MCAT Biochemistry Deb
DNA Binding Domain
- ______ ______ _______ binds to a specific nucleotide sequence in the promoter region or to a DNA response element to help in the recruitment of transcriptional machinery
Activation Domain
- ______ _______allows for the binding of several transcription factors and other important regulatory proteins (ie RNA pol., histone acetylases, etc)
Splicing, introns, exons, spliceosome
- _______ is the removal of noncoding ______ - ligating coding regions called______ - accomplished by the _________
Histone Deacetylation
- ________ ________ are proteins that function to remove acetyl groups from histines, which results in a closed chromatin conformation and overall decrease in gene expression
tRNA (Transfer RNA)
- ________ _________ is responsible for converting the language of nucleic acids to the language of amino acids and peptides each tRNA molecule has a folded strand of RNA which includes a three nucleotide anticodon which pairs with the appropriate codon of mRNA while in the ribosome. ________ _______ is found in the cytoplasm and is the second most abundant type of RNA in the cell, after mRNA
Ribozyme
- ________ enzyme made of RNA molecules instead of peptides
Codons
- ________ three nucleotide sequence in an mRNA molecule that pairs with an appropriate tRNA anticodon during translation
Nonsense Mutation. definiton and aka?
- _________ ________ is a mutation where the codon now encodes for a premature stop codeon. aka: truncation mutation
Wobble Position, what is it and why did it probably come about?
- _________ ________ is the variable third base and is an evolutionary development designed to protect against mutations in the coding regions of our DNA.
DNA Methylation
- _________ ___________addition of methyl groups to cytosine and adenine nucleotides and causes gene silencing - heterochromatin is more highly methylated than euchromatin
Gene
- _________ is a unit of DNA that encodes a specific protein or RNA molecule
Frameshift Mutation
- _________ mutation occur when an amino acid has been added or removed from the sequence causing the reading frame to shift - _______ mutations more serious than point mutations
Response Element
- ________ _______ are sequence of DNA that binds only to specific transcription factors
Missense Mutation
- __________ _________ is a mutation where one amino acid substitutes for another
TATA Box
- _________ box a site in the promoter region in eukaryotes with a high concentration of A and T
Prenylation
- __________ addition of lipids to certain membrane bound enzymes
Amplification
- __________ expression is increased as a result of specific signals such as hormones, growth factors, and other intracellular conditions How cells accomplish this: 1) enhancer 2) gene duplication
Operon
- __________ is a cluster of genes transcribed as a single mRNA ie trp operon
Acetylation
- __________ of histone proteins decreases the positive charge on lysine residues and weakens the interaction of the histone with the DNA results in an open chromatin conformation that allows for easier access of the transcriptional machinery to DNA
Structural Genes
- ___________ codes for the protein of interest
Promoter Site
- ___________ provides a place for RNA polymerase to bind, similar to eukaryotes
Promoters
- ___________ specialized DNA regions sought out by RNA polymerase
Operator Site
- _____________ nontranscribable region of DNA that is capable of binding a repressor protein
Carboxylation
- _______________addition of carboxylic acids to serve as calcium binding sites
Glycosylation
- ______________addition of oligosaccharides as proteins pass through the ER and Golgi to determine cellular destination
Phosphorylation
- ____________addition of phosphates by kinases to activate or deactivate proteins
Regulator Gene
- __________codes for proteins known as a repressor
Reading Frame
- the three nucleotides of a codon is referred to as the ________ ________
water-soluble peptide hormones
--------- hormones adjust the metabolic process of cells via second messenger cascades. (ex. insulin)
elongation factors (EF)
- elongation factors (EFs) assist by locating and recruiting aminoacyl tRNA along with GTP while removing GDP once the energy has been used
Lac operon, how it works
- falling levels of glucose increase levels of cAMP which binds to Catabolite activator protein (CAP) allowing it to bind to the promoter region so transcription is increased
What is the modified standard free energy state value of AMP? What is its function?
-9.2 kJ/mol, ATP synthesis
Function of Transcription Factors
- help the RNA polymerase locate and bind to the promoter region of DNA, helping to establish where transcription will start
RNA Polymerase II. what is it. where does it bind?
- main player in transcription of mRNA in eukaryotes synthesizes hnRNA (pre-processed mRNA) and some snRNA (small nuclear RNA) in nucleus - binds at the TATA box within the promoter region hnsn2
triiodothyronine (T3)
----- (---) is a thyroid hormone that increases the metabolic rate quickly but this increase last for a shorter span of time.
respirometry
----- allows accurate measurement of the respiratory quotient. ( used to measure metabolic rates. the RQ differs depending on the fuels being used by the organism)
leptin
----- is a hormone secreted by fat cells that decreases appetite by suppressing orexin production.
delta G
----- is the change in free energy that occurs at any concentration of products and reactants and at any temperature.
delta G= 0 when?
----- when the reaction is in equilibrium.
Internal energy (U)
------ (--) is the sum of all of the different interactions between and within atoms in a system (ie vibration, rotation, linear motion, stored chemical energies, etc)
thyroxine (T4)
------ (----) is a thyroid hormone that takes serval hours to increase an individual's metabolic rate, but once increased this heightened metabolic rate can last for several days.
catabolism
------ breakdown of biomolecules for energy.
hyperthyroidism
------ can cause rapid weight loss,anxiety, jitteriness and fever.
orexin
------ further increases our appetite and is involved in alertness and the sleep-wake cycle. Hypoglycemia is also a trigger for this hormone.
fat-soluble amino acid derivative hormones
------ hormones regulate metabolism at the transcriptional level. (thyroid hormones)
glucocorticoids
------ increase blood glucose in response to stress by mobilizing fat stores (fatty acids are released from adipocytes)and inhibiting glucose uptake (fight or flight response) They increase the impact of ---- and ------.
delta G*'
------ is a symbol that indicates that the reaction is in a modified standard state [ H+]= 10^-7 M --> pH=7
bioenergetics
------ is used to describe energy states in biological systems.
enthalpy (delta H)
------- (--) measures the overall change in heat of a system during a reaction.
entropy (delta S), J/K
------- (---) measures the degree of disorder or energy dispersion in a system. What are its units?
creatine phosphate
------- is a short-lived source of energy ( 2-7 seconds) which transfers a phosphate group to ADP to form ATP in active muscles.
ghrelin
------- is secreted by the stomach in response to signals of an impending meal (can be smell, sight, tast, etc). It increase our appetite and stimulates the secretion of orexin.
anabolism
------- is the synthesis of biomolecules/fuel storage
electron carriers: membrane bound or soluble?
------- may be soluble or membrane-bound.
hypothyroidism
-------- can cause symptoms including cold intolerance, fatigue, weight gain, and depression as metabolism suffers.
calorimeters
-------- can measure basal metabolic rate( BMR) based on heat exchange with the environment.
short bursts of high-intensity exercise are supported by what?
-------- exercise are supported by anaerobic glycolysis which uses up stored muscle glycogen.
What is the modified standard free energy state value of Glucose-6-phosphate? What is its function?
-13.9 kJ/mol, intermediate of glycolysis and gluconeogenesis
Pancreatic enzymes hydrolyze lipid components to...
-2-monoacylglycerol -free fatty acids -cholesterol
What is the modified standard free energy state value of ATP? What is its function?
-30.5 kJ/mol, energy turnover in all cell types
What is the modified standard free energy state value of creatine phosphate? What is its function?
-43.3 kJ/mol, direct phosphorylation in muscle
What is the modified standard free energy state value of cAMP? What is its function?
-50.4 kJ/mol, its a second messenger
The two major functions of liver:
1. maintain constant level of blood glucose under a wide range of conditions 2. synthesize ketones when excess fatty acids are being oxidized.
Side note: what are the rate limiting enzymes for the following processes? -Glycolysis -fermentation -glycogenesis -glycogenolysis -gluconeogenesis -pentose pphosphate pathway
-Glycolysis: phosphofructokinase-1 -fermentation: lactate dehydrogenase -glycogenesis: glycogen synthase -glycogenolysis: glycogen phosphorylase -gluconeogenesis: fructose-1,6-bisphosphatase -pentose pphosphate pathway: Glucose-6-phosphate dehydrogenase
How many carbons are lost in the TCA cycle
2
Transketolase and Transaldolase
2 enzymes responsible for the interconversions in the PPP
probe DNA/hybridization
(DNA with known sequence) Added to a mixture of target DNA sequences, when it binds to target DNA sequences, it may provide evidence of the presence of a gene of interest. This binding is called hybridization.
hnRNA
(Heterogenous Nuclear RNA is the primary transcript formed - Then it becomes mRNA after posttranscriptional modifications
Vitamin B5
(panto)thenic acid
Bile contains...
-bile salts -pigments -cholesterol
CETP
-cholesteryl ester transfer protein -catalyzes the transition from IDL to LDL by transferring cholesteryl esters from HDL
functions of carbohydrates on bilayer
-glycoproteins+water can make coat around cell -signaling -recognition ex: ABO blood typing, immune system
Lipoprotein lipase (LPL)
-necessary for metabolism of chylomirons and very-low-density lipoproteins (VLDL) -can release free fatty acids from triacylglycerols in these lipoproteins
How many protons are pumped in the intermembrane space in complex II?
0
Steps of southern blot
1) DNA is cut by restriction enzymes 2) separated by gel electrophoresis 3) DNA fragments carefully transferred to a membrane, retaining their separation 4) Membrane is probed w/ many copies of ssDNA. The probe will bind to its complementary sequence and form dsDNA. -probes are labeled w/ radioisotopes or indicator proteins which can be used to indicate presence of a desired sequence
What happens in complex II?
1) Succinate gets oxidized to fumarate, reducing FAD to FADH2. 2) FADH2 gets oxidized, reducing the iron-sulfur subunit. 3) Reduced iron-sulfur subunit is reoxidized as it transfers electrons to coenzyme Q (ubiquinone) (which gets reduced)
3 possible fates of pyruvate
1) conversion to acetyl-CoA by PDH 2) conversion to lactate by lactate dehydrogenase 3) Conversion to oxaloacetate by pyruvate carboxylase
How does the malate-aspartate shuttles work?
1) cytosolic oxaloacetate (which can't pass thru inner-mitochondrial membrane) is reduced to malate, which can (catalyzed by cytosolic malate dehydrogenase) 2) accompanying this reduction is the oxidation of cytosolic NADH to NAD+ 3) Once malate crosses into the matrix, mitochondrial malate dehydrogenase reverses the reaction to form mitochondrial NADH. 4) Now that NADH is in the matrix, it can pass along its e- toe the ETC via complex I and generate 2.5 ATP per molecule
what 2 ways does cortisol elevate blood glucose levels?
1) inhibits glucose uptake in most tissues (muscle, lymphoid, fat) and increases hepatic output of glucose via gluconeogenesis 2) has a permissive function that enhances the activity of glucagon, epinephrine and other catecholamines
How high can the potential rise to during depolarization?
+35mV
1. Spontaneous at high temperatures, 2. Spontaneous, 3. Nonspontaneous, 4. Spontaneous at low temperatures
+delta H - delta H +delta S 1. ---------- 2. ----------- -delta S 3. --------- 4. -----------
The liver also participates in the processing of --- and ----, ----, ----, and ----.
, bile, urea, and toxins
Start codon sequence?
- AUG (mnemonic: Are you Going or comes from the word au·gur which means to foretell)
5' cap
- At the 5' end of the hnRNA a 7-methylguanylate triphosphate cap.. added during the process of transcription - It is recognized by ribosomes as the binding site - protects mRNA from degradation in the cytoplasm
Aminoacyl- tRNA Synthetase, how it works. where it attaches
- Each type of amino acid is activated by a different Aminoacyl tRNA synthetase that requires TWO high energy bonds from ATP, implying that the attachment of amino acids in an energy-rich bond - _______-_______ ______ transfers the activated amino acid to the 3' end of the tRNA at a conserved nucleotide sequence (CCA)
Metasis
A migration to distant tissues by the bloodstream or lymphatic system
Activators of alpha-ketoglutarate dehydrogenase complex (2)
ADP, Ca2+
What is an isomerase?
An enzyme that catalyzes the rearrangement of bonds in a molecule.
What is an allosteric enzyme?
An enzyme with multiple binding sites, an active site and one or more allosteric binding sites for regulators.
DNA Polymerases δ and ε
Assisted by PCNA protein, which assembles into a trimer to form the sliding clamp. The clamp helps to strengthen the interaction between these DNA polymerases and the template strand.
Ways to test concentration determination
BCA assay, Lowry reagent assay, and Bradford protein assay each test for protein
How are hydrolases named?
By sticking the name of what they hydrolyze before the-ase!
empirical formula of carbs?
C,n,(H₂O),m, where n = m IF it is a simple monomeric sugar m ≠ n if its a a complex sugar (in which simple sugars have linked w/ a loss of water)
threshold
Changes in consumption or activity must surpass a ---- to cause weight change. ( Its lower for weight gain than for weight loss).
What are four common ways an enzyme helps to improve the environment of a reaction?
Charge pH Stabilize the transition state Bring reactive groups closer to one another
Purines
Contain two rings in their structure: 1) Adenine (A) 2) Guanine (G)
Lagging strand
Copied in the direction opposite of the direction of the replication fork. The parental strand is 5' to 3', which means DNA cannot simply read and synthesize strand. Thus, primate must add new Okazaki fragments in 5' to 3' manner, and DNA polymerase then goes back over it in the 3' to 5' manner filling any gaps that need to be filled.
Crystallography is used ___% of the time and ____ is used the other part
Crystallography is used 75% of the time and NMR is used the 25%
Enzyme that synthesizes mRNA
DNA-dependent RNA polymerase
How do insulin and GLUT 4 interact?
Exercise in skeletal muscle & insulin stimulation (increase of insulin) leads to the increased movement of GLUT4 transporters to the membrane by mechanism involving exocytosis = leads to an increase in glucose intake
Glycolysis Step 3
Glycolysis step 3: phosphofructokinase (PFK-1) is transfers phosphate group from ATP to form fructose 1,6-bisphosphate. irreversible step
Where is the pyruvate dehydrogenase complex located in the cell? (be specific)
Mitochondrion matrix
What happens when antioncogens are mutated?
Mutations of antioncogens result in loss of tumor suppression activity, and therefore promote cancer.
Each codon represents only ____ amino acid; however, most amino acids are represented by _______ codons
ONE multiple
Termination
Process of Termination: - a release factor (RF) binds to the termination codon whenever in any of three stop codons move into the A site causing a water molecule to be added to the polypeptide chain. The addition of this water molecule allows peptidyl transferase and termination factors to hydrolyze the complete polypeptide chain from the final tRNA the polypeptide chain will then be released from the tRNA in the P site and the ribosomal subunits will dissociate
Nucleotide excision
Repair will fix problems with 2-30 nucleotides.
Telomeres: sequence? purpose? ATCG content?
Repeating units (TTAGGG) at the end of DNA that protect eukaryotic chromosomes. 1) Have high GC content that creates strong attraction at end of chromosome and serves as a protection "knotting off" 2) Linked to aging due to shortening w/ each replication
DNA Polymerase γ
Replicates mitochondrial DNA
Why are nucleotides high energy compounds?
The close proximity of negatively charged phosphate groups create high energy compound that is exothermic upon bond breaking.
Origin of replication
The initiation site of replication. this is where DNA unwinds. generation of new DNA proceeds in both directions, creating replication forks on both sides of the origin
Where are errors in proofreading most likely?
The likelihood of mutations in the lagging strand is considerably higher due to the lack of proofreading ability of DNA ligase.
prosthetic groups
Tightly bound cofactors or coenzymes that are necessary for enzyme function
What is coenzyme Q also known as?
Ubiquionone
Alternative method to make transgenic mice?
Use embryonic stem cell lines. 1) introduce cloned gene into culture 2) select for cells w/ transgene successfully inserted 3) inject altered stem cells into developing blastocyst 4)implant blastocyst in surrogate RESULT = Chimera (offspring will have 2 types of stem cells, the transgene ones, and the original blastocyst cells)
18.5 and 25, Lower than normal, 25 and 30
What is the Body Mass Index (BMI) Equation What is a normal BMI What is an underweight BMI What is an obese BMI
Supercoiling
Wrapping of DNA on itself toward telomeres during replication. Creates tension via positive supercoils.
succinate dehydrogenase
a flavoprotein (covalently bonded to FAD, the e- acceptor in this rxn.
what does succinyl-CoA acetoacetyl-CoA transferase (thiophorase) do?
activates the acetoacetate = converts acetoacetate to acetoacetyl-CoA (which can be broken down into 2 aceytl-CoA)
------ and ----- tissues both require insulin for effective uptake of glucose.
adipose tissue and resting skeletal muscle
adtrenal cortex secretes ______ adrenal medulla?
adrenal cortex = steroid hormones (glucocorticoids, mineralocorticoids, sex hormones) medulla = catecholamines
secondary active transport
aka coupled transport no direct ATP usage use energy from one particle going down its concentration gradient to drive different particles up its concentration gradient symport antiport
Vitamin: Definition and 2 types
an essential nutrient that can't be adequately synthesized by the body and thus must be consumed in the diet. 2 types = water soluble (excreted thru urine) and lipid soluble (accumulate in stored fat)
Red blood cells can only use glucose ---- for all their energy needs.
anaerobically
Long-chain fatty acids are absorbed...
as micelles and assembled into chylomicrons for release into the lymphatic system
Post absorptive state
at night body is in postabsorptive state, utilizing energy stores instead of food for fuel fatty acids are released from adipose tissue and used for energy
structure of sphingosine
basis of sphingolipids
Vitamin B7 (7-1) NOT TESTED ON MCAT
biotin
why is column chromatography further useful
can separate other macromolecules besides proteins. like nucleic acids
example of glucocorticoid?
cortisol
sucrose structure
glucose-alpha-1,2-fructose
glycogen synthesis and degradation occur primarily where?
in liver and skeletal muscles, although other tissues store smaller quantities.
spontaneous redox reactions = +/- dG? how about E?
negative dG positive E (electromotive force
pentose phosphate pathway
pentose phosphate pathway
Vitamin B6 NOT TESTED ON MCAT
pyridoxal phosphate
enantiomers, brief summed up def
same sugars, different optical familes
t/f ungated channels are always open
t
Preferred food of RBCs when well fed vs fasting
well fed = Glucose fasting = Glucose
alditol
when aldehyde group of an aldose is reduced to an alcohol
why do cells need NADPH? (3 main reasons)
-Biosynthesis, mainly of fatty acids and cholesterol -Assisting in cellular bleach production in certain white blood cells. -maintenance of a supply of reduced glutathione to protest against reactive oxygen species which means to protect cells from free radicals from oxidative damage caused by peroxides.
What are the major monosaccharides that can be used in glycolysis... what is glycolysis?
-Glucose is the major monosaccharide that enters the pathwya but others (ie galactose and fructose) can be used. it is a cytoplasmic pathway all cell can carry out that converts glucose into two pyruvates, releasing a modest amount of energy captured in 2 substrate level phosphorylations and one oxidative reaction.
5 highly regulated enzymes in glycolysis:
-Hexokinase and Glucokinase -PhosphoFructoseKinase-1 and PhosphoFructoseKinase-2 -Glyceraldehyde-3-P deydrogenase -3-PhosphoGlycerate kinase -Pyruvate Kinase
Fatty-acyl-CoA synthetase
-activates fatty acids by attachment to CoA -product is referred to as fatty acyl-CoA or acyl CoA (ie palmitoyl-CoA has 16 carbon acyl group)
Acetyl-CoA shuttling
-after large meal, acetyl-CoA accumulates in mitochondrial matrix and needs to be moved to cytosol for fatty acid biosynthesis -acetyl-CoA = product of the pyruvate dehydrogenase complex and couples with oxaloacetate to form citrate (TCA) -isocitrate dehydrogenase is the rate-limiting enzyme of citric acid cycle; as cell becomes energetically satisfied, it slows the citric acid cycle which causes citrate accumulation -citrate diffuses across the mitochondrial membrane -in cytosol, citrate lyase splits citrate back into acetyl-CoA and OAA -OAA returns to mitochondrion to continue moving acetyl-CoA
Lipoproteins
-aggregates of apolipoproteins and lipids -how triacyl glycerol and cholesterol are transported in blood -named according to their density, which increases in direct proportion to the percentage of protein in the particle
Apolipoproteins
-aka apoproteins -form the protein component of lipoproteins -are receptor molecules involved in signaling -control interactions between lipoproteins
Fatty acid synthase
-aka palmitate synthase -large multienzyme complex in cytosol containing acyl carrier protein (ACP) -ACP requires pantothenic acid (vitamin B5) -also requires NADPH to reduce the acetyl groups added to the fatty acid
glucogenic AA
-all AAs except leucine and lysine -can be converted into intermediates that feed into GNG (gluconeogenesis).
Two important essential fatty acids
-alpha-linolenic acid -linoleic acid -important for maintaining cell membrane fluidity -humans can only synthesize a few unsaturated fatty acids, so the rest come from diet
Micelles
-clusters of amphipathic lipids that are soluble in the aqueous environment of the intestinal lumen -free fatty acids, cholesterol, 2-monoacylglycerol, and bile salts contribute to their formation -vital for digestion, transport, absorption of lipid soluble substances starting from dodenum to ileum
Methylmalonyl-CoA mutase
-converts methylmalonyl-CoA to succinyl-CoA -requires cobalamin (vitamin B12) -succinyl-CoA can go through TCA or be converted to malate to enter gluconeogenic pathway in cytosol
Propionyl-CoA carboxylase
-converts propionyl-CoA to methylmalonyl-CoA -requires biotin (vitamin B7)
Odd-numbered chain oxidation
-final cycle = yields one acetyl-CoA and one propionyl-CoA from the final 5-carbon fragment
Ketone bodies
-formed in the fasting state, when liver converts excess acetyl-CoA into ketone bodies -the ketone bodies are acetoacetate and 3-hydroxybutyrate -can be used for energy in various tissues
HDL
-high-density lipoprotein -synthesized in liver and intestines; released as dense, protein rich particles in the blood. -contain apolipoproteins for cholesterol recovery -main functions is cholesterol recovery: cleaning up of excess cholesterol from blood vessels for excretion -also delivers some cholesterol to steroidogenic tissues
Hormone-sensitive lipase
-hydrolyzes triacylglycerols yielding fatty acids and glycerol -activated by epinephrine, cortisol, and a fall in insulin levels -released glycerol may be transported to the liver for glycolysis or gluconeogenesis -doesn't respond to glucagon -effective in adipose cells but need LPL for metaboism of chylomicrons and VLDL
Write out the net reactions of the Pyruvate Dehydrogenase Complex, citric acid cycle ATP production
-in addition to the picture, glycolysis yields 2 ATP and 2 NADH (so another 7 molecules of ATP) so net yield for 1 glucose molecule from glycolysis and oxidative phosphorylation is 30-32 ATP
Regulation of cholesterol syntehsis
-inhibited by increased cholesterol (feedback inhibition) -stimulated by insulin -also dependent on HMG-CoA reductase gene expression in the cell
IDL
-intermediate-density lipoprotein, aka VLDL remnant -transition between triacylglycerol and cholesterol transport -some IDL = reabsorbed up by the liver by apolipoproteins on its exterior, some is further processed in the bloodstream
Chylomicrons
-least dense lipoproteins (highest fat:protein ratio) -highly soluble in both lymphatic fluid and blood -function in transport of dietary triacylglycerol, cholesterol, and cholesteryl esters to other tissues -assembled in the intestinal lining = results in nascent chylomicrons that contain lipids and apolipoproteins
LCAT
-lecithin-cholesterol acyltransferase -enzyme found in bloodstream that is activated by HDL apoproteins -adds a fatty acid to cholesterol to produce soluble cholesteryl esters (present in HDL... HDL cholesteryl esters can then be distributed to IDLs which become LDLs by acquiring these cholesteryl esters)
Bile is secreted by the... and stored in the ...
-liver -gallbladder
Thoracic duct
-long lymphatic vessel that empties into left subclavian vein at the base of the neck -responsible for the re-entry of chlyomicrons into the bloodstream
Fatty acids
-long-chain carboxylic acids -carboxyl carbon is carbon 1 -carbon 2 is referred to as alpha-carbon -occur as salts that are capable of forming micelles or are esterified to other compounds
LDL
-low-density lipoprotein -primarily transports cholesterol for use by tissues in biosynthesis and cell membrane maintenance
Urea cycle
-occurs in the liver -primary way of removing excess nitrogen from the body
Ketogenesis
-occurs in the mitochondria of liver cells when excess acetyl-CoA accumulates in the fasting state -requires the enzyme HMG-CoA synthase and HMG-CoA lyase -acetone = minor side product, not used as energy in tissues
Fatty acid synthesis
-occurs primarily in liver and products are transported to adipose tissue for storage (adipose tissue can also synthesize smaller quantities of fatty acids -synthesis occurs in the cytoplasm from acetyl-CoA transported out of the mitochondria -includes five steps: activation, bond formation, reduction, dehydration, and second reduction -repeated eight times to form palmitic acid (only fatty acid humans can synthesize)
Enzymes secreted by the pancreas
-pancreatic lipase -colipase -cholesterol esterase
steps of fatty acid synthase
-performs the following steps: 1. activation of growing chain and malonyl-CoA with ACP 2. bond formation between these activated molecules (releases CoA and CO2) 3. reduction of a carbonyl to a hydroxyl group (req. NADPH) 4. Dehydration (releases H2O) 5. Reduction to a saturated fatty acid (req. NADPH) REPEAT again and again until the molecule you want (ie palmitate) is made
Other fatty acid catabolisms
-peroxisomal beta-oxidation -alpha-oxidation of branched-chain fatty acids - ω oxidation in the ER, producing dicarboyxlic acids
beta-oxidatoin
-primary form of fatty acid catabolism -occurs in the mitochondria (also sometimes in peroxisome) -stimulated by glucagon -inhibited by insulin -opposite of fatty acid synthesis, by understaning 1 process you can answer questions about both
Acetyl-CoA carboxylase
-rate-limiting enzyme of fatty acid synthesis -activates acetyl CoA in the cytoplasm -requires biotin and ATP to function -adds CO2 to acetyl-CoA to form malonyl-CoA -activated by insulin and citrate
Ketolysis
-regenerates acetyl-Coa for use as an energy source in peripheral tissues -requires the enzyme succinyl-CoA acetoacetyl-CoA transferase (thiophorase), which is only found in tissues outside the liver -3-hydroxybutyrate is oxidized to acetoacetate
Fatty acid entry into mitochondria
-short-chain fatty acids (2-4 carbons) and medium chain fatty acids (6-12) carbons diffuse freely into mitochondria -long-chain fatty acids require transport via a carnitine shuttle Note: very long chain fatty acids (20+ carbons) are oxidized elsewhere
Nontemplate synthesis
-synthesis that do not rely directly on the coding of a nucleic acid -carbohydrate and lipid synthesis are most common examples
Emulsification
-the mixing of two normally immiscible liquids (in this case fat and water) -formation of an emulsion = increases the surface are of the lipid, which permits greater enzymatic interaction and processing -occurs upon entry into the duodenum -aided by bile
2,3-BPG effect on oxygen dissociation curve.
-this effect of 2,3-BPG is seen in the oxygen dissociation curve for HbA. the right shifting of the curve is sufficient for allowing unloading of oxygen in tissues but still allows 100% saturation in lungs. abnormal increase in erythrocyte 2,3 BPT might shift the curve far enough so that HbA is not fully saturated in lungs
Nomenclature rules for fatty acids
-total number of carbons is given along with number of double bonds, written as carbons:double bonds -further description can be given by indicating position and isomerism (cis or trans) of the double bonds in unsaturated fatty acid
Triacylglycerol synthesis
-triacylglycerols = storage form of fatty acids -formed by attaching three fatty acids (as fatty acyl-CoA) to glycerol -occurs primarily in the liver (then packaged and sent to adipose in VLDL) and somewhat in adipose tissue
Cholesterol
-ubiquitous component in human body -plays major role in synthesis of cell membranes, steroid hormones, bile acids, bile salts and vitamin D
Omega ( ω) numbering system
-used for unsaturated fatty acids - ω describes the position of the last double bond relative to the end of the chain and identifies the major precursor fatty acid
Enoyl-CoA isomerase
-used in monounsaturated fatty acids -rearranges cis double bonds at the 3,4 position to trans double bonds at the 2,3 positon once enough acetyl-CoA has been liberated to isolate the double bond w/in the first 3 carbons
2,4-dienoyl-CoA reductase
-used in polyunsaturated fatty acids -convert two conjugated double bonds to just one double bond at the 3,4 position, where it will undergo same rearrangement as monounsaturated
VLDL
-very-low-density lipoprotein -produced and assembled in liver cells -transport triacylglycerols from liver to tissues -contain fatty acids that are synthesized from excess glucose or retrieved from chylomicron remnants
Different ways to classify carbs? (4)
1) # sugar moieties that make them up 2) # carbons in each sugar 3) functional groups present on the molecule 4) stereochemistry of the sugar
Elongation (3 steps)
1) A site holds incoming aminoacyl tRNA 2) P site holds the tRNA that carries the growing polypeptide chain by formation of a peptide bond via peptidyl transferase, an enzyme from the LARGE SUBUNIT with energy from GTP 3) E site is where the inactivated tRNA is exited from the ribosome
Aromatic criteria:
1) Cyclic 2) Planar 3) Conjugated (alternating double/single bonds or lone pairs, creating at least one unhybridized p0orbital for each atom in the ring!) 4) Huckel's rule: 4n + 2 pi electrons
Why are telomeres necessary? (2)
1) DNA replication cannot extend all the way to the end of the chromosome and as a result, we lose sequences of information with each round of replication. 2) their high GC content creates exceptionally strong strand attractions at the end of the chromosomes to prevent unraveling, they "knot off" the end of the chromosome
What do the five histones do?
