Biochemistry Flashcards
What are the four groups attached to the central (alpha) carbon of a proteinogenic amino acid?
Amino group (NH2), carboxylic acid group (COOH), hydrogen and R group
Are eukaryotic amino acids L or D?
L
Are eukaryotic amino acids R or S?
S
What is the only eukaryotic amino acid that is R?
Cysteine
What is the only achiral amino acid?
Glycine
Nonpolar, non-aromatic amino acids
Glycine, alanine, valine, leucine, isoleucine, methionine, proline
Nonpolar, aromatic amino acids
Tryptophan and phenylalanine
Polar, aromatic amino acids
Tyrosine
Polar, non-aromatic amino acids
Serine, threonine, asparagine, glutamine and cysteine
Negatively charged (acidic) amino acids
Aspartate and glutamate
Positively charged (basic) amino acids
Lysine, arginine and histidine
What kind of amino acid is glycine?
Nonpolar, non-aromatic
What kind of amino acid is alanine?
Nonpolar, non-aromatic
What kind of amino acid is valine?
Nonpolar, non-aromatic
What kind of amino acid is leucine?
Nonpolar, non-aromatic
What kind of amino acid is isoleucine?
Nonpolar, non-aromatic
What kind of amino acid is methionine?
Nonpolar, non-aromatic
What kind of amino acid is proline?
Nonpolar, non-aromatic
What kind of amino acid is tryptophan?
Nonpolar, aromatic
What kind of amino acid is phenylalanine?
Nonpolar, aromatic
What kind of amino acid is tyrosine?
Polar, aromatic
What kind of amino acid is serine?
Polar, non-aromatic
What kind of amino acid is threonine?
Polar, non-aromatic
What kind of amino acid is asparagine?
Polar, non-aromatic
What kind of amino acid is glutamine?
Polar, non-aromatic
What kind of amino acid is cysteine?
Polar, non-aromatic
What kind of amino acid is aspartate?
Negatively charged (acidic)
What kind of amino acid is glutamate?
Negatively charged (acidic)
What kind of amino acid is lysine?
Positively charged (basic)
What kind of amino acid is arginine?
Positively charged (basic)
What kind of amino acid is histidine?
Positively charged (basic)
Glycine R group
H
Alanine R group
CH3
Valine R group
CH - (CH3)2
Leucine R group
CH2 - CH - (CH3)2
Isoleucine R group
CH - [CH3, CH2 - CH3]
Methionine R group
CH2 - CH2 - S - CH3
Proline R group
Cyclic
Tryptophan R group
CH2 - double ring system with N
Phenylalanine R group
CH2 - benzene ring
Tyrosine R group
CH2 - Phenyl
Serine R group
CH2 - OH
Threonine R group
C - [H, OH, CH3]
Asparagine R group
CH2 - C - [NH2, O]
Glutamine R group
CH2 - CH2 - C - [NH2, O]
Cysteine R group
CH2 - SH
Aspartic acid R group
CH2 - COO-
Glutamic acid R group
CH2 - CH2 - COO-
Lysine R group
(CH2)4 - NH3+
Arginine R group
(CH2)3 - NH - C - [NH, NH3+]
Histidine R group
CH2 - imidazole ring
Alanine
Ala, A, non polar, non-aromatic
Arginine
Arg, R, basic
Asparagine
Asn, N, polar, non-aromatic
Aspartate
Asp, D, acidic
Cysteine
Cys, C, polar, non-aromatic
Glutamate
Glu, E, acidic
Glutamine
Gln, Q, polar, non-aromatic
Glycine
Gly, G, non polar, non-aromatic
Histidine
His, H, basic
Isoleucine
Ile, I, nonpolar, non-aromatic
Leucine
Leu, L, nonpolar, non-aromatic
Lysine
Lys, K, basic
Methionine
Met, M, nonpolar, non-aromatic
Phenylalanine
Phe, F, nonpolar, aromatic
Proline
Pro, P, nonpolar, non-aromatic
Serine
Ser, S, polar, non-aromatic
Threonine
Thr, T, polar, non-aromatic
Tryptophan
Trp, W, nonpolar, aromatic
Tyrosine
Tyr, Y, polar, aromatic
Valine
Val, V, nonpolar, non-aromatic
Amino acid
Makes up peptide chains (i.e. proteins)
Dipeptide
Two amino acids joined by a peptide bond
Tripeptide
Three amino acids joined by peptide bonds
Oligopeptide
Less than 20 amino acids joined by peptide bonds
Polypeptide
More than 20 amino acids joined by peptide bonds
What molecule is released during the formation of a peptide bond?
