stereochemistry at last chiral C). In Fischer projections, the furthest -OH group from the carbonyl is to the LEFT for L, to the RIGHT for D
Enzyme Inhibition/Feedback Inhibition/ Zymogens are what? Why are they useful? What is an example?
are an inactive enzyme precursor. Useful b/c they can get activated quickly if needed, but are deadly if left on 24/7. Ex: Prothrombin (in blood coagulation).
What is an essential AA?
an AA that your body cannot synthesize. Must be ingested.
What’s the difference b/t an enzyme and a catalyst?
BOTH increase rate by lowering Ea. Enzymes are ORGANIC molecules, but catalysts CAN be inorganic. Neither are consumed during a rxn; both can be used & recycled again and again. Enzymes are HIGHLY specific, while catalysts CAN be universal”All enzymes are catalysts, but not all catalysts are enzymes”
Protein structure/3º:
Folding of alpha helices, Beta sheets, & other things to form a “functional” globular or structural protein.
Protein structure/3º/6 binding forces/Ionic interxns
aka “salt bridges.” Charge to charge interactions b/t a positive (+) AA and a negative (-) AA
Amino Acid Reactions
- Protein Hydrolysis
-
CHYMOTRYPSIN
- cleaves WHAT side
- …of WHAT AA’s?
-
CHYMOTRYPSIN
CHYMOTRYPSIN
Cleaves proteins on the CARBOXYL side of:
- Phenylalanine
- Tryptophan
- Tyrosine
Protein structure/4º definition & example
association of multiple folded proteins into a multi-subunit complex. classic example: Hb has 4 subunits, exhibits (+) cooperativity
Carbohydrates/Cyclic Structure & Conformation of hexoses/ what are hexoses? GGive 2 examples
class of simple sugars whose molecules contain 6 C atoms. Ex: glucose and fructose
Michaelis-Menten Kinetics/Lineweaver-Burke Plots/Applications (2)
used to calculate Vmax and Km experimentally, and used to identify enzyme inhibition
- Oligopeptide=?
- Polypeptide=?
How do they relate to each other when it comes to LENGTH?
- Oligopeptide= VERY SMALL chain of AAs
- Polypeptide= LONGER chain of AAs
When you see “protein” or “enzyme,” think: (2)
1) What AAs are present? 2) what is the chemistry of their R groups?
What is the isoelectric point? (pI)
- If a molecule is AT its isoelectric point, it must be in its ________ic form
when a molecule has 0 net charge
At its isoelectric point, a molecule is in its ZWITTERIONIC FORM
(Charges are all canceling each other out)
Enzyme classification by REACTION TYPE
- List the 6 types of enzymes
- MNEMONIC: “OVER THE HILL”*
- Oxireductases
- Transferases
- Hydrolases
- Isomerases
- Lyases
- Ligases
- Major (non-enzymatic) protein functions
MOTOR PROTEINS
- Name the 3 kinds
- Where are they found?
- What do they do?
Myosins
- Found in muscle cells (Thick portion of sarcolemma)
- Power stroke, cellular transport
Kinesins
-
Move along MICROTUBULES
-
from + end to the - end
- or from center of cell to periphery
-
from + end to the - end
Dyneins
- Move along MICROTUBULES
- From the - end to + end
- or from periphery to center of the cell
Carbohydrates/Stereochemistry/D-sugars
all human body sugars D-sugars
Carbohydrates
- Stereochemistry
- How are glucose and galactose related?
- Why are their names different?
- How are glucose and galactose related?
They’re EPIMERS
(more broadly, Diastereomers)
- Only differ at 1 chiral center (and it isnt the anomeric carbon– in that case, they’d be anomers)*
- Are different molecules, so they have different names!
Carbohydrates
Nomenclature & classification
- What suffix is given to all SUGARS?
- What prefix is used if the normal location of an OH group is replaced by a H?
“-ose” ending given to ALL SUGARS
“deoxy-“ prefix is used if normal location of an -OH group is REPLACED BY A H
Estimating pI
- pIacidic=?
