Irene Gold Biochemistry
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What form do amino acids exist in?
L-form, except glycine (which does not have D or L form because it is not optically active - center carbon does not have 4 different groups attached)
Which amino acids are essential (need in diet, cannot make)?
VAL MET LEU and took a TRP to an ILE but because of HIS LYS she had to pay THR PHE
Which amino acids are purely ketogenic?
leucine and lysine
Which amino acids are aromatic?
phenylalanine, tyrosine, tryptophan
Which amino acids contain sulfur?
cysteine, methionine, cystine
Which amino acids are branched chain?
isoleucine, leucine, valine
What is maple syrup urine disease?
can't break down branched chain amino acids --> viscous, dark, sweet smelling urine
Which amino acids are acidic?
aspartic acid (aspartate) and glutamic acid (glutamate)
What amino acids are basic?
histidine, lysine, arginine
What can amino acids make?
- Phe --> Tyr --> L-dopa
- L-dopa --> dopamine --> norepinephrine --> epinephrine (catecholamines)
- L-dopa --> melanin (skin pigment)
- Histidine --> histamine
- Tryptophan --> serotonin, niacin, melatonin
What type of bond holds protein together?
peptide bond (type of amide bond)
What is the primary structure of proteins?
linear sequence of amino acids
What is the secondary strucuture of amino acids?
alpha helices and beta pleated sheets (both structures are held together by hydrogen bonds between atoms of the polypeptide backbone (ex. fibrous proteins - collagen and silk)
What is the tertiary structure of amino acids?
folding of a single polypeptide chain in solution. Myoglobin is a classic example of a globular protein with tertiary structure
What is the quaternary structure of amino acids?
association of two or more polypeptide chains to make a functional protein. Hemoglobin is a classic example
What are enzymes?
catalysts, they increase the rate of a reaction by lowering the activation energy
What factors affect the reaction velocity of an enzyme?
substrate concentration, temperature, pH
What is Vmax?
the maximal velocity of an enzyme catalyzed reaction
What is Km?
the amount of substrate required to reach 1/2 of Vmax (low Km indicates high affinity for enzyme)
What does a competitive inhibitor do?
increase the Km, no effect on Vmax
What does a noncompetitve inhibitor do?
no change in Km, decrease Vmax
What do vitamins and minerals become in the body?
vitamins --> coenzymes and minerals --> cofactors
What is Vitamin B1? What reaction is it involved in? Deficiency?
Thiamine (Thiamine pyrophosphate or TPP), decarboxylation (remove CO2) reactions, beri-beri
What is vitamin B2? What type of reactions is it involved in?
Riboflavin (FAD and FMN), oxidation/reduction
What is vitamin B3? What type of reactions is it involved in? Deficiency?
Niacin (NAD and NADP), oxidation/reduction, pellagra (dermitis, diarrhea, dementia and death)
What is vitamin B5?
Pantothenate (pantothenic acid) -structural component of coenzyme A (CoA)
What is vitamin B6? What type of reactions is it involved in?
Pyridoxine (pyridoxal phosphate), transamination (amino acid metabolism) "My trans am has a B6 engine"
What is vitamin B7? What type of reactions is it involved in?
Biotin (biocytin), carboxylations (add CO2)
What is vitamin B9? What type of reactions is it involved in? Deficiency?
folic acid (tetrahydrofolate), one carbon transfers, megaloblastic anemia
What is vitamin B12? Deficiency?
Cobalamin (methylcobalamin), pernicious anemia
What is vitamin C? Reaction? Deficiency?
ascorbic acid, hydroxylation of proline and lysine in collagen, enhances iron absorption, scurvy
What vitamins are fat soluble (in order of depletion in the liver)?
K, D, E, A
What is vitamin A? What is it involved in? Deficiency?
retinal, retinoic acid, vision/growth, night blindness
What is vitamin D? What is it involved in? Deficiency?
1,25-dihydroxycholecalciferol, calcium and phosphate metabolism, rickets, osteromalacia
What is vitamin E used for?
What is vitamin K used for?
blood clotting, precursor to coenzyme Q
What vitamins are antioxidants?