Water
Primary protein structure
Linear amino acid sequence
Secondary protein structure
Local structure determined by nearby amino acids
Subtypes of secondary protein structure
Alpha-helices and beta-pleated sheets
Stabilizing bonds of the primary protein structure
Peptide (amide) bonds
Stabilizing bonds of the secondary protein structure
Hydrogen bonds between amino groups and nonadjacent carboxyl groups
What role does proline serve in the secondary protein structure?
Its rigid structure causes it to introduce kinks in alpha-helices, or create turns in beta-pleated sheets
Tertiary protein structure
Protein folding (three-dimensional shape of protein)
Quaternary protein structure
Interaction between separate subunits of a multisubunit protein
Subtypes of tertiary protein structure
Hydrophobic interactions, acid-base/salt bridges, disulfide links
Stabilizing bonds of the tertiary protein structure
Hydrogen bonds, van der Waals forces, ionic bonds and covalent bonds
Stabilizing bonds of the quaternary protein structure
Hydrogen bonds, van der Waals forces, ionic bonds and covalent bonds
Why are proteins denatured by heat?
Heat increases the average kinetic energy, thereby distrusting hydrophobic interactions
Why are proteins denatured by solutes?
Solutes disrupt elements of secondary, tertiary and quaternary structures
Isoelectric point (pI) of neutral amino acid
= (pKa, NH3+ group + pKa, COOH group) / 2
Isoelectric point (pI) of acidic amino acid
= (pKa, R group + pKa, COOH group) / 2
Isoelectric point (pI) of basic amino acid
= (pKa, R group + pKa, NH3+ group) / 2
What does the R group on an amino acid do?
Determine the chemistry and function of that amino acid
Are prokaryotic amino acids D or L?
D
What happens to an amino acid in low (acidic) pH?
It is fully protonated
What happens to an amino acid in pH closer to the amino acid’s pI?
The amino acid is neutral (zwitterion)
What happens to an amino acid in high (basic) pH?
It is fully deprotonated
What does the titration curve of an amino acid look like?
Flat at pKa values and vertical in pI values
How to form a peptide bond?
Through a condensation or dehydration reaction, releasing one molecule of water
The nucleophile (amino group) of one amino acid attacks the electrophile (carboxyl group) of another amino acid
What is the nucleophilic group on an amino acid?
Amino group
What is the electrophilic group on an amino acid?
Carbonyl carbon of the carboxyl group
Why are amide bonds rigid?
Because of resonance
How to break a peptide bond?
Hydrolysis reaction
Alpha-helices
Clockwise coils around a central axis
Beta-pleated sheets
Rippled strands that can be parallel or antiparallel
Can proline interrupt secondary protein structure?
Yes because of its rigid structure
Hydrophobic interactions
Push hydrophobic R groups to the interior of a protein, which increases entropy of the surrounding water molecules and creates negative Gibbs free energy
What do hydrophobic interactions result in?
Increase in entropy of the surrounding water and negative Gibbs free energy
When do disulfide bonds occur?
When two cysteine molecules are oxidized and create a covalent bond to form cystine
Conjugated proteins
Proteins with covalently attached molecules
Prosthetic group
Tightly bound cofactors or coenzymes that are necessary for enzyme function
The molecule attached to a conjugated protein
Can be metal ion, vitamin, lipid, carbohydrate or nucleic acid
Denaturation
Loss of three-dimensional protein structure
Which amino acids have chiral carbons in their side chain?
Threonine and isoleucine
What is the reason behind protein conjugation?
Directing protein to a particular organelle, directing protein to the cell membrane and adding a cofactor needed to protein activity
How do enzymes function as biological catalysts?
Improve the environment in which a particular reaction takes place, which lowers its activation energy
They are regenerated at the end of the reaction to their original form
They can form transient covalent bonds with substrates
They can act as electron donors or receptors to allow the reaction to proceed
Enzyme specificity
Enzymes are specific for certain kinds of compounds and perform certain kinds of reactions
The six classes of enzymes
Ligase, isomerase, lyase, hydrolase, oxidoreductase and transferase
Ligase
Addition or synthesis reactions, generally between large molecules (often of the same type); often require ATP
Isomerase
Rearrangement of bonds within a compound
Catalyze the interconversion of isomers, including both constitutional isomers and stereoisomers
Lyase
Cleavage of a single molecule into two products, or synthesis of small organic molecules
Does not use water or transfer electrons
The opposite of synthesis
Often form cyclic compounds or double bonds in products
Hydrolase
Breaking of a compound into two molecules using the addition of water
Oxidoreductase
Oxidation-reduction reactions (transferring electrons)
Transferase
Movement of a functional group from one molecule to another
In what ways to enzymes affect the thermodynamics vs. the kinetics of a reaction?
Enzymes only affect the kinetics of a reaction, by lowering the activation energy (i.e. lowering the transition state energy). Enzymes do not affect the thermodynamics of a reaction since they do not change delta G, delta H, the equilibrium constant, the equilibrium position or the concentrations of reactants and products.