1) H2A, H2B, H3, and H4 (the first 4) form a protein complex and have chromosomes wind around them. about 200 base pairs of DNA are wrapped around protein complex. 2) H1 seals off the ends of the DNA as it enters and leaves the nucleosome, adding stability to the structure
What factors can cause DNA denaturation? (3)
1) Heat 2) alkaline pH 3) Chemicals like urea or formaldehyde
DNA replication steps:
1) Helicase- unwinds the parental double helix 2) DNA topoisomerase - upstream of helices alleviating torsional strain 3) Single-strand binding proteins (SSBP) stabilize unwound DNA, aided by DNA gyrase. 4) Primase synthesizes a short RNA primer for DNA polymerase to bind to in the 5' to 3' direction to start replication on each strand. 5) DNA polymerase synthesizes the leading strand in 5' to 3' direction while the lagging strand is made discontinuously by primate making short pieces and then DNA polymerase extending these to make Okazaki fragments. 6) DNA ligase joins the Okazaki fragments together
Stability to DNA?
1) Intermolecular hydrogen bonds and hydrophobic interactions between base pairs 2) Delocalization of electrons in p orbitals of base pairs 3) Increased entropy due to sequestered hydrophobic base pairs + exposed - charged phosphate groups.
Why don't RBCs have mitochondria?
1) Maximizing volume available for hemoglobin, the primary oxygen carrying protein 2) Stopping the red blood cell from utilizing the oxygen it's suppose to be carrying to oxygen depleted bodily tissues
Ethical issues of biotechnology?
1) Pathogen resistance 2) Selecting child's traits 3) unethical gene therapy 4). Communicating with family about disease-causing gene
Acetyl-CoA regulates what 2 enzymes? How
1) Pyruvate dehydrogenase 2) pyruvate carboxylase (mitochondrial enzyme that uses pyruvate) -the buildup of acetyl-CoA (happens during B-oxidation) causes a shift in metabolism: pyruvate is no longer convertedinto acetyl-CoA (to enter citric acid cycle) rut rather into oxaloacetate (to enter gluconeogenesis
regulators of the PDH complex (3)
1) Pyruvate dehydrogenase kinase = phosphorylates PDH which inhibits acetyl-CoA production (happens when ATP levels RISE) 2) Pyruvate dehydrogenase phosphatase = removes phosphate from PDH so acetyl CoA production is reactivated (happens in response to high levels of ADP) 3) Acetyl CoA has negative feedback on its own production
Summary of RNA Pol I RNA pol II RNA Pol III (function and location)
1) RNA polymerase I - located in the nucleolus and synthesizes rRNA 2) RNA polymerase II - located in the nucleus and synthesizes pre-mRNA (hnRNA) and snRNA 3) RNA polymerase III - located in the nucleus and synthesizes tRNA and some rRNA
Watson-Crick model (5 key features
1) Two stands of DNA are anti-parallel (5'-3' and 3' to 5') 2) Sugar-phospahte backbone is on outside (nitrogenous bases are on the inside) 3) Complementary base paring (A-T, G-C) 4) Due to complementary pairing, [A]=[T],[G]=[C] 5) Right handed double helix
How do enzymes work to lower Ea?
1) can provide favorable microenvironment in terms of charge or pH 2) stabilize transition state 3) bring reactive groups nearer to one anotehr in the active site
Why are lipids good for storing energy?
1) carbons atoms of fatty acids are more reduced than those of sugars (which contain alcohol groups) 2) tracylglycerols are hdyrophobic = do not draw in water or require hydration for stability (helps decrease their weight, ie in comparison to hydrophilic polysaccharides)
Exact steps in Complex I
1) e- of NADH transferred to FMN -results in-> NAD+ and FMNH2 2) Flavoprotein becomes reoxidized while the iron-sulfur subunit is reduced 3) the reduced iron-sulfur subunit donates the e- t received from FMNH2 to coenzyme Q (aka ubiquinone). 4) Coenzyme Q becomes CoQH2. 4 protons moved to intermembrane space Net reaction = NADH + H+ + CoQ -> NAD+ + CoQH2
2 examples of votage gated channels
1) excitable cells ,such as neurons, possess voltage gated csodium channels = closed under resting conditions, but membrane depolarization causes a protein conformation change that allows them to quickly open and then quickly close as the voltage increases 2) voltage gated,nonspecific sodium potassium channels are in cells of the sinoatrial node of the heart where they serve as the pace maker current; as the voltage drops, these channels open to bring the cell back to threshold and fire another action potential
glycogenesis process
1) glucose 6-p is converted to glucose 1-p. 2) glucose 1-p is activated by coupling to a molecule of uridine diphosphate (UDP) which permits integration into glycogen chain by glycogen synthase 3) this activation occurs when glucose 1-p interacts w/ uridine triphosphate (UTP) forming UDP-glucose and a pyrophosphate
what 2 things does the branching enzyme do?
1) hydrolyzes one of the alpha-1,4 bonds to release a block of oligoglucose which is then moved and added in a slightly different location 2) forms an alpha-1,6 bond to create a branch
3 post transcriptional modifications. necessary for what?
1) splicing (Intron/exon) 2) 5' capping 3) 3' poly A tail necessary for the RNA to leave the nucleus
2 major systems of biosignaling
1) take advantage of existing gradients (ion channels) 2) second messenger cascades (enzyme linked receptors/G protein coupled receptors
DNA sequencing
1) template DNA 2) Primers 3) appropriate DNA polymerase 4) deoxyribonucleotide triphosphates (normal) 5) dideosyribonucleotide (ddATP, ddCTP, etc)...no -OH on C-3', just H instead) DNA sequencing in which ddNTP's randomly add and terminate sequence. Then can separate by gel electrophoresis (by size) and read ddNTP ends for sequence.
Advantages of using embryonic stem cell lines?
1) the cloned genes can be introduced in cultures, and then one can select for cells w/ the transgene successfully inserted. 2) chimeras are evident if the two cell lineages come from mice w/ different coat colors (the offspring will have patchy coats). if this is the case, the chimeras can then be bred to produce mice that are heterozygous for the transgene and mice that are homozygous for the transgene.
how does glycerol 3-p shuttle work?
1) the cytosol contains 1 isoform of glycerol 3-phosphate dehydrogenase, which oxidizes cytosolic NADH to NAD+ while forming glycerol 3p from DHAP 2) on the outer face of the inner mitochondrial membrane, there exists another isoform of glycerol-3p dehydrogenase that is FAD dependent. this mitochondrial FAD is the oxidizng agent and ends up being reduced to FADH2 3) Once reduced, FADH2 proceeds to transfer its e- to the ETC via complex II, generating 1.5 ATP for every molecule of cytosolic NADH
Initiation (3 steps)
1) the small ribosomal subunit binds to the mRNA (at Shine-Dalgarno in prokaryotes and 5' cap in eukaryotes) 2) The charged initiator tRNA binds to AUG start codon (Methionine in eukaryotes and N-formylmethionine in prokaryotes = fMet) through base-pairing with its anticodon within the P site (!!!) of the ribosome 3) the large subunit then binds to the small subunit as assisted by initiation factors (IFs)
3 types of sphingolipids and their characteristics
1. Sphingomyelin -phospholipid; has a func group of phosphatidylcholine/ethanolamine 2. Glycosphingolipid -glycolipid; sugars 3. Ganglioside -glycolipid; oligosaccharide and N-acetylneuraminic acid (NANA)
Which component of membrane lipids contribute to their structural role in membranes?
1. amphipathic: allows for formation of bilayers in aqueous solution 2. fatty acid tails form the bulk of the phospholipid bilayer
Roles of quaternary structures
1. be more stable by reducing the surface area of the protein complex 2. reduce amount of DNA needed to encode the protein complex 3. bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction 4. induce cooperativity or allosteric effects = one subunit can undergo conformational or structural changes which either enhance or reduce the activity of he other subunits
How many ATP molecules do NADH that go through the glycerol-3-phosphate shuttle generate?
1.5
How many ATP molecules are generated by each FADH2? NADH?
1.5, 2.5
Four steps of beta-oxidation
1.oxidation of fatty acid to form a double bond (creates FADH2) 2. hydration of the double bond to form a hydroxyl group (req. H2O) 3. oxidation of the hydroxyl group to form a carbonyl; called a beta-ketoacid (generates NADH) 4. splitting of the beta-ketoacid into a shorter acyl-CoA and acetyl-CoA (req. CoA-SH) -process continues until chain has been shortened to two carbons (for even chained fatty acids)
How many cytochrome C molecules are needed to transfer the electrons from CoQH2 to cytochrome C?
2
How many protons are pumped in the intermembrane space in complex IV?
2
pka of carboxyl group?
2
Overall reaction for Complex IV?
2 cytochrome c [w/ Fe2+] + 2H+ + 1/2 O2 --> 2 cytochrome c [w/ Fe3+] + H2O
What is the Q cycle?
2 e- are shuttled from a molecule of ubiquinol (CoQH2) near the intermembrane space to a molecule of ubiquinone (CoQ) near the mitchondrial matrix. another 2 e- are attached to the heme moieties, reducing two molecules to cytochrome c
products of glycosis?
2 pyruvate, 2 NADH, 2 net (4 total) ATP
2,3-BPG in fetal Hb
2,3 BPG binds well to HbA but not to fetal hemoglobin (HbF). Thus, HbF has a higher affinity for oxygen than maternal HbA = allow for transpacental passage of oxygen from mother to fetus
How many ATP molecules do NADH that go through the malate-aspartate shuttle generate?
2.5
How many amino acid are in eukaryotic proteins? Each of which is represented by at least _____codon.
20 amino acids, one
cholesterol abundance in bilayer (by mass and by mole fraction)
20% of cell membrane by mass 50% by mole fraction ensures membrane fluidity
Prostaglandins
20-C molecules that are unsaturated carboxylic acids derived from arachidonic acid and contain 5 carbon ring;
4 strands of rRNA present in the ribosome?
28S 18S 5.8S 5S
Irreversible enzymes
3 enzymes in the pathway catalyze reactions that are irreversible. this keeps the pathway moving in only 1 direction. BUT the liver must be able to generate new glucose from other biomolecules thru gluconeogenesis (basically revers of glycolysis) the 3 irreverisble enzymes = -glucokinase or hexokinase -PFK-1 -Pyruvate Kinase
how much energy does ATP provide under physiological conditions
30kJ/mol (this is at pH7 and w/ excess magnesium)
Biological T optima in humans
37 C, 310 K, 98.6 F
Tertiary Structure
3D shape; determined by hydrophilic and hydrophobic interactions between R groups of amino acids; the hydrophilic N-H and C=O bonds found in the polypeptide chain get pulled in by these hydrophobic residues. the hydrophilic bonds can then form electrostatic interactions and hydrogen bonds that further stabilize the protein from the inside
How many protons are pumped in the intermembrane space in complex I?
4
How many protons are pumped in the intermembrane space in complex III?
4
How many and which cofactors/coenzymes are involved with metabolic reactions?
4! thiamine (decarboxylation), biotin (carboxylation), magnesium (ATP), and NAD (for oxidation)
What are 3 things a vector has?
4) Vectors contain the origin of replication, the fragment of interest, and at least one gene for antibiotic resistance.
How many NADH and FADH2 molecules are formed by the pyruvate dehydrogenase complex and the citric acid cycle?
4, 1
Messenger RNA is synthesized in the _______ direction and ribosomes translates the mRNA in the _______ direction, as it synthesizes the protein from the _________ _________ (___-terminus) to the ________ _________ (___-terminus)
5'→3' direction, 5'→3' direction, amino terminus (N-terminus), carboxy terminus (C-terminus)
Each codon consists of three bases thus there are how many codons
64
What pH is considered neutral biologically?
7.4, not 7
pka of amino group?
9
How many kcal/gram does fat, carbs, and proteins have?
9 kcal/gram, 4 kcal/gram, 4 kcal/gram
Fat-Soluble Vitamins and their Functions
A (carotene) - retinal: vision; retinoic acid: epithelial development D (cholecalciferol) - calcitriol: calcium and phosphate regulation E (tocopherols) - antioxidants, using aromatic ring K (phylloquinone and menaquinones) - posttranslational modification of prothrombin, addition of calcium-binding sites on many proteins
Deoxyribonucleic acid (DNA)
A biological macromolecule that encodes the genetic information for living organisms and is capable of self‐replication and the synthesis of ribonucleic acid (RNA). DNA is a polydeoxyribonucleotide that is composed of many monodeoxyribonucleotides linked together
colloid
A mixture containing small, undissolved particles that do not settle out.
Nucleotides
A nucleoside to which one or more phosphate groups are added at C-5' of pentose. High energy compounds.
What does a phosphorylase do that a hydrolase does not?
A phosphorylase breaks bonds using an inorganic phosphate instead of water. the glucose 1-p formed by glycogen phosphorylase is converted to glucose 6-p by the same mutase used in glycogen synthesis
Vector
A piece of nucleic acid. Usually bacterial or viral plasmids that can be transferred to a host bacterium after insertion of DNA of interest.
Replication complex or Replisome
A set of specialized proteins that assist the DNA polymerases.
Chromosomes
A single piece of coiled DNA and associated proteins found in linear forms in the nucleus of eukaryotic cells and circular forms in the cytoplasm of prokaryotic cells; contains genes that encode traits. Each species has a characteristic number of chromosomes.
Fat soluble vitamins
A, D, E, and K
Major fat soluble vitamins?
ADEK
Vitamin A: Aka, structure, use
AKA: Carotene unsaturated hydrocarbon that is important in vision, growth, development, and immune function;
Terpenoids: Aka?
AKA: isoprenoid derivatives of terpenes that have undergone oxygenation or rearrangement of the carbon skeleton
What is the AP site? AKA?
AP = Apurinic/apyrimidinic site aka abasic site.
# H bonds between AT? GC?
AT = 2 H bonds GC = 3 H bonds
What enzyme synthesizes ATP using the proton-motive force?
ATP synthase
Inhibitors of isocitrate dehydrogenase (2) activators?
ATP, NADH (note: ADP and NAD+ are allosteric activators = enhance affinity of enzyme for its substrates)
Inhibitors of alpha-ketoglutarate dehydrogenase complex (3)
ATP, NADH, succinyl-CoA
Inhibitors of citrate synthase (4)
ATP/NADH,succinyl-CoA, citrate = all allosteric inhibitors
The pyruvate dehydrogenase complex is inhibited by what two molecules?
Acetyl-CoA, NADH. which can accumulate if the e- transport chain is not properly functioning
Vitamin D: Aka? purpose?
Aka: cholecalciferol can be consumed or formed in a UV-driven reaction in the skin; lack of this can result in rickets
How does alcohol form acetyl-CoA?
Alcohol dehydrogenase and acetaldehyde dehydrogenase convert it to acetyl-CoA
Hypertension and Aldosterone
Aldosterone is a hormone which triggers greater reabsorption of water from the kidneys. This causes increases in both blood volume and pressure and this can cause hypertension. Aldosterone is a mineralocorticoid that whose release may be caused by stress OR may be caused by a chain of reactions in which Angiotensin I is converted by Angiotensin-converting Enzyme (ACE) into Angiotensin II which directly triggers blood vessel constriction AND the release of aldosterone. A way to treat hypertension is via the prescription of an ACE inhibitor. It thus prevents Angiotensin II from trigger blood vessel constriction, but it also prevent Angiotensin II from triggering the release of aldosterone which increases blood volume and pressure.
How D/L naming works
All D-sugars have the HYDROXIDe of their highest numbered chiral center on the RIGHT All L sugars have the hydroxide on the left
Are all DNA replication processes from 5' to 3'?
All processes (DNA synthesis/repair, RNA transcription/translation <- the reading of codons) in the 5' to 3' direction except DNA polymerase reading direction (which is 3' to 5'
DNA topoisomerases
Alleviate the torsional stress and reduce the risk of strand breakage in DNA by introducing negative supercoils.
What are the two types of allosteric binders?
Allosteric inhibitors = make active site LESS accessible Allosteric activators = make active site MORE accessible
Alternative Splicing
Alternativesplicing is a process in which the primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene (more proteins with limited number of genes) ie we make apprx 100,000 proteins from ~20-25,000 genes
Amino acids w/ acidic side chains will have pI values (above/below) 6 AAs w/ basic side chains will have pI value (above/below) 6
Amino acids w/ acidic side chains will have pI values BELOW 6 AAs w/ basic side chains will have pI value ABOVE 6
immunoglobulin. overall shape and usage
An antibody (AB), also known as an immunoglobulin (Ig), is a large, Y-shape protein produced by plasma cells (B cells) that is used by the immune system to identify and neutralize pathogens such as bacteria and viruses and then recruit other cells to help
What chemical property do these bases posses?
Aromaticity!
What is most common form of DNA (ie A, B, Z?)
B-DNA
What do you think would happen if structure of collagen was messed up? Example
BAD!! ex: osteogenesis imperfecta = brittle bone disease. Collagen - a major component of bone - forms a unique and specific secondary helical structure based on the abundance of AA glycine. The replacement of glycine w/ other AAs can cause improper folding of the collagen protein and cell death, leading to bone fragility
Under intermediate conditions (2 < pH < 9), will AA's (w/o ionizable side chains) be + or - charged?
BOTH, will be zwitterion!!! carboxylic acids become deprotonated at neutral pH, forming zwitterions--two charges neutralize each other; molecule that has both positive and negative charge; pH is above pKa of carboxylic acid so it is deprotonated, but pH is below pKa of amine group so, protonated
Bacterial origin of replication vs Eurkayote formation?
Bacteria have circular dsDNA: -form two circular molecules. Eukaryotic formation: One linear sequence requires multiple origen sites. As they move toward each other, sister chromatid are created and remain bound to centromere.
Where do restriction enzymes come from? What was their original purpose
Bacteria. they act as part of a restriction and modification system that protects the bacteria from infection by DNA viruses
Uncompetitive inhibition Line Weaver Burke Values
Because Km decreases, -1/Km gets larger and further from zero. The decrease in Vmax causes a proportional increase in 1/Vmax, so the y intercept is higher. The two lines will be parallel and not intersect anywhere
Why does a catalyst, by neither affected H, S, or Stand. G, not affect Keq?
Because Stand. G is a constant and Keq is a constant in accordance with the conditions which gave Stand. G to begin with (T).
Competitive Inhibition Line Weaver Burke Values
Because Vmax stays the same, 1/Vmax stays the same (all lines will pass through same point on the y axis) Because Km increases, -1/Km gets smaller and approaches zero (competitive line will start closer to zero and hit same point on y axis, so steeper line)
open systems
Biological systems are ----- because they can exchange both energy and matter with the environment.
What charge does an RNA backbone have?
Both DNA and RNA backbones carry a negative charge due to phosphate groups.
T/F: mRNA is complementary and parallel to the DNA template strand
Bothish, it is complementary and ANTIparallel to the template strand
Reanneal
Bringing single-stranded DNA back together. 1) Must be performed slowly to get correct use pairing 2) Important step in PCR
Write the reduction and oxidation half reactions of the following oxidation-reduction reaction: (lactic acid formation) C3H4O3 +NADH ---> C3H6O3 + (NAD+)
C3H4O3 + (2H+) + (2e-) ----> C3H6O3, reduction; NADH ----> (NAD+) + (H+) + 2e-, oxidation
What is a by-product of the formation of acetyl-CoA from pyruvate?
CO2
When someone has high blood sugar, the GLUT4 transporters will permit ___(increase,decrease, etc)_ rate of glucose influx... why?
CONSTANT rate of glucose influx bc they will be saturated (zero order kinetics)
Pyrimidine Mnemonic
CUT the Pye (as C, U, and T are pyrimidines). Pie is one circle, like pyrimidines.
cadherins
Calcium-dependent adhering of cells a group of glycoproteins that mediate calcium-dependent cell adhesion; often hold similar cell types together, such as epithelial cells; are type-specific
Ketoses
Carbohydrates that contain a ketone group as their most oxidized functional group
Aldoses
Carbohydrates that contain an aldehyde group as their most oxidized group
From what end does beta-oxidation occur (breaking of 2 carbon units)
Carboxyl-end
catabolic vs anabolic
Catabolic reactions usually release energy that is used to drive chemical reactions. Anabolism refers to chemical reactions in which simpler substances are combined to form more complex molecules. Anabolic reactions usually require energy. Anabolic reactions build new molecules and/or store energy.
The ideal temperature for a reaction changes depending on whether or not a what is present?
Catalyst. Reactions will typically favor very high temperatures, but if there is an enzyme involved, the enzyme will denature if the temp is too high!
Mismatch repair: used in which phase of cell cycle? What happens?
Cells also have machinery in G2 phase of cell cycle for mismatch repair. Enzymes detect and remove errors in replication that were missed during S phase.
Duplicating
Cells can also increase the expression of gene product by _________the relevant gene in series on the same chromosome
Free energy
Changes in _______ energy (delta G) provide information about chemical reactions and can predict whether a chemical reaction is favorable and will occur
Heterochromatin
Chromatin that remains compact and appears dark under light microscopy. 1) Transcriptionally silent 2) Often has DNA with repetitive sequence
summary of lipoprotein classes
Chylomicrons and VLDL primarily carry triacylglycerols but also small quantities of cholesteryl esters LDL and HDL primarily cholesterol transport
Step 1 of TCA cycle?
Citrate formation. acetyl-CoA and oxaloacetate undergo a condensation rxn to form citryl-CoA. then, hydrolysis of citryl-CoA yields citrate and CoA-SH (catalyzed by citrate synthase). this second step energetically favors the formation of citrate and helps the cycle revolve in the forward direction
3 control pts of citric acid cycle?
Citrate synthase isocitrate dehydrogenase a-ketoglutarate dehydrogenase complex
Name of complex III. generally what happens?
CoQH2-cytochrome C oxidoreductase aka cytochrome reductase generally facilitates the transfer of e- from coenzyme Q to cytochrome c the Q cycle
NAD and NADP are called enzyme whats?
Cofactors! Also called electron carriers because they can take electrons and hold on to them for later!
Four types of reversible inhibition
Competitive, noncompetitive, mixed, uncompetitive
Optical isomers=? aka?
Compounds that have the same chemical formula, but differ from spatial arrangement of their component atoms aka stereoisomers
What type of reaction is the formation of citryl-CoA from acetyl-CoA and oxaloacetate?
Condensation
On test day, the concentration of the enzyme will always be what?
Constant!
Genomic libraries
Contain large fragments of DNA, including both coding and noncoding regions on the genome. They cannot be used to make recombinant proteins or for gene therapies.
Dideoxyribonucleotide
Contains a hydrogen at the C-3'
An atypical MM graph due to enzyme BLANK is shaped how?
Cooperativity! S-shaped, or sigmoidally shaped
Knockout mice
Created by deleting a gene of interest
Name of complex IV? what else is in it?
Cytochrome C oxidase -includes subunits of cytochrome a, cytochrome a,3, and Cu2+ ions. together, cytochromes a and a3 make up cytochrome oxidase
What happens in complex IV?
Cytochrome oxidase gets oxidized and oxygen gets reduced to water
Important intermediates of glycolysis (3)
DHAP 1,3-bisphosphoglycerate (1,3-BPG) phosphoenolpyruvate
What type of gel is used for DNA vs Protein electrophoresis
DNA = Agarose gels Proteins = Polyacrylamide (usually, at least)
B-DNA: #bases/turn and distance btwn turns? left/right handed?
DNA forming a right-handed helix. 1) Makes turn every 3.4 nm and ~10 bases 2) Turns create major and minor grooves and are sites of protein binding.
How to make a DNA library?
DNA fragments, often digested randomly, are cloned into vectors and can be utilized for further study.
Name of prokaryotic enzyme that adds DNA after primer has been removed
DNA polymerase I
Name of prokaryotic enzyme that removes the RNA that was used as a primer?
DNA polymerase I
Name of main PROKARYOTIC DNA polymerase?
DNA polymerase III
Name of EUKARYOTIC enzyme that adds DNA after primer has been removed
DNA polymerase δ
cis vs trans regulators
DNA regulatory base sequences (promoters, enhancers, response elements) are known as cis regulators bc the yare in same vicinity as the gene they control TFs, however, have to be produced and translocated back into the nucleus, so they are called trans regulators, bc they travel thru the cell to their point of action
At what stage does DNA replicate?
DNA replicates in S phase. At this phase, the majority of DNA needs to be uncondensed and accessible to make the process more efficient.
Recombinant DNA
DNA that has been formed artificially by combining constituents from different organisms.
Chromatin
DNA that is wound around a group of small basic proteins
Central dogma of Molecular Biology
DNA→RNA→proteins
spingolipids
DON"T have glycerol. but similar in structure to glycerophospholipids (have hydrophilic region and two fatty acid-derived hydrophobic tails)
- The genetic code is _________ because more than one codon can specify an amino acid - except for the amino acids _______ and _______
Degenerate, methionine, tryptophan
Oxidoreductases may be recognized by what common names?
Dehydrogenase and reductase.
Type I diabetes and Type II diabetes cause?
Diabetes mellitus is caused by diruption of insulin/GLUT4 mechanism Type I: insulin is absent and can't stimulate the inuslin receptor Type II: the receptor becomes insensitive to insulin and fails to bring GLUT4 transporters to cell surface in both cases, glood glucose rises leading to immediate symptoms (increase urination, increased thirst, ketoacidosis_ and long term symptoms (blindness, heart attacks, strokes, nerve damage)
Epimers
Diastereomers that differ in configuration at exactly one chiral center only
__ and __ canbe converted into glucose in the liver.
Dietary Fructose and galactose
Examples of zymogens
Digestive enzymes such as trypsinogen and pepsinogen as well as apoptotic enzymes (caspases)
Chemiosmotic coupling
Direct relationship between proton gradient and ATP synthesis predominant mechanism accepted in the scientific community when describing oxidative phosphorylation
Euchromatin
Dispersed chromatin, which appears light under light microscopy. Contains genetically active DNA.
What is a Line-Weaver Burke plot, and what are some important points on that graph?
Double reciprocal of Michaelis Menten graph... the actual data is represented by the portion of the graph to the right of the y-axis but the line is extrapolated into the upper left quadrant to determine its intercept w/ the x-axis y axis = 1/v x axis = 1/[S] x intercept = -1/Km y intercept = 1/Vmax
Chargoff's rule
Due to complementary base pairing, the amount of A in and DNA sequence must equal the amount of T, and the the amount of G must equal amount of C. (so total purines will equal total pyrimidines)
Helicase and topoisomerase
During initiation of transcription, several enzymes including ______, and _________ are involved in unwinding the double stranded DNA and preventing the formation of supercoils
DNA proofreading
During synthesis, DNA polymerase will proofread. Can detect incorrectly paired H-bonds, and excises/ replaces with correct pair.
Anticodon
During translation, the codon of the mRNA is recognized by a complementary anticodon on the transfer RNA (tRNA).
What is the reaction equation explaining how enzymes work
E + S <--(k₁→/k₂←)---> ES --(k₃)--> E + P So basically you have ur Enzyme and Substrate which form the ES complex with a rate of k₁, and dissociate with the rate of k₂.... alternatively, it can proceed and result in the Enzyme and a Product at rate k₃ Note, either way the enzyme is available again
Oxidant is what?
Electron Acceptor
Reductant is what?
Electron Donor
What are some synonymous words for enzyme activity?
Enzyme rate or enzyme velocity
Helicase
Enzyme responsible for unwinding DNA, generating two ssDNA template strand ahead of DNA polymerase. Causes positive supercoiling that strains the DNA helix.
What are the five enzymes in the pyruvate dehydrogenase complex?
Enzymes that work together to convert pyruvate to acetyl CoA Pyruvate dehydrogenase, dihydropropyl transacetylase, dihydrolipoyl dehydrogenase, Enzymes that regulate the actions of PDH pyruvate dehydrogenase kinase, pyruvate dehydrogenase phosphatase
What are lyases?
