Biochem 1 Flashcards
Estimating pI:
- pIbasic=?
pIbasic =
AVERAGE of pKa -AMINE group
+
pKa -BASIC R group
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)
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
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”*
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!!
Enzyme classification by reaction type
- Hydrolases do what kind of rxn?
Hydrolysis
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
LIPIDS are:
“Hydro_____ __________s”
“Hydrophobic Biomolecules”
Carbohydrates
- List the “8 Common Monosaccharides”
- glyceraldehyde
- dihydroxyacetone
- ribose
- deoxyribose
- glucose
- fructose
- galactose
- mannose
Enzyme classification by rxn type
- What kind of reactions do ISOMERASES participate in?
- Describe & give examples
REARRANGEMENTS
Examples:
- Phosphoglucose isomerase
- Epimerases
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.
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
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
Protein structure:
- 1º Structure consists of solely…?
AA sequence
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
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
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.
Carbohydrates/Carbohydrate Rxns/ Hydrolysis of Glycoside linkage
Polymer (n) + H2O–>Polymer (n-1)+monomer
When pH is near the pKa of one of the acidic protons, the AA acts as what?
a buffer
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
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
Protein Folding/Proline Turns: either considered to ___ _º or ___ to _º structure.
disrupt 2º or contribute to 3º structure
Substrate-Enzyme specificity/substrate=?
molecule that is acted upon by an enzyme (or, is converted to product BY the enzyme)
Michaelis-Menten Kinetics/Lineweaver-Burke Plots/Applications (2)
used to calculate Vmax and Km experimentally, and used to identify enzyme inhibition
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!
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/3º:
Folding of alpha helices, Beta sheets, & other things to form a “functional” globular or structural protein.
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].
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
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)
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!
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*
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
Draw a mechanism for:
FORMATION OF A PEPTIDE BOND BETWEEN GLYCINE AND ALANINE
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*
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
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*
