Biochem Flashcards
Aromatic Amino Acids
WYF (Tryptophan, Phenylalanine and Tyrosine)
Basic (+) Amino Acids
His Lies Are basic (Arginine, Histidine, Lysine)
Nonpolar Amino Acids
LIMP VAG (Leucine, Isoleucine, Methionine, Proline and Valine, Alanine, Glycine)
Polar Amino Acids
STQNC (Serine, Threonine, Glutamine, Asparagine, Cysteine)
Acidic (-) Amino Acids
Aspartic Acid and Glutamic Acid
All amino acids are chiral except for __
glycine
All amino acids are S configuration except for __
cysteine
Thiols are prone to __.
oxidation
Amides (Asp and Glu) do not become charged with __ changes.
pH
Serine and Threonine are often found __ bonding.
hydrogen
All proteinogenic amino acids are __.
L
Peptide bonds are formed via ___ which involves removing H2O.
condensation / dehydrogenation
Hydrolysis of peptide bonds breaks the __ bond by adding H to the amide nitrogen and OH to the carbonyl carbon.
C-N
Primary protein structure consists of the __ . It is stabilized by __ bonds.
order of amino acids ; peptide
Secondary protein structure consists of the __ . It is stabilized by __ bonds.
alpha helices and beta pleated sheets ; hydrogen (proline introduces kinks and usually is not in the middle)
Tertiary protein structure consists of the __ . It is stabilized by __ bonds.
folded protein; disulfide
Quaternary protein structure consists of the __ .
more than one polypeptide chain (subunits)
If you lose tertiary structure than the protein is said to be __. Heat can cause hydrophobic interactions to break with increased kinetic energy. Solutes like urea can break cystine, H bonds and SDS solubilizes the protein.
denatured
GLUT2
1) hepatocytes and pancreatic
2) high Km
3) liver picks up excess glucose and stores it preferentially post meal when high glucose
4) Beta cells: glut 2 and glucokinase –> glucose sensors
5) 1st order kinetics
GLUT4
1) adipose tissue, muscle
2) incr. insulin incr. GLUT4
3) saturated when higher than normal blood glucose levels because close to normal glucose levels
4) 0 order kinetics
Glycolysis is necessary for RBC because they lack __
mitochondria
Glycolysis overall can be defined as glucose –> __
2 pyruvate
Glycolysis : Hexokinase
1) irreversible or reversible
2) inhibited by _
3) forms _
IRREVERSIBLE
Glucose-6-Phosphate
Forms glucose-6-phosphate
Glycolysis : Glucokinase (RATE LIMITING STEP)
1) irreversible or reversible
2) works with __
3) induced by __
1) Irreversible
2) works with Glut 2
3) insulin, senses glucose
Glycolysis : PFK-1
1) irreversible or reversible
2) inhibited __
3) activated __
1) Irreversible
2) ATP, citrate, glucagon
3) activated by AMP , f-2,6 bisphosphate, insulin
Glycolysis : Glyceraldehyde-3- Phosphate Dehydrogenase
1) irreversible or reversible
2) generates _
1) reversible
2) generates NADH
Glycolysis : 3 Phosphoglycerate Kinase
1) irreversible or reversible
2) forms __
1) reversible
2) ATP and 3-phosphoglycerate
Glycolysis : Pyruvate Kinase
1) irreversible or reversible
2) activated by_
3) forms _
1) irreversible
2) 1,6 bisphosphate
3) forms ATP and pyruvate
Monosaccharides can under glycolysis instead of glucose. This happens through __ and __.
trapping ; linking
Galactose is trapped by __ and linked by __
galactokinase ; galactose-1 p uridyltransferase
Fructose is trapped by __ and linked by aldolase B –> DHAP –> Glyceraldehyde –> Glyc-3-Phosph.
fructokinase
Pyruvate dehydrogenase is activated by __ in the liver. It Causes pyruvate to become Acetyl-CoA and releases CO2 and converts NAD+ to NADH.
insulin
Pyruvate dehydrogenase is inhibited by __.