Catalysts
Reduce the activation energy of a reaction, thus speeding up the reaction
They are not used up in the course of the reaction
Lock and key model
Active site of enzyme fits exactly around substrate
No alterations to tertiary or quaternary structure of enzyme
Less accurate model
Induced fit model
Active site of enzyme molds itself around substrate only when substrate is present
Tertiary and quaternary structure is modified for enzyme function
More accurate model
Cofactors
Inorganic (minerals) activators of enzymes
Induce conformational change in the enzyme to promote its activity
Coenzymes
Organic (vitamins) activators of enzymes
Induce conformational change in the enzyme to promote its activity
What are the effects of increasing substrate concentration on enzyme kinetics?
When the substrate concentration is low, an increase in substrate concentration causes a proportional increase in enzyme activity
When the substrate concentration is high and the enzyme is saturated, increasing substrate concentration will have no effect on enzyme activity since v max has already been attained
What are the effects of increasing enzyme concentration on enzyme kinetics?
Increasing enzyme concentration will always increase v max, regardless of the starting concentration of enzyme
Michaelis-Menten plot
v vs [S]
Hyperbolic curve for monoatomic enzymes
Lineweaver-Burk plot
1/v vs 1/[S]
Linear plot
Km
A measure of an enzyme’s affinity for its substrate
The substrate concentration at which an enzyme is functioning at half of its maximal velocity
What does an increase Km signify?
Decrease in an enzyme’s affinity for its substrate
What is the x-intercept of a Lineweaver-Burk plot?
- 1/Km
What is the y-intercept of a Lineweaver-Burk plot?
1/v max
Enzyme cooperativity
The interactions between subunits in a multi-subunit enzyme or protein
The binding of a substrate to one subunit induces a change in the other subunits from the T(tense) state to the R (relaxed) state, which encourages binding of substrate to the other subunits
The unbinding of a substrate from one subunit indices a change from R to T in the remaining subunits, promoting unbinding of substrate from the remaining subunits
Temperature’s effect on enzyme function
As temperature increases, enzyme activity generally increases (doubling approximately every 10 C)
Above body temperature, however, enzyme activity quickly drops off as the enzyme denatures
pH’s effect on enzyme function
Enzymes are maximally active within a small pH range
Outside of the range, enzyme activity drops quickly with changes in pH as the ionization of the active site changes and the protein is denatured
Salinity
Changes in salinity can disrupt bonds within an enzyme, causing disruption of tertiary and quaternary structure, which leads to loss of enzyme function
Ideal temperature for enzyme function
98.6 F = 37 C = 310 K
Ideal pH for most enzymes
7.4
Ideal pH for gastric enzymes
2
Ideal pH for pancreatic enzymes
8.5
Feedback inhibition
The product of an enzymatic pathway turning off enzymes further back in that same pathway
Helps maintain homeostasis: as product levels rise, the pathway creating that product is appropriately down-regulated
Types of reversible inhibitors
Competitive, noncompetitive, mixed and uncompetitive
Irreversible inhibition
The prolonged or permanent inactivation of an enzyme, such that is cannot be easily renatured to gain function
New enzyme molecules must be synthesized for the reaction to occur again
Transient enzyme modifications
Allosteric activation
Allosteric inhibition
Covalent enzyme modifications
Phosphorylation
Glycosylation
Why are some enzymes released as zymogens?
It is critical that certain enzymes (like the digestive enzymes of the pancreas) remain inactive until arriving at their target site
Is allosteric activation a transient or covalent enzyme modification?
Transient
Is allosteric inhibition a transient or covalent enzyme modification?
Transient
Is phosphorylation a transient or covalent enzyme modification?
Covalent
Is glycosylation a transient or covalent enzyme modification?
Covalent
Zymogens
Precursors of an active enzyme
They are secreted in an inactive form and are activated by cleavage
Michaelis-Menten rates
E + S ES –(K3)–> E + P
Michaelis-Menten equation
v = ( v max [S]) / (Km + [S])
Synthesis
The opposite of lyases
Exergonic reaction
Release energy
delta G is negative
Delta G is negative
Exergonic reaction
Do enzymes stabilize the transition state?
Yes
They provide a favorable micro-environment or bonding with substrate molecules
Active site
The site of catalysis in an enzyme
Saturation kinetics
As substrate concentration increases, the reaction rate does as well until a maximum value is reached
What kind of Michaelis-Menten graph do cooperative enzymes make?
Sigmoidal because of the change in activity with substate binding
Does temperature affect enzyme activity in vivo or in vitro?
In vivo
Does pH affect enzyme activity in vivo or in vitro?