Enzymes which cleave a substrate into two pieces WITHOUT the use of water OR redox reaction types (often forming double bonds and cyclic molecules to do this). They also do the opposite of cleavage, meaning they combine two molecules without water or redox (when fulfilling this function they are referred to as synthases).
What are covalently modified enzymes?
Enzymes which require the covalent binding of something in order to get into their active conformation.
Esterification rxn
Esterification is the reaction by which a hydroxyl group reacts with either a carboxylic acid or carboxylic derivative to form an ester;
What enzymes do mismatch repair (probably don't need to know) (2 eukaryotes; 2 prokaryotes)
Eukaryotes = MSH2 and MSH1 prokaryotes = MutS and MutL PRobably don't need to know)
Expressed Mutations. Definition and the two types?
Expressd mutation is a mutation that effects the primary amino acid sequence of the protein What are the two catergories: 1) Missense mutation 2) Nonsense mutation
waxes: structure, purpose
Extremely hydrophobic. composed of a long chain fatty acid and long chain alcohol (leads to high melting point) provide stability and rigidity when present in cell membranes (but ONLY in NONPOLAR TAIL REGIONS)
T/F: Citrate synthase, which converts citryl-CoA to citrate and CoA requires energy
F
T/F: Formation of acetyl-CoA from pyruvate is reversible
F (irreversible, which is why we can't make glucose from acetyl-CoA)
F-1,6BP is activated by what? inhibited by what (2)
F-1,6-BP is activated by ATP and inhibited by AMP and F-2,6-BP. makes sense bc when there are high levels of ATP, the cell is energetically satisfied enough to produce glucose for the rest of the body, whereas low levels of AMP imply that a cell needs energy and can not afford to produce.
T/F: Oxygen molecules are used in the Krebs cycle
F. oxygen is not used directly, but the cycle is considered aerobic because NADH and FADH2 will build up w.o oxygen and will inhibit the cycle, hence oxygen is an oxidizing agent)
Portion of ATP synthase that spans the membrane
F0
What are the two portions of ATP synthase?
F0, F1
T/F: acetyl CoA from fatty acids can be converted to glcuose... what can happen?
FALSE, it can't BUT, it can be converted to ketone bodies as an alt. fuel for cells extended periods of low blood sugar are thus usually accompanied by high levels of ketones in the blood
T/F: cooperative enzymes are not subject to activation and inhibition
FALSE: they ARE subject to activation and inhibition, both competitively and thru allosteric sites
metabolic profile of the postabsorptive (Fasting) state
FIND PICTURE!
T/F: all AA's are derived from codons
False, not every amino acid found in the human body is specified by a codon in the genetic code or incorporated into proeins ie: ornithine = one of he intermediates in he urea cycle, the metabolic process by which the body excretes excess nitrogen. also, some AA's sometimes modified = lysine -> pyrrolysine and cysteine -> selenocysteine
Aconitase requires ____ to function
Fe2+
What is the most common form of regulation? what specifically?
Feedback regulation is most popular, Negative, or feedback inhibition, is most common. Positive, or feedback activation, is less common.
Nucleosides
Five-carbon sugar (pentose) bonded to nitrogenous base (A,T,G,C,U) and formed by covalently linking C-1' of sugar to base.
Nucleotide Excision Repair. using Thymine dimers as example
Formation of thymine dimers interfere with DNA replication (caused by UV light) Proteins scan the DNA molecule and recognize the lesion because of a bulge in the strand. An excision nuclease makes nicks in the backbone of the damaged strand on both sides of the thymine dimer and removed the defective oligonucleotide. DNA pol can fill in gap by synthesizing in the 5' to 3' direction, using undamaged strand as template. DNA ligase seals the nick
Rate limiting enzyme in gluconeogensis
Fructose-1,6bisphosphatase
Step 6 of TCA cycle
Fumarate formation = happens on the inner membrane 1) succinate undergoes oxidation to yield fumarate = catalyzed by sccinate dehydrogenase 2) as succinate is oxidized to fumarate, FAD is reduced to FADH2. each molecule of FADH2 then passes the e- to the e- transport chain
Relationship of G and Keq
G = G° + RTln(Q). G is the free energy exchange at the given current temperature and pressure at the given current concentrations (Q). G° = is the free energy exchange at standard temperature and pressure at the equilibrium concentrations (which are constant at that temperature and pressure only)
G-3-P is converted to DHAP by
G-3-P dehydrogenase
Hydrogen bonds in bases?
G-C has three H bonds and is stronger. A-T has two and is therefore weaker. DNA with a higher denaturation point will have more G-C base pairs because intermolecular forces are higher!
The hydrolysis of succinyl-CoA converts ___ to ___. Nucleosidediphosphate kinase catalyzes transfers a phosphate from ____ to ____ to make ____, the only one made in the Krebs cycle
GDP, GTP, GTP, ADP, ATP
______ are the most significant of the glucose transporters because they are located only in specific cells and are highly regulated
GLUT 2 and GLUT4
How many glucose transporters? Names?
GLUT1, GLUT2, GLUT3, and GLUT4
DNA cloning: Goal and 5 steps to doing so
GOAL: To produce a large quantity of homogenous DNA 1) Introduce DNA fragment into a vector (via ligation) = forms a "recombinant vector 1a)A restriction enzyme (restriction endonuclease) cuts both the plasmid and fragment, which are left at stick ends. Enzyme recognizes palindromic sequences. 3) Fragment inserted into plasmid (vector), and can be introduced into bacterial cell and permitted to replicate, generating multiple fragment copies. 5) Once replicated, bacterial cell can be used to create a protein of interest, or lysed to allow isolation of magnified fragment.
counter regulatory hormones. examples and what they do
Glucagon, cortisol, epinephrine, norepinenphrine, and growth hormone are all ------ because their effects on skeletal muscle, adipose tissue, and the liver oppose the actions of insulin.
what 4 things increase blood sugar levels
Glucagon, epinephrine, cortisol, and GH (growth hormone) act to ______ blood sugar levels by stimulating gluconeogensis
Amino acids can be sub-classified as 3 things:
Glucogenic Ketogenic Both
what is the rate limiting step in pentose phosphate pathway (PPP)? induced by What?
Glucose 6 phosphate dehydrogenase induced by insulin
Where is G-6-P found?
Glucose-6-phosphate is found only in the lumen of the ER in liver cells. G-6-P is transported into the ER, and free glucose is transported back into the cytoplasm, from where it can diffuse out of the cell using the GLUT transporters.
Important substrates for gluconeogensis
Glycerol 3-Phosphate or G-3-P (from stored fats, or triglycerols, in adipose tissue) Lactate (from anaerobic glycolysis) Glucogenic AA (from muscle proteins)
what are the 2 main shuttles?
Glycerol 3-phosphate shuttle malate aspartate shuttle
Muscles store excess glucose as __________ and adipose tissue requires glucose to form ________ _______ which is converted into ______ to store incoming fatty acids as triacylglycerols
Glycogen, dihydroxyacetone phosphate (DHAP), glycerol phosphate
pros/cons of glycogen? triacylglycerols?
Glycogen: it offers access to metabolic energy in a faster, water-soluble form BUT has low energy density (so can only provide energy for a bit less than one day Triacylglycerols: can live on 20kg of triacylglycerols (ie moderately obese person) for months BUT takes more time to mobilize this energy
Glycolysis step 1
Glycolysis step 1: Glucose is phosphorylated by the enzyme hexokinase. In this process, ATP molecule is consumed. A phosphate group from ATP is transferred to the glucose molecules to produce glucose-6-phosphate
Glycolysis step 2 (an isomerization)
Glycolysis step 2: glucose-6-phosphate is rearranged into fructose-6-phosphate by the enzyme glucose phosphate isomerase_. This is a reversible reaction under normal conditions of the cell
What is the driving force in the e- transport chain?
H+ concentration gradient (proton-motive force generated by the e- transport chain)
why are free radicals bad and how do they arise?
H2O2 (hydrogen peroxide) is produced as a byproduct in aeroic metabolism. can break apart to form hydroxide radicals (OH.-).. free radicals can attack lipids, including those in the phospholipids of the membrane when oxidized, these lipids lose their function and can weaken the membrane, causing cell lysis (esp true in RBCs which have high levels of oxygen. when oxidized by other fre radicals they become superoxide radicals (O2.-) free radicals can also damage DNA, potentially causing cancer
How does salinity or osmolarity affect enzyme activity?
High concentrations of salt can disrupt H-bonds and ionic bonds, causing partial change in conformation of enyzymes or denaturation of the enzyme
Transcription factors that bind to DNA can recruit other coactivators such as ______ _________ and these proteins are involved in _____ remodeling because they acetylate ______ residues found in the amino terminal tail regions of histone proteins
Histone Acetylation, chromatin, lysine
Mnemonic for irrevesible steps of glycolysis
How Glycolysis Pushes Forward the Process: Kinases. Hexokinase Glucokinase PFK-1 Pyurate Kinase
What is a hydrolase?
Hydrolases are enzymes that catalyze hydrolysis. The breaking of a molecule into two pieces by the addition of water
so hw can cells w/ GLUT4 transporters increase their intake of glucose?
INCREASE # of GLUT4 transporters on their surface!
Mixed Inhibition Line Weaver Burke Values
If inhibitor preferentially binds enzyme, then Km increases and -1/Km approaches zero. (The line will start closer to zero). Vmax also decreases, causing 1/Vmax to increase. (The line will intercept the y axis at a higher point). Overall, the line will cross with the uninhibited enzyme at a point in the fourth quadrant. If inhibitor preferentially binds enzyme-substrate complex, then Km decreases and -1/Km gets larger and further from zero. Vmax still decreases, so 1/Vmax increases. The line will start further from zero and intercept the y axis at a higher point, only intersecting the original line in the first quadrant.
Mixed Inhibition Michaelis Menton Values
If the inhibitor binds the enzyme better than the enzyme-substrate complex, then it lowers the enzyme's overall affinity for its substrate. This causes an increase in Km (lowers affinity) and a decrease in Vmax (less product is able to be produced in a given amount of time). If the inhibitor binds the enzyme-substrate complex better than the enzyme, then it increases the enzyme's overall affinity for its substrate = decrease in Km and still a decrease in Vmax (less product is able to be produced in a given amount of time).
DNA Polymerases β and ε
Important to the process of DNA repair
Inducible Systems
In ______ Systems - the repressor is bound tightly to the operator system and thereby acts as a roadblock (RNA pol can't get from promoter to structural gene) - an inducer must bind to the repressor protein inhibiting it from binding to the operator so the structural genes can be transcribed
closed systems
In a ------ there is no exchange of energy with the environment.
Structure of the spliceosome
In spliceosomes, small nuclear RNA molecules couple with proteins known as small nuclear ribonucleoproteins (snRNPs) The snRNP/snRNA complex recognizes both the 5' and 3' splice sites of the introns
Are tumor suppressor genes dominant or recessive
Inactivation of BOTH alleles is necessary for the loss of function bc, in most cases, even one copy of the normal protein can function to inhibit tumor formation
How does DNA polymerase extend the primer strands?
Incoming nucleotides in the form of 5' deoxyribonucleotide triphosphate: dATP, dCTP,dGTP, and dTTP. As the new phosphodiester bond is formed, pyrophosphate (PPi) is released.
Conformational coupling
Indirect relationship between proton gradient and ATP synthesis in which ATP is released by the synthase as a result of conformational change caused by the gradient. in this mechanism, the F1 portion of ATP synthase is reminiscent of a turbine, spinning w/in a stationary compartment to facilitate the harnessing of gradient energy for chemical bonding
Which model is more accurate scientifically, lock and key or induced fit?
Induced fit
Uncompetitive inhibition Michaelis Menton Values
Inhibition by binding the enzyme-substrate complex causes an overall increase in the enzyme's affinity for its substrate, so Km decreases. Vmax decreases because the amount of substrate converted to product over a given time is decreased.
Uncompetitive inhibition
Inhibitor binds an allosteric site on the enzyme-substrate complex only. it is the FORMATION fo the ES complex that creates a conformational change that allows the uncompetitive inhibitor to bind
Noncompetitive Inhibition Michaelis Menton Values
Inhibitor binds to an allosteric site on the enzyme or enzyme-substrate complex, causing Vmax to decrease because the addition of more substrate will not overcome the inhibitor, and the effective enzyme concentration has decreased. Km stays the same because the inhibitor binds the enzyme and lowers its substrate affinity at an equal amount to binding the enzyme substrate complex and increasing the enzyme's affinity for its substrate.
As opposed to all the step in the Krebs cycle, which occur in the mitochondrial matrix, where does fumarate formation occur?
Inner membrane
beta-cells produce what? where are they located?
Insulin is a peptide hormone secreted by the ----- of the pancreatic islets of langerhans.
three types of membrane proteins
Integral proteins = associate w/ interior of plasma membrane (usually assisted by one or more membrane-associated domains that are partially hydrophobic. 2 types = 1. transmembrane proteins 2. embedded proteins 3. peripheral proteins = bound thru electrostatic interactions w/ lipid bilayer (esp lipid rafts or to other transmembrane/embedded proteins
High concentration of H+ is found in the _______________________________, returning to the _______________________ to create ATP
Intermembrane space, matrix
What enzyme is the rate-limiting step of the Krebs cycle?
Isocitrate dehydrogenase IMPORTANT TO KNOW FOR MCAT
When looking at a michaelis-menton plot with reaction velocity on the y axis, what does that velocity mean?
It means rate! Each point (or tangent line) on the curve was an initial velocity taken at that substrate concentration. The rate (velocity) is increasing at a decreasing rate
Rate of enzyme catalytic reaction means what?
It's not the literal amount of time a single enzyme takes to convert a substrate, it's the amount of substrate changed in a period of time (so both the concentration of an enzyme, and the concentration of a substrate play a role)
Alpha-ketoglutarate dehydrogenase complex carries out the reaction to convert ____________________ to ____________________, while releasing ____ and _______
Ketoglutarate, succinyl-CoA, CO2, NADH
What other ___ase is a transferase?
Kinase!
Are ketose sugars also reducing sugars?
Kinda so ketones can't be oxidized directly to carboxylic acids, BUT they can tautomerize to form aldoses under basic conditions (keto=enol shift_.. in the aldose form they can react w/ Tollen's or Benedict's reagents to form the carboxylic acid
Given that equation for v, what does Km equal when V = Vmax/2
Km = [S]
Km of GLUT 4? meaning what?
Km is about 5mM, transporter is saturated when blood glucose levels are just a bit higher than normal. when a person has high blood sugar, these transporters will still permit only a constant rate of glucose influx because they will be saturated.
Chiral Amino Acids Characteristics
L-amino acids and have (S) absolute configuration; except for cysteine which has (R)
Lactate is converted to pyruvate by ____ Alanine?
Lactate is converted to pyruvate by lactate dehydrogenase Alanine is converted to pyruvate by alanine aminotransferase
DNA libraries. Made up of what (RNA, DNA, cDNA, etc)
Large collections of known DNA; basically the sum of the sequences could equate to the genome of an organism can consist of either genomic DNA or cDNA
Z-DNA: #bases/turn and distance btwn turns? left/right handed? How might it form? Is it commonly occurring in nature?
Left-handed helix. 1) No biological activity attributed to it because it is unstable. not common in nature 2). 12 bases per turn (4.6nm) 3). High GC content or high salt concentration may contribute to this form.
what is it called when a protein has a lipid prosthetic group? carbohydrate? nucleic acid?
Lipid = lipoprotein carbohydrate = glycoprotein nucleic acid = nucleoprotein
How do amino acids get converted to acetyl-CoA?
Lose their amino group via transamination, form ketone bodies, which can be converted to acetyl-CoA
Step 7 of TCA cycle
Malate formation: 1) the enzyme fumarase catalyzes the hydrolysis of the alkene bond in fumarate giving rise to L-malate (both enantiomeric forms are possible, but only L forms)
Polymerase chain reaction (PCR): materials (3). steps (3)
Material: primers, nucleotides, temperature dependent enzymes (Taq) 1) Denature DNA 2) Anneal primer / extend ssDNA 3) Cool down to dsDNA Repeat
What about feedforward regulation?
Means that intermediates prior to the enzyme in a pathway may regulate the enzyme's activity
The start codon AUG codes for
Methionine
Ligases
Much like synthases (lyases), ligases combine molecules without necessarily being redox or water-related (addition or synthesis reactions). Difference: lyases typically deal with small molecules, and ligases deal with large molecules and greater repeated polymerization. AND ligases ONLY deal in addition and synthesis (no breaking or reversing!).
Oncogenes
Mutated genes that cause cancer. Oncogens primarily encode cell cycle-related proteins. Tthe abnormal alleles encode proteins that are more active than normal proteins, promoting rapid cell cycle advancement
What is NANA?
N-acetylneuraminic acid. aka sialic acid
NAD+ vs. NADH (NADP+ vs. NADPH)
NAD+ (oxidized form) is an oxidant and gets reduced (accepts electrons) JUST LIKE OXYGEN DOES. When it accepts electrons, is also gains a proton so it can keep the electrons comfortably and becomes NADH (the reduced form). This may then act as a reductant by DONATING electrons. (Just like when C-OH gets oxidized to C=O, it LOSES electrons!) LEO says GER
NADPH vs NADH
NAD+ = high energy e- acceptor (is a potent oxidizing agent) NADPH = an e- donor in biochemical reactions. a potent reducing agent....used in biosynthesis, immune system, and to help prevetn oxidative damage
give a rund down of aerobic respiration
NADH and FADH2 transfer their e to carrier proteins on the inner mitochondrial membrane these e- are given to oxygen in the form of hydride ions (H-) and water is formed. energy released from transporting e- facilitates proton transport at 3 specificlocations in the chain (Complex I, ) protons are moved from the mitochondrial matrix into the intermembrane space
six high energy e carriers
NADH, NADPH, FADH2, ubiquinone, cytochromes, and glutathione
Complex I name? how big? important subunits? coenzymes?
NADH-CoQ oxidoreductase 20+ subunits 2 important Complex I subunits = 1) iron-sulfur clustor 2) flavoprotein that oxidizes NADH (flavoprotein has a coenzyme called flavin mononucleotide (FMN) covalently bonded to it
composition of inner mitochondrial membrane?
NO cholesterol lots of cariolipin
is glucose from gluconeogenesis in the hepatic cells an energy source for liver?
NO! gluconeogenesis requires expenditure of ATP that is provided by the Beta-oxidation of fatty acids. therefore, hepatic gluconeogenesis is always dependent on Beta-oxidation of fatty acids in liver. during periods of low blood sugar, adipose tissue releases these fatty acids by breaking down triacylglycerols to glycerol (which can also be converted to the gluconeogenic intermediate, DHAP) and free fatty acids
does protein digestion happen frequently for metabolism?
NO! metabolism is directed toward conserving tissues, esp heart and brain digestion of proteins compromises muscle (potentially the heart) so its unlikely to occur under normal circomstances. also proteins are v. important in other functions
is acetyl CoA and fatty acids a good source of glucose?
NO, its not possible in humans to convert acetyl-CoA back to glucose. since most fatty acids are metabolized solely to acetyl CoA, they are not a major source of glucose either exception = fatty acids w/ an odd number of carbon atoms (ie a fatty acid tail w/ 17 carbons). these yield a small amount of prpionyl-CoA which is glucogenic
Side Note: are coenzyme Q and cytochrome C part of the complexes?
NO, bc are able to move freely in the innermitochondrial membrane
GENERALLY: Reactions with more products than reactants have _____ delta G compared to reactions with more reactants than products have a more _______ delta G. but always check the numbers to double check!!!
Negative, Positive
Gel electrophoresis
Negatively charged nucleic acids travel toward the anode (positive end). Smaller strands travel faster than larger chains.
Do we need enzymes active all the time? give an example
No, we need to turn certain ones off sometimes ie enzymes in mitosis should be turned off whne cells are no longer dividing (ie are in G0 phase)
How do remember difference between Noncompetitive and Uncompetitive
Noncompetitive inhibitors bind both the enzyme and enzyme-substrate complex, so the word has more letters. Uncompetitive inhibitors bind only the enzyme-substrate complex, so the word has less letters.
Diastereomers
Not identical and not mirror images of one another in biochemistry, if 2 sugars are the same family (both ketoses or aldoses) that are not identical now, but
fructose metabolism
Note: bc DHAP and glyceraldehyde, the products of fructose metabolism, are downstream from the key regulatory and rate-limiting enzymes of glycolysis (PFK-1), a high-fructose drink supplies a quick source of energy in both aerobic and anaerobic cells.
What two molecules regulate oxidative phosphorylation the most? how?
O2 = if O2 is limited, the rate of oxidative phosphorylation decreases and concetration of NADH and FADH2 increase. accumulation of NADH inhibits the citric acid cycle ADP = in the presence of adequate O2, the rate of oxidative phosphorylation is dependent on availability of ADP. ADP allosterically activates isocitrate dehydrogenase, increasing rate of citric acid cycle and prodcution of NADH and FADH2 -> increases rate of e- transport and ATP synthesis
Can vmax be increased?
ONLY if the ENZYME concentration is increased. Remember that rate is simply substrates converted over time, not enzyme turnover rate itself
Proto-oncogens
Onco-Genes before they are mutated. These are responsible for regulating cell cycle division and turning off when division is finished. "Gas Pedal".
glycosylation
One which needs to be glycosylated (a sugar group added). This can cause an enzyme to be transported somewhere important OR can modify protein activity/selectivity
Pyrimidines
Only one ring in there structure: 1) Thymine 2) Cytosine 3) Uracil
Step 8 of TCA cycle (final)
Oxaloacetate formed anew 1) the enzyme malate dehydrogenase catalyzes the oxidation of malate to oxaloacetate. A 3rd and final molecule of NAD+ is reduced to NADH
From a metabolic standpoint, does it make sense for carbohydrates to get oxidized or reduced? Purpose?
Oxidized because they will be able to reduce other groups. Aerobic metabolism requires reduced forms of electron carriers to facilitate processes such as oxidative phosphorylation
Six General Classes of Enzymes
Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases. Can be remembered by Li'l Hot (ligase, isomerase, lyases, hydrolases, oxidoreductases, and transferases.)
What is the final electron acceptor in the electron transport chain?
Oxygen
What is PAGE gel most useful for?
PAGE is most useful to compare the molecular size or the charge of proteins known to be similar in size from other analytic methods like SDS-PAGE or size-exclusion chromatography
Purine Mnemonic
PURe As Gold (A and G are PURines) Think of gold wedding rings. It takes two gold rings at a wedding, just like two rings in purines.
paracellular
Paracellular transport refers to the transfer of substances across an epithelium by passing through the intercellular space between the cells. It is in contrast to transcellular transport, where the substances travel through the cell, passing through both the apical membrane and basolateral membrane.
type I diabetes
Patients with ------ are unable to synthesize insulin but can still synthesize glucagon, this combination leads to drastically high blood sugar levels.
Chymotrypsin breaks down what?
Peptide bonds near Phenylalanine, Tryptophan, and Tyrosine, (all aromatic, hence class of substrates rather than a single substrate)
Mnemonic for remembering substrates of citric acid cycle
Please Can I Keep Selling Seashells For Money Officer? Pyruvate Citrate Isocitrate a-Ketoglutarate Succinyl CoA Succinate Fumarate Malate Oxaloacetate
Components of phospholipids
Polar head: 1. a phosphate 2. an alcohol Hydrophobic fatty acid tail -polar head is joined to tail via phosphodiester linkage
What does F1 do?
Portion of ATP synthase that phophorylates ADP to make ATP.
Base Excision Repair
Problem: cytosine deamination (caused by absorption of thermal energy) The affected base recognized and removed by a glycolyase enzyme, leaving an AP site. The AP site recognized by AP endonuclease that removes the damaged sequence from the DNA. DNA polymerase and ligase can fill in the gap and seal the strand.
DNA Replication conserved?
Process is semi-conserved because one parental strand is retained in each of the two resulting identical double stranded DNA molecules.
So talk about subunits for prokaryotes vs eukaryotes? Important why?
Prokaryotes = 70S total large = 50S small = 30S Eukaryotes = 80S total large = 60 small = 40 differences in pro vs eukaryotes = important bc allows us to target w/ antibioics w/ fewer side effects for us
Eukaryotic vs Prokaryotic: Removal of RNA primers
Prokaryotic: DNA Polymerase I (5' to 3' exonuclease) Eukaryotic: RNase H (5' to 3' exonuclease)
Eukaryotic vs Prokaryotic: Synthesis of DNA
Prokaryotic: DNA Polymerase III Eukaryotic: DNA Polymerases α, δ, and ε
Eukaryotic vs Prokaryotic: Removal of positive supercoils ahead of advancing replication forks
Prokaryotic: DNA Topoisomerase II (DNA gyrase) Eukaryotic: DNA Topoisomerase II (DNA gyrase)
Eukaryotic vs Prokaryotic: Joining of Okazaki fragments
Prokaryotic: DNA ligase Eukaryotic: DNA Ligase
Eukaryotic vs Prokaryotic: Replacement of RNA with DNA
Prokaryotic: DNA polymerase I Eukaryotic: DNA polymerase δ
Eukaryotic vs Prokaryotic: Unwinding of DNA double helix
Prokaryotic: Helicase Eukaryotic: Helicase
Eukaryotic vs Prokaryotic: Synthesis of telomeres
Prokaryotic: Not applicable Eukaryotic: Telomerase
Eukaryotic vs Prokaryotic: Origin of Replication
Prokaryotic: One per chromosome Eukaryotic: Multiple per chromosome
Eukaryotic vs Prokaryotic: Synthesis of RNA primers
Prokaryotic: Primase Eukaryotic: Primase
Eukaryotic vs Prokaryotic: Stabilization of unwound template strands
Prokaryotic: Single-stranded DNA-binding protein Eukaryotic: Single-stranded DNA-binding protein
Nucleoproteins
Proteins that associate with DNA. most are acid soluble and tend to stimulate processes such as transcription
What do the allosteric binders do to the allosteric enzyme?
Put it in its active or inactive conformations
What enzyme complex converts pyruvate into acetyl-CoA and CO2?
Pyruvate dehydrogenase complex = a multienzyme complex located in the mitochondrial matrix
Primer, 3'→5', 5'→3'
RNA does not require a _______ to start generating a transcript and it travels along the template strand in the ___'→___' direction. Synthesis of the transcript occurs in the ___'→___' direction.
Shine dalgarno sequence
RNA sequence helps recruit the ribosomes to the mRNA to initiate protein synthesis by aligning the ribosome with the start codon
Name of EUKARYOTIC polymerase that removes the RNA that was used as a primer?
RNase H
What is the formula for the respiratory quotient?
RQ= (CO2 produced)/ (O2 consumed)
_________ _____ ______ glycolysis is used exclusively because they lack a mitochondria, which is required for __(4 things
Red blood cells. required for Citric acid cylce, Eelectron Transport chain, Oxidative phosphorylation, and Fatty acid metabolism (Beta oxidation).
After carrying out its function, lipoic acid is in its _________________ (red/ox) form
Reduced
Centromeres
Region of DNA found in the center of a chromosome. 1) Composed of heterochromatin, w/ tandem repeat sequences with high GC content. 2) Allows sister chromatids to remain connected there until microtubules pull the chromatids apart in anaphase.
DNA polymerase
Responsible for reading the DNA template, or parental strand, and synthesizing the new daughter strand. 1) Reads 3' to 5' 2) Synthesizes 5' to 3' *results in new double helix that is antiparallel.
How do ketones form acetyl-CoA?
Reverse of ketone body formation. outside of MCAT scope
Ribosome
Ribosome is composed of proteins and rRNA. Both prokaryotes and eukaryotes, there are large and small subunits that only bind together during protein synthesis.
Example of Gene therapy in kids w/ SCID
SCID = severe combined immunodeficiency. have a mutation in the gene encoding the gamma chain common to several interleukin receptors. we put working copy of gene for the gamma chain into a virus which can transmit the functional gene into human cells
Where does most lipid digestion occurs?
Small intestine (duodenum = where emulsification occurs)
Histones: definition and 5 main types
Small, basic proteins that chromosomes wind around. Five basic histones: H2A, H2B, H3, and H4 form histone core The last histone, H1, seals off the DNA as it enters and leaves the nucleosome, adding stability to structure.
What is SDS?
Sodium Dodecyl sulfate = SDS is a detergent that disrupts all noncovalent interactions in a protein
Competitive inhibition
Something binds an enzymes active site, making it impossible for a substrate to bind that active site and go on with the reaction.
Can enzymes that have been overheated return to their original state if cooled?
Sometimes! Depends on the enzyme!
Stand. G in terms of H and S
Stand. G = H - TS
Isomerases may deal with what kinds of isomers?
Stereoisomers as well as constitutional isomers
Enantiomers
Stereoisomers that are nonidentical, nonsuperimposable mirror images of each other any molecule w/ a chiral carbon(one w/ 4 different groups attached to it) AND no internal planes of symmetry has an enantiomer
Reducing agent is what?