pIacidic=
AVERAGE of pKa of ACIDIC R group
+
pKa of CARBOXYL group
Enzyme classification by rxn type/Oxireductases
are REDOX rxns (O and H are gained or lost)
Protein Folding: a _____ed protein assumes ___ structure almost instantly, and then folds into its ___ or ___ _º state
a translated protein assumes 2º structure almost instantly, then folds into its globular or structural 3º state
Carbohydrates/Carbohydrate Rxns/ Polymerization/Beta Linkage
Mono. & Disac. are linked through Oxygen on the same side as (ie, is cis to) the CH2OH group
Proteins
Absolute Configuration
- While it is TRUE that L- and D- do NOT correlate DIRECTLY with R and S, among all 20 of the common amino acids…
- there are ONLY TWO CASES in which an amino acid CANNOT be said to be BOTH L- and S*
- Name the two exceptions and explain why, specifically, they are exceptions
GLYCINE & CYSTEINE
To answer this question, first we need to define what L, D, R, and S are
L and D
- For amino acids, L and D refer to the glyceraldehyde molecule that the amino acid could theoretically be synthesized from
- D-glyceraldehyde or L-glyceraldehyde
R and S
- R and S refer to the absolute stereochemistry of the molecule
- To designate a molecule as R or S, you must rank each R group of a chiral carbon for priority
- For almost all the amino acids, the L designation and the S designation occur together
- This makes sense, because if they all could theoretically derive from the same glyceraldehyde molecule
- they would all end up with the same stereochemical orientation
- Two amino acids, however, differ from this rule
Glycine
The tetrahedral carbon of glycine is not a chiral center
- because it has TWO hydrogens attached
- ∴ does NOT have four DIFFERENT R groups
Because it does NOT have a chiral center, glycine CANNOT be designated as EITHER R or S
Cysteine
Since cysteine has a SULFUR at the second position in its side chain,
- the side chain has a HIGHER RANKING than the other side chains (when considering whether to designate it as R or S)
- due to cysteine’s HIGHER atomic mass*
- This means that L – cysteine will be R – cysteine
- …Because the SULFUR has changed the direction the priorities of the R groups turn*
Substrate-Enzyme specificity/substrate=?
molecule that is acted upon by an enzyme (or, is converted to product BY the enzyme)
What type of rxn is a peptide bond formation? Describe it.
dehydration synthesis and acyl substitution. amine group N (Nu:) from the NEW AA attacks the carboxyl C (E:) on the C-terminus of the growing peptide chain (aided by enzymatic function of the ribosome).
Mechanisms of Catalysis/Prosthetic Groups are what?
Non-protein species that ARE (!!) permanently attached to the enzyme and are req’d for the protein to function.
What 2 things do R groups DETERMINE in an AA?
It determines an AA’s…
- Chemistry &
- Folding pattern
Enzyme Inhibition/Feedback Inhibition/ Allosteric enzymes
enzymes whose activity is influences by the reversible, NON-covalent binding of ANOTHER molecule
Protein Folding/Proline Turns: either considered to ___ _º or ___ to _º structure.
disrupt 2º or contribute to 3º structure
Enzyme classification by rxn type/Lyases
AB A+B. (Cleavage/synthesis, NO H2O, NOT hydrolysis).
Protein Folding/Hydrophobic Core: What folds into the interion of a globular protein? Why? What do they often bring with them? What happens as a result of this?
Hydrophobic R groups fold into the interior of a globular protein in order to escape H2O. Often bring other smaller POLAR groups with them, which interact in a complementary way to further stabilize protein folding.
Michaelis-Menten Kinetics/MM saturation curve is a graph of ___ vs ___. Reveals connection b/t what?
graph of velocity vs [S]. Reveals connection b/t 1/2 Vmax and Km
Substrate-Enzyme specificity/what is the active site?
part of an enzyme where substrate is converted to product
Carbohydrates/Cyclic Structure & Conformation of hexoses/Pyranose vs Furanose
Pyranose is a 6-membered ring, Furanose is 5-membered
Carbohydrates/Common Disaccharides/maltose
maltose=glucose+glucose
Protein structure: 2º
includes alpha helices, Beta sheets.
In what fashion do proteins fold?
Hydrophobic R groups fold INTO the protein core.Hydrophilic R groups are more common on surface of the protein.
Lipids/What are the 9 types to know for the MCAT?
1) Fatty Acids. 2) Triaglyerols (aka triaglycerides). 3) Phospholipids. 4) Steroids. 5) Terpenes (Terpenoids). 6) Sphingolipids. 7) Waxes. 8) Prostaglandins.
Protein structure/3º/6 binding forces/Hydrophobic or hydrophilic interxns: Where will hydrophobic/philic AAs be in soluble proteins and membrane proteins?
1) in soluble proteins, hydrophobic AAs collapse into protein core. 2) In membrane proteins, hydrophilic membranes will either be outside the membrane in the cytoplasm or inside the core of the protein, away from the membrane bilayer, with hydrophobic AAs located w/in the membrane bilayer
Vitamins & Minerals/Vitamins: which are fat soluble & water soluble?
Fat soluble=A,D,E,K. Water soluble=all the rest.
