Metabolism Flashcards
What does Catabolism/Anabolism do?
Catabolism - breaking down/exergonic/oxidation
Anabolism - building/endergonic/reduction
Define Catabolism/Anabolism:
Catabolism - generation of energy to drive vital reactions
Anabolism - synthesis of biological molecules
What are 3 properties of Catabolic pathways?
- Exergonic (release energy)
- Oxidative (e- transferred to NAD+ or NADP+_
- Energy captured as ATP
What are the 3 stages of Catabolism?
- hydrolysis of complex molecules to monomers
- conversion of building blocks to acetyl CoA in the mitochondria
- oxidation of acetyl CoA to carbon dioxide and water in ATP through Oxidative Phosphorylation (ETC)
Name 3 properties of anabolic pathways:
- Endergonic
- Reductive (hydride ion from NADPH used)
- ATP consumed
What type of reactions are carried out by dehydrogenase reactions?
oxidize a substrate by transfering Hydride ion to NAD+ and FAD
(dehydrogenase = think oxidation and NAD+ and FAD)
What are the major differences between Catabolism and Anabolism?
Catabolic products are similar, low molec. weight, and energy poor
Anabolic products are diverse, large, and energy rich
What is futile cycling?
Simultaneous synthesis and degradation
think Sisyphean
At least one of the steps in paired anabolic/catabolic pathways has a different…
enzyme
T/F
Paired pathways often occur right next to each other
False
they are often in different cellular compartments
i.e. - Fatty acid degradation occurs in Mitochondria
Fatty acid synthesis occurs in cytoplasm
Delta G Exergonic
Delta G Endergonic
less than 0
greater than 0
When delta G=0, then
equilibrium
forward rate=reverse rate
What 3 things do free energy changes predict?
- Direction of chemical reactions
- Equilibrium positions
- Amount of work that can be performed
(the further from equilibrium the more work can be performed)
What can’t free energy changes tell us?
anything about the RATE of rxn
and is independent of the PATH of rxn
Can a rxn proceed if delta G(not) is positive
yes.
If delta G is negative
How can a thermodynamically unfavorable reaction be driven in the forward direction?
If coupled to highly exergonic rxn through a common intermediate.
What 3 things facilitate ATP hydrolysis?
Charge separation
Inorganic phosphate product stabilzed by resonance
direct product of hydrolysis ADP is ionized
Does ATP provide energy through hydrolysis?
NO
by group transfers
What are 2 ways to produce ATP?
Substrate level phosphorylation (minority)
Oxidative phosphorylation (mitochondria - ETC)
What are 3 levels of metabolic pathway regulation?
Allosteric (non-covalent bonding)
Hormonal
Concentration of enzyme (longest time frame)
What are two practical principles of bioenergetics (in terms of delta G and delta G0)?
A rxn can move forward even if delta G0 is positive (delta G has to be negative)
chemical rxns can be additive (coupling)
What are the 3 families of lipids?
Glycerophospholipids
Sphingolipids
Cholesterol
What is the prefix for a Glycerophospholipid?
Phasphatidyl… (or phosphatidic)
What are the 4 Sphingolipids?
Ceramide
Sphingomyelin
Glucosylcerebroside
Ganglioside
What molecule is both a phospholipid and a sphingolipid?
sphingomyelin
What are the microdomains made up of cholesterol and sphingomyelin in the bilayer?
Lipid Rafts
What is a transmembrane protein called?
Integral
The membrane spanning part of an IMP (integral membrane protein) is usually ________(property) and ________ (structurally)?
Hydrophobic
alpha - helices
An aquaporin is an example of
An IMP
What substances easily permeate membranes?
Gases and ethanol
What substances are slightly permeable to membranes?
Urea and water
Are ions permeable?
no
What are 6 ways to get something across a membrane?
Simple diffusion - gases and ethanol
Facilitated diffusion - down electrochemical gradient
Primary active transport (ATP)
Secondary active transport (driven by ion moving down gradient carrying substrate)
Ion channel
Ionophore-mediated ion transport
Is ATP required for secondary active transport?
No. Not directly.
because it relies on a concentration gradient set up by Na/K pump which does rely on ATP
What type of transport goes against a concentration gradient?
Active Transport and Cotransport (with ions)
What are the 3 major types of membrane anchors?
Which are on the cytosolic side?