Substrate that gets oxidized as a result of getting rid of electrons, or bonding to something that is more electronegative than it.
Oxidizing agent is what?
Substrate that gets reduced as a result of taking on more electrons, or bonding to something that is less electronegative.
What is the name of the molecule that enzymes typically act on?
Substrates
What is the net effect of complex II?
Succinate + CoQ + 2H+ ---> fumarate + CoQH2
Why does fumarate formation take place in the inner mitochondrial membrane?
Succinate dehydrogenase (enzyme that catalyzes fumarate formation) is an integral membrane protein on the inner mitochondrial membrane
Hydrolysis of succinyl-CoA into __________________ and _________________ is carried out by _________________________________
Succinate, CoA, succinyl-CoA synthetase
name of complex II
Succinate-CoQ oxidoreductase (also succinate dehydrogenase is part of complex II.. .succinate was responsible for oxidizing succinate to fumarate in the citric acid cycle)
Step 4 of TCA cycle
Succinyl-CoA and CO2 formation succinyl-CoA is formed, alpha-ketoglutarate and CoA come together and produce a molecule of CO2 (the second and last carbon lost from acetyl CoA) NAD+ reduced to NADH carried out by alpha-ketoglutarate dehydrogenase complex
When a lyase combines to molecules it is called a?
Synthase
Primase, how long are the primers?
Synthesizes a short primer (~10bp) in the 5' to 3' direction to start replication on each strand. Lagging strand needs on to start each Okazaki fragment. Leading strand theoretically just needs one.
T/F: Formation of acetyl-CoA from pyruvate is exergonic
T. the dG(biochemical standard) = -33.4kJ/mol
T/F: as our body mass increases so does our Basal metabolic rate
T: so BMR = energy required for one sedentary day.. so it increases as our body mass increases. thus a caloric excess will cause an increase in body mass until equilibrium is reached btwn the new BMR and the existing intake
The TATA box is found (using the numbering system to identify the location of important bases in the DNA strand) where? Transcription happens where? Promoter region is where?
TATA = around -25 transcription = +1 Promoter = around -70
What is required for the function of PDH? (2)
TPP = a coenzyme held by noncovalent interactions to PDH also Mg2+
Changes in what parts of protein structure alter in induced fit model?
Tertiary and quaternary
Feedback regulation
That an enzyme is either activated or deactivated (regulated) by products produced later in the pathway
proton motive force, oxidative phosphorylation
The ----- created by electrons as they are passed down the electron transport chain supplies the energy needed to trigger the ----- of ADP to ATP.
How can you distinguish 5' vs 3'?
The 5' end has a -OH or phosphate group on C-5' of sugar. The 3' has a -OH on the C-3' of the sugar.
How would you write the following DNA stand? (Answer)
The DNA stand must be written: 5'--ATG--3' They can also be written in a few different ways: 1) Written backwards: 3'--GTA--5' (must label the ends 3' and 5' in this case) 2) Showing phosphate position: pApTpG 3) "d" to denote deoxy: dAdTdG ALWAYS CHECK NUCLEIC ACIDS FOR POLARITY!
Competitive inhibition Michaelis Menton Values
The addition of more substrate can cause the substrate to outcompete the inhibitor and run the reaction at the same maximum rate. Vmax does not change, but Km increases because the substrate concentration has to be higher to reach the max velocity in the presence of the inhibitor
Denaturation
The disruption of hydrogen bonding and base-pairing, resulting in a "melting" of the double stranded helix into two single strands. NO covalent links in the backbone break during this process
Hybridization
The joining of complementary base pair sequences (can be DNA/DNA or DNA/RNA) vital for PCR and Southern blots
Transferases catalyze what?
The movement of a functional group from one molecule to another!
DNA backbone?
The negatively backbone of DNA is composed of alternating sugar and phosphate groups. 1) It determines the directionality of DNA and is always read from 5' to 3'. Meaning the Phosphate group links the 3' carbon of one sugar to the 5' phosphate group of the incoming sugar in the chain.
Proofreading: How does DNA polymerase discriminate between template strand and incorrect daughter strand?
The template strand has a higher level of methylation.
What happens to the chromosomes that do not have histone H1?
They begin to unravel and are susceptible to nuclease.
Changes in pH affect enzymes in what two ways?
They can affect ionization in the active site, and they denature the enzyme
Why do cytosolic NADH need shuttle mechanisms? what is a shuttle mechanism?
They can't cross directly into the mitochondrial matrix shuttle mechanism = transfers the highenergy e- of NADH to a carrier that can cross the inner mitochondrial membrane
Isomerases use what kinds of mechanisms?
They may use redox, transfer of functional groups, cleavage or combination without water. AS IN THEY CAN ALSO BE CALLED oxidoreductases, transferases, or lyases.
Catalysts only do what and do not affect what?
They only change the activation energy of a rxn and thus increase the RATE. They do not alter the thermodynamics in any way (no change in H, S, regular G, or Keq = equilibrium constant)
How do cofactors/coenzymes bind in an active site?
They range from weak noncovalent to strong covalent
Coenzyme A (CoA) contains which reactive group?
Thiol
Leading strand
This parental strand will be read 3' to 5' and its compliment will be synthesized in a 5' to 3' manner.
How do we detect presence of reducing sugars?
Tollen's reagent benedict's reagent
Histone acetylases
Transcription factors that bind to the DNA can recuit other coactivators such as ________ ________ and these proteins are involved in chromatin remodeling because they acetylate lysine residues found in the amino terminal tail regions of histone proteins
- _________ is the conversion of the mRNA transcript into a functional protein - occurs in the _________ Processes of Translation: 1) ________ 2) ________ 3) __________
Translation, cytoplasm 1) initiation 2) elongation 3) termination
famous repressible system?
Trp operon. when tryptophan is in high concentration, it acts as a corepressor/ binding of 2 molecules of Tryptophan cause the repressor to bind the operator
T/F: amino and carboxyl groups can be on different carbons
True. AA's don't NEED to have both the amino and carboxyl groups bonded to the same carbon. ie γ-aminobutyric acid (GABA) = has the amino group on the gamma carbon (3 carbons away from the carboxyl group) *Side note: if they are on the same carbon = an alpha-amino acid
Antioncogenes
Tumor supressor genes like p53, that encode proteins that inhibit the cell cycle. Mutations in these genes promote cancer. It's like "cutting the breaks"
Enzymes named -ase
Typically have the name of the substrate ahead of the -ase. Like lactase breaks down lactose.
Stop codons
UAA (mnemonic: U Are Annoying) UGA (mnemonic: U Go Away) UAG (mnemonic: U Are Gone)
Why is mRNA more error prone?
Unlike DNA polymerase, RNA polymerase does not _proofread its work
How do cells recognize cytosine deamination?
Uracil should not be found in a DNA molecule and is thus easily detected There are detection systems for other, small, non helix-distorting mutations as well)
Urease breaks down what and only what?
Urea
Gene therapy
Used for diseases in which a given gene is mutated or inactive The insertion of working copies of a gene into the cells of a person with a genetic disorder in an attempt to correct the disorder
Southern blotting: purpose
Used to detect presence and quantity of various DNA strands in a sample.
After a meal fatty acid are converted to triacylglycerols and released into the blood as -------.
VLDL
Water soluble vitamins, blank and blank, must be replenished regularly because they are
Vitamins B and C (ascorbic acid) excreted easily
membrane potential
Vm difference in electrical potential across membranes resting potential for most cells is between -40 and -80 mV
Noncompetitive Inhibition Line Weaver Burke Values
Vmax decreases, so 1/Vmax increases Km stays the same, so -1/Km stays the same Lines will start at same point on x axis, but non competitively inhibited line will be steeper to hit a higher y intercept
DNA Polymerases α, δ, and ε
Work together to synthesize both the leading and lagging strands; δ also fills in the gaps left behind when RNA primers are removed.
how does crystallography work?
X-ray crystallography => crystallography measures e- density on an extremely high resolution cale anc can also be used for nucelic acids X-ray diffraction pattern is generated in this method small dots in the diffraction pattern can then be interpreted to determine the proteins structure
Is a pH of 7.35 bad?
YES considered acidemia
Do D-AA's exist?
Yes, ie gramicidin = an antibiotic produced by a soil bacterium called Bacillus brevis in which D and L AA's alternate in the primary structure
At saturation of [S], reaction rate does not change as a result of
[S] the reaction rate is independent of [S]
At high [S] (above Km), reaction rate changes less rapidly as a result of
[S] the reaction rate is less dependent of [S]
At low [S] (below Km), reaction rate changes rapidly as a result of
[S] the reaction rate is very dependent on [S]
Fructokinase
_____ is the important enzyme used in Fructose metabolism. convert Fructose into fructose-1-phosphate, trapping it in the cell
DNA Methylases
______ _______ add methyl group to cytosine and adenine nucleotides; play an important role in silencing gene that no longer need to be activated
glycogen storage disease
_______ _______ ________accumulation of glycogen in one or more tissues can be cause by many factor such as enzyme isoform malfunction
Glycogen Phosphorylase = activated by what? inhibited?
_______ ___________ is activated by glucagon (liver), epinephrine (liver and muscle), AMP (muscle) inhibited by ATP
de-branching enzyme
_______ enzyme it is a two enzyme complex that deconstructs the branches in glycogen that have been exposed by glycogen phosphorylase.
RNA Polymerase III
________ ________ III synthesize tRNA and some 5S rRNA Located in nucleus
2 functions of rRNA
________ ________ helps catalyze the formation of peptide bonds and splice out its own introns within the nucleus
pyruvate carboxylase
________ _______it is a mitochondrial enzyme that is activated by acetyl-CoA (from beta oxidation), producing oxaloacetate. also, pyruvate will be shunted through pyruvate carboxylase to help generate additional glucose through Gluconeogenesis.
Km of GLUT 2?
________ of _______is high, around 15mM. this means that the liver will pick up glucose in proportion to its concentration in the blood. in other words, the liver will pick up excess glucose and store it only after a meal, when blood glucose levels are high.
GLUT 4 transporter
________ transporter is in adipose tissue and muscle. it responds to the glucose concentration in peripheral blood.
Euchromatin
_________ are looser and appears light under the microscope; transcription machinery can access the genes of interest, so these genes are active.
sucrase
_________ hydrolyze sucrose. is a duodenal brush border enzyme products = glucose and fructose (absorbed into hepatic portal vein... go to liver where fructose is phosphorylated w/ fructokinase)
Heterochromatin
__________ are tightly coiled DNA that appears dark under the microscope; its tight coiling makes it inaccessible to the transcription machinery, so genes are inactive.
Enhancer
__________ transcriptional regulatory sequence that function by enhancing the activity of RNA polymerase at a single promoter site - grouping of several response elements - allow for the control of one's gene expression by multiple signals - can be up to 1 kB away from the gene they regulate... can be in an intron/noncoding region of the gene (DNA must be in a hair pin loop to bring them closer together)
Ketogenic AA
___________ AA that can be converted into Ketone bodies, which can be used as an alternative fuel, particularly during periods of prolonged starvation.
aldolase B
___________ cleaves fructose-1-phosphate to DHAP and glyceraldehyde which then can enter glycolysis, glycogenesis and gluconeogenesis
hexokinase
___________ phosphoralates glucose and is present in most tissues. Low Km (reaches maximum velocity at low [glucose]) and inhibited by glucose-6-phosphate (negative feedback)
glucokinase\
___________ phosphorylate glucose and -is present in hepatocytes (liver cells) and pancreatic B-islet cell (along with GLUT 2, act as the glucose sensor) - High Km (acts on glucose proportionally to its concentration) - induced by insulin in hepatocytes
GLUT 2 transporter: located where?
___________ transporter it is a low-affinity transporter in hepatocytes (liver) and pancreatic cells. After a meal, blood traveling through hepatic portal vein from the intestine is rich in glucose. GLUT 2 captures the excess glucose primarily for storage.
Pyruvate dehydrogenase
_____________ _________ convert pyruvate to acetyl CoA require many cofactors and coenzyme including thiamine, pyrophoshate, lipoic acid, CoA, FAD, and NAD+. inhibited by acetyl-CoA irreversible step
Fructose
_____________ found in honey, fruit, and part of the disaccharide sucrose (table sugar) quick source of energy for both aerobic and anaerobic cells
gluconeogenesis
____________the process by which the liver maintains glucose levels in blood during a period of fasting. (also occurs in the kidney, but to a lesser degree)
glycogen
___________a branched polymer of glucose in storage.
glycogenolysis
___________the process of breaking down glycogen
glutathione
__________reducing agent that help reverse radical formation before damage is done to the cell
Glycogenesis
__________the synthesis of glycogen granules. starts w/ a core protein called glycogenin
Glycogen synthase
______is the rate limiting step in glycogenesis. forms the alpha-1,4 lycosidic bond found in the linear glucose chains of the granule. is stimulated by glucose 6-p and insulin. inhibited by epinephrine and glucagon thru a protein kinase cascade that phosphorylates and inactivates the enzyme
How are nucleotides joined together?
a 3'-5' phosphodiester bond
How is the cytosekelton formed?
a 3D web for the cell comprised of proteins that are anchored to the cell membrane by embeded protein complexes. in addition to intracellular support, extracellular matrices composed of proteins also support the tissues of the bodies
what else is needed to help w/ the Q cycle?
a carrier containing iron and sulfur
peptide bond
a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acid
Terpenes
a class of lipids build from isoprene (C5H8) moieties. are metabolic precursors to steroids and other lipid signaling molecules have a smell
If Stand. G is positive, then Keq is
a decimal
Typical MM graph is in the shape of a
a flipped/upside down hyperbola
G protein-coupled receptors (GPCRs)
a large family of integral membrane proteins involved in signal transduction; characterized by their seven membrane-spanning α-helices; in order for these receptors to transmit signals to an effector in the cell, they utilize a heterotrimeric G protein
amylose
a linear glucose polymer linked via alpha-1,4 glycosidic bonds
retinal
a metabolite of vitamin A... is an aldehyde component of light sensing molecular system in the human eye
PAGE (polyacrylamide gel electrophoresis)
a method for analyzing proteins in their native states; it is limited by the varying mass-to-charge and mass-to-size ratios of cellular proteins because multiple different proteins may experience the same level of migration; in this type of electrophoresis, the functional native protein can be recovered from the gel after electrophoresis, but only if the gel has not been stained because most stains denature proteins
carnitine
a molecule that can cross the inner membrane w/ a fatty acyl group in tow.
colligative property
a physical property that depends on the concentration of dissolved particles but not the chemical identity of those particles ex: osmotic presure
biosignaling
a process in which cells receive and act on signals
actin
a protein that makes up microfilaments and the thin filaments in myofibrils; it is the most abundant protein in eukaryotic cells; it has both a positive side and a negative side, this polarity allows motor proteins to travel unidirectionally along one of these protein filaments, like a one-way street
Monoterpenes
a single terpene unit which consists of TWO isoprene units (C10H16)
antibody. detailed structure. origen?
a specialized protein molecule produced by lymphocytes (B cells) for interaction with antigens; antibodies consist of two identcial heavy and two identical light chains that have constant and variable regions; disulfide linkages and noncovalent interactions hold the heavy and light chains together
amylopectin
a starch which starts off w/ same linkage as amylose but also contains branches via alpha-1,6 glycosidic bonds
Edman degradation
a stepwise process for determining the amino acid sequence in an isolated protein
soaps can act as surfactants, what are those?
a surfactant lowers the surface tension at the surface of a liquid, serving as a detergnt or emulsifier
facilitated diffusion: what is it and why is it a thing? example of types of molecules that use it
a type of passive transport; the diffusion of molecules down a concentration gradient through a pore in the membrane created by a transmembrane protein; this type of diffusion allows integral membrane proteins to serve as channels for substrates to avoid the hydrophobic fatty acid tails of the phospholipid bilayer molecules that need it = large, polar or charged
SDS-PAGE
a useful tool because it separates proteins on the basis of mass alone; SDS binds to proteins and creates large chains with net negative charges, thereby neutralizing the protein's original charge and denaturing the protein; as the proteins move through the gel, the only variable affecting their velocity is f, the frictional coefficient, which depends on mass
starches, how are the D-glucoses linked?
aalpha-D-glucose monomers in plants starchers are mainly stored as amylose
emulsion is followed by ____
absorption of fats by intestinal cells. free fatty acids, cholesterol, 2-monoacylglycerol, and bile salts contribute to the formation of micelles
major enzymes of fatty acid synthesis?
acetyl CoA carboxylase fatty acid synthase
the fact that acetyl CoA activates pyruvate carboxylase is important why?
acetyl CoA inhibits pyruvate dehydrgenase b/c e a high level of acetyl-CoA implies that the cell is energetically satisfied and need not run the CAC in the forward direction. in other words, the cell should stop burning glucose. rather, pyruvate will be shunted thru pyruvate carboxylase to help generate additional glucose thru gluconeogenesis
Would you expect AAs w/ acidic side chains to have pI above or below 6? basic AAs?
acidic = below 6 basic = 6
Aspartic Acid aka?, 3 letter code and 1 letter code and structure
acidic, polar (negatively charged) hydrophobic aka aspartate asp D
Glutamic Acid aka? , 3 letter code and 1 letter code and structure
acidic, polar (negatively charged) hydrophobic glu E
Short-chain fatty acids are absorbed...
across the intestine via simple diffusion directly into the blood
during fasting state, decreased levels of insulin/increased levels of epinetrhine activate __what enzyme--....result
activate hormone-sensitive lipase in fat cells. allows fatty acids to be released into circulation
steps of beta oxidation process?
activation faty acid entry into mitochondria beta oxidationin mitochondria
How do fatty acids get converted to acetyl-CoA?
activation causes a thioester bond to form btwn carboxyl groups of fatty acids and CoA. the activated fatty acyl-CoA is then transported to the intermembrane space of the mitochondrion. bc fatty acyl-CoA can't cross the inner mitochondrial membrane, the fatty acyl group is transferred to carnitine via a transesterification rxn
catalytic domain other molecules involved? (3-4_
activation of this domain often results in the initiation of a second messenger cascade like: RTKs (receptor tyrosine kinases) serine/threonine-specific protein kinases receptor tyrosine phosphatases
what can affect activity levels?
activity is correlated w/ concentration but also affected by purification methods used and conditions of the assay
How can u determine activity levels for enzymes? what is also helpful?
activity levels for enzymatic samples are determined by following the process of a KNOWN reaction w/ a GIVEN concentration of substrated and comparing it to a standard helpful if there is a color change b/c then microarrays can rapidly ID the samples from a chromatographic analysis that contains the compound of interest
To catalyze hydrolysis for N terminus
add H atom to the amide nitrogen
To catalyze hydrolysis for C terminus
add OH group to carbonyl group
2 other names for the Citric acid cycle, where it occurs and the main function/products of it
aka Krebs cycle or tricarboxylic acid cycle (TCA cycle) main function = oxidation of acetyl-CoA to CO2 and H2O. also makes high energy e-carriers (NADH and FADH2)
expression libraries
aka cDNA libraries. Constructed by reverse-transcribing processed mRNA. Contain smaller fragments of DNA , and only include exons of genes expressed in the sample tissue. Can be used to reliably sequence specific genes and identify disease-causing mutations, produce recombinant proteins or produce transgenic animals.
Phospholipids (aka
aka glycerophospholipid (the correct name) replace one of the fatty acid chains of triglycerides with phosphate this gives polar head for interaction on outer surface of lipid bilayer bc of hydrophobic interactions they spontaneously make micelles, liposomes
branching enzyme. aka?
aka glycosyl alpha-1,4:alpha-1,6 transferase -is responsible for introducing alpha-1,6-linked branches into the granule as it grows.
Coding strand... aka?
aka the Sense strand of DNA is not used as a template during transcription is identical to the mRNA transcript except that all the thymine nucleotides in DNA have been replaced with uracil
Structure of triacylglycerols? Aka?
aka triglycerides. composed of 3 fatty acids bound by ester linkages to glycerol.. usually in naturally occurring triacylglycerols = the fatty acids are not the same. fatty acids are hydrophobic. have a polar hydroxyl group in the glycerol component and polar carboxylates of fatty acids which decreases their polarity
postprandial state?
aka well-fed( absorptive) state Our bodies enter the ---/----- (-----) state after we have eaten, this state is characterized by high amounts of insulin secretion, greater anabolism, and more fuel storage than catabolism.
Glucogenic amino acids
alanine is the major glucogenic AA, tho almost all the others are as well most are converted b individual pathways to citric acid cycle intermediates thento malate, follwing the same path from there to glucose
Hydrophobic Amino Acids
alanine, isoleucine, valine, phenylalanine (ie AAs with long alkyl side chains)
free fatty acids are transported thru blood in association w/ _____
albumin, a carrier protein
Benedict's Reagent
aldehyde group of an aldose is readily oxidized, indicated by red precipitate of cupric oxide (Cu₂O)
what would you call a 6 carbon sugar w/ an aldehyde group? what is a ketopentose?
aldohexose ketopentose = 5 carbon sugar w/ a ketone group
lactones vs aldonic acids
aldonic acids = come about when aldehyde is oxidized in its OPEN CHAIN FORM lactones = come about when aldoes is in RING FORM
What is a complex carbohydrate?
all carbs w/ at least 2 sugar molecules linked together (ie disaccharide, oligosaccharide, polysaccaraide)
Are AA's D or L? What does this mean? What about absolute configuration? Exceptions?
all chiral AA's are L-amino acids... so amino group is drawn on the left in a Fischer projection (in Cahn-Ingold prelog system
affinity
all chromatography is about the ___ of a substance for the mobile and stationary phases, except for size-exclusion chromatography
saturated fatty acids
all single bonds solids at room temperature main part of animal fats decrease membrane fluidity
hybridization of benzene
all six of the carbon atoms in benzene are sp2 hybridized and each of the six orbitals overlaps equally w/ its two neighbors. Result = delocalized e- form 2 pi electron clounds (one above and below the plane of the ring
Repressible Systems
allow constant production of a protein product - the repressor maintains inactive until bound with a corepressor, this complex then binds to the operator to prevent transcription negative control mechanism
glycogen and amylopectin uses what linkages?
alpha 1,4 and alpha 1,6 linkages
How to differentiate between the alpha and beta anomer
alpha = down (fish in sea) beta = up (birds in the sky)
important essential fatty acids for humans
alpha linolenic acid linoleic acid
How is amylose degraded in our body?
alpha-amylase or beta amylase
Step 3 of TCA cycle
alpha-ketoglutarate and CO2 formation: 1) isocitrate is oxidized to oxalosuccinate by isocitrate dehydrogenase 2) oxalosuccinate is decarboxylated to produce alpha-ketoglutarate and CO2 the first of the 2 carbons from acetyl CoA is lost here. als othe 1st NADH produced IMPORTANT TO KNOW FOR MCAT
cholesterol is a precursor to what?
also is a vitamin D precursor which can be produced in the skin in a UV-driven reaction
Under basic conditions (pH > 9), will AA's (w/o ionizable side chains) be + or - charged?
amino groups become deprotonated at basic pH, forming an anion (NEGATIVE CHARGE pH is above pKa of COOH so deprotonated (COO- = charge of -1), and pH of amino group is above pKa so deprotonated
Which of the two forms of starch (amylose vs amylopectin) is more soluble in the solution? Why?
amylopectin is more soluble in solution than amylose because of its branched structure; it decreases intermolecular bonding between polysaccharide polymers and increases interaction with the surrounding solution
What is a kinase?
an enzyme that catalyzes the transfer of a phosphate group from one molecule to another (it usually takes from ATP)
importance of thiamin
an essential cofactor for several enzymes involved in cellular metabolism and nerve conduction. Thiamine deficiency, often a result of excess alcohol consumption, results in diseases (ie wernicke Korsakoff syndrome) in this disorder, patients suffer from a variety of neurologic deficits, incl delirium, balance problems, and - in sever cases - the inability to form new memories
what is prothrombin
an important clotting factor in blood
keratin
an intermediate filament protein found in epithelial cells; it contributes to the mechanical integrity of the cell and also functions as a regulatory protein; it is the primary protein that makes up hair, skin, and nails
glycolysis/fermentation/anaerobic processes happen where? aerobic respiration?
anaerobic = cytosol aerobic = mitochondria
glycolysis in erythrocytes:
anaerobic glycolysis =only pathway for ATP production, yields net 2 ATPs per glucose
anode; cathode
anions always move toward the ___ and cations always move toward the ___
elastin
another important component of the extracellular matrix of connective tissue; its primary role is to stretch and then recoil like a spring, which restores the original shape of the tissue
What is the key example of a covalently modified enzyme?
any enzyme that can be activated/deactivated by dephosphorylation/phosphorylation (one cannot predict whether phosphorylation or dephosphorylation will actiavte an enzyme w/o experimental determination.
brief summary of apolipoproteins (don't need to know for MCAT
apoA-I: activates LCAT, an enzyme that catalyzes cholesterol esterification apoB-48: mediates chylomicron secretion apoB-100: permits uptake of LDL by liver etc
enzymes without their needed cofactors/coenzymes are called what? and the opposite?
apoenzymes holoenzymes = enzymes with their needed cofactors
Cancer cells = different how?
are able to proliferate excessively bc the yare able to divide w/o stimulation from other cells and are no longer subject to the normal controls on cell proliferation. tend to accumulate mutations
Tocopherols are helpful in our body how? what do they do?
are biological antioxidants... aromatic ring reacts w/ free radicals and destroys them this prevents oxidative damage (an important contributor to development of cancer and aging)
Phenylalanine, 3 letter code and 1 letter code and structure
aromatic, nonpolar hydrophobic phe F
Tryptophan, 3 letter code and 1 letter code and structure
aromatic, nonpolar trp W
Tyrosine, 3 letter code and 1 letter code and structure
aromatic, polar (bc of -OH group) tyr Y
electrochemical gradient
as [H+] increases in intermembrane space 1) pH drops in intermembrane space 2) voltage difference btwn the intermembrane space and matrix increases
aspartate/glutamate vs aspartic acid/glutamic acid... which is more common in our body?
aspartate/glutamate: anion form aspartic acid/glutamic acid: acidic form usually in anion form (most acids in cells exist in the deprotonated form)
Negatively Charged Amino Acids
aspartic acid (aspartate) and glutamic acid (glutamate); negatively charged at physiological pH 7.4
Common example of irreversible inhibition
aspirin! = acetylsalicyclic acid (aspirin) irreversibly modifies cyclooxygenase-I. the enzyme can no longer bind its substrate to make its product (prostaglandins) which are involved in modulating pain and inflammatory responses to make more prostaglandins, new cyclooxygenase-1 will have to be synthesized thru transcription and translation
When does change in enthalpy( delta H) = thermodynamic heat exchange (Q) ?
at constant pressure and volume
What must occur for a polymer to branch?
at least 2 glycosidic bonds are formed on a monosaccharide
How does cholesterol work to maintain membrane fluidity
at low T, it keeps the cell membrane from solidifying; at high T, it holds the membrane intact and prevents it from becoming too permeable;
what linkage cannot be cleaved in the human body?
b-glycosidic linkage
Cori cycle
b/c RBCs lack mitochondria, they can't carry out aerobic metabolism instead, pyruvate is converted to lactic acid to regenerate NAD+. BUT lactate is acidic, it must be removed from blood to avoid acidifying the blood. RBCs deliver lactate to liver where its converted back to pyruvate and, thru gluconeogenesis, becomes glucose for the RBCs to use. basically: glucose is converted to lactate in red blood cell, lactate is converted to glucose in liver cells.
fate of side chains?
basic AA side chains feed into urea cycle other side chains act like carbon skeletons and produce energy via gluconeogenesis or ketone production
Histidine, 3 letter code and 1 letter code and structure
basic, positively charged, polar his H Is aromatic ring w/ 2 nitrogen atoms (the ring is called an imidazole
Arginine, 3 letter code and 1 letter code and structure
basic, positively charged, polar hydrophobic arg R Has 3 nitrogen atoms in its side chain + positive charge is delocalized over all three nitrogen atoms
Lysine, 3 letter code and 1 letter code and structure
basic, positively charged, polar hydrophobic lys K has terminal primary amino group
glycerol structure
basis of phosphoglycerides (ie glycerophospholipids)
why are the sedimentation constants not additive?
bc S is determined experimentally by studying behavior of particles in ultracentrifuge based on size AND SHAPE!!
What is the charactristic of the peptide bond
bc amide groups have delocalizable pi e- in the carbonyl and in the lone pair on the amino nitrogen, they can exhibit resonance; thus the C-N bond in the amide has partial double bond character. as a result rotation of the protein backbone around its C-N amide bonds is restricted which makes the protein more rigid. Rotation around the remaining bonds in the backbone, however, is not restricted as those remain in single (sigma) bond
Why don't we know the exact number of ATP created from 1 glucose (ie its around 30-32, but we don't know what)
bc efficiency of NADH shuttles from cell to cell is variable
What is the formula associated with Newton's First Law of Thermodynamics?
bc system is closed, the change in internal energy can come only in the form of work or heat so: delta U = Q - W, Q= heat exchange, W= work (work in thermodynamics refers to changes in pressure and volume which are constant in most living system so the only quality of interest = heat!)