Acetyl-CoA
Pyruvate has three potential fates 1) Acetyl CoA by pyruvate dehydrogenase 2) lactate by __ 3) oxaloacetate by __.
lactate dehydrogenase ; pyruvate carboxylase
Glycogenesis is the synthesis of _ .
glycogen
Glycogenesis is inhibited by __ and __ via a protein kinase cascade.
epinephrine, glucagon
(Glycogenesis) a alpha 1,4 linkage attaches to glucose because of __
glycogen synthase
(Glycogenesis) a alpha 1,6 linkage breaks _ and moves block of __.
alpha 1,4 linkage ; oligoglucose
Glycogenolysis results in the breaking down of __
glycogen
What breaks down alpha 1,4 linkages and creates glucose-1-phosphate (Glycogenolysis)
glycogen phosphorylase
The break down of alpha 1,6 linkages forms __(Glycogenolysis)
free glucose
Glycogenolysis is activated by AMP and epinephrine but inhibited by __.
ATP
(Gluconeogenesis) occurs when fasting glycogen levels __
decrease
Gluconeogenesis Pyruvate Carboxylase replaces __.
pyruvate kinase
Gluconeogenesis PEPCK replaces __.
pyruvate kinase
Gluconeogenesis F-1,6 bisphosphatase replaces __.
PFK-1
Gluconeogenesis 6-6-phosphatase replaces __.
glucokinase
Gluconeogenesis occurs as it reverses the steps of glycolysis including bypassing the 3 irreversible steps. It depends upon __.
beta oxidation for acetyl-coA and ketone bodies
The Pentose Phosphate Pathway has two major products. What are they?
1) Ribose -5- Phosphate 2) NADPH
The Pentose Phosphate Pathway NADPH Product has what functions?
1) biosynthesis of fatty acid + cholesterol
2) cellular bleach production
3) maintain supply of reduced glutathione against ROS
Acetyl-CoA is comprised of thioester bonds which are __ in energy.
high
Acetyl-CoA is inhibited by __ and __.
acetyl CoA and NADH
Acetyl-CoA is activated by __ then PDH and then dihydrolipoyl x2
pyruvate dehydrogenase phosphatase
The Citric Acid Cycle generates __
NADH, FADH2, GTP
The Citric Acid Cycle oxidizes __
carbons, intermediates to CO2
The Citric Acid Cycle begins with 1) citrate synthase 2) __ 3) __ 4) __ 5)__ 6)__ 7)__ 8) malate dehydrogenase
2) aconitase
3) isocitrate dehydrogenase
4) alpha ketoglutarate dehydrogenase
5) succinyl- coA- synthetase
6) succinate dehydrogenase
7) fumarase
The Electron Transport chain takes place in the __
inner mitochondrial membrane , facing the matrix
The Citric Acid cycle is a part of __
mitochondrial matrix
Electron Transport Chain (Complex I) translocates __ protons. NADH to FMN to CoQ results in __. The key components are iron-sulfur
4 ; CoQH2
Electron Transport Chain (Complex II) translocates __ protons. Succinate to FAT to CoQ results in __ . The key components are iron-sulfur
0 ; CoQH2
Electron Transport Chain (Complex III) translocates __ protons. CoQH2 to heme leading to __. The key components are iron-sulfur
4 ; cytochrome C
Electron Transport Chain (Complex IV) translocates __ protons. H+ ions lead to cytochrome C to oxygen making __. The key components are cytochrome and Cu2+
2; H2O
ETC NADH cannot cross and needs a shuttle. One path leads to glycerol-3-phosphate and one leads to malate.
1) gly-3-phosphate NADH to DHAP to glycerol-3-phosphate
2) malate aspartate NADH to oxaloacetate to malate
Oxidative Phosphorylation - proton motive force
The proton-motive force is the electrochemical gradient generated by the ETC across the inner mitochondrial membrane.
Oxidative Phosphorylation- ATP synthase
ATP Synthase is the enzyme responsible for generating ATP from ADP and an inorganic phosphate (Pi).
Oxidative Phosphorylation- F0 portion
Is an ion channel. allowing protons to flow down the gradient from the intermembrane space to the matrix.
Oxidative Phosphorylation- F1 portion
Uses the energy released by the gradient to phosphorylate ADP into ATP
Lipid Mobilization in adipocytes involves __ and is regulated by insulin, epinephrine and cortisol
Hormone sensitive lipase
Lipid Mobilization in lipoprotein involves __.
lipoprotein lipase
Short chain fatty acids are __ whereas long chain fatty acids are absorbed into micelles and chylomicrons.
absorbed into blood
Chylomicrons
triacylglycerols that transport long chain fatty acids via the lymph system
VLDL is a triacylglycerol that transports from liver to __.
peripheral tissue
IDL is a VDL remnant and transports between triacylglycerol and cholesterol. It picks up __ from HDL.