In vivo
Does salinity affect enzyme activity in vivo or in vitro?
In vitro
In vitro
In the lab
In vivo
In the body
Reversible inhibition
The ability to replace the inhibitor with a compound greater affinity or to remove it using mild laboratory treatment
Competitive inhibition
Results when the inhibitor is similar to the substrate and binds at the active site
How can competitive inhibition be overcome?
Adding more substrate
What happens to v max in competitive inhibition?
Nothing
What happens to Km in competitive inhibition?
Increases
Noncompetitive inhibition
Results when the inhibitor binds with equal affinity to the enzyme (at an allosteric site) and the enzyme-substrate complex
What happens to v max in noncompetitive inhibition?
Decreases
What happens to Km in noncompetitive inhibition?
Nothing
Mixed inhibition
Results when the inhibitor binds with unequal affinity to the enzyme (at an allosteric site) and the enzyme-substrate complex
What happens to v max in mixed inhibition?
Decreases
What happens to Km in mixed inhibition?
Increases if the inhibitor prefers to bind to the enzyme at an allosteric site
Decreases if the inhibitor prefers to bind to the enzyme-substrate complex
Uncompetitive inhibition
Results when the inhibitor binds only with the enzyme-substrate complex
What happens to v max in uncompetitive inhibition?
Decreases
What happens to Km in uncompetitive inhibition?
Decreases
Allosteric activation
Activators bind to the allosteric site of an enzyme, increasing enzyme affinity to substrate
Allosteric inhibition
Inhibitors bind to the allosteric site of an enzyme, decreasing enzyme affinity to substrate
Phosphorylation
Covalent modification of an enzyme with phosphate
Can alter the activity or selectivity of an enzyme
Glycosylation
Covalent modification of an enzyme with carbohydrate
Can alter the activity or selectivity of an enzyme
Apoenzyme
An enzyme devoid of its necessary cofactor and is catalytically inactive
What determines enzyme specificity?
The three-dimensional shape of the active site
Cytoskeletal proteins
Fibrous
Have repeating domains
Function in cellular motility
Motor proteins
Have one or more heads capable of force generation through a conformational change
Have catalytic activity, acting as ATPases to power movement
Are motor proteins enzymes?
No
What could permit a binding protein involved in sequestration to have a low affinity for its substrate and still have a high percentage of substrate bound?
If the binding protein is present in sufficiently high quantities relative to the substrate, nearly all substrate will be bound despite a low affinity
Cell adhesion molecules (CAM)
Allow cells to bind to other cells or surfaces
Cadherin, integrin and selectin
What type of cell adhesion does cadherin form?
Two cells of the same or similar type using calcium
What type of cell adhesion does integrin form?
One cell to proteins in the extracellular matrix
What type of cell adhesion does selectin form?
One cell to carbohydrates, usually on the surface of other cells
When an antibody binds to its antigen, what are the three possible outcomes of this interaction?
Antigen-antibody interactions can result in neutralization of the pathogen or toxin, opsonization (marking) of the antigen for destruction, or creation of insoluble antigen-antibody complexes that can be phagocytize and digested by macrophages (agglutination).
Enzyme
A protein or RNA molecule with catalytic activity
Do motor proteins have catalytic activity?
No
Enzyme-linked receptors
Participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades Autoactivity Enzymatic activity Extracellular domain Transmembrane domain Ligand binding
G protein-coupled receptors
Have membrane-bound protein associated with a trimetric G protein Initiate second messenger systems Two-protein complex Dissociation upon activation Extracellular domain Transmembrane domain Ligand binding
What type of ion channel is active at all times?
Ungated channels
How do transport kinetics differ from enzyme kinetics?
Transport kinetics display both Km and v max values. They also can be cooperative, like some binding proteins. However, transporters do not have analogous Keq values for reactions because there is no catalysis.
What separation methods can be used to isolate a protein on the bases of isoelectric point?
Isoelectric focusing and ion-exchange chromatography can separate proteins based on charge
What are the relative benefits of native PAGE compared to SDS-PAGE?
Native PAGE allows a complete protein to be recovered after analysis; it also more accurately determines the relative globular size of proteins. SDS-PAGE can be used to eliminate conflation from mass-to-charge ratios.
What are two potential drawbacks of affinity chromatography?
The protein of interest may not elute from the column because its affinity is too high
The protein may be permanently bound to the free receptor in the eluent
In size-exclusion chromatography, do the largest or the smallest molecules elute first?
The largest molecules elute first since the size-exclusion chromatography trap smaller particles, retaining them in the column
How does isoelectric focusing separate proteins?
Separate proteins by charge
The protein migrates towards an electrode until pH = pI of the protein
How does ion-exchange chromatography separate proteins?
Separate proteins by charge
How is the charge of a protein determined?