Antidepressants increase levels of neurotransmitters in the brain, but effects take longer to appear than the changes in neurochemistry. Why?
bc the nervous system must still upregulate its postsynaptic receptors to respond to the new levels of neurotransmitters
Why is FAD the e- acceptor in fumarate formation?
bc the reducing power of succinate is not great enough to reduce NAD+
Why does soap appear to dissolve in water, and how is this fact important in cleaning?
because amphiphatic free FA acid salts form micelles; so 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
why is G-6-P dehydrogenase induced by insulin?
because the abundance of sugar entering the cell under insulin stimulation will be shunted into both fuel utilization pathways (glycolysis, aerobic resp.) as well as fuel storage pathways (FA's synthesis, glycogenesis, PPP).
first part of PPP starts with ___ and ends with ___... it is _(irreversible or reversible)
begins w/ Glucose 6p, ends w/ ribulose 5p is irreversible. also produces NADPH and involves the important rate-limiting enzyme Glucose-6Phosphate dehydrogenase (G6PD)
second part of pathway begins w/ what? it is _(irreversible or reversible)
begins w/ ribulose 5p. represents a series of reversible rxns that produce an equilibrated pool of sugars for biosynthesis, including ribose 5p for nucleotide synthesis. also fructose 6p and glyceraldehyde 3p. these intermediates can feed back into glycolysis. conversely, pentoses can be made from glycolytic intermediates w/o going thru the G6PD reaction. these interconversions are primarily accomplished by the enzymes transketolase and transaldolase
postranslational processing (4, 4)
begins w/ the proper folding of the newly synthesized protein permitted by a specialized class of proteins called chaperone proteins. Also cleavage events Also subunits coming together to form a quaternary structure Other biomoleculs may be added to the peptide via the following processes: 1) phosphorylation 2) carboxylation 3) glycosylation 4) prenylation
cellulose uses what linkage?
beta-1,4 linkage
when does the liver releases glucose into the blood.
between meals and during prolonged fasts
why is acetyl CoA being a thioester important?
bic thioesters are more highenergy (so when a thioester undergoes hydrolysis or other rxns a significant amount of energy is released which can drive other rxns forard (like citric acid cycle)
What does BCA stand for?
bicinchoninic acid
at the end of the ileum what happens?
bile salts are actively reabsorbed and recycled; any fat that remains in the intestine will pass into the colon and end up in stool.
desmosomes
bind adjacent cells by anchoring to their cytoskeletons interaction between transmembrane proteins and intermediate filaments inside adjacent cells interface between two layers of epithelial tissue
How carriers work
binding of substrate to transporter induces a conformational change... for a brief time, the carrier is in the occluded state (carrier is not open to either side of the phospholipid bilayer) opens to otherside, releasing substrate
explain how cooperativity works
binding of substrateencourages transition of other subunits from the T state to the R state, which increases the likelihood of substrate binding by these other subunits. conversely, los of substrate can encourage the transition from the R state to the T state and promote dissociation of substrate from the remaining subunits. think of it like a party, as more ppl start arriving, it is more relaxed and party seems appealing. but as ppl start going, the party dies down and more ppl are encouraged to leave so the tense hosts can clean up
examples of binding proteins (4)
binding proteins include hemoglobin, calcium-binding proteins, DNA-binding proteins (often transcription factors), Cell Adhesion Molecules (CAMs)m and others
Enzymes =? sensitive to __(2)__
biological catalysts that are NOT used up or changed in the rxn they are temp and pH sensitive (optimal activity at specific pH and temp
roles of cholesterol
biosynthesis, cell memrbane stability/fluidity, bile acids and salts are made from cholesterol in the liver many tissues require cholesterol for steroid hormon synthesis (steroidogenesis)
glycolysis in erythrocytes, process:
bisphosphoglycerate mutase (produces 2,3-BPG from 1,3 BPG in glycolysis) -2,3-BPG binds allosterically to the beta-chains of hemoglobin A (HbA) and decreases its affinity for oxygen.
7.4 pH is the pH of what fluid in human bodies
blood
Is bon breaking usually endo or exothermic? How bout bond making? exceptions?
bond breaking = usually endothermic bond making = usually exothermic ATP = exception to this rule. Due to all the negative charges in close proximity, remobing the terminal phosphate =releases energy
things of note about serine and threonine
both have -OH group in side chain which makes them highly polar and able to participate in H bonding
things of note about asparagine and glutamine
both have amide side chains. unlike the amino group common to all amino acids, the amide nitrogens do NOT gain or lose protons w/ changes in pH and they do not become charged
why is glycogen so branched? (2)
branching of glycogen optimizes the energy efficiency of glycogen, makes it more soluble in solution, allows more glucose to be stored in the body 2. allows enzymes (ie glycogen phosphorylase) which vleave glucose from glycogen to work on many sites w/in the molecule simultaneously
HMG-CoA lyase
breaks down HMG-CoA into acetoacetate, which can subsequently be reduced to 3-hydroxybutyrate
glycogen phosphorylase does what?
breaks the alpha-1,4 glycosidic bonds, releasing glucose 1-p from the periphery of the granule. it canNOT break alpha 1,6 bonds so stops at the outermost branch points
Micelles difusse to the...
brush border of the intestinal mucosal cells where they are absorbed. the digested lipids pass thru the brush border where they are absorbed into mucosa and re-esterified to form triacylglycerols and cholesteryl esters -they are packaged, along w/ apoproteins, fat soluble vitamins and other lipids, into chylomicrons
btwn meals, glucose is supplied to the brain by what>... when does the brain use ketone bodies?
btwn meals, glucose is supplied by either hepatic glycogenolysis or gluconeogenesis uses ketone bodies only in periods of extreme fasting
How are alpha helices stabilized?
by H-bonds btwn carbonyl Oxygen atom and the amide hidrogen FOUR resideus away
How is pyruvate kinase activated?
by fructose 1,6-bisphosphate from the PFK-1 reaction this is a feed-forward activation
uptake and release of glucose by ____. ↑ [glucose] and Km in blood → _____?
by the liver Beta- islet cell glucose sensor ↑ [glucose] and Km in blood → ↑[glucose] picked up by the liver
How is steroid functionality determined? Are they polar or not?
by the oxidation status of these rings/functional groups that they carry. are NONpolar
cDNA Library vs. Genomic Libraries: enzymes used to make the library
cDNA = Reverse transcriptase and DNA ligase Genomic = Restriction endonuclease and DNA ligase
cDNA Library vs. Genomic Libraries: Source of DNA
cDNA Library: mRNA Genomic Libraries: Chromosomal DNA
cDNA Library vs. Genomic Libraries: Promoter and Enhancer sequences present
cDNA Library: noo Genomic Libraries: Yes but not necessarily in the same clone
cDNA Library vs. Genomic Libraries: Contains nonexpressed sequences of chromosomes? yes or no
cDNA: No Genomic: Yes
cDNA Library vs. Genomic Libraries: Can be used for gene therapy or constructing transenic animals. Y/N
cDNA: Yes Genomic: No
cDNA Library vs. Genomic Libraries: genes can be expressed in cloning host (recombinant proteins). Y or N
cDNA: Yes Genomic: No
cDNA Library vs. Genomic Libraries: Cloned genes are complete sequences?
cDNA: Yes Genomic: Not necessarily
respiratory quotient for carbs? lipids? resting individuals? indicates? (don't need to know these numbers, just a reference)
cabs = 1.0 lipids = 0.7 resting = 0.8 indicating taht both fat and glucose are consumed
Amphoteric species
can accept or donate a proton (ie amino acids)
beta-pleated sheets
can be parallel or antiparallel peptide chains forming rows or strands held together by intramolecular H bonds between carbonyl oxygen atoms and amide H atoms in an adjacent chain; ex. fibroin - primary protein component of silk fibers
How do you get your gene of interest out of the vector?
can be processed by restriction enzymes to release cloned DNA from vector
ketone bodies
can be thought of as a transportable form of acetyl CoA that is primarily utilized in periods of extended starvation
are sphingolipids phospholipids?
can be, if they containe a phosphodiester linkage but others contain glycosidic linkages to sugars = a glycolipid
how to elute out protein afterwards. and then to further isolate it?
can change polarity, pH, or salinity to elute out ur protein then, evaporate solvent to get compound
What can we ascertain from knowing the DNA sequence and AA sequence
can determine where on a chromosome the gen coding a particualr protein resides
WHat can the aldehyde carbon do?
can participate in glycosidic linkages; sugars acting as substituents via this linkage are called glycosyl residues
Once you run ur proteins on using SDS PAGE. what do you do?
can stain gel to visualize protein bands
Why are fatty acids not used as an energy source for the brain?
can't cross the blood-brain barrier. btwn meals, glucose is supplied by either hepatic glycogenolysis or gluconeogenesis
glycoprotein coat
carbohydrates associated with membrane-bound proteins cell wall of plants, bacteria, and fungi have higher levels of this than on membranes of animal cells
what is C1' vs C1?
carbon atoms in the sugar are labeled w/ a prime symbol to distinguish them from the carbon atoms in the nitrogenous base
Anomeric Carbon
carbonyl group becomes chiral and forms a ring in the process
fatty acids
carboxylic acids with hydrocarbon chain and terminal carboxylic acid
cariac myocytes most closely parallel ____ muscle during extended periods of exercise. in patients w/ cardiac hypertropy (______), the situation reverses to some extent. In a failing heart, _____ increases and _____ falls
cariac myocytes most closely parallel skeletal muscle during extended periods of exercise. in patients w/ cardiac hypertropy (thickening of the heart muscle), the situation reverses to some extent. In a failing heart, glucose oxidation increases and beta-oxidation falls
Citrate shuttle
carries mitochondrial acetyl-CoA into the cytoplasm, where cholesterol synthesis occurs NADPH (from the pentose phosphate pathway) supplies reducing equivalents
Oxidoreductases
catalyze oxidation-reduction reactions, that is, the transfer of electrons between biological molecules. They often have a cofactor that acts as an electron carrier, such as NAD+ or NADP+
Glyceraldehyde-3-phosphate dehydrogenase?
catalyzes an oxidation and addition of inorganic phosphate (Pi) to its substrate,glyceraldehyde 3-phosphate. this results in the production of a high energy intermediate: 1,3-bisphosphoglycerate and the reduction of NAD+ to NADH.
peptidyl transferase
catalyzes the formation of peptide bond amide linkage
endocytosis
cell membrane invaginates and engulfs material to bring it into the cell vesicle brings it in because stuff might be toxic
cell-cell junctions
cells w/in a tissue can form a cohesive layer via intercellular junctions. can provide direct pathways of communication btwn neighboring cells or btwn cells and extracellular matrix. usu made of cell adhesion molecules (CAMs) 1. gap junctions 2. tight junctions 3. desmosomes
3 major polysaccharides, their composition, and how they differ
cellulose, starch, glycogen all composed of D-glucose differ in configuration about the anomeric carbond, position of glycosidic bonds
What are the 4 classes of sphingolipids?
ceramide sphingomyelins glycosphingolipids (cerebrosides or globosides) gangliosides
What are 2 types of glycosphingolipids and how do they differ? where are glycosphingolipids usually found?
cerebrosides = have a single sugar globosides have 2+ sugars glycosphingolipids are mainly on the outer surface of the plasma membrane... are NOT phospholipids bc no phosphodiester linkage
Definition of a lipid
characterized by insolubility in water and solubility in non-polar organic solvents
Vitamin E
characterizes a group of closely related lipids called tocopherols and tocotrienols; characterized by substituted aromatic ring with long isoprenoid side chain; hydrophobic
when is it preferred over electrophoresis
chromatography is preferred over electrophoresis when large amounts of protein are being separated
Step 2 of TCA cycle?
citrate isomerized to isocitrate: achiral citrate is isomerized to 1 of 4 possible isomers of isocitrate. 1) citrate binds at 3 points to the enzyme aconitase 2) water is lost from citrate, yielding cis-aconitate 3) water is added back to form isocitrate results in a switching of a hydrogen and a hydroxyl group, needed to facilitate the subsequent oxidative decarboxylation
side note: fatty acid synthesis starts from what?
citrate, produced in the citric acid cycle
Classification of AAs in catabolism
classified by their ability to turn into specifc metabolic intermediates -glucogenic AAs (all but leucine and lysine) = can be converted into glucose via gluconeogenesis -ketogenic AAs (L,K,I,F,T,W,Y) = can be converted to acetyl-CoA and ketone bodies
Common lyase example
cleavage of ATP to form Pi and cyclic AMP
how does beta amylase work?
cleaves amylose at the reducing end of the polymer (the end w/ the free anomeric carbon) to yield maltose
alpha-amylase
cleaves anywhere along the chain to yield polysaccharides, maltose, and glucose
beta-amylase
cleaves at the nonreducing end of the polymer to yield maltose only
how does alpha amylase work?
cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, and glucose
The small difference between cofactors and coenzymes
cofactors are inorganic molecules or metal ions. Usually called minerals! usually ingested thru dietary minerals coenzymes are organic molecules! Usually vitamins or vitamin derivatives such as NAD⁺ and FAD and Coenzyme A. also incl. water soluble vitamins including B complex vitatmins and ascorbic acid (vitamin C) = important coenzymes that must be replenished regularly bc they are easily excreted...
where does the glycerol phosphate that is required for triacylglycerol synthesis come from?
comes from glucose which is metabolized in adipocytes as an alternative product of glycolysis.
Describe the structure and function of triacylglycerol
composed of glycerol backbone esterified to 3 FA; used for energy storage
Glucose entry in most cell is driven by ______ and is independent of ____, unlike absorption from the digestive tract.
concentration sodium
Catabolism of cellular proteins occurs only under...
conditions of starvation
explain how osmotic pressure works
consider a container separated into 2 compartments (1 w/ water, 1 w/ solute) separated by semipermeable membrane thats permeable to water but not the solute. water will flow into the concentrated compartment, causing the water level to rise. bc the solute can't pass thru the membrane, the concentration of solute will never be equal, but the hydrostatic pressure exerted by the water level in the concentrated compartment will eventually oppose the influx of water. the water will only rise to the point at which it exerts sufficient pressure to counterbalance the tendency of water to flow across the membrane. this pressure = osmotic pressure
Sesquiterpenes
contain 3 isoprene units (Sesqui = 1.5)
Diterpenes
contain 4 isoprene units; ex. vitamin A
deoxy sugar
contains a hydrogen that replaces a hydroxyl group on the sugar (ie D-2-deoxyribose = the carbohydrate found in DNA
membrane protein concentration
controlled by gene regulation, endocytotic activity, protein insertion biosignaling cells can up or down regulate the number of specific cell receptors on surface to meet cellular requirements
semipermeable
controls what comes in and out through the membrane and individual channels
What happens to vitamin D in liver and kidneys
converted to calcitriol (1,25-(OH)2D3) = the biologicaly active form of vitamin D
What does aminotransferase?
converts aspartate and α-ketoglutarate, as a pair, to glutamate and oxaloacetate by moving the amino group from aspartate to α-ketoglutarate
amino group removed by trans/de-amination = potential toxen, how? How is it taken care of?
could turn into ammonia? excreted via urea cycle
where is FAD when its being oxidized?
covalently bonded to complex II
Transgenic mice
created by integrating a gene of interest into a germline or embryonic stem cell of developing mouse. The cloned gene that is introduced is referred to as a transgene. 1) Can be mated to select for transgene
Vitamin B12 NOT TESTED ON MCAT
cyanocobalamin
cysteine vs cystine
cysteine = an AA cystine = what is formed when 2 cysteins form disulfide bonds
Absolute configuration: what is it and how is it named by organic chemists vs biochemists
def: the particular 3D arrangement of the groups attached to the chiral carbon organic chemists = R/S system biochemists = D/L
Write the formula used to find the change in free energy using standard free energy.
delta G= delta G* + RT ln(Q), R= universal gas constant, T= temperature, Q= reaction quotient
Write out the Gibbs free energy equation.
delta G= delta H - T (delta S)
What about cells w/ few mitochondria (ie RBCs)? what do they use for energy?
depend on glucose still
Conjugated proteins
derive part of their function from covalently attached molecules called prosthetic groups; the prosthetic groups can help direct the delivery of the proteins to a particular organelle or cell membrane, can also be a cofactor needed for their activity
Jacob-Monod Model
describes the structure and function of operons - contains: (most downstream) structural genes, an operator site, a promoter site, and a regulator gene (most upstream)
What is the haworth projection and what is it used for?
describing the 3D conformations of cyclic structures. depicts cyclic sugars as planar rings
Nernst Equation
determines membrane potential from intra and extracellular concentrations of various ions z=charge assuming T is 310K (body temp) then you can also say; E = 61.5/z * (log [ion,out]/[ion,in])
concentration gradients
dictates whether membrane transport is passive or active
What is the difference between an amino acid, dipeptide, tripeptide, oligopeptide, and a polypeptide?
differ by the number of amino acids that make them up: amino acid = 1, dipeptide = 2, tripeptide = 3, oligopeptide = few (<20), polypeptide = many >20
What is another way that enantiomers differ and how is it denoted?
differ in optical rotation (denoted by +/- rotation)... it is NOT correlated w/ D/L designation of sugar and must be determined experimentally
sphingosine classes (4)
different sphingolipid head region makes different sphingosine class ceramide, sphingomyelin, cerebroside, ganglioside
What three things generally increase in rate as temp increases?
diffusion, facilitated diffusionand osmosis. active transport may or may not be affected by temp, depending on the enthalpy (delta H) of the process
gap junctions
direct cell-cell communication. intercellular transport aka connexons (formed by the alignment and interaction of pores compoesed of six connexin molecules that line up on the pores) transfer of water and solutes between cells proteins generally do not transfer
by convention, AA's are drawn from ____ to ____. why?
drawn from N-terminus to C-terminus b/c that is the way it is synthesized by ribosomes
osmotic pressure. what is it and equation
driving force behind osmosis Π=iMRT i=vant Hoff factor M=molarity R=ideal gas constant T=absolute temperature (in kelvins) colligative property sucking: water moves towards the part with the higher osmotic pressure
why are pyranose/furanose so common?
due to ring strain the only cyclic molecules that are stable in soln are pyranose/furanose
antibody/antigen specificity.. what about the rest of the antibody?
each antibody has an antigen-binding region at the tips of the "Y"; within this region, there are specific polypeptide sequences that will bind one, and only one, specific antigenic sequence rest of antibody = known as constant region and is involved in recruitment and binding of other cells of the immune system (ie macrophages
glycogen granule
each granule has a central protein core with polyglucose chains radiating outward to form a sphere. glycogen granules w/ entirely linear chains have highest density of glucose near the core. if the chains are branched, the glucose density is highest at the periphery of the granuse, allowing more rapid release of glucose on demand
How many acetyl CoA groups are needed to produce palmitate (16:0)
eight
1. NADH, 2. NADPH, 3. Ubiquinone (Coq), 4. Cytochromes, 5. Glutathione
electron carrier Metabolic Pathway 1.---- Glycolysis, fermentation, citric acid cycle, ETC 2. ----- Pentose phosphate pathway, lipid biosynthesis, bleach formation, oxidative stress, photosynthesis 3. ------- ETC 4. ----- ETC 5. ----- Oxidative stress
what happens in peptide bond formation?
electrophilic carbonyl carbon on the 1st AA is attacked by the nucleophilic amino group on the 2nd AA. after that attack, the hydroxyl group of the carboxylic acid is kicked off. result = formation of a peptide amide bond
What type of cell does electrophoresis use? what is the dG? the E?
electrophoresis uses an electrolytic cell (∆G>0, Ecell<0)
endergonic vs exergonic
endergonic = energy input is required (∆G > 0) exergonic = energy is given off (∆G < 0)
pinocytosis
endocytosis of fluids or dissolved particles
phagocytosis
endocytosis of large solids/ bacteria
Typical naming protocol for zymogens
ends in -ogen
How is energy derived during moderately high-intensity continuous exercise
energy is derived from the oxidation of glucose and fatty acids.
Carbon skeletons are used for...
energy, either through gluconeogenesis or ketone body formation
fate of pyruvate from aerobic glycolysis?
enters mitochondria where either 1) converted to acetyl-CoA for entry into citric acid cycle (if ATP is needed) 2) fatty acid synthesis (if sufficient ATP)
Why do hydrophobic residues tend to occupy the interior of a protein while hydrophobic residues tend to accumulate on the exterior portions?
entropy; hydrocarbons are more stable in aqueous solution than in organic ones (H<0) when hydrophobic side chain is placed in aqueous soln, the h2o molecules have to rearrange themselves in specific arrangements to maximize H bonding = -S (negative entropy, decrease in disorder) unfavorable, nonspontaneous G > 0 putting hydrophilic residues on exterior = lets nearby h2o molecules more latitude in their positioning and thus increases entropy, making overal solvation process spontaneous.
the debranching enzyme does what?
enzyme 1 = alpha-1,4:alpha-1,4 transferase 1) breaks an alpha-1,4 bond adjacent to the branch pt and moves the small oligo glucose chain that is released to the exposed end of the other chain 2) forms a new alpha-1,4 bond enzyme 2 = alpha-1,6 glucosidase 3)hydrolyzes the alpha-1,6 bond, releasing the single residue at the branch pt as a free glucose. this represents the only free glucose produced directly in glycogenolysis (as opposed to the glucose produced from glucose 1-phosphate which must be converted by a mutase to glucose 6-p becore it can be converted to glucose via the enzyme glucose 6-phosphatase
Pyruvate dehydrogenase
enzyme from the pyruvate dehydrogenase complex that oxidizes pyruvate, yielding CO2 and while the other two carbons to bind to thiamine pyrophosphate (vitamin B1/TPP)
lock and key enzyme
enzyme is in specific conformation ready for specific substrate no alteration of the tertiary or quaternary structure is necessary upon inding of the substrate
induced fit enzyme... what's going on w/ the energy?
enzyme is relaxed conformation that only gets into substrate specific conformation once the substrate begins to bind. Then, if the substrate is right, the enzyme and substrate fit perfectly together so just like squeezing a stress ball. When you squeeze it changes shape (when the substrate binds, the enzyme changes shape) and this takes ENERGY (endergonic) When you let go, it is exergonic
flippase
enzyme that helps flip a phospholipid from one side of membrane to the other. it is energetially unfavorable bc polar head group of the phospholipid must be forced thru the nonpolar tailr region. so doesn't happen spontaneously that quickly
3 primary protein domains of enzyme linked receptors
enzyme-linked receptors have three primary protein domains: a membrane-spanning domain, a ligand-binding domain, and a catalytic domain
epimerases
enzymes that catalyze the conversion of one sugar epimer to another
epimer
epimers are diastereomers that differ at exactly ONE chiral carbon
ex of catecholamines?
epinephrine/norepinephrine (aka adrenaline/noradrenaline)
If Stand. G is 0, then Keq is
equal to 1
If G is 0, then Q is and Keq is
equal to 1 (but not necessarily Keq, because Keq could be 1000 at a very different temperature and pressure or time of the rxn. Q is only for a current situation that is perturbed from equilibrium and not necessarily at standard temp and pressure)
equlibrium vs homeostasis
equilibrium = a fixed state which prevents us from storing any energy for later use or creating an excitable environment. homeostasis = a physiological tendency toward a relativvely stable state that is maintained and adjusted, often with the expenditure of energy. (our bodies are able to store potential energy in this state)
What bonds are broken during saponification?
ester bonds of triacylglycerols are broken to form a glycerol molecule and salts of fatty acids (soap)
Saponification
ester hydrolysis of triacylglycerols using a strong base (Iye - common name for NaOH or KOH); the result is the cleavage of fatty acid, leaving the sodium salt of the FA and glycerol
Waxes
esters of long-chain fatty acids with long-chain alcohols; protection for plants and animals; prevent excessive evaporation and against parasites; prevent dehydration for animals
examples of motor proteins and where they are
examples = myosin, kinesins and dyneins motile cilia/flagella of bacteria/sperm contraction of the sarcomere in muscle
What are some things we can derive fatty acids from?
excess carbs and proteins from diet can be converted to fatty acids and stored as energy reserves in the form of triacylglycerol
what causes a right shift in the oxygen dissociation curve?
exercise is the right thing to do -high 2,3BPG -low pH -high H+ -high pCO2
HOW IS EXOCYTOSIS IMPORTANT IN NEVEROUS SYSTEM?
exocytosis of neurotransmitters from synaptic vesicles is a crucial aspect of neuron physiology
isoelectric focusing exploits what? how? what else is needed
exploits the acidic and basic properties of amino acids by separating on the basis of isoelectric point; the mixture of proteins is placed in a gel with a pH gradient (acidic gel at the positive anode, basic gel at the negative cathode, and neutral in the middle); an electric field is then generated across the gel
Why are aromatic compounds particularly stable?
extra stability is due to the delocalized pi e-, which can travel throughout the entire compound using available p-orbitals.
t/f motor proteins are not enzymes
f, enzyme is protein w/ catalytic activity, which motor proteins have
phospholipid movement
fast across plane of a membrane through diffusion flippase to move between membrane layers (SLOW)
During times of starvation most tissue will begin relying predominately on ----- for fuel and the brain will begin using ---- for energy. At maximum, ---- of the brain's energy can be derived from this energy source.
fatty acids, ketones, 2/3.... (1/3 is from glucose)
how are hormones levels regualted?
feedback loops /w other endocrine structures
fibrous vs globular proteins? Examples for both
fibrous = proteins w/ structures that resemble sheets ro long strands (ie collagen) globular = spherical (ie hemoglobin)
keratin
fibrous structural protein found in human skin, hair and fingernails. HAS A LOT OF ALPHA HELICES
Dihydrolipoyl dehydrogenase
flavin adenine dinucleotide (FAD) is used as a coenzyme in order to reoxidize lipoic acid, allowing lipoic acid to facilitate acetyl CoA formation in future reactions as lipoic acid is reoxidized, FAD is reduced to FADH2 In subsequent reactions, this FADH2 is reoxidized to FAD while NAD+ is reduced to NADH
cristae
foldings on inner mitochondrial membrane that increase the surface area for integral proteins associated with the membrane
Vitamin B(9) NOT TESTED ON MCAT
folic acid
Besides looking at loss/gain of electrons, how can we tell if a biomolecule is being reduced or oxidized?
for biochemistry, generally increasing bonds to oxygen or other heteroatoms (atoms besides C and H) is oxidation reduction is usually increasing bonds to hydrogen. so conversion of NAD+ to NADH is a reduction reaction
explain concept of zwitterion
for individual AAs the electrically neutral form is called a zwitterion in which the amino group is protonated, the carboxyl group is deprotonated and any side chain is electrically neutral
How can you do larger proteins? Also what is the downside/
for larger proteins, digestion w/ chymotrypsin, trypsin and cyanogen bromide (a synthetic reagent) may be used this digestion selectively cleaveds proteins at specific AA residues, creating smaller fragments which can then be analyzed by electrophoresis or Edman degradation downside: b/c disulfide bridges are broken to reduce the protein to its primary structure, their positions cannot be determined by these methodes
ligand-gated channels
for these channels, the binding of a specific substance or ligand to the channel causes it to open or close; ex. neurotransmitters such as the inhibitory neurotransmitter GABA which binds to a chloride channel and opens it
draw formation of a disulfide bond
formation of disulfide bond requires the loss of 2 protons and 2 electrons (oxidation)
HMG-CoA synthase
forms HMG-CoA from acetyl-CoA
How does acetyl CoA form?
forms via covalent attachment of the acetyl group to the -SH group, resulting in the formation of a thioester (has -SR rather than -OR linkage)
how much energy was required to generate ATP?
free energy change (dG*') of the protons going down their gradient = -220kJ/mol =highly exergonic (makes sense bc phosphorylating ADP to ATP = highly endergonic so needs a lot of energy)
What does F0 do?
functions as an ion channel, so protons travel thru F0 along their gradient back into the matrix. as this happens, a process called chemiosmotic coupling allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP, thus forming ATP
glycogen phosphorylase
functions by cleaving glucose from the nonreducing end of a glycogen branch (the end w/ no free anomeric carbon) and phosphorylating it = produces glucose 1-phosphate
furanosides vs pyranosides
furanosides = glycosides derived from furanose rings pyranosides = gycosides derived from pyranose rings
How do we know phospholipid movment is fast across the plane of the membrane?
fuse 2 membranes that are tagged w/ different labels together tabs will migrate w/ their associated lipids until both types are equally intermixed
Ionizable groups in acidic condition, low pH
gain proton; protonated
galactose metabolism enzymes to remember?
galactokinase galacto-1-phosphate uridyltransferase
lactose structure
galactose-beta-1,4-glucose
secondary lactose intolerance
gastrontestinal disturbances that cause damage to the intestinal lining where lactase is found. occur at any age
The making of a ribosome (the rRNA portion)
genes for 28S, 18S, and 5.8S are found in nucleolus. RNA pol I transcribes them as a single unit w/in nucleolus results in 45S ribosomal precursor. the 45S pre-rRNA is procesed to become either: 1) the 18S rRNA of 40S ribosomal subunit (small subunit) 2) the 28S and 5.8S rRNAs of the 60S (large) subuit Meanwhile: RNA pol II transcribes the 5S rRNA (found in the 60S subunit(. this happens outside the nucleolus
How does glucagon causeincreased lipolysis in liver
glucagon actiavtes hormone-sensitive lipase in the liver. bc action is on the liver and not the adipocyte, glucagon is NOT considered a major fat-mobilizing hormone
How does glucagon cause increased glycogenolysis
glucagon activates glycogen phosphorylase and inactivates glycogen synthase
----- and ---- levels rise when the body is starving.
glucagon and epinephrine
How does glucagon cause increased liver gluconeogenesis
glucagon promotes the conversion of pyruvate to phosphoenolpyruvate by pyruvate carboxylase and phosphoenolpyruvate carboxykinase (PEPCK) -it also increases conversion of fructose 1,6bp to fructose 6p by fructose 1,6bisphosphatase
glucocorticoids increase the impact of ---- and ------.
glucagon, catecholamines
glucagon vs insulin
glucagon= is associated with the fasting post absorptive metabolic state. insulin = well-fed, absorptive metabolic state enzymes taht are phosphorylated by glucagon are generally dephosphorylated by insulin and vice versa
source of acetyl CoA
gluconeogenesis requires acetyl CoA to occur (to inhibit pyruvate dehydrogenase and stimulate pyruvate carboxylase). so gluconeogenesis is inextricably linked to fatty acid oxidation the source of acetyl CoA can't be glycolysis bc this would just burn the glucose that's being generated in gluconeogenesis
Glucagon increases blood glucose levels by promoting ----- and ------ in the liver.
gluconeogenesis, glycogenolysis
--------- plays an important role in maintaining blood glucose levels during prolonged fasting.
gluconeogenesis... after 24 hours, gluconeogenesis is predominant source of glucose for body
the major fuels of skeletal muscles are _ and _ does skeletal muscle use a lot of fuel?
glucose and fatty acids. skeletal muslce is the body's major consumer of fuel
Insulin increases ---- and ---- in muscle and fat.
glucose uptake and carbohydrate metabolism
maltose structure
glucose-alpha-1,4-glucose
Nonpolar, Nonaromatic Side Chains
glycine, alanine, valine, leucine, isoleucine, methionine, proline (GAVLIMP)
Between glycogen and amylopectin, which one have a higher rate of enzyme activity from enzymes that cleave side branches? Why?
glycogen has higher rate of enzymatic branch cleavage because it contains more branching than amylopectin
rate limiting enzyme in glycogenolysis
glycogen phosphorylase
How is glycogen stored
glycogen stored as granules_ in the cytoplasm of the liver
Insulin promotes ------ synthesis in liver and muscle.
glycogen synthesis
Insulin also increases ------- in the liver by increasing the activity of ----- and -------, while decreasing the activity of enzymes that promote --------- ( ex. ------ and -----).
glycogen synthesis, glucokinase, glycogen synthase, glycogen breakdown, glycogen phosphorylase and glucose-6-phosphatase
Resting muscle conserves carbohydrates in ----- stores and uses ----- from the bloodstream.
glycogen, free fatty acids
pathways to making acetyl CoA
glycolysis, fatty acid oxidation, amino acid catabolism, ketone bodies, alcohol
Draw α,α-1,1 linkage
glycosidic bond btwn 2 anomeric carbons
Are transgenic mice good for studying dominant genes? recessive?
good for studying dominant genes. bc transgene coesxists in the animals w/ their own copies of the gene, which have not been deleted. not so good for studying recessive diseases bc # of copies of the gene that insert into genome cannot be controlled.