ACE and selenium
What are monosaccharides?
aldehydes (carbon 1) and ketones (carbon 2), single sugar units
What are the 5 most common monosaccharides?
Fructose (ketohexose), ribose (aldopentose), glucose, galactose and mannose (all aldohexose)
What are isomers?
compounds with the same chemical formula (ex. glucose and fructose)
What are epimers?
monosaccharides which differ in their configuration around one specific carbon, glucose and galactose are C4 epimers, glucose and mannose are C2 epimers
What are enantiomers?
mirror images of the same compound (L and D-glucose)
What are anomers?
anomeric carbons are formed with sugars cyclize. For an aldehyde the anomeric carbon is C1. For a ketone the anomeric carbon is C2. Anomeric carbons are designated as alpha or beta.
What projections can be used to represent a monosaccharide?
fischer projection (linear stick figure), haworth projection (cyclized form)
What are the most common disaccharides and their linkages?
- Sucrose - glucose + fructose (alpha 1, beta 2)
- Lactose - galactose + glucose (beta 1,4)
- Maltose - glucose + glucose (alpha 1,4)
What is glycogen?
storage form of glucose in animals, contains alpha 1,4 bonds and alpha 1,6 bonds
What forms of polysaccharides are present in plants?
- amylose - contains alpha 1,4 links
- amylopectin - contain alpha 1,4 and alpha 1,6 links
- cellulose - contains beta 1,4 links
What are glycosaminoglycans (GAGs)?
large complexes of negatively charged heteropolysaccharides which bind large amounts of water, repeating disaccharide unit of sugar-amino, most common are hyaluronic acid and chondroitin sulfate
What are lipids?
triacylglycerols have three fatty acids esterified to a glycerol backbone (acid + alcohol), this is the most predominant form of fats/lipids in the body
What are fatty acids?
nonpolar hydrocarbon tails attached to a polar carboxylic acid, unsaturated fatty acids contain double bonds which decrease their melting point. The presence of unsaturated fatty acids in the phospholipid bilayer helps maintain the fluid nature of the membrane, naturally occuring double bonds exist in the cis configuration
What are the essential fatty acids?
linoleic acid, linolenic acid and arachidonic acid (precursor to prostagladins)
What are phospholipids?
contain 2 fatty acids and a polar head group which are esterified to glycerol-3-phosphate. The fatty acid chains are esterified at C1 and C2 of the glycerol-3-phosphate. The alchol is esterified to the phosphate of C3. Phospholipids are the major component of membrane lipids
What are nonglycerol lipids?
spingolipids and steroids
What are sphingolipids?
sphingosine backbone, sphingomyelin is the major lipid component of the myelin sheath that surrounds and insulates cells of the nervous system
What is niemann-pick disease?
deficiency of spinomyelinase (a lysosomal enzyme involved in the degradation of sphingomyelin)
What is cholesterol?
most abundant sterol in humans, derived from acetyl-CoA (acetyl-CoA --> HMG-CoA --> Mevalonate --> squalene --> cholesterol --> steroid hormones)
What is HMG-CoA reductase?
rate limiting enzyme of cholesterol synthesis, converts HMG-CoA to mevalonate
What is desmolase?
rate limiting enzyme in steroid biosynthesis, enzyme that converts cholesterol to pregnenolone which is then converted to progesterone, from which all other steroid hormones are derived
What are lipoproteins?
monolayer shell of polar lipids and proteins which surrounds hydrophobic core containing cholesterol esters and/or triglycerides
What are chylomicrons?
produced and secreted from intestinal mucosal cells in response to intake of fats, carry triacylglycerides to peripheral tissues
What is VLDL?
synthesized and secreted from the liver, transports triacylglycerides to peripheral tissues form the liver
What is LDL?
derived from VLDL (VLDL --> IDL --> LDL), the function of LDL is to transport cholesterol from the liver to peripheral tissues
What is HDL?
synthesized and secreted from the liver, transports cholesterol from peripheral tissues back to the liver
What indicates increased risk of heart disease?
high levels of LDL, low levels of HDL
What is lipoprotein lipase?
required for uptake of triglycerides/fatty acis that are carried by VLDL and chylomicrons
What are nucleic acids made of?
phosphate, pentose sugar (ribose for RNA and deoxyribose for DNA), and a nitrogenous base
What are the nitrogenous bases?
adenine and guanine are purines, cytosine, thymine and uracil are pyrimidines
What is a nucleoside?
pentose sugar + nitrogenous base
What is a nucleotide?
pentose sugar + nitrogenous base + phosphate
What base pairs are used in DNA?