By the protein’s isoelectric point (pI)
Why are proteins analyzed after isolation?
Protein isolation is generally only the first step in an analysis. The protein identity must be confirmed by amino acid analysis or activity. With unknown proteins, classification of their features is generally desired.
What factors would cause an activity assay to display lower activity than expected after concentration determination?
Contamination of the sample with detergent or SDS could yield an artificially increased protein level, leading to lower activity than expected (because the protein concentration was calculated as higher than its actual value). Alternatively, the enzyme could have been denatured during isolation and analysis.
Does the Edman degradation proceed from the carboxy (C-) terminus or the amino (N-) terminus?
Amino (N-) terminus
Migration velocity (v)
= Ez / f
Structural proteins
Compose the cytoskeleton, anchoring proteins and must of the extracellular matrix
Fibrous
Common structural proteins
Collagen, elastin, keratin, actin and tubulin
Applications of motor proteins
Muscle contractions, vesicle movement within cells, cell motility
Common motor proteins
Myosin, kinesin and dynein
Binding proteins
Bind a specific substrate, either to sequester it in the body or hold its concentration at steady state
Cadherins
Calcium-dependent glycoproteins that hold similar cells together
Integrins
Have two membrane-spanning chains and permit cells to adhere to proteins in the extracellular matrix. Some also have signaling capabilities
Selectins
Allow cells to adhere to carbohydrates on the surfaces of other cells and are most commonly used in the immune system
Antibodies (immunoglobulins, Ig)
Used by the immune system to target a specific antigen, which may be a protein on the surface of a pathogen (invading organism) or a toxin
Structure of antibodies (immunoglobulins, Ig)
Contain a constant region and variable region; the variable region is responsible for antigen binding
Two identical heavy chains and two identical light chains form a single antibody; they are held together by disulfide linkages and non covalent interactions
How are the light and heavy chains of an antibody held together?
By disulfide linkages and non-covalent interactions
Ion channels
Used to regulate ion flow into or out of the cells
Types of ion channels
Ungated, voltage-gated and ligand-gated
Ungated channels
Are always open
Voltage-gated channels
Open within a range of membrane potentials
Ligand-gated channels
Open in the presence of a specific binding substance, usually a hormone or neurotransmitter
How does a G-protein- coupled receptor work?
Ligand binding engages the G protein –> GDP is replaced with GTP –> The alpha subunit dissociates from the beta and gamma subunits –> The activated alpha subunit alters the activity of adenylate cyclase or phospholipase C –> GTP is dephosphorylated to GDP –> The alpha subunit rebinds to the beta and gamma subunits
Electrophoresis
Uses a Gell matrix to observe the migration of proteins in response to an electric field
Native PAGE
Maintains the protein’s shape, but results are difficult to compare because the mass-to-charge ration differs for each protein
SDS-PAGE
Denatures the proteins and masks the native charge so that comparison of size is more accurate, but the functional protein cannot be recaptured from the gel
Chromatography
Separates protein mixtures on the basis of their affinity for a stationary phase or a mobile phase
Column chromatography
Uses beads of a polar compound, like silica or alumina (stationary phase), which a non polar solvent (mobile phase)
Ion-exchange chromatography
Uses a charged column and a variably saline eluent
Size-exclusion chromatography
Relies on porous beads
Larger molecules elute first because they are not trapped in the small pores
Affinity chromatography
Uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest
How is protein structure determined?
X-ray crystallography (after the protein has been isolated)
NMR can also be used
How is amino acid composition determined?
Simple hydrolysis
How is amino acid sequence determined?
Sequential degradation
Example of methods of protein degradation
Edman degradation
How is enzyme activity determined?
Following the process of a known reaction and color change
How is protein concentration determined?
Colorimetrically (either by UV spectroscopy or color change in a reaction)
Bradford protein assay test
BCA assay
Lowry reagent assay
Bradford protein assay
Uses color change from brown-green to blue
BCA Assay
The principle of this method is that proteins can reduce Cu+2 to Cu+1 in an alkaline solution (the biuret reaction) and result in a purple color formation by bicinchoninic acid.
Lowry reagent assay
The Lowry protein assay uses copper, which bonds with the peptide bonds in proteins under alkaline conditions. This forms a monovalent copper ion which can then react with the Folin reagent, which in turn can be reduced into a blue colored substance. This blue color can be measured using a spectrophotometer to determine the concentration of blue in the sample. Thus, the concentration of protein can be determined.
What is the function of sodium dodecyl sulfate (SDS) in SDS-PAGE?
It stabilizes proteins to give them uniformly negative charges, so the separation is based purely on size
What are the most prevalent extracellular proteins?
Keratin, elastin and collagen
What are the primary cytoskeletal proteins?
Tubulin and actin
What kind of protein is myosin?