If Stand. G is negative, then Keq is
greater than 1
Vitamin K
group of compounds including phylloquinone (K1) and menaquinones (K2); important to the posttranslational modification required to form prothrombin
How are terpenes grouped?
grouped according to #isoprene units present
How to go from fischer to haworth projection
groups on right in fischer projection will point down
Km, because it is described at 1/2 Vmax, is the blank point
half saturation point. It is the rate when 50% of active sites are being used by the substrate. This makes it a constant for the reaction that can be scaled up or down (change enzyme concentration or substrate concentration and it will never change)
In addition to the 5' cap, exons, and 3' cap, what else does mRNA have?
has 5' and 3' Untranslated regions (UTRs)
Triterpenes
has 6 isoprene units; can be converted to cholesterol and various steroids
Tetrapeterpenes
has 8 isoprene units; ex. carotenoids, b-carotene and lutein
collagen
has a characteristic trihelical fiber (three α-helices woven together to form a secondary helix) and makes up most of the extracellular matrix of connective tissue; it is found throughout the body and is important in providing strength and flexibility
Things of note about cystein
has a thiol (-SH) group in its side chain b/c sulfur is larger and less EN than oxygen, the S-H bond is weaker than the OH bond. THis leaves the thiol group in cystein prone to oxidation
Saturated fatty acid
have only single bonds; have great van der Waals forces and a more stable structure; solid in R/T
Sphingolipids
have sphingosine or sphingoid backbone; long chain, nonpolar fatty acid tails and polar head groups; can either have a phosphodiester bond, therefore be phospholipids or glycosidic linkage, therefore be glycolipids ex. ceramide, sphingomyelin, cerebrosides, globosides, ganglioside
where do hemiacetals derive from? hemiketals?
hemiacetals = from aldoses hemi ketals = from ketoses
Glycoside formation... reactants? leaving group?
hemiacetals react w/ alcohols to form acetals. The anomeric hydroxyl group is transformed into an alkoxy group, yielding a mix of α and β-acetals (w/ water as a leaving group. The resulting carbon-oxygen bonds are called glycosidic bonds and the acetals formed are glycosides
what else does glucagon stimulate?
hepatic gluconeogenesis. but response is slower than that of glycogenolysis (glycogenolysis begins as soon as the body enters the post absorptive state, while gluconeogenesis takes about 12 hours to hit its maximum velocity.)
primary lactose intolerance
hereditary deficiency of lactase
The Pentose phosphate pathway (PPP) is also known as the
hexose Monophosphate shunt (HMP)
why is ATP so high energy?
high energy phosphate bonds. the (-) charges on the phosphate groups experience repulsive forces w/ one another and the ADP and Pi molecules that form after hydrolysis are stabilized by resonance
1,3-BPG and PEP?
high-energy intermediates used to generate AATP by substrate-level phosphorylation. this is the only aTP gained in anaerobic respiration.
outer mitochondrial membrane
highly permeable bc of large pores which allow for passage of ions and small proteins -completely surrounds inner mito membrane with intermembrane space between them
What are some common ways of isolating proteins
homogenization -> centrifugation (crude isolation) electrophoresis, chromatography (Can be used for native or denatured proteins
generally what occurs in chromatography? why is it valuable?
homogenized protein mixture to be fractionated thru a porous matrix is valuable b/c the isolated proteins are immmediately available for ID and quantification
fischer projection conventions
horizontal lines are OUT of page vertical lines are INTO page
thyroid hormone activity is largely permissive, meaning what?
hormone levels are kept more or less constant, rather than undulating w/ changes in metabolic state
How does the human body store spare energy? Why doesn't the human body store most energy as sugar?
human body stores energy as glycogen and triacylglycerol; triacylglycerols are preferred because their C are more reduced, resulting in a larger amount of energy yield per unit weight and due to their hydrophobic nature, they do not need to carry extra weight from hydration
2 examples of hydrophobic side chin 2 examples f hydrophilic side chain
hydophobic = phenylalanine and leucine philic = serine or lysine
What helps enzymes bind to their substrates?
hydrogen bonding, ionic interactions and transient covalent bonds w/in the active site all help stabilize the enzyme substrate complex and contribute to the efficiency of the enzyme
ATP provides energy through ----- and ----- to energetically unfavorable reactions.
hydrolysis and coupling
How are the high-energy phosphate bonds of ATP stabilized?
hydrolysis by resonance, ionization, and loss of charge repulsion
cholesterol structure
hydrophobic and hydrophilic regions
in hypoglycemic conditions, what happens to maintain brain glucose concentrations?
hypothalamic centers sense fall in Blood glucose level and release of glucagon and epinephrine is striggered
example of how cadherins are type specific
ie epithelial cells use E-cadherin while nerve cells use N-cadherin
example of a conjugated protein
ie hemoglobin (and myoglobin) contains prosthetic group called heme = contians an iron atom in its core, binds to and carries oxygen. as such, it is inactive w/o the heme group
example of an integrin
ie integrin α,IIb,β₃ = allows platelets to stick to fibrinogen = a clotting factor, which causes activation of platelets to stabilize the clot
ex of equilibrium vs homeostasis
ie we keep the Na concentrations much higher outside a neuron than in bc it makes a gradient that stores energy.. it is NOT at equilibrium
Explain WHY isoelectric focusing works w/ an example
ie: lets say we had a protein w/ pI = 9. if we put it in the middle of the gel (pH = 7) there will be a lot of protons around the protein. the protons will attach to available basic sites on protein, creating a net positive charge on molecule this charge will then cause the protein to be attracted to the negatively charged cathode, which is located on the basic side of the gradient as the protein moves closer to the cathode, the pH of the gel slowly increases. Eventually, as the protein nears the pH of 9, the protons creating the positive charge will dissociate and the protein will become neutral again and thus be unaffected by the electric field
fate of glycolysis products?
if a cell has a mitochondria, and oxygen, the energy carriers produced in glycolysis (NADH) can feed into the aerobic respiration pathway to generate energy for the cell. if mitochondria or oxygen is lacking (ie in erythrocytes or exercising skeletal muscles respectively) glycolysis may occur anaerobically, tho some of the available energy is lost
Fate of NADH from this step?
if glycolysis is aerobic, the NADH can be oxidized (indirectly) by the mitochondrial e- transport chain, providing energy for ATP synthesis by oxidative phosphorylation.
How does soap work?
if we try to combine aqueous soln w/ oil, the soln won't mix. but if we add soap, the two phases would appear to combine into a single phase, forming a colloid. this occurs bc of the formation of micelles = nonpolar compounds can dissolve in the hydrophobic interior of the water soluble miclle, meaning that our cleaning agents can dissolve both water soluble and insoluble messes and wash them away together
how are micelles important in our body?
important for absorption of fat-soluble vitamins (ADEK) and complicated lipids like lecithins. fatty acids and bile salts secreted by the gallbladder form micelles that can deliver the fatty acids/vitamins/cholesterol to the cells of the small intestine
When do Nucleotide excision repair/Base Excision repair occur (ie what phase)
in G1 and G2 cell cycle phases
fermentation
in absence of oxygen, fermentation will occur. the key fermentation enzyme in mammalian cells = lactate dehydrogenase which oxidizes NADH to NAD+, replenishing the oxidized coenzyme for G3P dehydrogenase. there is no net loss of carbon in the process of fermenting.
types of chromatography
in chromatography for protein separation, common properties include charge, pore size, and specific affinities
retention time high vs low retention times
in chromatography, the amount of time a compound spends in the stationary phase components w/ high retention times migrate slowly those w/ low = migrate faster
where is PEPCK? what is it induced by?
in cytoplasm, induced by Glucagon and cortisol (act to raise blood sugar levels)
How can you predict where the compounds will go in electrophoresis
in electrophoresis, negatively charged compounds will migrate toward the positively charged anode, and positively charged compounds will migrate toward the negatively charged cathode
Ex of cleavage event
in insulin, insulin needs to be cleaved from a larger, inactive peptide. also, in peptides w/ signal sequences, the signal sequence must be cleaved if the protein is to enter the organelle and accomplish its function
When does the protein stop moving?
in isoelectric focusing, a protein stops moving when pH=pI
How do you know which way proteins move and when do they stop?
in isoelectric focusing, proteins that are positively charged will begin migrating toward the cathode and proteins that are negatively charged will begin migrating toward the anode; as the protein reaches the portion of gel where the pH is equal to the protein's pI, the protein takes on a neutral charge and will stop moving
fate of acetyl CoA in different places?
in muscle and adipose = enters citric acid cycle in liver = stimulates gluconeogeneiss by activating pyruvate carboxylase (remember, it can't be converted back to glucose) In fasting state = liver produces more acetyl CoA from beta oxidation than is used in TCA cycle so it is used to make ketone bodies (basically 2 acetyl CoA molecules linked together)
the threshold level is higher in negative energy balance than positive energy balance.... this means what?
in other words, larger changes must be made to lose weight than to gain it
Which compounds will migrate
in regards to chromatography, components that have a high affinity for the stationary phase will barely migrate at all; components with a high affinity for the mobile phase will migrate much more quickly
partitioning
in regards to chromatography, varying retention times of each compound in the solution results in separation of the components within the stationary phase, or ___. each component can then be isolated individually
Which end of the gel is +/-?
in relation to isoelectric focusing, a quick way to remember pH of each end of the gel is to recall that we associate acids with protons, which carry a positive charge, and thus the anode is positively charged; we associate bases with the negatively charged hydroxide ion, which gives us the negatively charged cathode
digstion of prteins begins where?
in stomach w/ pepsin. continues w/ pancreatic proteases: trypsin, chymotrypsin, and carboxypeptidases A and B (all are secreted as zymogens)
Where is PFK-2 mostly found? WHY is it important??
in te liver... by activating PFK-1, it allows these cells to override theinhibition caused by ATP so that glycolysis can continue, even when the cell is energetically satisfied. the metabolites of glycolsysis can thus be fed into the production of glycogen, fatty acids, and other storage molecules rather than just being burned to produce ATP
How does GLUT 2 also help regulate insulin
in the Beta-islet cells of the pancreas, GLUT 2, along w/ the glycolytic enyzme glucokinase, serves as the glucose sensor for insulin release
When is fatty acid synthase/palmitate synthase induced?
in the liver folowing a meal high in carbs bc of elevated insulin levels
other uses for glycolysis intermediates
in the liver, glycolysis is part of the process by which excess glucose is converted to fatty acids for storage
voltage-gated channels
in these channels, the gate is regulated by the membrane potential near the channel
What are zymogens?
inactive forms of dangerous enzymes that must not be active until absolutely necessary. They have a catalytic (active) domain and a regulatory domain. the regulatory domain must be either removed or altered to expose the active site
Unsaturated fatty acid
includes one or more double bonds which introduces kinks into the chain that makes it difficult fro them to stack and solidify; liquids in R/T
thyroid hormones do what?
increase basal metabolic rate (which leads to increased O2 consumption and heat production)
catecholamines do what to adipose tissue?
increase lipolysis by increasing the activity of hormone sensitive lipase
glucagon causes what?
increased glycogenolysis increased liver gluconeogenesis -increased liver ketogenesis and decreased lipogenesis -increased lipolysis in liver
6 adaptions the body goes through when at higher altitude elevations (low pO₂):
increased respiration increased oxygen affinity for hemoglobin, increased rate of glycolysis increased 2,3BPG in RBC normalized oxygen affinity for hemoglobin restored by the increase of 2,3BPG increased hemoglobin.
Insulin's effect on metabolism of fats = Increases ___?
increases glucose and triglyceride uptake by fat cells -lipoprotein lipase activity which clears VLDL and chylomicrons from the blood. -triacylglycerol synthesis (lipogenesis) in adipose tissue and the liver from acetyl-CoA.
epinephrine does what to heart?
increases basal metabolic rate thru sympathetic nervous system ("adrenaline rush"
what does calcitriol do?
increases calcium and phosphate uptake in the intstines = promotes bone production
Leading up to a temperature optima, temperature increases of BLANK degrees Celsius cause the velocity to BLANK
increaseses of 10*C tend to lead in a doubling of enzyme velocity until optimum temp is reached
How can someone increase enzyme concentration biologically?
induce the expression of genes coding for that enzyme
2 types of operons
inducible systems repressible systems
Inhibitors of PFK1? Activators?
inhibited by ATP and Citrate, activated by AMP. this is because the cell should turn off glycolysis when it has sufficient energy (high ATP) and turn on glycolysis when it needs energy (highAMP). citrate is an intermediate of the Citric acid Cycle so high levels of citrate also imply that the cell is producing sufficient energy.
Why is cyanide toxic?
inhibitor to cytochrome c oxidase (specifically subunits a and a,3,). the cyanide anion is able to attach to the iron group and prevents the transfer of e-. tissues that rely heavily on aerobic respiration (ie heart/CNS) are greatly impacted
what lowers blood sugar levels?
insulin
lipoprotein lipase is induced by what hormone?
insulin lipoprotein lipase = found incapillary bed of adipose tissue.
Pyruvate dehydrogenase is activated by what?
insulin (in liver) = bc high insulin levels signal to the liver than the individual is in a well-fed state; thus the liver should not only burn glucose for energy but shift the fatty acid equilibrium toward production and storage rather than oxidation - in nervous system, the enzyme is not responsive to hormones
after a meal, what happens with insulin and skeletal muscles?
insulin promotes glucose uptake in skeletal muscle which replenishes glycogen stores and AAs for protein synthesis. both excess glucose and AAs can be oxidized for energy
Insulin interactions w/ PFK1 and intermediates? what about glucagon?
insulin stimulates PFK-1. glucagon inhibits PFK1 -both do so by inderect mechanisms involving PFK-2 and fructose 2,6 bisphosphate -INSULIN: activates PFK-2 which converts a tiny amount of fructose -6phophate to fructose 2,6 bisphosphate...F2,6-BP activates PFK 1 -GLUCAGON: inhibits PFK-2, which lowers F2,6-BP and thereby inhibits PFK-1
Adipose tissue stores lipids under the influence of ---- and releases them under the influence of --------.
insulin, epinephrine
carriers
integral membrane proteins used in facilitated diffusion open to one side of the membrane or the other (not both at the same time!)... like a revolving door. bind to extracellular-->conformational change-->open on other side occluded state: when closed on both sides
channels
integral membrane proteins used in facilitated diffusion rapid transport kinetics either open to both sides or closed to both sides... like a tunnel
integrins? Structure?
integrated in the membrane and bind the extracellular matrix a group of proteins that all have two membrane-spanning chains called α and β;
Quaternary Structure. how is it stabilized? examples?
interaction between separate subunits of a multisubunit protein; stabilized by van der Waals forces, H bonds, ionic bonds, covalent bonds not necessarily present in all proteins. ex = hemoglobin/immunoglobins hemoglobin structure = 4 subunits, each of which binds 1 molecule of O2 immunoglobin G (IgG) antibodies = 4 total subuits each
Where in the cell does beta-oxidation (fatty acid oxidation) occur?
intermembrane space
how do we test for presnece of starch?
iodine it fits inside the helix conformation amylose typically makes, forming a starch-iodine complex
Pyruvate dehydrogenase Complex (PDH) reaction
irreversible and can't be used to convert acetyl CoA to pyruvate or glucose
Draw alpha-1,6 glycosidic bond
is btwn 2 D-glucose molecules, the alpha anomeric carbon of the 1st glucose (C-1) attaches to the C-6 of the second glucose the second glucose can be either alpha or beta
glycogen: where is it found, structure
is carbohydrate storage in animals similar to starch except it has more alpha-1,6 glycosidic bonds (1/10 glucose molecules vs amylopectin = 1/25 glucose molecules)
"charged tRNA
is considered charged or activated when bound with an amino acid
Alpha Carbon
is the carbon adjacent to the carboxyl carbon; chiral center - except for glycine
Which two purification methods are based on the same principle? why?
isoelectric focusing and ion-exchange chromatography both separate proteins based on charge; the charge of a protein in any given environment is determined by its isoelectric point (pI)
explain cooperative binding of hemoglobin
it acts as a transport protein rather than an enzyme, resulting in a characteristic sigmoidal binding curve
How is proline unique
it forms a CYCLIC amino acid in all other AAs the amino group is attached ONLY to the alpah carbon. In proline, the amino nitrogen becomes part of the side chain, forming a 5 membered ring the ring places notable constraints on the flexibility of proline which limits where it can appear in a protein and can have significant effects on proline's role in secondary structure
Fructose 2,6BP is sometimes thought of as a marker for satisfactory energy levels in cells, why?
it helps cells override the inhibition of phosphofructokinase-1 that occurs when high levels of acetyl=CoA are formed, signaling to the liver cell that it should shift its function from burning to storing fuel
source of acetyl CoA in gluconeogenesis is what?
it is NOT from glycolysis and pyruvate dehydrogenase, but from fatty acids so to produce glucose in liver during gluconeogenesis, fatty acids must be burned. also, the forward flow of the citric acid cycle must be stoped
what does F-1,6-BP do?
it is in the cytoplasm and is a key control point of GNG and represents the rate limiting step of the process. it reserves the action of PFK-1 (the rate limiting step of glycolysis) by hydrolyzing phosphate from F-1,6-BP to produce F-6-P.
glyceraldehyde is a ____ _______ =a ___(aldose or ketose)_____
it is polyhydroxylated aldehyde = it is an aldose
Is Methionine polar or not, why?
it is relatively nonpolar despite having a sulfur so Methionine is one of only 2 AA's hat contain a sulfur atom in its side chain. Nevertheless, bc the sulfur has a methyl group attached, it is relatively nonpolar
If the Km is high, then
it needs a lot of substrate to reach half-saturation. This implies that it has low affinity for its substrate.
If the Km is low, then
it needs very little substrate to reach half saturation. This implies that it has a high affinity for its substrate.
what happens once acyl-carnitine crosses the inner membrane?
it transfers the fatty acyl group to a mitochondrial CoA-SH via another transesterification rxn. once acyl-CoA is formed in the matrix, Beta oxidation can occur which removes 2 carbon fragments from the carboxyl end
where is lactase present?
its a brush-border enzyme of the duodenum.
how is amylopectin degraded?
its branched, so debranching enzymes degrade the polysaccharide chain
What happens to the resulting galactose 1-phosphate?
its converted to glucose 1-phosphate by Galactose-1-phosphate uridyltransferase (GALT) and epimerase
importance of ribulose 5p?
its created in the PPP and is isomerized to ribose 5-p = the backbone of nucleic acids when coupled to a nitrogenous base, it forms a nucleotide that can be integrated into RNA
what inhibits the PPP or HMP shunt? what activates it?
its product, NADPH. it is activated by its reactant, NADP+.
What does proline serve in secondary structure?
its rigid cyclic structure causes it to introduce kinks in alpha helices or create turns in beta-pleated sheets bc it causes the kinks in the alpha helices, it is rarely found in them, except in helices that cross the cell membrane similarly, it is rarely found in the middle of peated sheets. more often found in the turns btwn the chains of the beta-pleated sheets or as the residue at the start of an alpha helix
For the following reaction E + S --> ES --> E + P, how do the rates relate to Km?
k1 is first forward reaction k2 is reverse of first reaction k3 is second forward reaction Km = k2 + k3 / k1 SO! Km will be large when the dissociation of ES happens more rapidly than its formation (low affinity). Km will be small when the formation of ES happens more rapidly than its dissociation (high affinity).
famous inducible system?
lac operon = contains gene for lactase. bacteria can digest lactose, but it is energetically expensive than digesting glucose. so bacteria only want to use it if lactose is high and glucose is low so induced by presence of lactose.
What are the 3 important gluconeogenic intermediates in the gluconeogenesis pathway?
lactate, alanine, glycerol 3-phosphate. each have enzyems that convert them into glycolytic intermediates.
Lactose
lactose (a disaccharide) is hydrolyzed into galactose and glucose by lactase. lactose = important source of galactose
pyruvate kinase
last enzyme in aerobic glycolysis. catalyzes a substrate-level phosphorylation of ADP using the high-energy substrate phosphoenolpyruvate (PEP)
Physiological concentrations are much -(less/more)-- than standard concentrations.
less
inducible systems are like __(positive or negative) control/ what type of inhibition...how?
like positive control or competitive inhibition as the concentration of the inducer increases, it will pull more copies of the repressor off of the operator region, freeing up the genes for transcription. useful bc allows gene products to be produced only when they're needed
Primary Structure
linear arrangement of amino acids coded in an organism's DNA; stabilized by formation of covalent peptide bonds between amino acids
Common examples of hydrolases
lipases (hydrolyze lipids) phosphatases (hydrolyze something to cleave off a phosphate group, commonly seen on MCAT) peptidases (hydrolyze peptide bonds in proteins) nucleases (hydrolyze nucleic acids)
names of proteins w/ lipid prosthteic groups? carbohydrates? nucleic acid?
lipid prosthetic groups = lipoproteins carbohydrates = glycoproteins nucleic acid = nucleoproteins
lipid raft movement
lipid rafts are colections of similar lipids w/ or w/o associated proteins that serve as attachment points for other biomolecules. often serve roles in signaling. travel slowly across the plane of a membrane
general membrane structure and function
lipid rafts contain proteins and signaling areas glycoprotein coat has carbohydrates phospholipid bilayer
Starvation also leads to rapid amounts of -----, which results in ______
lipolysis, excess acetyl-CoA that is used in the synthesis of ketone bodies.
After glycogen stores are filled, what happens?
liver converts excess glucose to fatty acids and triacylglycerols
glycogen in liver vs skeletal muscle
liver glycoen is broken down to maintain a constant level of glucose in the blood/prevent low blood sugar muscle glycogen is broken down to provide glucose in the muscle during vigorous exercise
Name the 3 major target tissues for insulin.
liver, muscle, and adipose tissue
Secondary Structure
local structure determined by the hydrogen bonding between nearby amino acids; alpha-helices and beta-pleated sheets
RNA Polymerase I
located in nucleolus. synthesize rRNA
lipid storage
long term changes in body fat result from changes in -----.
are these transcriptional level regulations long or short term?
longer range effects.
Ionizable groups in basic condition, high pH
lose proton; deprotonated
What is cytosine deamination?
loss of an amino group from cytosine resulting in a uracil
Transamination
loss of an amino group from the amino acid. remaining carbon skeleton can be used for energy loss of an amino group from the amino acid can also happen via deamination
-------- and the ingestion of a meals rich in ------ both lead to glucagon secretion.
low blood sugar (hypoglycemia), protein (hypoglycemia = most important physiological promoter of secretion and hyperglycemia = most important inhibitor!