Acylation - fatty acyl to Gly
Prenylation - NH3+ to Cys
(both cytosolic)
GPI anchor - PI, PE, and several sugars anchored through Asp
(exterior cell)
How does glucose enter a cell?
Facilitated diffusion
Membrane protein changes conformation (simple hand movement)
What are the 3 general classes of cell-surfaced receptors?
second-messenger
catalytic
intracellular
What are 4 approaches to cell signalling?
Endocrine
Paracrine
Autocrine
plasma membrane-attached proteins (to adjacent cell)
What are 2 G protein coupled second messengers?
Adenylate Cyclase pathway (glucagon and epinepherine) Phosphoinositide pathway (growth hormone)
What is the function of the Nitric Oxide pathway?
Relaxation of smooth muscle
Give an example of a Sell-Surfaced Receptor and an Intracellular Receptor.
Insulin
Steroids
What is another name for 7TM receptors?
G protein coupled receptors (GPCR)
G-protein coupled receptor:
Hormone binds receptor in plasma membrane
G-protein binds receptor
GDP > GTP
dissolution of complex, conformational change in G alpha
G alpha to effector in plasma membrane
GTP > GDP puts back together
Explain the Adenylate Cyclase cAMP pathway:
Epinephrine binds Beta-andrenergic receptor
GDP > GTP
activated Adenylate cyclase (protein/protein interaction)
Adenylate cyclase causes ATP > cAMP,
which activates Protein Kinase A
How do stimulatory and inhibitory (Gs and Gi) heterotrimers work in regards to cAMP
Gs activates cAMP
Gi inhibits cAMP
(through separate stimulatory/inhibitory receptors and G-complexes), affecting Adenylyl cyclase
T/F
cAMP inhibits Protein Kinase A
False
cAMP activates the regulatory subunits of PKA to release its catalytic subunits
it phosphorylates the targets Ser and Thr, and stimulates transcription activator CREB
Describe how Acetylcholine opens an ion channel (in neurotransmitter)
Acetylcholine binds,
GDP > GTP in G-complex dissociates the complex
G-beta binds adjacent channel, allowing K to flow out
How does the inactivation of a receptor work (two steps)?
- Dissociation of signalling molecule
2. phosphorylation of cell-side of receptor, followed by binding of Beta-Arrestin
How are GTP and cAMP inactivated?
GTP - hydrolyzed by intrinsic GTPase
cAMP - by cAMP phosphodiesterase
What are two pathologies arising from a failure to inactivate signal?
Cholera and whooping cough (pertussis)
both cases activate G-proteins, which increases cAMP, which leaves ion channels open
8 steps of phosphoinostide cascade
alternative 2nd messenger system for 7TM Receptors
- GCPR/ligand dissociates G-beta inside cell,
- PIP2 (phosphatidylinositol) > IP3 (inositol)
- IP3 binds Ca+ ion channel
- IP3- gated Ca2+ channel open
5-8. PKC (protein kinase C) activated by Ca, phosphorylates substrates
What does IP3 cause?
rapid release of Calcium from the endoplasmic reticulum
which further activates PKC and Calmodulin
Flow of Nitric Oxide pathway:
Ach > Ach GPCR > Phospholipase C > Ca/Calmodulin > NO synthase > NO receptor > PKG
relaxation of muscle cell
What is the function of NO
Relaxes smooth muscle
prevents platelet aggregation
neurotransmitter in brain
mediates tumoricidal/bactericidal actions of macrophage
What type of receptor is the insulin receptor?
Catalytic
What receptor has a protein kinase as part of its structure and is a good example of transduction?
Insulin
Describe 2 ways how a signal is relayed via intracellular receptors:
Hormone enters nucleus > binds receptor > transcription > translation > new protein >altered cell function
Peptide or amine binds outside of cell and acts via 2nd messengers to alter gene expression
Name 5 Glycerophospholipids
Phosphatidic acid Phosphatidylethenolamine Phosphatidylcholine Phosphatidylserine Phosphatidylinositol
What is the free energy of a reaction?
Energy available to do work
NADH serves to carry…
electrons
[conc] 10 -2 M to 10 -4 M
Spontaneous
Which lipid is both a phospholipid and sphingolipid?
Sphingomyelin
Which variety of membrane transport coupling involves one species in and another out?
Antiporters
T/F
Signal transduction by catalytic receptors and intracellular receptors are both mediated by G-proteins
False
Which rxn pathways transform fuels into energy?
Catabolic
Exergonic rxns are:
spontaneous
Which enzyme begins the phosphoinositol cascade?