When pH is near the pKa of one of the acidic protons, the AA acts as what?
a buffer
Lipids/Fatty acids are what?
COOH with a long hydrocarbon chain
Protein Folding/Neither alpha helices nor Beta sheets can contain WHAT internally w/o its 2º structure being disrupted?
Proline!
Two theories of enzyme specificity/Induced fit/ resulting conformational changes do what?
stabilize transition state and lower Ea
Estimating pI: pI neutral
=average of pKa amine group + pKa carboxyl group
Enzyme Inhibition/Feedback Inhibition/ Positive feedback=?
Positive feedback is where the product of a rxn acts as an AGONIST for one of the enzymes earlier in the chain
Protein Folding/Entropy: how does volume relate to radius of globular protein during unfolding? (Equation)
Volume is inversely related to the radius^3
AAs: Order of Deprotonation (1-5)
1) alpha COOH group, pKa~2. 2) -R group, ACIDIC. pKa~4. 3) -R group, His. pKa~6. 4) alpha NH3+ group. pKa~9.5) -R group, BASIC. pKa~11-12.
Carbohydrates/Common Disaccharides/sucrose
sucrose=glucose+fructose
Protein structure:
- 1º Structure consists of solely…?
AA sequence
Mechanisms of Catalysis/Coenzymes are what? Give an example
Non-protein species that are NOT permanently attached to the enzyme, but ARE req’d for the protein to function. ex: NAD+
Protein structure
- Where will you usually find PROLINE in α-helices and β-sheets?
- WHY?
Is usually the FIRST residue at the VERY END of an α-helix
- …but is rarely found inside the helix*
- (because it induces a KINK/TURN)*
Found at the END of β sheets
- where “TURNING” happens because of it
Two theories of enzyme specificity/induced fit/as ___ binds, ____ for it __es. This is an example of what?
as substrate binds, affinity for substrate increases. This is an example of Positive (+) Cooperativity.
Protein Folding/Define globule, premolten globule, molten globule
globule=fully folded. Premolten=just starting to unfold. Molten (aka denatured)=fully UNfolded
Enzymes=____ _____s
=Biological catalysts
Enzyme classification by rxn type/ Ligases
addition or synthesis of LARGE molecules. Usually ATP-dependent. Ex: DNA ligase
Enzyme classification by rxn type
- What kind of reactions do ISOMERASES participate in?
- Describe & give examples
REARRANGEMENTS
Examples:
- Phosphoglucose isomerase
- Epimerases
Protein Folding/Di-sulfide bonds: ____ed ___ residues form a disulfide (R-S-S-R) bond. What other important thing should you remember?
oxidized cysteine residues form a DSB. This is the STRONGEST TYPE OF FOLDING INTERACTION!
Vitamins & Minerals/Vitamins: define them
are small, organic molecules that are essential nutrients req’d in SMALL amts for proper metabolism
Michaelis-Menten Kinetics/Lineweaver-Burke Plots are a ___ ___ graph of?
are a double-inverse graph of the rxn rate (v inverted to 1/v) and substrate concentration ([S] inverted to 1/[S])
AA rxns: protein hydrolysis. What 2 things cleave proteins on the carboxyl side of certain AA residues?
trypsin & chymotrypsin cleave proteins on the CARBOXYL side.
Protein structure/3º/6 binding forces/Proline turns
b/t of proline’s bulky, cyclical shape, putting a Pro in an alpha helix or Beta sheet causes KINKS. Proline can aid in Beta turns
Major (non-enzymatic) protein functions/Binding proteins: name the 7 we’re supposed to know
1) Hemoglobin (Hb). 2) Calmodulin. 3) Troponin. 4) Tropomyosin. 5) Histones. 6) Transcription factors (TFs). 7) Cell Adhesion molecules.
Protein Folding/H-bonds: b/t what, and what 2 things does it do?
(JUST LIKE ELECTROSTATIC INTERXNS,) H-bonding are b/t charged R groups and both 1) encourage folding and 2) stabilize the protein once folded.
Enzyme Inhibition
-
Reversible Inhibition
-
MIXED INHIBITORS do what?
- Effect on Vmax or Km
-
MIXED INHIBITORS do what?
A MIXED INHIBITOR has UNequal affinity
Favors either ES > E (or vice versa)
Effect on Vmax
- Vmax DECREASES NO MATTER WHAT it favors
Effect on Km
- If favors ES over E
Km DECREASES
- If favors E over ES
Km INCREASES
Enzyme Inhibition/Reversible Inhibition/Uncompetitive Inhibition does what? Effect on Vmax and Km
inhibitor binds ONLY with ES complex. Vmax=DECREASES. Km=DECREASES.