Surfactant
lowers the surface tension at the surface of a liquid, serving as a detergent or emulsifier; ex. soap
Positively Charged Amino Acids
lysine, arginine, histidine (LAH)
Hydrophilic Amino Acids
lysine, arginine, histidine, glutamate, aspartate, asparagine, glutamine ie AAs w/ charged side chains and the amides
Translation requires what 5 things
mRNA tRNA ribosomes AAs energy in the form of GTP
Monocistronic, polycistronic
mRNA (Messenger RNA) is monocistronic in eukaryotes - is polycistronic in prokaryotes
mRNA
mRNA (messenger RNA) carries the information specifying amino acid sequence of protein to the ribosome and is transcribed from template DNA in the nucleus BY RNA polymerase!!! then undergoes post-transcriptional modifications and carries the message from DNA in the nucleus, travels into the cytoplasm to be translated
What are the three main types of RNA found in cells:
mRNA (most abundant by far), tRNA, and rRNA
Polycistronic
mRNA codes into different products depending on where translation starts. so in prokaryotes, they can sometimes start the process of translation at different locations in the mRNA which will result in different proteins
Monocistronic
mRNA codes into only one product. thus, in eukaryotes, the cell has a different mRNA molecule for each of the thousands of different proteins in that cell
cellulose, where is it found, how are the D-glucoses linked?
main structural component of plants a chain of Beta-D-glucose molecules linked by B-1,4 glycosidic bonds Hydrogen bonds hold the actual polymer chains together for support
Terpenes are mainly produced by what?
mainly produced by plants and some insects can be a protective mechanism
Na/K pump
maintains low Na, high K concentration inside the cell 3 Na out for every 2 K in maintains negative resting potential
Sphingomyelins
major class of sphingolipids; have either phosphatidylcholine or phosphatidylethanolamine as a head group and bound by a phosphodiester bond are phospholipids ("sphingophospholipids)
how does human calorimetry work
makes use of large insulated chambers w/ specialized heat sinks to determine energy expenditure. is expensive so usually other measures of BMR are used
Cofactors are what? aka? concentration in the cell?
many enzymes require nonprotein molecules called cofactors/coenzymes to be effective. they are usu. small in size so they can bind to the active site of the enzyme and participate in the catalysis of the rxn (usu by carrying charge thru ionization, protonation, or deprotonation usually in low conectrations in the cell so they can be recruited only when needed
role of CAMs in cancer other role?
many medications target selectins and integrins. ie research shows that ability of cancer cells to metastasize = assoc w/ unique expression patterns of CAMs. by targeting these CAMs, metastatsis may be avoided also: to stop clotting process during heart attacks, other medications target CAMs used by platelents
opsonization
marking the pathogen for destruction by other white blood cells immediately, this marking function is also called opsonization
exocytosis
material is released from inside the cell to extracellular environment nervous system and intercellular signaling
sources of cholesterol
may be obtained through dietary sources (LDL or HDL) or through de novo synthesis in the liver (driven by acetyl-CoA and ATP)
Silent Mutation
means that there is no effect on the synthesis and expression of proteins Most mutations w/in introns also don't change protein sequence bc they are spliced out prior to translation
What can get thru the membrane itself/
membrane = 2 layers of phospholipids. permits fat soluble compounds to cross easily.
peripheral proteins
membrane associated does not actually touch the proteins bound through electrostatic interactions with lipid bilayer or other transmembrane embedded proteins signaling/recognition
cholesterol
membrane fluidity/membrane stability necessary for synthesis of all steroids which are derived from cholesterol.
enzyme linked receptors
membrane receptors that also display catalytic activity in response to ligand binding
what are glycerophospholipids used for?
membrane synthesis can produce hydrophilic surface layer on lipoproteins (i.e. very-low-density-lipoprotein, VLDL, a lipid transporter)) main component of cell membranes, structural function but also serve as second messengers in signal transduction phosphate group serves as point of attachment for water soluble groups
Steroids
metabolic derivatives of terpenes; have 4 cycloalkane rings fused together: three cyclohexane and 1 cyclopentane
how do we get the acetyl CoA
metabolism of carbs, fatty acids, AAs
Common way of making a transgenic mouse
microinject the cloned gene into the nucleus of a newly fertilized ovum 2) Implant ovum into surrogate mother. the resulting offspring should contain the transgene in all of their cells, including germ line cells (gametes). thus transgene will also be passed to their offspring
ATP is a ------- energy carrier. why is this a good thing?
mid-level energy carrier. think about your wallet, if you never had the ability to get change back acter a purchase, what type of bill would you want? $1!! similarly, ATP can't get back "leftover" free energy after a reaction, so its best to use a charrier w/ smaller free energy
Most of the ATP in a cell is produced by -------, but some ATP is produced during ---- and the -----.
mitochondrial ATP synthase, glycolysis, citric acid cycle
Mixed vs Noncompetitive inhibitors
mixed inhibition rexults when an inhibitor can bind to either the enzyme or the enzyme substrate complex BUT HAS A DIFFERENT AFFINITY FOR EACH!! if the inhibitor had the SAME affinity for both, it would be a NONcompetitive inhibitor
connexins
molecules that align and interact with pores to make gap junction
Amino Acids
molecules that contain three functional groups: an amino group (-NH2) and a carboxyl group (-COOH) and a variable R group
most basic form of carbs?
monosaccharides
what rxns can monosaccharides undergo
monosaccharides contain alcohols and either aldehydes or ketones thus can undergo redox, esterification, and nucleophilic attack (creates glycosides)
in the postprandial state would there be more anabolism or catabolism? what happens in our body? how long does it last?
more anabolism -nutrients flood in from gut and make their way via hepatic portal vein to the liver. lasts 3-5 hours after eating
Enzymes often require BLANK cofactors or coenzymes
more than one!
Gangliosides
most complex sphingolipids. glycolipids that have polar head groups composed of oligosaccharides with one or more NANA (aka sialic acid) molecules at the terminus and a negative charge
active transport
movement of solute against its concentration gradient always uses energy primary and secondary non-spontaneous positive deltaG rate depends on change in H and T
Which direction does the ribosome move?
moves in 5' to 3' dirction along the mRNA (synthesizes protein from N to C terminus
inner mitochondrial membrane
much more restrictive permeability. has numerous infoldings (cristae) = increase available surface area for integral proteins associated w/ the membrane -encloses the mitochondrial matrix -where the e- transport chain is
body protein is catabolized mainly where?
muscle and liver
after 1-3 hours of continuous moderately straining exercise, what happens?
muscle glycogen stores become depleted and intensity of exercise declines to a rate that can be supported by oxidation of fatty acids
What is an example of a non-coding mutation that could be lethal?
mutations in splice sites can lead to abnormal proteins. ie: mutations that interfere w/ proper splicing of Beta-globulin mRNA are responsible for some cases of Beta-thalassemia (blood disorder that hinders the production and efficacy of hemoglobin)
Naming of disaccharides: how are they named?
named for the configuration of the anomeric carbon and the numbers of hydroxyl containing carbons involved in the linkage]]IF glycosidic bond is formed btwn 2 anomeric carbons, this must be specified in the name
G protein: what are they? how do they bind/how is it helped, what does it do?
named for their intracellular link to guanine nucleotides (GDP and GTP) the binding of a ligand increases affinity of the receptor for the G protein. the binding of the G protein represents a switch to the active state and affects the intracellular signaling pathway
At the pI, what would you expect the titration curve to look like?
nearly vertical
When the metabolic phosphate compound is on the reactant side its modified standard free energy state value is -----.
negative
----- and ----- are insensitive to insulin.
nerve tissue and red blood cells
Insulin does not effect the glucose uptake of what parts of our body?
nervous tissue, kidney tubules, intestinal mucosa, red blood cells, and beta cells of the pancreas
Vitamin B3
niacin (NAD).. THREE letters
common stationary phases for affinity chromatography
nickel (used in separation of genetically engineered proteins w/ histidine tags; antibodies/antigens enzyme substrate analogues (which mimic the natural substrate for an enzyme of interest)
Native PAGE/how it works/benefits?
no denaturants in the gel benefits = functional native protein can be recovered from the gel after electro phoresis BUT ONLY IF THE GEL HAS NOT BEEN STAINED (most stains denature proteins
Do sphingomyelin head groups have a charge? what are they used for?
no net charge are a major component in the plasma membrane of cells producing myelin (oligodendrocytes and Schwann cells), the insulating sheath for axons
can we digest cellulose?
no, we lack cellulase enzyme needed to hydrolyze cellulose to glucose monomers. thus they serve as a good source of fiber, drawing water into the gut
allosteric site
non catalytic regions of the enzyme that bind regulators
----- reactions proceed in the reverse direction and have a +(delta G).
non-spontaneous
Alanine: characteristics, 3 letter code and 1 letter code and structure
nonpolar, nonaromatic hydrophobic ala A
Isoleucine: characteristics, 3 letter code and 1 letter code and structure
nonpolar, nonaromatic hydrophobic ile I
Leucine: characteristics, 3 letter code and 1 letter code and structure
nonpolar, nonaromatic hydrophobic leu L
Valine: characteristics, 3 letter code and 1 letter code and structure
nonpolar, nonaromatic hydrophobic val V
Methionine: characteristics, 3 letter code and 1 letter code and structure
nonpolar, nonaromatic met M
Proline: characteristics, 3 letter code and 1 letter code and structure
nonpolar, nonaromatic pro P
Glycine: characteristics, 3 letter code and 1 letter code and structure
nonpolar, nonaromatic, Achiral hydrophobic gly G
positive delta G
nonspontaneous energy is incresing
salinity's effect on enzymes
not generally of physiologic signficance, but IN VITRO, can be a factor. increasing levels of salt can disrupt H bonds and ionic bonds causing denaturation
function of introns?
not well understood. hypothesized that introns are important in regualtion of cellular gene expression levels and in maintaining the size of our genome. Existence of introns has also been hypothesized to allow for rapid protein evolution. 3) many eukaryotic proteins share peptide sequences, suggesting that the genes encoding for these particular peptides may employ a modular function (ie contain standard sequences that can be swapped in and out, depending on the needs of the cell.
Once the mRNA transcript is created and processed it can exit the nucleus through _______ _______
nuclear pores
Ligases are most often found during
nucleic acid synthesis and repair
So are AMP/ADP/ATP nucleosides or nucleotides?
nucleotides
i van't hoff factor
number of particles obtained from the molecule when in solution ex: NaCl is 2 glucose is 1
cholesterol function in bilayer
occupies space between phospholipids to prevent formation of crystal structures in the membrane = increase its fluidity increases stability by linking interactions at polar head group and hydrophobic interactions at tails
what are the 2 major functions of the Pentose phosphate pathway (PPP) Where does it happen
occur in cytoplasm of all cell production of NADPH and serving as a source of ribose-5-phosphate for nucleotide synthesis.
What is another way to separate proteins? What is it called
on the basis of their isoelecetric point, pI called isoelectric focusing
what happens when GDP is replaced w/ GTP (2possibilities)
once GDP is replaced with GTP, the α subunit is able to dissociate from the β and γ subunits; the activated α subunit alters the activity of adenylate cyclase; if the α subunit is αs, then the enzyme is activated; if the α subunit is αi, then the enzyme is inhibited
What happens when GTP -> GDP?
once GTP on the activated α subunit is dephosphorylated to GDP, the α subunit will rebind to the β and γ subunits, rending the G protein inactive
unsaturated fatty acids
one or more double bonds or other multiple bonds at room temperature make kinks fluidity in membrane regarded as "healthier"
Enzyme specificity essentially means that an enzyme will only catalyze ____ or ______.
one reaction or a set of similar reactions for a class of substrates
What is another example of a rgulatory enzyme?
one that is covalently modified (phosphorylation or dephosphorylation OR glycosylation/deglycosylation)
embedded proteins
only associated with cytoplasmic or extracellular surface of cell membrane catalytic activity linked to nearby enzymes
How would you duplicate a gene in parallel?
open the gene w/ helicases and permit DNA replication ONLY of that gene; cells can continue replicating the gene until hundreds of copies of the gene exist in parallel on the same chromosome
Enzymes have a temperature BLANK, where they function best
optima
possible prosthetic groups of conjugated proteins
organic molecules (ie vitamins) or even metal ions like iron also: lipid, carbohydrate, and nucelic acids
example of a prosthetic group
organic molecules (ie vitamins) or even metal irons (ie iron)
Chimeras
organisms that contain cells from two different lineages
In cells, what is different from example above?
osmotic pressure is maintained against the cell membrane, rather than the force of gravity. if osmotic pressure created by solutes w/in cell exceeds the pressure that the cell membrane can w/stand, the cell will lyse. osmotic pressure is kinda like a "sucking" pressure, drawing water into cell
examples of colligative properties?
osmotic pressure, vapor pressure depression, bp elevation, freezing point depression
product of pyruvate carboxylase? its significance?
oxaloacetate, is a citric acid intermediate and can not leave the mitochondria, so it is converted into malate, exits through the malate-aspartate shuttle, than converts (oxidizes) back to Oxaloacetate when in the cytoplasm.
Oxidoreductases which facilitate oxygen being the last oxidant (ie last e- acceptor) are often called
oxidases/ have oxidase in their names
Aldonic Acids
oxidation of aldolases during open-chain aldehyde form
After the consumption of a meal how does the liver acquire most of its energy?
oxidation of excess amino acids
Compared to carbs, how much more energy can triacylglycerols store?
oxidation of triacylglycerols yield twice the amount of energy per gram as carbs, so are far more energy dense storage mechanism compared to polysaccharides
retinoic acid
oxidized form of retinol. is a hormone that regulates gene expression during epithelial development
Beta oxidation overview
oxidizes and releases molecules of acetyl-CoA (reverse of fatty acid synthesis. has 4 steps. each 4 step cycle releases one acetyl CoA and reduces NAD+ and FAD (producing NADH and FADH2 which are oxidized in the e- transport chain)
How do nerve tissues acquire most of their energy? when does it do this (ie well fed, fasting, etc) when does it change?
oxidizing glucose to CO2 and water. does so in both well fed and normal fasting states. (changes after proonged fasting
Catalysts are sensitive to what?
pH and temperature changes. Remember that they are proteins and can denature!
Isoelectric point (pI) and eq for neutral amino acids
pH at which the molecules is electrically neutral; makes the molecule be sensitive to pH changes and titration curve is nearly vertical; pI of amino acids with non-ionizable side chains is 6
What are some places in the human body where pH is vastly different?
pH of 2 in the stomach for pepsin pH of 8.5 in the small intestines for pancreatic juices
Isoelectric point of acidic amino acid
pI acidic amino acid = (pKa R group + pKa COOH group) / 2 have low pI
P15: Given the following pKa values, what is the value of the pI for each of the AAs listed below Aspartic acid: pka1 = 1.88, pka2 = 3.65, pka3 = 9.60) arginine: pka1 = 2.17, pka2 = 9.04, pka3 =12.48 valine: pka1 = 2.32, pka2 =9.62
pI aspartic acid: 1.88+3.65/2 = 2.77 pI arginine: 9.04 +12.48/2 = 10.76 pI valine: 2.32+9.62/2 = 5.97
Isoelectric point of basic amino acid
pI basic amino acid = (pKa R group + pKa NH group) / 2 have higher pI
pKa2
pKa for amino group ~ 9 or 10
pKa1
pKa for carboxyl group ~2
pKa3
pKa for ionizable group
Glucagon secretion by --- ----. It is stimulated by both ------ and ----- levels.
pancreatic alpha cells (in islets of Langerhans), low glucose, high protein
Are prostaglandins paracrine or autocrine hormones? what is their function?
paracrine and autocrine hormones; function = regulate synthesis of cAMP = important second messenger; release of prostaglandins result in downstream effects on smooth muscle function, influence over the sleep-wake cycle, elevation of body Temp associated with fever and pain
endocytosis and exocytosis are used when
particles are too big or too numerous to use simply through active/passive transport systems
transmembrane proteins
pass completely through lipid bilayer transporters, channels, receptors
leak channels
passive diffusion of ions into cell more K leak channels than Na channels so favors K movement into cell more
hers' disease = glycogen storage disease = a condition characterized by a deficiency in liver of glycogen phosphorylase, result?
patients can't break down glycogen in their livers and thus have hepatomegaly (swollen liver) also may have hypoglycemia (low blood sugar) between meals bc they can't use glycogen to maintain blood glucose concentrations
long term exposure to glucocorticoids may be required clinically but cause ______
persistent hyperglycemia, which stimulates insulin (which promotes fat storage in adipose tissue rather than lipolysis)
ex of some common head groups
phosphatidylcholine phosphatidylethanolamine
PEPCK
phosphoenolpyruvate carboxykinase
Two popular cooperative proteins are
phosphofructokinase-1 (enzyme) and hemoglobin (transport protein)
Glycerophospholipids
phospholipids that contain a glycerol backbone bound by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head group; ex. phosphatidylcholine and phosphatidylethanolamine
starch
plant storage of excess glucose 1,4 alpa-linked chain
most important controller of insulin secretion?
plasma glucose above 100mg/dL (5.6mM glucose) insulin secretion is directly proportional to plasma glucose. -for glucose to promote insulin secretion, it must not only enter the Beta cells but also be metabolized, increasing intracellular ATP concentration Increased ATP promotes exocytosis of insulin thru several ion and voltage gated channels.
Role of gangliosides w/in the cell?
play major role in cell interaction, recognition, signal transduction
Asparagine, 3 letter code and 1 letter code and structure
polar asn N
Cysteine, 3 letter code and 1 letter code and structure
polar cys C
Glutamine, 3 letter code and 1 letter code and structure
polar gln Q
Serine, 3 letter code and 1 letter code and structure
polar ser S
Threonine, 3 letter code and 1 letter code and structure
polar thr T
what is usually used in electrophoresis as a medium?
polyacrylamide gel
Proteins
polypeptides; main actors in cells; the genetic code
homopolysaccharide
polysaccharide conposed entirely of the same monosaccharide (ie glucose)
heteropolysaccharide
polysaccharide made up of more than 1 type of monosaccharaide
When the metabolic phosphate compound is on the product side its modified standard free energy state value is -----.
positive
fasting state. aka?
post absorptive state = ------
tight junctions
prevent solutes from leaking into space between cells via paracellular route found in epithelial cells function as a physical link between cells as they form a single layer of tissue can limit permeability enough to create a trans-epithelial voltage difference based on differing concentrations of ions on either side of the epithelium. to be effective, need to make a continuous band around cells (or else, they would just leak through random parts)
break down of saturated vs unsaturated fatty acids
previous processes = for saturated fatty acids unsaturated fatty acids = need 2 additional enzymes bc double bonds disturb stereochemistry needed for oxidative enzymes to act on the fatty acid. to function, these 2 enzymes can have at most 1 double bond in their active site and the bond MUST be located between carbons 2 and 3 2 enzymes = enoyl-CoA isomerase and 2,4-dienoyl CoA reductase
what else do thyroid hormones do?
primary effects = in lipid and carb metabolism accelerate cholesterol clearance from plasma and increase rate of glucose absorption from small intestine. epinephrine requires thyroid hormones to have a significan metabolic effect.
snRNA
primary function is in the processing of hnRNA to mRNA in the nucleus
F2,6-BP is produced by what? what does it control?
produced by PFK-2 controls gluconeogenesis and lgycolysis (in liver). PFK is activated by insulin and inhibited by glucagon. so glucagon will lower F2,6-BP and stimulate gluconeogenesis. insulin will increase F2,6BP and inhibit gluconeogenesis
Benefit of PCR
produces millions of copies of DNA w/o having to use bacteria
what do catecholamines do?
promote glycogenolysis in liver and muscles (increases glucose output by liver... in muscles = there is no glucose-6-phosphatase so glucose can't be released by skeletal muscles into blood stream... instead its metabolized by the muscle tissue itself)
pathway is promoted by what? inhibited by what?
promoted = glucagon and epinephrine (raise blood sugar levels) inhibited = insulin (lowers blood sugar levels)
cell membrane function
protect interior of cell from outside regulate traffic intercellular and intracellular communication and transport proteins: cell receptors during signal transduction; regulate cell activity
Denaturation. what it is and 2 main causes
protein loses its 3D shape and functionability (can't catalyze rxns); often irreversible; 2 main causes are heat and solutes
how is protein strucutre determined
protein structure can be determined through X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy
Insulin increases amino acid uptake by muscle cells, thereby increasing levels of ---- and decreasing ----------.
protein synthesis, breakdown of essential proteins
lipid raft
proteins and signaling parts of phospholipid bilayer
CAMs
proteins that allow cells to recognize each other and contribute to proper cell differentiation and development
motor proteins.. what are the, what do they include (3)
proteins that are involved in cell motility through interactions with structural proteins; motor proteins have enzymatic ATPase activity and include myosin, kinesin, and dynein
structural proteins
proteins that are involved in the cytoskeleton and extracellular matrix; they are generally fibrous in nature and include collagen, elastin, keratin, actin, and tubulin
ion channels: what is it and 3 eamples and what do they have in comon?
proteins that create specific pathways for charged molecules; they can be classified into three main groups: ungated channels, voltage-gated channels, and ligand-gated channels ALL permit facilitated diffusion of charged particles
binding proteins? binding affinity?
proteins that transport or sequester molecules. (ie hemoglobin) each binding protein has an affinity curve for its molecule of interest the curve differes depending on goal of binding protein. ie when sequestration of molecuel is the goal, the binding protein usually has high affinity for its target across a large range of concentrations wo it can keep ti bound at nearly 100% tranpsort protein= must be able to bind or unbind its target to maintain steady state concentrations
what are cytochromes? reaction?
proteins w/ heme groups in which iron is reduced from Fe2+ and reoxidized to Fe3+ CoQh2 + 2 cytocrhome c [w/ Fe3+] --> CoQ + 2 cytochrome c [w/ Fe2+] + 2H+
Under acidic conditions (pH < 2), will AA's (w/o ionizable side chains) be + or - charged?
protonated, positively charged; pH is lower than pKa, both amino and carboxyl group will be protonated (so +1 for NH₃⁺ and 0 for COOH)
there is no net loss of carbon in the process of fermenting <- explain this
pyruvate and lactate are both 3-carbon molecules
what 4 enzymes are important for reversing gluconeogenesis?
pyruvate carboxylase phosphoenolpyruvate carboxykinase (PEPCK) Fructose-1,6-bisphosphatase Glucose-6-Phosphatase
Partition coefficient
quantify the ability of a molecule to dissolve in a polar vs nonpolar environment.This helps localize where certain vitamins will be found!
Issues w/ gene therapy
randomly integrated DNA poses a risk of integrating near, and activating, a host oncogene. among kids treated for SCID, a small # have developed leukemias (cancer of white blood cell)
Carnitine acyltransferase I
rate limiting enzyme of fatty acid oxidation
RTKS
receptor tyrosine kinases = composed of monomer that dimerizes upon ligand binding. the dimer is the active form that phosphorylates additional cellular enzyems, including the receptor itself (autophosphorylation)
How is malate recycled?
recycling the malate requires oxidation to oxaloacetate, which can be transaminated to form aspartate. aspartate crosses into the cytosol and can be reconverted to oxaloacetate to restart the cycle
why can we not give water intravenously?
red blood cells have osmolarity ~300mOsm/L... pure water has osmolarity of 0mOsm/L... water would rush into the RBCs causing them to burst
If you pair 2 molecules w/ different reduction potentials, the molecule w/ the greater potential will be ____
reduced!, the other molecule will be oxidized so NADH is a good e- donor and the high reduction potential of oxygen makes it a great final acceptor in the e- transport chain
Since aldolases can be oxidized, they are called ____
reducing agents
Any monosaccharides with a hemiacetal ring is considered ____
reducing sugar
Tautomerization
refers to the rearrangement of bonds in a compound, usually by moving a hydrogen and forming a double bond
Catalysts are _______ after a reaction has run its course
regenerated
The more a substrate binds to a cooperative enzyme, the more BLANK states occur, resulting in what for affinity and rxn rate?
relaxed states. SO affinity for the substrate increases and the rate increases at an increasing rate prior to reaching vmax!! hence s curve!
debranching enzyme
removes oligosaccharides from a branch in glycogen or starch
Base excision
repair fixes a single nucleotide
maintaining membrane potential
requires energy b/c ions may passivly diffuse thru the cell membrane over time using leak channels ion transporter or pump like the sodium-potassium pump (Na/K ATPase) is used Chloride ions also participate in establishing membrane potential
What is a downside to using alcohol as a source of acetyl-CoA? How is this problem overcome?
results in NADH build up (stops Krebs cycle), thus acetyl-CoA formed thru this process is used primarily for the synthesis of fatty acids
Vitamin B2 NOT TESTED ON MCAT
riboflavin
Given what we know about vitamin D, what would a lack of it result in?
rickets = often seen in kids, characterized by underdeveloped, curved long bones and impeded growth
Heterocycles
ring structures that contain at least two different elements in the ring. Ex) Purines and pyrimidines (which have at least 1 nitrogen in their aromatic rings)!
Structure of alpha helices?
rod like, peptide chain coils clockwise around central axis. side chains of AAs point AWAY fro mthe Helix core
alpha-helices
rodlike structure in which the peptide chain coils clockwise around a central axis; H bonds stabilization; important structure of keratin
sarcolemma membrane
sarcolemma of muscle cells must maintain a membranepotential for muscle contractions to occur.
When vmax is reached, the enzyme is
saturated
what is it called when, say, you have 100 enzymes and 200 substrates
saturation, the rate of the rxn will not increase b/c it can't go any faster. the enzyme is working at maximum velocity (v,max,)... the only way to increase v,max, is by increasing the enzyme concetration
symport
secondary active transport both particles flow the same direction across the membrane
antiport
secondary active transport particles flow in opposite directions
basic idea of how proteins fold
secondary structures probably form first, then hydrophobic interactions and h bonds cause the protein to "collapse" into its proper 3D shape along the way, it adopts intermediate states known as molten globules it is extremely rapid process, from start to finish = takes much less than a second
where would proteins to be secreted go?
secreted peptides (ie hormones and digestive enzymes) direct the ribosome to go to the ER so that the protein can be translated directly into the lumen of the RER. from there protein can be sent to golgi and secreted from a vesicle via exocytosis
cortisol
secreted w/ many forms of stress (exercise, cold, emotional stress, etc) promotes mobilization of energy stores thru degradation and increased delivery of AAs and increased lipolysis. also elevates blood glucose levels
selectins
selectively bind carbohydrates on other surface, such as glycoproteins in the matrix unique because they bind to carbohydrate molecules that project form other cell surfaces; these bonds are the weakest formed by the CAMs; they are expressed on white blood cells and the endothelial cells that line blood vessels; like integrins, they play an important role in host defense, including inflammation and white blood cell migration
Leukocyte extravasation
selectrin and integrin regulate neutrophil movement
cell (plasma) membrane
semipermeable phospholipid bilayer. follows a fluid mosaic model
Amino Acids with Polar Side Chains
serine, threonine, asparagine, glutamine, cysteine (STAGC)
Hydroxyl group of monosaccharide
serves as a nucleophile
Carbonyl group of monosaccharide
serves as an electrophile
Okazaki fragment
short pieces of new DNA on lagging strand
Mutations in the wobble position are called ___ or ___. meaning what?
silent, degenerate means there is no effect on the expression of the amino acid and therefore no adverse effects on the polypeptide sequence
Structure of FMN
similar to FAD
What reaction is esterifaction very similar to?
similar to phosphorylation of glucose = phosphate ester forms
Naming of terpenoids
similar to terpene naming. ie diterpenoids derive from four isoprene units
hemidesmosomes
simlar to desmosomes, but attach epithelial cells to underlying (basement) membrane
types of passive transport?
simple diffusion osmosis facilitated diffusion
facilitated diffusion
simple diffusion for molecules that are impermeable to the membrane (large, charged, polar). energy barrier is too high for them to cross freely use integral membrane proteins (Carriers or channels)
What is the simplest ketone sugar. where is the carbonyl?
simplest = dihydroxyacetone carbonyl is most oxidized so it should have the lowest number it can (2)
simplest monosaccharides? and from there?
simplest = those w/ 3 carbon atoms = trioses from ther = tetroses (4), pentoses and hexoses
Ceramide
simplest type of sphingolipid which has a single hydrogen atom as its head group
SSBPs = what type of proteins?
single-stranded DNA binding proteins Bind to the unraveled strand, preventing both the reassociation of the DNA strands (which are very "sticky) and the degradation of DNA by nucleases.
Gel electrophoresis separates macromolecules based on what?
size and charge
What situation would molecules move slow fast?
slow = biger/more convoluted/electrically neutral molecules move slowly fast = small, highly charged or placed in a large electric field
threshold (body weight
small adjustments in intake, even over a prolonged period of time, are partially or fully compensated by changes in energy expenditure. so deliberate alterations of body mass require alterations above this threshold level
How are small proteins best analyzed? (what is a "small protein"
small proteins are best analyzed with the edmund degradation degradation can be used for proteins 50-70AA's long
where do you start the numbering for the sugar?
so that the most oxidized carbon can have the lowest number it can (in this case the carbonyl carbon of the aldehyde should proably have 1)
How does the bradford protein assay work? when is it most accurate? least accurate? other shortcomings?
so: samples of known protein concentrations are reacted w/ Bradford reagent then absorbance is measured to create a standard curve the unknown sample is then exposed toe the same conditions and the conentration is determined based on the standard curve v/ accurate when only one type of protein is present less accurate when more than one protein is present b/c of variable binding of Coomassie dye w/ different AA's also limited by presence of detergent in sample or excessive buffer
isotonic
solute concentration inside and outside the cell are the same there is still movement of particles, but NO net movement (kinda like a dynamic equilibrium
hypertonic
solute concentration is LOWER in the cell than surroundings. water will move out of cell
hypotonic
solute concentration is higher in the cell than surrounding concentration. such a soln will cause a cell to swell as water rushes in, sometimes to the point of bursting
example of IDL being processed in bloodstream?
some IDL picks up cholesteryl esters from HDL to become LDL. so is transition particle btwn triacylglycerol transport and cholesterol transport
How do proteins know where to go?
some eukaryotic proteins contain signal sequences, which designate a particular destination for the protein
Telomerase?
some of the sequence is lost in each round of replication and can be replaced by telomerase telomerase is more highly expressed in rapidly dividing cells
Noncompetitive inhibition
something binds an allosteric site on both the enzyme and enzyme-substrate complex with equal affinity
Why use ketones?
spares proteins that are vital for other functions
what are adipocytes
special cells in animals that store large amounts of fat and are found primarily under the skin/around mammary glands/in abdominal cavity
cell adhesion molecules (CAMs).. where? what? 3 common CAMs
specialized structural proteins found on surface of cell (are integral membrane proteins) are involved in cell-cell junctions as well as transient cellular interactions; common CAMs are cadherins, integrins, and selectins
osmosis
specific kind of simple diffusion othat concerns water. water moves from a region of lower solute to higher solute concentration. important when solute is impermeable to membrane. in this case, water will move to try to bring solute concentrations to equimolarity
How can you determine concentraion of proteins what are the draw backs?
spectroscopy: b/c proteins contain aromatic side chains, they can be analyzed w/ UV spectroscopy w/o any treatment; however, this type of analysis is particularly sensitive to sample contaminants
what is a sphingoid backbone?
sphingosine like
lariat
spliceosomes are formed when snRNA couples with snRNPs excising introns into a lariat (lasso-shaped structure) form that is then degraded
Citrate lyase
splits citrate back into acetyl-CoA and OAA in the cytoplasm
------ reactions proceed in the forward direction and have a -(delta G).
spontaneous
negative delta G
spontaneous energy is going down
passive transport
spontaneous (negative delta G) movement DOWN the concentration gradient energy given by Potential Energy of concentration gradient primary thermodynamic motivator is an increase in enthalpy (deltaS) facilitated diffusion osmosis
Mutarotation
spontaneous change of configuration on C-1 to form alpha or beta anomer. will happen in water and occurs more rapidly when the reaction is catalyzed with an acid or base; interconversion between anomers of a compound
dG* = ?
standard free energy the energy change tha toccurs at standard concentration of 1M, pressure = 1atm, temp =25*C
Cholesterol
steroid. mediates membrane fluidity; amphipathic (is hydrophilic and phobic
3 important signaling lipids
steroids prostaglandins fat-soluble vitamins
Steroids vs Steroid hormones
steroids: a group defined by a particular chemical structure steroid hormones: steroids taht act as hormones (secreted by endocrine glands into bloodstream and travel on protein carriers to distant sites where they bind to specific high affinity receptors and alter gene expression levels
retinol
storage form of vitamin A
triglycerides
storage lipid in human metabolic process aka triacylglycerols. structure = 3 fatty acid chains esterified to a glycerol molecule
motif
structural proteins generally have highly repetitive secondary structure and a supersecondary structure - a repetitive organization of secondary structural elements together sometimes referred to as a motif; this regularity gives many structural proteins a fibrous nature
flavoproteins
subclass of e- carriers contain modified vitamin B2 (aka riboflavin) -nucleic acid derivatives, -gnereally either flavin adenine dinucleotide (FAD) or Flavin mononucleotide (FMN)
T4 vs T3
subscript = number of iodine atoms in the hormone T4 = precursor to T3.. deiodonases (enzymes that remove iodine from a molecule) are located in target tissues and convert T4 to T3
what is a substrate level phosphorylation? in contrast to what?
substrate level phosporylation - ADP is directly phosphorylated to ATP using a high-energy intermediate... only means of ATP generation in anaerobic tissue. in contrast to oxidative phosphorylation which is in mitochondria and depends on oxygen.