Motor protein
Do antibodies label antigens for targeting by other immune cells?
Yes
Do antibodies cause agglutination by interaction with antigen?
Yes
Do antibodies have two heavy chains and two light chains?
Yes
Can antibodies bind to more than one distinct antigen?
No
Which ion channels are responsible for maintaining the resting membrane potential?
Ungated channels
Which ion channels are involved in cell signaling and pacemaker potentials?
Ligand-gated and voltage-gated channels
How does the gel for isoelectric focusing differ from the gel for traditional electrophoresis?
Isoelectric focusing uses gel with a pH gradient that encourages a variable charge
Which protein properties allow UV spectroscopy to be used as a method of determining concentrations?
Proteins contain aromatic groups in certain amino acids
What property of protein-digesting enzymes allows for a sequence to be determined without fully degrading the protein?
Selectivity
D-stereoisomers of glucose
D-allose, D-altrose, D-glucose, D-mannose, D-gulose, D-idose, D-galactose and D-talose
Which of the diastereomers of D-glucose are considered to be epimers of glucose?
D-allose, D-mannose and D-galactose
What is the enantiomer of D-glucose?
L-glucose
D-allose structure
RRRR
Is D-allose an epimer of D-glucose?
Yes
D-altrose structure
LRRR
Is D-altrose an epimer of D-glucose?
No
D-glucose structure
RLRR
D-mannose structure
LLRR
Is D-mannose an epimer of D-glucose?
Yes
D-gulose structure
RRLR
Is D-gulose an epimer of D-glucose?
No
D-idose structure
LRLR
Is D-idose an epimer of D-glucose?
No
D-galactose structure
RLLR
Is D-galactose an epimer of D-glucose?
Yes
D-talose structure
LLLR
Is D-talose an epimer of D-glucose?
No
What is the less stable anomer of D-glucose in Haworth projection form?
OH at C1: pointing down OH at C2: pointing down OH at C3: pointing up OH at C4: pointing down CH2OH at C5: pointing up
What is the less stable anomer of D-glucose in chair configuration?
All the hydroxyl groups are in the axial position
What is the difference between esterification and glycoside formation?
Esterification is the reaction by which a hydroxyl group reacts with either a carboxylic acid or a carboxylic acid derivative to form an ester. Glycoside formation refers to the reaction between an alcohol and a hemiacetal (or hemiketal) group on a sugar to yield an alkoxy group.
From a metabolic standpoint, does it make sense for carbohydrates to get oxidized or reduced?
Oxidized; because aerobic metabolism requires reduced forms of electron carriers to facilitate processes such as oxidative phosphorylation. Because carbohydrates are a primary energy source, they are oxidized.
Which of the two forms of starch is more soluble in solution?
Amylopectin is more soluble in solution than amylose because of its branched structure. The highly branched structure of amylopectin decreases intermolecular bonding between polysaccharide polymers and increases interaction with the surrounding solution.
Regarding glycogen and amylopectin, which of these two polymers should experience a higher rate of enzyme activity from enzymes that cleave side branches?
Glycogen has a higher rate of enzymatic branch cleavage because it contains significantly more branching than amylopectin.
Number of stereoisomers with common backbone
= 2^n, where n = the number of chiral carbons
How are carbohydrates organized?
By their number of carbon atoms and functional groups
Trioses
Three-carbon sugars
Tetroses
Four-carbon sugars
Aldoses
Sugars with aldehydes as their most oxidized group
Ketoses
Sugars with ketones as their most oxidized group
What is the nomenclature of sugars based on?
D- and L-forms of glyceraldehydes
D-sugars
Sugars with the highest-numbered chiral carbon with the -OH group on the right in a Fischer projection
L-sugars
Sugars with the highest-numbered chiral carbon with the -OH group on the left in a Fischer projection
Enantiomers of sugars
D- and L-forms
Diastereomers
“Nonsuperimposable configurations of molecules with similar connectivity
Differ in at least one, but not all, chiral carbons”
Subtypes of diastereomers
Epimers and anomers
Epimers
A subtype of diastereomerts that differ at exactly one chiral carbon
Anomers
A subtype of diastereomers that differ at the anomeric carbon
Cyclization
Describes the ring formation of carbohydrates from their straight-chain forms
Anomeric carbon
The new chiral center formed in ring closure; it was the carbon containing the carbonyl in the straight-chain form
Alpha-anomers
Have the -OH on the anomeric carbon trans to the free -CH2OH group
Beta-anomers
Have the -OH on the anomeric carbon cis to the free -CH2OH group
Haworth projections
Provide a good way to represent three-dimensional structures
Mutarotation
“Cyclic compounds shift from one anomeric form to another with the straight-chain form as an intermediate
The hemiacetal ring of the sugar will break open spontaneously and then re-form. When the ring is broken, bond rotation occurs between C-1 and C-2 to produce either the alpha- or beta- anomer”
Monosaccharides
Single carbohydrate units, with glucose as the most commonly observed monomer
What is the most commonly observed monomer?