Carbohydrates/Stereochemistry/how are alpha and beta glucose related to e/o?
They’re anomers. (Same molecule, different stereochem at anomeric carbon). **Since they’re the same molecule, they’re still both called glucose**
Enzyme Inhibition/Feedback Inhibition/ Phosphorylation: If phosphorylation (by what?) activates a protein, what deactivates it? & VICE VERSA
If phosphorylation (by a kinase) activates it, de-phosphorylation (by a phosphatase) deactivates it, and vice-versa
Two theories of enzyme specificity/induced fit
as substrate begins binding to product, conformational changes occur, so that final shape and characteristics of active site arent “final” until substrate is completely bound
Carbohydrates/Carbohydrate Rxns/ Polymerization/alpha linkage
monosaccharides & disaccharides linked through an Oxygen that is on the OPPOSITE side of the plane from the CH2OH group (ie, is trans)
Proteins
Absolute Configuration
-
ALL amino acids are designated as either__ or __
- …depending on the side on which the _____ _____ is located in a Fischer Projection (__= Left; __= Right)
- ALL NATIVE human AA’s are __-amino acids
Absolute Configuration:
All amino acids are designated as either L- or D-
- depending on the side on which the AMINE GROUP (!!) is located in a Fischer Projection
- (L = Left; D = Right)
- ALL NATIVE human amino acids are L-amino acids
What is a non-essential AA?
an AA that your body CAN synthesize on its own.
Draw a mechanism for:
FORMATION OF A PEPTIDE BOND BETWEEN GLYCINE AND ALANINE
Protein structure/3º/6 binding forces/VDWs
IMFs that repel atoms away from e/o (due to steric hindrance)
Enzyme classification by reaction type
- Hydrolases do what kind of rxn?
Hydrolysis
Carbohydrates/Stereochemistry/ R&S vs D&L
R/S≠D/L!!
AA’s are ___ acids
weak
Major (non-enzymatic) protein functions/Motors/Kinesins & Dyneins: Differentiate
Kinesins move along MTs from the (+) to the (-) end, or from center of cell to periphery or nerve cell body towards the dendrite. Dyneins are the exact opposite.
Enzyme Inhibition/Reversible Inhibition=?
Inhibitor is not permanently bound & enzyme is not permanently disabled
Resonance during AA rxns: what 2 things resonate? What does this mean?
Resonance b/t π bonds of C=O bond and N’s lone pair. The C-N bond yields 2 reso scrutcs for any peptide bond. BOTH the C=O bond and the C-N bond in a peptide have double bond character.
Lipids/ Triaglycerols (aka triaglycerides) look like what? What are the 2 types of triaglycerols?
Have a glycerol backbone with 3 FA’s attached via ESTER linkages. 2 types are saturated and unsaturated
KINASES are a type of _______ase that does WHAT?
A type of TRANSFERASE
that transfers an R group
(In this case, a phosphate)
On a pH scale, if you ONLY are seeing ZWITTERIONS, that means you MUST have reached….?
Why is this?
the ISOELECTRIC POINT, pI
- Think about it!*
- Zwitterions are variations that have NO formal charge, therefore they are AT their isoelectric point*
- Small oligopeptides are often dominated by one or two amino acid residues*
- An oligopeptide made up primarily of which pair of amino acids would be LEAST likely to require a protein carrier for transport in the blood?*
- A. glycine and tryptophan
- B. tyrosine and lysine
- C. arginine and phenylalanine
- D. histidine and glutamine
D
- The oligopeptide which is least likely to require a protein carrier for transport in the blood will be composed of hydrophilic, or polar amino acids
- Thus, we are looking for an answer choice with two polar amino acids
Answer D is correct, both histidine and glutamine are polar charged amino acids
- Answer A is incorrect, tryptophan is a large nonpolar amino acid
- Answer B is incorrect, tyrosine is a large nonpolar amino acid
- Answer C is incorrect, phenylalanine is a large nonpolar amino acid
Aspartate has a pKa of 3.7, while the structurally similar glutamate has a pKa of 4.5
Which phenomenon best explains this difference?
- The structural difference between aspartic acid and glutamic acid is the fact that glutamic acids sidechain carboxylic acid group is ONE carbon FURTHER AWAY from the amino acid backbone
- The amino acid backbone contains electronegative groups
- which are capable of withdrawing electron density from the sidechain carboxylic acid groups
- A greater degree of induction results in a more stable conjugate base (better charge distribution, more stable molecule)
Because inductive effects decrease with distance from the electronegative element, glutamic acid experiences less charge induction than aspartic acid
How do “ANTIOXIDANTS” prevent OTHER things from getting oxidized?