cholesteryl ester
LDL
A cholesterol for tissue use
HDL
“good cholesterol” reverse cholesterol transport
Apoprotein are important for interactions with lipoproteins forming apolipoproteins. If you had no apolipoproteins then we could expect:
1) cannot secrete lipid transport lipoprotein
2) inability to endocytose
3) decreased ability to remove excess cholesterol
The key enzyme of cholesterol biosynthesis
HMG-CoA reductase
Cholesterol metabolism - LCAT
Cholesteryl esters for HDL transport
Cholesterol metabolism- CETP
IDL to LDL transfer esters from HDL
An unsaturated fatty acid contains __
one or more double bonds
A saturated fatty acid contains _
no double bonds
Fatty Acid Synthesis
1) activation 2) bond formation 3) reduction 4) dehydration 5) reduction
(x8)
Palmitic Acid
16 carbon acid and the only fatty acid that humans can synthesize
Fatty Acid Mitochondria Oxidation- Saturated
1) Oxidation 2) Hydration 3) Oxidation 4) Cleavage
Fatty Acid Mitochondria Oxidation- Unsaturated
This requires 1) isomerase 2) additional reductase at cleavage
Ketone Bodies are formed due to __ and occurs in the liver.
excess acetyl coA during starvation and regenerates acetyl coA
Ketolysis generates acetyl coA but
does not occur in the liver and only occurs in low energy muscle and brain tissues
Protein catabolism occurs during starvation and is fed __
into urea cycle for excretion
Protein catabolism - Amino Acids pathways
1) gluconeogenesis 2) ketone body formation
Enzymes lower the activation energy and increase the rate of a reaction. However, what other features should we know about enzymes?
1) no change in the equilibrium constant
2) appear in both reactants and products- unchanged
3) no change in deltaG
4) pH and temperature sensitive
5) specific to rxn or rxn class
Oxidoreductases catalyze _ reactions.
redox
Transferases catalyze __.
movement of functional groups (i.e. kinases transfer phosphate from ATP to another molecule)
Hydrolases catalyze __
breaking into two using the addition of water (i.e. phosphatase, lipase, nuclease)
Lysases catalyze __ reactions.
cleaving 1 molecule into 2 products w/o water (ex. synthases 2 molecules into a single molecule)
Isomerases catalyze __
the rearrangement of bonds within a molecule ; (aka synthases 2 molecules into a single molecule)
Ligases catalyze __
addition or synthesis reactions between large molecules and require ATP (i.e. nucleic acid synthesis and repair)
Mnemonic for Enzyme Classes
LIL Hot (Ligase, Isomerase, Lysase & Hydrolase, Oxidoreductase and Transferase)
A holoenzyme is an enzyme with _
a cofactor
An apoenzyme is an enzyme with _
no cofactor
Tightly bound groups attached to cofactors or coenzymes
prosthetic groups
Cofactors are __ or metal ions digested as __.
inorganic ; dietary minerals
Coenzymes are __ and are vitamins and their derivatives.
organic
Water soluble vitamins (coenzymes), which are __ and __ ,are easily secreted.
Vitamin B and C
Fat soluble vitamins (coenzymes) are __ and __
A, D, E, K
Michaelis- Menten Kinetics state that if substrate concentration increases then the rate will __ until the ___ also known as saturation.
increase ; Vmax
The rate of a reaction depends upon the concentration of __ and __.
enzyme and substrate
At 1/2vmax we have km. Km indicates the __ of a substrate.
affinity
A low km indicates __ substrate efficiency
high
A high km indicates __ substrate affinity
low
kcat/Km is a measure of _
catalytic efficency
a large kcat indicates __ combined with a small Km this would mean high catalytic efficiency
high turnover
Km cannot be altered by altering
the concentration of enzyme or substrate
Lineweaver- Burke plots are useful for __. It is a double reciprocal plot of a Michaelis Menten plot.