Phospholipase C
cAMP releases inhibition of, thereby activating…
PKA
Protein Kinase A
Glc enters most cells via
Facilitated diffusion
3 ways metabolism can be regulated:
Hormone
Allosteric
Compartmentalization
Ceramide is a…
Sphingolipid
What do both active transport and facilitated diffusion require?
Integral membrane protein
AA review. What 2 things does every Amino Acid have?
Amino group and Carboxyl group attached to alpha-C
pH=
-log [H+]
Why is pH biologically important?
charges in environment affect charge of molecule (and therefore shape)
Which acid is stronger,
Formic acid pKa=3.75
Acetic acid pKa=4.76
Formic
Henderson-Hasselbach equation:
pH = pKa + log [A-]/[HA]
When is buffering optimal?
when acid = base
When acid = base,
pH = Pka
What is the term for an amino acid that can act either as an acid or a base?
Amphoteric
aka - zwitterion
What does an Amino Acid titration curve look like, and what is in the middle?
Two plateaus, each representing the pKa of the carboxyl and amino group.
pI = average of the pKa’s
Generally, the pKa’s of carboxyl groups are around ______ , while the pKa’s of Amino groups tend to be around ___.
carboxyl = around 2
amino = around 9
The pI, or isoelectric point, is defined as the _________.
What will a molecule do in an electric field (like electrophoresis) at the isoelectric point?
point in which there is no net charge on a molecule
won’t move
In terms of charge, how is Histadine different than other AA’s?
It has three dissociations (and therefore 3 pKa’s)
Around how many polar and non-polar R groups are there for AA’s?
10 polar
10 non-polar
Which amino acid makes serotonin?
which makes dopamine?
Tryptophan
Tyrosine
What are the 5 amino acids that carry a charge?
Lysine, Arginine, and Histidine (positive)
Aspartate and Glutamate (negative)
What is special about a peptide bond?
partial double bond character
rigid and planar
trans configuration
uncharged but polar
What is the conventional direction of an Amino Acid?
From N (amino) to C (carboxyl)
Primary, secondary, and tertiary structure
AA sequence
Beta sheets, alpha helix (can be parallel or antiparallel), Beta bends and turns.
Folding (intra-structural interactions) - nonpolar usually inside, polar outside
What are structural motifs?
This is a supersecondary structure in which individual elements of secondary structure are combined into stable, geometrical arrangements (like helix bundles)
What stabilizes tertiary structure?
Non-covalent interactions (hydrophobic, ionic, and H-bonds)
Covalent interactions (peptide bonds, disulfide bonds)
What is the difference between a polypeptide and a protein?
Polypeptide is one chain of AA’s
Protein can be made from multiple polypeptides.
(this is Quaternary Structure)
What is the main driving force for the assembly Quaternary Structure?
Hydrophobic interactions
What is the difference between a fibrous and globular protein?
Fibrous - water insoluble, lack tertiary structure (think hair)
Globular - water soluble (most proteins, etc)
If a molecule has a pKa, it is by definition a…
weak acid
At a pH below the pI, proteins carry a net ______ charge, and above the pI, proteins carry a net _____ charge.
positive
negative
What does a large pKa tell you about an acid?
It is very weak
What is in a conjugated protein?
a Prosthetic Group, such as lipids, metal (blood), phosphate groups, etc.
How do temperature and pH affect enzymes?
Temp - increase rate of rxn up to point
pH - change charge, conformation, shape
What is the turnover number?
The maximum number of molecules of substrate an enzyme can convert to product
(molecules converted/sec.)
How is catalytic efficiency determined?
Kcat/Km
low Km means high efficiency/high affinity for substrate
T/F
Enzymes only bind one substrate
False.
Enzymes have a range of specificity
Give an example of an enzyme with high specificity.
Low specificity?
Urease - absolute specificity
Chymotrypsin - breaks peptide bonds in a broad range (most specific for phenylalanine)
What is the additional ingredient many enzymes require to function?
A cofactor
Define Holoenzyme, Apoenzyme
Holoenzyme - Enzyme with its cofactor
Apoenzyme - protein portion of the holoenzyme (no cofactor and inactive)
T/F
Coenzymes are non-protein organic molecules
True
What is the term for a tightly bound nonpolypeptide non-dissociating structure in an enzyme?