ATP is formed as a result of ------ as well as -----.
substrate-level phosphorylation, oxidative phosphorylation
simple diffusion
substrates move down concentration gradient directly across membrane only particles that are freely permeable to membrane are able to undergo simple diffusion there is potential energy in a chemical gradient, some of the energy is dissipated as the gradient is utilized during simple diffusion like a ball rolling down a hill
Dehydrogenases are a subtype of _____. when you see one, look out for a ___ being formed
subtype of oxidoreductases (enzymes that catalyze redox reactions) -dehydrogenases transfer a hydride ion (H-) to an e- acceptor (usually NADH or FADH2) so when you see one, look out for a high energy e- carrier being formed
types of interactions causing tertiary strucutre stabilizing forces of tertiary structure
subtypes: hydrophobic interactions, acid-base interactions (which create salt bridges), disulfide links (2 cystein molecules become oxidized to form cystine = creates loops in protein chain stabilized by: van der Waals forces, H bonds, Ionic bonds, covalent bonds
Step 5 of the TCA cycle
succinate formation 1) hydrolysis of thioester bond on succinyl-CoA yields succinate and CoA-SH. is coupled to the phsphorylation of GDP to GTP bc the thioester hydrolysis releases a lot of energy (thioesters = high energy!) 2) once GTP is formed, nucleosidediphosphate kinase catalyzes phosphate transfer from GTP to ADP producing ATP (only time that ATP is produced directly by TCA cycle)
synthase vs synthestase?
synthases = enzymes that form new covalent bonds w/o needing significant energy synthetases = enzymes that create new covalent bonds WITH energy input
rate-limiting step of cholesterol biosynthesis?
synthesis of mevalonic acid in the smooth ER. -catalyzed by 3-hydroxy-3-methylglutaryl (HMG) CoA reductase
rRNA (Ribosomal RNA): Made where?
synthesized in the nucleolus and functions as an intregral part of the ribosomal machinery used during protein assembly in the cytoplasm. - functions as a ribozyme
general concept of chromatography?
t/f in all forms of chromatography, the concept is identical: the more similar the compound is to its surroundings (by polarity, charge, and so on), the more it will stick to and move slowly through its surroundings
how does chromatography start?
t/f the chromatography process begins by placing the sample onto a solid medium called the stationary phase or adsorbent; the next step is to run the mobile phase through the stationary phase; this will allow the sample to run through the stationary phase, or elute; depending on the relative affinity of the sample for the stationary and mobile phases, different substances will migrate through at different speeds
benefits (depending on what you are going for) of PAGE vs SDS PAGE
t/f the relative benefits to native PAGE compared to SDS-PAGE is that native PAGE allow 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 happens when antibodies bind to antigens (3)
t/f when antibodies bind to their targets, called antigens, they can cause one of three outcomes: 1) neutralizing the antigen, making the pathogen or toxin unable to exert its effect on the body; 2) opsonization; 3) clumping together (agglutinating) the antigen and antibody into large insoluble protein complexes that can be phagocytize and digested by macrophages
3' Polyadenosyl (Poly-A Tail)
tail is added to the 3' end - It protects against rapid degradation its like a fuse for a time bomb. as soon as mRNA leaves the nucleus, it will start to get degraded from its 3' end. The longer the poly-A tail, the more time the mRNA will be able to survive. also helps w/ export of the mRNA
Goldman-Hodgkin-Katz voltage equation
takes account the relative contribution of each major ion to the membrane potential if ion has a different relative charge to the other ions, it is inverted (see Cl-)
affinite of binding of noncompetitive inhibitors
tehy bind equally to the enzyme and enzyme substrate complex, unlike mixed inhibitors... once the enzymes conformation is altered, no amount of extra substrate will be conducive to forming an ES complex....
Having a temperature optima is also referred to as being what?
temperature dependent
What affects enzyme activity/rate/velocity?
temperature, pH, salt (salinity)
Transcription results in a single strand of mRNA, synthesized from one of the two nucleotide strands of DNA called _______ _______
template strand or anti sense strand
what parts of our body are "proteinaceous
tendons, ligaments, cartilage, bacement membranes
Ex of steroid hormones
testosterone, various estrogens, cortisol, aldosterone
Vitamin B1 NOT TESTED ON MCAT
th1amine
Dihydrolipoyl transacetylase
the 2 carbon moelcule bonded to tPP is oxidized and transferred to lipoic acid, a coenzyme that is covalently bonded to the enzyme. Lipoic acid's disulfide group acts as an oxidizing agent, creating the aceytl group. the acetyl group is now bonded to lipoic acid via thioester linkage. after this, dihydropropyl transacetylase catalyzes the CoA-SH interaction w/ the newly formed thioester link, causing transfer of an acetyl group to form acetyl CoA. Lipoic acid is left in its reduced form
proteinogenic AAs
the 20 alpha AA's encoded by the human genetic code
Which end of the chromosome can DNA polymerase NOT replicate?
the 5' end (bc it works in the 5' to 3' direction)
What makes it hard to do AA sequencing? What can we do instead? how do we sequence the AA's'
the AAs that compose a proteincan be determined by complete protein hydrolysis and subsequen chromatographic analysis HOWEVER< actually determining the SEQUENCE of the AAs in the protein is difficult b/c of the random nature of hydrolysis to determine the sequence, we can do a sequential digestion of the protein w/ specific cleavage enzymes
How does the Edman degradation work?
the Edman degradation selectively and sequentially removes the N-terminal amino acid of the protein, which can be analyzed via mass spectroscopy
How does it detect the incorrectly paired H bonds?
the H bonds btwn the strands can be unstable. detected by polymerase
Talk about thermodynamics/kinetics of transporters
the K,m, and v,max, parameters that apply to enzymes are also applicable to transporters such as ion channels in membranes the kinetics of transport can be derived from the Michaelis=Menten and Lineweaver-Burk equations where K,m, = solute concentration at which the transporter is functioning at half of its max activity
What does the absence of G-6-P in skeletal muscle imply??
the absence means that glycogen cannot serve as a source of blood glucose and rather is for use only within the muscle. G-6-P is used to bypass hexo or glucokinase which convert glucose to G-6-P.
write what Km is again?
the concentration of substrate when an enzyme is active at half of its maximum velocity (v,max) the lower the Km, the higher the enzymes affinity for the substrate
yeast fermentation
the conversion of pyruvate (3 carbons) to ethanol (2 carbons) and carbon dioxide (1 carbon) result = replenishes NAD+, just like mammalian fermentation
respiratory control
the coordinated regulation of the citric acid cycle and oxidative phosphorylation
Which component of membrane lipids contribute to their function?
the difference between membrane lipids are determined by the polar head group, due to its constant exposure to the exterior environment; the degree of unsaturation of fatty acid tails
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
If the rate of a reaction, or v, is increasing with increasing substrate concentration, then
the enzyme concentration is constant. Remember that if you have 100 enzymes and 2 substrates, the reaction RATE (amount of substrate converted over time) is low. If you have 100 enzymes and 50 substrates, the rate is faster. If you have 100 enzymes and 75 substrates, it's even faster. If you have 100 enzymes and 100 substrates, it's at a maximum. If you have 100 enzymes and 150 substrates, you are still at that maximum.
saponification
the ester hydrolysis of triacylglycerols using a strong base (usually lye = NaOH/KOH) -result = the basic cleavage of the fatty acid, leaving the sodium salt of the fatty acid and glycerol. -the fatty acid salt is what we know as soap
primary target of glucagon action?
the hepatocyte acts thru second messengers.
What provides the energy to make peptide bonds during translation?
the high-energy aminoacyl=tRNA bond will suply the energy
final perk of lipids?
the layer of lipids seres a dual purpose of energy storage and insulation = helps to retain body heat so that less energy is required to maintain constant internal temp.
disulfide bonds in hair. also structure/rxn of disulfide bond formation
the more disulfide bons, the culier the hair is Note: forming a disulfide bond requires the loss of 2 protons and 2 electrons (oxidation)
kinesin
the motor protein associated with microtubules; has two heads, at least one of which remains attached to tubulin at all times; plays key roles in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis; important for vesicle transport in the cell; brings vesicles toward the positive end of the microtubule; bring vesicles of neurotransmitters to the positive end of the axonal microtubules (toward the synaptic terminal) "karry+out"
dynein
the motor protein associated with microtubules; has two heads, at least one which remains attached to tubulin at all times; involved in the sliding movement of cilia and flagella; important for vesicle transport in the cell; bring vesicles toward the NEGATIVE end of the microtubule; bring vesicles of waste or recycled neurotransmitter back toward the negative end of the microtubule (toward the soma) through retrograde transport "dyne-in"
pKa
the pH at which half of the molecules are deprotonated; [HA] = [A-] =-log(Ka) if pH is less than pKa = protonated if pH is higher than pKa = deprotonated
What is the pI?
the pI is the pH at which he protein or amino acid is electrically neutral, with an equal number of positive and negative charges
how is pKa of AA groups related to pH?
the pKa of a group is the pH at w/, on avg, half of the molecules of that species are deprotonated, that is [HA] = {A-] if pH is less than pKa, most species w/ be protonated, if pH is higher than pKa, most will be deprotonated
How can histidine acquire a positive charge?
the pKa of the side chain is relatively close to 7.4 (apprx 6) so at physiologic pH, one nitrogen atom is protonated and the other isn't. under more acidic conditions, the 2nd nitrogen can become protonated, giving the side chain a positive charge
myosin
the primary motor protein that interacts with actin; in addition to its role as the thick filament in a myofibril, this protein can be involved in cellular transport; each subunit has a single head and neck; movement at the neck is responsible for the power stroke of sarcomere contraction
What are the primary structural proteins in the body?
the primary structural proteins in the body are collagen, elastin, keratin, actin, and tubulin TCAKE
homogenization
the process of breaking cell membranes and creating a uniform mixture of cell components for further separation; may be accomplished chemically or physically
centrifugation
the process of separating components on the basis of their density and resistance to flow by spinning a sample at very high speeds; the highest density materials form a solid pellet and the lowest density materials remain in the supernatant (liquid portion)
electrophoresis
the process of separating compounds on the basis of size and charge using a porous gel and an electric field; this technique generally uses polyacrylamide, while nucleic acid electrophoresis uses agarose
chromatography relies on what/what is the basis of the process?
the process of separating molecules by their interactions with a stationary phase and a mobile phase; most chromatographic methods rely on the similarity of molecules w/ the stationary vs mobile phases, with the exception of size-exclusion chromatography
feed forward activation
the product of an earlier reaction of glycolysis (F1,6BP) stimulates or prepares a later reaction in glycolysis (by activating pyruvate kinase).
tubulin
the protein that makes up microtubules; microtubules are important in providing structure, chromosome separation in mitosis, and intracellular transport with kinesin and dynein; like actin, this protein has polarity: the negative end of the protein is usually located adjacent to the nucleus, whereas the positive end is usually in the periphery of a cell
Phosphofructokinase-1 KNOW THIS ENZYME!!!
the rate limiting enzyme and main control point in glycolysis. -fructose 6-phosphate is phosphorylated to fructose 1,6-bisphosphate using ATP
a decrease in insulin and an increase in epinephrine stimulates what 2 changes?
the release of amino acids from skeletal muscle and fatty acids from adipose tissue... once carried into the liver, AAs and fatty acids can provide the necessary carbon skeletons and energy required for gluconeogenesis
what is 1 thing you NEED to know before PCR?
the sequences that flank the desired region
Protein digestion is completed where? enzymes (2)? products
the small intestine by the brush-border enzymes dipeptidase and aminopeptidase products = amino acids, di/tripeptides
polyacrylamide gel
the standard medium for protein electrophoresis; a slightly porous mixture, which solidifies at room temperature; this gel acts like a sieve, allowing smaller particles to pass through easily while retaining large particles
Point Mutation
the substitution of one nucleotide for another in codon (can have a severe and detrimental effect depending upon where the mutation occurs in the genome)
How many subunits comprise the G protein and what are they? how are they inactivated/activated
the three subunits that comprise the G protein are α, β, and γ; in its inactive form, the α subunit binds GDP and is in a complex with the β and γ subunits; when a ligand binds to the GPCR, the receptor becomes activated and, in turn, engages the corresponding G protein
ATP cleavage
the transfer of a high energy phsopahte group from ATP to another molecule... generally activates or inactivates the target molecule. W/ these phosphoryl group transfers, the overall free energy of the reaction will be determined by taking the sum of the free energies of the individual reactions
drawbacks of affinity chromatography
the two potential drawbacks of affinity chromatography are that the protein of interest may not elute from the column because its affinity is too high or it may be permanently bound to the free receptor in the eluent
3 maintypes of G proteins
there are three main types of G proteins: Gs, Gi, and Gq
What are the chains for?
these chains are very important in binding to and communicating with the extracellular matrix; they also play a very important role in cellular signaling and can greatly impact cellular function by promoting cell division, apoptosis, or other processes; others are used for white blood cell migration, stabilization of epithelium on its basement membrane, and other processes
ungated channels. what are they, examples?
these channels have no gates and are therefore unregulated; ex. potassium channels so there will be a net efflux of potassium ions thru these channels unless potassium is at equilibrium
What do NADH, NADPH, FADH2, ubiquinone, cytochromes, and glutathione have in common?
they are all high energy electron carriers
What are free fatty acids and where are they found in our body?
they circulate in the blood bound noncovalently to serum albumin. also in soap
Cooperative enzymes have ______ that exist in two states, what are they?
they have multiple subunits 2 states = tense state (less likely to bind substrate) relaxed state (more likely to bind substrate)
deficiency in thaimine can result in what 2 symdromes/
thiamine = vitamin B1 1) Beriberi = characterized by congestive heart failure or nerve damage 2) Wernicke-Korsakoff syndrome = characterized by difficulty walking, confusion, etc giving glucose to an individual w/ thiamine deficiency can lead to severe lactic acidosis and other metabolic derangements bc pyruvate can't be converted into acetyl CoA w/o the vitamin. so thiamine must be given before an infusion of glucose
What is the chemical basis of the bradford protein assay/overview of general procedure
this assay mixes protein in soln w/ coomassie Brilliant Blue dye in its protonated form, this dye exists as a brown/green color. The dye is DEprotonated by the protein and gives up protons to the ionaizable groups in the protein, turning blue in the process noncovalent attractions btwn the deprotonated dye and the protein then stabilize this blue form of the dye thus, increased protein concentrations correspond to a larger concentration of blue dye in soln
membrane-spanning domain
this domain anchors the receptor in the cell membrane
ligand-binding domain
this domain is stimulated by the appropriate ligand and induces a conformation change that activates the catalytic domain
Irreversible inhibition
this means that the enzyme is either inactive for a super long time, or it will never be active again. If the body needs the enzyme, it will have to simply make more. it is a prime drug mechanism and something that will appear often in med school
why is it considered a cycle?
tho acetyl CoA is oxidized to CO2 and energy (GTP) and energy carriers (NADH and FADH2) are produced, all other substrates/products are reused!!!
Why can't genomic libraries be used to reliably sequence specific genes or produce recombinant proteins
though they have the whole genome, genes may by chance be split into multiple vectors
how do we break down peptides?
thru hydrolysis via acid or base catalysis (in orgo lab) in nature = hydrolyss catalyzed by hydrolytic enzymes like trypsin and chymotrypsin which cleave at specific points in the peptide chain (trypsin cleaves at carboxyl end of arginine and lysine, etc... don't need to know this) breaks bond by adding a hydrogen atom to the amide nitrogen and an -OH to he carbonyl carbon
absorption of amino acids/small peptides = ?
thru luminal membrane via secondary active transport linked to sodium at the basal membrane = simple and facilitated diffusion transport AAs into bloodstream
how does galactose get to the liver? what happens then?
thru the hepatic portal vein. once in the tissues, galactose is phosphorylated by galactokinase, trapping it in the cell.
structure of beta pleated sheets
to accomodate as many H bonds as possible, the beta pleated sheets assume a pleated, or rippled, shape the R groups of the amino residues point above and below the plane of the beta pleated sheet
What is the function of PEPCK with the combination of pyruvate carboxylase?
to convert oxaloacetate back to PEP (avoids pyruvate kinase).uses GTP (once converted back to PEP, goes down pathway to F-1,6-BP)
Why is the phosphorylation of glucose necessary?
to prevent glucse from leaving via the transporter... glucose enters the cell via facilitated diffusion or active trasport... B/c GLUT transporters are specific ffor glucose (not *phosphorylated* glucose), the glucose gets trapped in the cell.
Transcription Factors
transcription activating proteins that search the DNA looking for specific DNA binding motifs Examples of two: 1) DNA binding domain 2) activation domain
What happens in complex I?
transfer of e- from NADH to coenzyme Q (CoQ).
3-phosphoglycerate Kinase
transfers the high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate this is a substrate level phosphorylation
integral proteins
transmembrane and embedded proteins associated with interior of plasma membrane with the assistance of one or more membrane associated domains that are partially hydrophobic
dietary fats consist mainly of ____.. but also what?
triacylglycerol (primary), also cholesterol, cholesteryl esters, phopholipids, and free fatty acids
Insulin's effect on metabolism of fats = decreases ___?
triacylglycerol breakdown (lipolysis) in adipose tissue. -formation of ketone bodies by liver
Insulin promotes ------ in adipose tissue and ---- in muscle, as well as _____ entry into both tissues.
triacylglycerol synthesis, protein synthesis, glucose entry
What do we use for energy storage (what type of lipid?
triacylglycerols
what are the 2 main methods of energy storage in the body?
triacylglycerols in adipose tissue 2. carbs in glycogen
Which is biggest of the AA's w/ aromatic side chains? structure? smallest? structure? the third?
tryptophan which has a double ring system that contains a nitrogen smallest = phenylalanine = has a benzyl side chain (benzene and -CH2 group) third = tyrosine = basically phenylalanine w/ -OH group
Amino Acids with Aromatic Side Chains
tryptophan, phenylalanine, tyrosine (TPT)
Nucleosome
two copies of each histone protein (H2A, H2B, H3, and H4 form a histone core and about 200 bps of DNA wrap around the protein complex to form a nucleosome.
Gq
type of G protein; activates phospholipase C, which cleaves a phospholipid from the membrane to form PIP2; PIP2 is then cleaved into DAG and IP3; IP3 can open calcium channels in the endoplasmic reticulum, increasing calcium levels in the cell (mind you'r P's and Q's)
Gi
type of G protein; inhibits adenylate cyclase, which decreases levels of cAMP in the cell i = Inhibits
Gs
type of G protein; stimulates adenylate cyclase, which increases levels of cAMP in the cell (S = stimulates)
size-exclusion chromatography what is it? how can it be specialized when is it usually performed?
type of chromatography that relies on porous beads; larger molecules elute first because they are not trapped in the small pores size of pores can be varied so that molecules of diff melecualr weights can be fractioned usually done after ion exchange chromatography
affinity chromatography
type of chromatography that uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest
ion-exchange chromatography: what it uses. what is the eluent
type of chromatography that uses a charged column (ie if its positively charged, then negatively charged proteins will bind to it) a variably saline eluent
column chromatography
type of chromatography that uses beads of a polar compound, like silica or alumina (stationary phase), with a nonpolar solvent (mobile phase)
Cerebroside
type of sphingolipid which has a single sugar in its head
Globoside
type of sphingolipid which has two or more sugar residue in its head; no net charge
are mutations in oncogenes dominant or recessive?
typically mutation in only ONE copy is sufficient to promote tumor growth and therefore is considered dominant.
Km describes what
under certain conditions, Km is a measure of the enzyme's affinity for its substrate... can be used to compare enzymes it is intrinsic property of ES system and can't be altered by changing the concentration of substrate or enzyme
which is more likely to be liquid at room temp, saturated or unsaturated fatty acids
unsaturated, have kinks so difficult to stack and solidify
Brain can derive...
up to 2/3 of its energy from ketone bodies during prolonged starvation
enhancers vs promoter elements?
upstream promoter elements must be w/in 25 bases of the start of a gene
role of insulin
uptake and storage of glucose (which is absorbed by peripheral tissues via facilitated transport mechanisms that utilize glucose transporters in cell membrane)
How do you test specifically for glucose?
use the enzyme glucose oxidase which does not react w/ other reducing sugars...
dihydroxyacetone phosphate (DHAP)
used in hepatic and adipose tissue for triacylglycerol synthesis formed from fructose 1,6-bisphosphate can be isomerized into glycerol 3-phsophate which can then be converted to glycerol, the backbone of triacylglyerols
primary active transport
uses ATP or another energy molecule to directly transport molecules across a membrane (usually involves the use of a transmembrane ATPase.
Tollen's reagent
uses silver nitrate = Ag(NH₃)⁺₂ ... as an oxidizing agent; positive test results in aldehydes reducing Ag+ to metallic silver
carbohydrates on bilayer
usu attach to proteins on extracellular surface usu hydrophilic so interactions betwn glycoproteins+water can make coat around cell signaling
Isoelectric point of AAs w/ nonionizable side chains?
usually around pH ~6
What do cofactors/coenzymes typically contribute to a rxn?
usually carry charge thru ionization, protonation or deprotonation
How might binding affinity change?
usually has varying affinity depending on evironmental conditions
where are waxes usually found?
usually serve an extracellular function in protection or waterproofing rarely found on animal cell membrane found more on plant cell membrane
what is often the corepressor?
usually the final structural product. so as its levels increase, it can bind the repressor to prevent further transcription of the same gene
membrane receptors
usually transmembrane proteins, some are carbohydrates and lipids can activate/deactivate facilitated diffusion or active transport biosignaling -generally are proteins, but there are some carbohydrate and lipid receptors, esp in viruses
When enzyme concentration is constant, velocity equals
v = (vmax*[S]) / (Km + [S]) Km = mihaelis-Menton constant = the substance concentration at which 1/2 of the enzyme's active sites are full (ie half the stress balls are in use)
What is the equation to figure out how fast a compound will migrate in Electrophoresis?
v = Ez / f v = migration veloity E = electric field strength z = net charge on the molecule f = frictional coefficient (depends on mass and shape of migrating molecules REMEBER THIS!
After the temperature optima, any temperature increase causes what? Due to what?
very steeply decreases the velocity due to denaturation
Lacteals
vessels of the lymphatic system. chylomicrons leave the intestine via lacteals and re-enter the bloodstream via the thoracic duct
Example of how vitamins and their solubility affect us
vitamins come in 2 major classes: fat and water soluble this is important to consider in digestive diseases, where different parts of the gastrointestinal tract may be affected by different disease processes b/c different parts of the gastrointestinal tract specialize in the absorption of different types of biomolecules, loss of different parts of the gastrointestinal tract or its accessory organs may result in different vitamin deficiencies
symptoms of lactose intolerance and why?
vomiting, bloating, explosive and watery diarrhea, cramps, dehydration. attributed to bacterial fermentation of lactose producing a mix of CH4 and H2 and small organic acids. the acids are oxmotically active and result in the movement of water to the intestinal lumen.
membrane lipids
w/in cell membrane ther aer lots of phospholipids w/ few free fatty acids. main components: 1. phospholipids: primary component 2. steriods/ cholesterols: fluidity 3. waxes: membrane stability 4. few fatty acids
Why is this fermentation necessary?
w/o mitochondria and oxygen, glycolysis would stop when all the available NAD+ had been reduced to NADH. by reducing pyruvate to lactate and oxidizing NADH to NAD+, lactate dehydrogenase prevents this potential problem from developing
how to elute out proteins from affinity chromatography?
wash column w/ a free receptor 9or target or antibody) which will compete w/ the bead bound receptor and ultimately free the protein from the column or use eluent of specific pH or salinity level that disrupts the bonds btwn the ligand and the protein of interst
What molecule is released during formation of a peptide bond? what is the bond make up.. what type of rxn is it?
water bond formed = -C(O)NH- is a condensation/dehydration rxn... also can be seen as an acyl substitution, which can occur w/ all carboxylic acid derivatives
body mass is determined by
water, carbs, proteins, lipids. -but carbs and protein mass tend to be stable over time and water is quickly adjusted by the endocrine system/kidneys.. therefore lipids, stored in adipocytes are primary factor in gradual change of body mass. nucleic acids don't contribute significiantly
how do we get unsaturated fatty acids?
we can only synthesize a few unsaturated fatty acids. the rest come from essential fatty acids in the diet that are transported as triglycerides from the intestine inside chylomicrons
Preferred food of cardiac musclewhen well fed vs fasting
well fed = Fatty acids fasting = fatty acids and ketones
Preferred food of brain when well fed vs fasting
well fed = Glucose fasting = Glucose (ketones in prolonged fast)
Preferred food of adipose tissue when well fed vs fasting
well fed = Glucose fasting = fatty acids
Preferred food of resting skeletal muscle when well fed vs fasting
well fed = Glucose fasting = fatty acids and ketones
Preferred food of liver when well fed vs fasting
well fed = Glucose and amino acids fasting = fatty acids
How does GLUT2 regulation work?
when glucose concentration drops below the Km for the transporter, much of the remainer leaves the liver and enters the peripheral circulation. The Km of GLUT2 is quite high (~15mM) so the liver wil pick up glucose in proportion to its concentration in the blood (first order kinetics). So basically, the liver will pick up excess glucose and store it only after a meal, when blood glucose levles are high.
Draw the titration curve for glycine. explain caption
when pH is close to pKa of the solute, the soln acts as a buffer. the titration curve is relatively flat
Lactone
when the aldose is in ring form and gets oxidized; it is a cyclic ester with a carbonyl group persisting on the anomeric carbon
mitochondrial matrix
where the citric acid cycle produces high energy e- carriers used in the e- transport chain
Is it common for enzymes to be able to do the reverse of their reaction?
yes
Are terpenoids similar to terpenes
yes in terms of biological prefursor function and aromatic properties, contributing to steroid biosynthesis
What does the oxidation of carbohydrates result in?
yields energy
what are 3 CAMs
3 Cell adhesion molecules = Cadherins integrins selectins
How many carbons does pyruvate have? Acetyl-CoA?
3, 2
Codons are written in which direction?
5' to 3' direction
So if the aminoacyl tRNA "Ile-tRNA" has the anticodon sequence 5'-GAU-3', what will the isoleucine codon be?
5'-AUC-3'
Normal glucose concentration in peripheral blood is_______
5.6mM (normal range: 4-6mM)
How many carbons does citrate have?
6
What does the A P E sites stand for
A = Amino acyl P = peptidyl E = exit