determining type of inhibition
Hill Coefficient > 1
positive ; after one is bound the affinity for more to bind increases
Hill Coefficient < 1
negative ; after one ligand is bound the affinity for more decreases
Hill Coefficient = 1
enzyme is not exhibiting cooperative binding
The impact of temperature on enzyme activity
increased temperature and increased enzyme activity 2x every 10 celsius until it denatures
The impact of pH on enzyme activity
there is maximal activity in small pH range (pH= 7.4 ; gastric = 2 ; pancreas = 8.5). Outside of this range because ionization of active site changes it denatures
The impact of salinity on enzymes
It can disrupt tertiary and quaternary structures
Competitive Inhibition (looks like a gas pedal on lineweaver)
Km: increased
Vmax: unaffected
Slope: 1/ Vmax
Uncompetitive Inhibition
Km: decreased
Vmax: reduced
Slope: Km/ Vmax
Noncompetitive Inhibition
Km: unaffected
Vmax: reduced
Slope: -1/ Km
Mixed Inhibition
Km: increases or decreases
Vmax: reduced
Irreversible inhibition, unlike reversible, alters the enzyme in a way that the active site is unavailable permanently ; new enzymes must be synthesized for the reaction to occur again. An example is __
suicide inhibitors and their covalent bonding
Regulatory enzymes can experience activation and inhibition. Allosteric sites __
can be occupied by activators which increase affinity or enzymatic turnover
Regulatory enzymes can experience activation and inhibition. Phosphorylation, covalent modifications with phosphate, or glycosylation, covalent modifications with carbohydrate, can __
alter the selectivity of enzymes
Regulatory enzymes like __ are secreted in an inactive form and are activated by cleavage
zymogens
Carbohydrate Metabolism- Glycolysis generates
2 NADH and 2 ATP
Carbohydrate Metabolism- Pyruvate dehydrogenase generates
1 NADH per pyruvate
Carbohydrate Metabolism- Citric Acid Cycle generates
3 NADH, 1 FADH2, and 1 GTP
Carbohydrate Metabolism- Each NADH generates
2.5 ATP ; 10 NADH ; 25 ATP
Carbohydrate Metabolism- Each FADH2 generates
1.5 ATP ; 2 FADH2 ; 3 ATP
Carbohydrate Metabolism- Each molecule of glucose generates
32 ATP if completely efficient (2 glycolysis, 2 citric acid cycle, 25 NADH, 3 FADH2)
Keratin
in epithelial cells ; intermediate filament
Tubulin
makes up microtubules; periphery + and nucleus -
Actin
microfilament and myofibril ; has + and - sides
Myosin
motor protein with movement at neck due to sarcomere contraction
Kinesins
aligning chrom. in metaphase and depolymerizing during anaphase: bring vesicles to +
Dyneins
aligning chrom. in metaphase and depolymerizing during anaphase: bring vesicles to -
Cell Adhesion Molecule: Cadherins
Ca+ dependent binding protein
Cell Adhesion Molecule: Integrins
cell signaling and host defense binding protein
Cell Adhesion Molecule: Selectins
binding to carbohydrates as a binding protein
Immunoglobulins
antibodies specific to antigens
1) neutralize
2) opsonization- marking for destruction
3) agglutinate - clumping together and then phagocytosis
GPCR
Gs stimulates cAMP levels rise
Gi inhibits cAMP levels lower
Gq activates phospholipase C
binding of G switches to active state
Electrophoresis separates proteins based by __ . Negative molecules go to the positive anode and positive go to the negative cathode.
charge
V= Ez / f
electric field x net charge / frictional coefficent
Electrophoresis uses an electrolytic cell where delta G is __ 0 and E cell is __ 0
> ;
Native PAGE
complexes stay together and we can compare molecular size or charge of proteins
SDS Page
SDS disrupts all noncovalent interactions which means the functional protein cannot be recaptured. separation is based on molecular mass
the SDS solubilizes the protein uniformly negative charges
Isoelectric Focusing
protein stops when pH = pI and separation occurs based on PI. the anode has acidic gel and + charge
you use a gel with a pH gradient that encourages a variable change
Chromatography: Column
polar composition like silica, alumina with a nonpolar solvent
Chromatography: Size-Exclusion
porous beads larger molecules will elute first as not trapped in small pores
Chromatography: Affinity
bound receptor or ligand and eluent with receptor for protein of interest
Edman Degradation
1) breaks disulfide bonds
2) separate polypeptide chains by chromatography
3) use a method to generate peptides (chemical)
4) use another method to generate peptides (enzymatic)
5) separate peptides by chromatography
6) determine sequence by Edman degradation
7) use overlapping peptide sequences to reconstruct the polypeptide sequence
done at N terminus for amino acid sequencing
BCA Assay
quantitation of total protein in a sample. 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
Bradford Protein Assay
measure the concentration of total protein in a sample. The principle of this assay is that the binding of protein molecules to Coomassie dye under acidic conditions results in a color change from brown to blue.
You can use UV to determine concentration for __ amino acids
aromatic