Prosthetic Group
Define:
Vmax
Km
Kcat
max rate enzyme activity at substrate saturation
substrate [conc] at 1/2 Vmax
turnover number (substrate converted/time)
What term defines catalytic efficiency (how effective an enzyme is at catalyzing rxns)
Kcat/Km
What are 3 types of enzymatic reactions?
Random (creatine kinase)
Sequential displacement (defined order)
Double Displacement (enzyme > intermediate > enzyme)
What are the 5 key landmarks of a Michaelis-Menten graph
Vmax 1/2 Vmax Km 1st Order linear rxn zone 0 Order
The Km is referred to as the:
Michaelis constant
In a Lineweaver-Burke plot, what do the following indicate
The x-intercept
the y-intercept
the slope
-1/Km
1/Vmax
Km/Vmax
Describe the rxn when [S] is less than, equal to, and greater than Km
[S] less - optimal rxn velocity
[S]=Km - half max velocity
[S] greater - rxn approaches Vmax
What are the 3 types of enzyme inhibition?
What are their effects on a lineweaver-burke plot
Competitive - goes for same active site (Vmax same, Km increases)
Increase slope around the y-axis
Noncompetitive - binds other site on Substrate, changes conformation
Increase slope, but rotates at x-axis
Uncompetitive - Vmax and Km decrease (traps enzyme)
parallel slope
What are the effects of Allosteric positive and negative modifiers?
Allosteric positive - Increases affinity of enzyme for substrate
Allosteric negative - Decreases affinity for enzymes to substrate
What is a proenzyme (aka zymogen), and what is an example?
Inactive enzyme precursor
pancreatic and blood-clotting pathways (Trypsinogen)
What are isoenzymes?
Alternate forms of enzymes existing in different proportions in different tissues (tissue specificity)
Define: Aldose Ketose Enantiomer Epimer Glycosidic bond
aldose - carbohydrate with aldehyde as oxidized functional group
ketose - carb with keto as oxidized functional group
enantiomer - non-super imposable mirror images (hands)
epimer - single carbon atom configuration difference
glycosidic bond - carb/carb bond (hemiacetal to hydroxyl)
What is an oligosaccharide?
2-12 monosaccharides
under - mono
over - poly
What is a pyranose?
Furanose?
pyranose - hexagonal sugar
furanose - pentagonal sugar
What is an anomer?
example?
special type of epimer
alpha and beta-D-Glucose are anomers
Where is the hydroxyl group oriented in Alpha D glucopyranose?
Beta D glucopyranose?
alpha - hydroxyl on bottom
beta - hydroxyl on top
What can humans digest, alpha or beta glc?
Alpha = glycogen chains
Beta = cellulose
How is glycogen branched?
Alpha 1,4 (linear) AND Alpha 1,6 (branched) linkages
What is starch made from?
Amylopectin (highly branched Alpha 1,4 and Alpha 1,6) and
Amylose (spiral polymer of D glc)
What is cellulose made from
Linear chain of Beta 1,4 D Glucose
What makes up the disaccharides Maltose and Lactose?
Sucrose?
Maltose - 2 glc (Alpha 1,4)
Lactose - 2 BETA D glc (Beta 1,4)
glc/frc (Alpha 1, Beta 2)
What calcium dependent enzyme is found in saliva and what does it break down?
Salivary Amylase
breaks down Alpha 1,4
What breaks Alpha 1,4 glycosidic bonds in the mouth?
What breaks them in the small intestine?
Salivary Amylase
Pancreatic Amylase
What 4 brush border enzymes break down disaccharides?
Isomaltase, maltase, lactase, and sucrase
What does Isomaltase break down?
Alpha 1,6 glycosidic bonds
How does glc move from the lumen to the blood?
Symporter (secondary active transport) into enterocyte (cytosol)
Glc then moves through basolateral membrane through GLUT2 transporters (integral membrane proteins) by Facilitated Diffusion
Describe the role of glc transporters in sugar metabolism.
GLUT2 IMP’s move glc down concentration gradient through Facilitated Diffusion
What are 4 effects of fiber in the the diet?
Increase stool volume
Increase stool softness
Decrease transit time
Increase satiety
What 2 things does passage of undigested carbohydrate into the large intestine cause?
Osmotic diarrhea
Bacterial fermentation of carbohydrate to 2 and 3 C fragments (plus carbon dioxide and hydrogen gas)
What is the most common disaccharide enzyme deficiency?
What disaccharide enzyme deficiency hasn’t been observed?
Lactase
Maltase