What does this mean with regards to their REDUCTION potential when comparing it to a similar, non-antioxidant molecule?
Anti-oxidants inhibit the oxidation of other molecules by being oxidized THEMSELVES
- This means they should have a lower reduction potential
- …than a similar molecule that is not an antioxidant
Classes of Lipids
Draw the general structure of TRIAGLYCEROLS, aka “________s”
- _____backbone with three _____ _____s attached via _____ linkages
- What are the 2 forms TAGs can come in?
HINT: think H-bonds
TRIGLYCEROLS**
aka “TRIAGLYCERIDES“
- Glycerol backbone (HOCH2CHOHCH2OH) with three fatty acids attached via ester linkages
2 FORMS:
- Saturated FAs
- Unsaturated FAs
Classes of Lipids
Draw the general structure of STEROIDS
-
Have a characteristic molecular structure containing _\_#__ rings of carbon atoms, consisting of:
- 3 ___-membered rings
- All steroids are four-membered ring structures. In the figure below, the rings are labeled, and carbons are numbered.
Classes of Lipids
Draw the general structure of PHOSPHOLIPIDS
- is a ____ containing a _______ group
a lipid containing a phosphate group in its molecule
Classes of Lipids
PHOSPHOLIPIDS
- What is the most common type of phospholipid?
- What are the only 2 things that make it up?
What is the phosphate head directly attached to?
MOST COMMON TYPE: PHOSPHATIDS
Consists of:
- 2 FATTY ACID sections
- A PHOSPHATE group
- …which is attached directly to the glycerol backbone
Classes of Lipids
PHOSPHOLIPIDS
- Most phospholipids in biological membranes have other________ _____s attached to the ______head
- Give an example of this, using PhosphaTIDS ( the most common type of phospholipid) as an example
- Most phospholipids in biological membranes*
- have OTHER FUNCTIONAL GROUPS attached*
- to the phosphate head*
Example of this: Phosphatids (most common type of Phospholipids), which consist of:
- 2 FATTY ACID sections
- A PHOSPHATE group
- …which is attached directly to the glycerol (R GROUP!) backbone
Classes of Lipids
Draw the general structure of STEROIDS
-
Each contain HOW MANY carbon rings?**
- What 2 types of cycloalkanes are found in steroids?
All steroids have 4 carbon rings!!
- three six-membered
- one five-membered ring
Classes of Lipids
- Draw the general structure of TERPENES, a class of lipid
Classes of Lipids
Draw the general structure of STEROIDS
-
Each contain HOW MANY carbon rings?**
- What 2 types of cycloalkanes are found in steroids?
All steroids have 4 carbon rings!!
- three six-membered
- one five-membered ring
Classes of Lipids
TERPENES
- What are the building blocks of terpenes?
- What is the only difference between:*
- a TerpENE and a TerpeNOID?*
Terpenes are made from:
ISOPRENE units
The only difference between terpenes and terpenoids:
Terpenes are hydrocarbons
THINK: TerpENES are made up of alkENES
TerpenOIDS contain additional R groups
Classes of Lipids
Draw the general structure of SPHINGOLIPIDS
- Are a class of lipids that contain a backbone of _____ bases
are a class of lipids containing a backbone of SPHINGOSINE bases
Classes of Lipids
Draw the general structure of WAXES
- Waxes are ESTERS (ROOR) made up of WHAT R-GROUPS?
Waxes are ESTERS of:
- Fatty Acids
- Long-chain monohydric ALCOHOLS
(“Monohydric” =have one hydroxyl group)
Classes of Lipids
Draw the general structure of GLYCOLIPIDS
- Are _____s with a _______ attached
are LIPIDS with
a CARBOHYDRATE attached
Classes of Lipids
PROSTAGLANDINS
- Are lipid _______ors that have ________ and ______ functions throughout the body
- Another way to think of Prostaglandins is as “_____ Hormones”
What 2 things make Prostaglandins different from Hormones?
- Are lipid MEDIATORS that:*
- have AUTOcrine and PARAcrine functions*
- throughout the body*
Prostaglandins are like LOCAL Hormones!
UNLIKE hormones:
1) PRODUCED and RELEASED (by tissues)
THROUGHOUT the body!
….not _JUST_ in specialized glands (like hormones)
2) ACT:
LOCALLY!
- …rather than traveling* via the bloodstream
- to a distant target*
Estimating pI:
- pIbasic=?
pIbasic =
AVERAGE of pKa -AMINE group
+
pKa -BASIC R group