Glucose
What reactions can monosaccharides undergo?
Oxidation-reaction, esterification and glycoside formation
Oxidation of aldoses result in:
Aldonic acids
Reduction of aldoses result in:
Alditols
Reducing sugars
Sugars that are oxidized and act as reducing agents
How can reducing sugars be detected?
Tollen’s reagent or Benedict’s reagent
Deoxy sugars
Sugars with a -H replacing an -OH group
Esterification
Sugars can react with carboxylic acids and their derivatives, forming esters
Phosphorylation
“Similar to esterification
Phosphate ester is formed by transferring a phosphate group from ATP onto a sugar”
Glycoside formation
The basis for building complex carbohydrates and requires the anomeric carbon to link to another sugar
Disaccharides
Form as result of glycosidic bonding between two monosaccharide subunits
How do polysaccharides form?
By repeated monosaccharide or polysaccharide glycosidic bonding
Common disaccharides
Sucrose, lactose and maltose
Sucrose
Glucose-alpha-1,2-fructose
Lactose
Galactose-beta-1,4-glucose
Maltose
Glucose-alpha-1,4-glucose
Polysaccharides
Cellulose, starches and glycogen
Cellulose
The main structural component for plant cell walls and is a main source of fiber in the human diet
Starches subtypes
Amylose and amylopectin
Starches
Function as a main energy storage form for plants
Glycogen
Functions as a main energy storage form for animals
Aldohexose
Sugar that has one aldehyde group and six carbons, e.g. glucose
Is glucose an aldohexose?
Yes
How many chiral carbons does glucose have?
4
Glycosidation
The addition of a sugar to another compound
Tautomerization
A rearrangement of bonds to undergo keto-enol shifts
Anomerization
Refers to ring closure of a monosaccharide, creating an anomeric carbon
What happens when glucose reacts with ethanol with an acid catalyst?
The hemiacetal is converted to an acetal via replacement of the anomeric hydroxyl group with an an alkoxy group, the result is a type of acetal known as a glycoside
Beta-amylase
Cleaves amylose at the nonreducing end of the polymer to yield maltose
Alpha-amylase
Cleaves amylose anywhere along the chain to yield short polysaccharides, maltose and glucose
Debranching enzyme
Removes oligosaccharides from a branch in glycogen or starches
Glycogen phosphorylase
Yields glucose 1-phosphate (GMP)
How to convert a straight-chain Fischer projection into a chair/ring conformation?
- Draw out the Haworth conformation
- All the groups on the right in the Fischer projection will go on the bottom of the Haworth projection
- All the groups on the left in the Fischer projection will go on the top of the Haworth projection
- Draw out the chair structure, with the oxygen in the back right corner
- Label the carbons in the ring 1 through 5 from the oxygen and moving clockwise around the ring
- Draw in the lines for all the axial substituents, alternating above and below the ring
- What was pointing down in the Haworth projection, will also point down for the chair conformation
- What was pointing up in the Haworth projection, will also point up for the chair conformation
Which polysaccharides display branching structure?
Glycogen and amylopectin
What linkages does glycogen use?
Alpha-1,4 and alpha 1,6
What linkages does amylopectin use?
Alpha-1,4 and alpha 1,6
What linkages does cellulose use?
Beta-1,4
What linkages does amylose use?
Alpha-1,4
Can humans digest maltose?
Yes
Can humans digest cellobiose?
No
Why can’t humans digest cellobiose?
Because cellobiose contain beta-glycosidic linkages and humans do not have the enzymes to cleave them
What are the cyclic forms of monosaccharides?
Hemiacetals and hemiketals
Which components of membrane lipids contribute to their structural role in membranes?
The fatty acid tails form the bulk of the phospholipid bilayer and play a predominantly structural role
Which components of membrane lipids contribute to function?
“The polar head group determines the function of the membrane lipid due to its constant exposure to the exterior environment of the phospholipid bilayer
The degree of unsaturation of fatty acid tails can also play a small role in function”
What is the difference between a sphingolipid that is also a phospholipid and one that is not?
The difference is the bond between the sphingosine backbone and the head group. When this is a phosphodiester bond, it’s a phospholipid. Nonphospholipid sphingolipids include glycolipids, which contain a glycosidic linkage to a sugar.
Types of sphingolipids
Sphingomyelin, glycosphingolipid and ganglioside
What would happen if an amphipathic molecule were placed in a nonpolar solvent rather than an aqueous solution?
In a nonpolar solvent, we would see the opposite of what happens in a polar solvent like water: the hydrophilic, polar part of the molecules would be sequestered inside, while the nonpolar, hydrophobic part of the molecules would be found on the exterior and exposed to the solvent
Phospholipid structure
Phosphodiester bond between the sphingosine backbone and the head group
Are phospholipids sphingolipids?
Yes
Glycolipid structure
Glycosidic linkage between sphingosine backbone and a sugar
Are glycolipids sphingolipids?
Yes
Is sphingomyelin a phospholipid or a glycolipid?
Phospholipid
Is glycosphingolipid a phospholipid or a glycolipid?
Glycolipid
Is ganglioside a phospholipid or a glycolipid?
Glycolipid
What is the functional group of a sphingomyelin?
Phosphatidylethanolamine / phosphatidylcholine
What is the functional group of a glycosphingolipid?
Sugars (mono- or polysaccharides)
What is the functional group of a ganglioside?
Oligosaccharides and N-acetylneuraminic acid (NANA)
How many carbons are in a diterpene?
20
What is the difference between a steroid snd a steroid hormone?
"A steroid is defined by its structure: it includes 3 cyclohexane rings and one cyclopentane ring A steroid hormone is a molecule within this class that also functions as a hormone, meaning that it travels in the bloodstream, is active at low concentrations, has high-affinity reception and affects gene expression and metabolism."
NSAIDs block prostaglandin production in order to reduce pain and inflammation. What do prostaglandins do to bring about these symptoms?
Prostaglandins regulate the synthesis of cAMP, which is involved in many pathways, including those that drive pain and inflammation
Fat-soluble vitamins
Vitamin A (carotene), vitamin D (cholecalciferol), vitamin E (tocopherols) and vitamin K (phylloquinone and menaquinones)
Terpene unit
Made of 2 isoprene units
How many carbons are in an isoprene?
5
Vitamin A (carotene)
“Metabolized to retinal for vision
Metabolized to retinoid acid for gene expression in epithelial development”
Vitamin D (cholecalciferol)
Metabolized to calcitriol in the kidneys to regulate calcium and phosphate homeostasis in the intestines (increasing calcium and phosphate absorption) and promoting bone formation
Vitamin E (tocopherols)
Metabolized to biological antioxidants, using their aromatic rings to destroy free radicals, preventing oxidative damage
Vitamin K (phylloquinone and menaquinones)
“Important for the formation of prothrombin, a clotting factor
Performs posttranslational modification to a number of proteins, creating calcium-binding sites”
How does the human body store spare energy?
The human body stores energy as glycogen and triacylglycerols
Why doesn’t the human body store most energy as sugar?
Triacylglycerols are preferred because their carbons are more reduced, resulting in a larger amount of energy yield per unit weight. In addition, due to their hydrophobic nature, triacylglycerols do no need to carry extra weight from hydration.
Describe the structure of triacylglycerols (triglycerides)
One glycerol attached to three fatty acids by ester bonds
The carbon atoms in lipids are more reduced than those in carbohydrates, giving them twice as pure energy per gram during oxidation
Hydrophobic, so they are not hydrated by body water and do not carry additional water weight
What bonds are broken during saponification?
The ester bonds of triacylglycerols (triglycerides) are broken to form a glycerol molecule and the salts of fatty acids (soap)
Why does soap appear to dissolve in water, and how is this fact important to cleaning?
Soap appears to dissolve in water because amphipathic free fatty acid salts form micelles, with hydrophobic fatty acid tails towards the center and carboxylate groups facing outward towards the water. Fat-soluble particles can then dissolve inside micelles in the soap-water solution and wash away. Water-soluble compounds can freely dissolve in the water.
What are triacylglycerols (triglycerides) used for?
Energy storage
Are lipids soluble in water?
No
Are lipids soluble in nonpolar organic solvents?
Yes
Phospholipids
“Amphipathic
Form the bilateral of biological membrane
Contain a hydrophilic (polar) head group and hydrophobic (nonpolar) tails
The head group is attacked by a phosphodiester linkage”
Are saturated fatty acids more or less fluid than unsaturated fatty acids?
Less
Glycerophospholipids
Phospholipids that contain a glycerol backbone
Sphingolipids
Contain a sphingosine or sphenoid backbone
Can have a phosphodiester bond (phospholipids) or glycosidic bonds (glycolipids)
Used in ABO blood typing
Sphingophospholipids
Sphingolipids that are phospholipids because they have a phosphodiester bond
Sphingomyelins
"A major class of sphingophospholipids and contain a phosphatidylcholine or phosphatidylethanolamine head group A major component of the myelin sheath"
Glycosphingolipids
Attached to sugar moieties instead of a phosphate group
Cerebrosides
Have one sugar connected to a sphingosine