A and T, G and C (note: in RNA uracil replaces thymine, RNA is single stranded so no base pairing)
What is replication?
DNA to DNA, occurs during the S phase of the cell cycle, proceeds in the 5' to 3' direction
What is transcription?
DNA to mRNA, proceeds in the 5' to 3' direction, every set of three bases in mRNA is called a codon (encodes for a single amino acid
What is translation?
mRNA to protein, occurs on the rough endoplasmic reticulum (RER), involves mRNA, transfer RNA (tRNA) and ribosomes (surround mRNA and expose 2 codons at a time), the codon on mRNA is recognized by the anticodon on tRNA which is also bound to a specific amino acid, peptidyl transferase links amino acids together
What is a catabolic pathway?
exergonic (releases energy), breaks down macromolecules to simple precursors, ex. glycolysis, lipolysis, glycogenolysis
What is an anabolic pathway?
synthesis of macromolecules from simple precursors, endergonic (use energy), ex. gluconeogenesis, lipogenesis, nucleic acid synthesis
What is glycolysis? Where does it occur? What stimulates it?
- breakdown of glucose to pyruvate
- aerobic = glucose --> 2 pyruvate (pyruvic acid), 2 ATP and 2NADH
- anaerobic = glucose --> 2 lactate (lactic acid), 2 ATP (lactate dehyrogenase uses NADH)
- occurs in the cytosol (cytoplasm)
- insulin stimulates, glucagon inhibits
What are the regulatory enzymes of glycolysis?
- Hexokinase (everywhere else)/glucokinase (liver): glucose + ATP --> glucose-6-phosphate + ADP (step 1)
- Phosphofructokinase (PFK): rate limiting enzyme of glycolysis, fructose-6-phosphate + ATP --> fructose 1,6 bisphosphate + ADP (step 3)
- Pyruvate kinase: phosphoenolpyruvate (PEP) + ADP --> pyruvate + ATP (step 9)
Reactions of glycolysis.
See hand out
What is the cori cycle?
occurs under anaerobic conditions, involves both the muscle and the liver, lactate from anaerobic glycolysis travels to the liver where it is converted back to glucose (2 lactate + 2NAD --> 2NADH + 2 pyruvate --> glucose --> back to muscle where it can be used for energy
What is pyruvate dehydrogenase complex?
link between glycolysis and kreb cycle, converts pyruvate to acetyl-CoA in the mitochondrial matrix (pyruvate + NAD + CoA --> acetyl-CoA + NADH + CO2)
What type of reaction does PDH catylze? What hormones effect it? What coenzymes are required?
oxidative decarboxylation, stimulated by insulin, inhibited by glucagon, uses NAD, FAD, TPP, lipoic acid and CoA as coenzymes
Other names for the Krebs cycle? Where does it occur?
citric acid cycle, Tricarboxylic acid cycle (TCA), occurs in the mitochondria, See hand out for steps.
What is the yield from two turns of the TCA cycle? (two acetyl-CoA or 1 glucose)
- 6 NADH (18 ATP)
- 2 FADH2 (4 ATP)
- 2 GTP (2 ATP)
- Total: 24 ATP
What is the electron transport chain?
synthesis of ATP, oxidative phosphorylation, occurs innermitochondrial membrane (need oxygen), oxygen is the ultimate acceptor of electrons, coenzyme Q is a component of ETC
What is the mitchell hypothesis?
chemiosmotic hypothesis, hypothesis that ETC is coupled to ATP synthesis
Where does gluconeogenesis occur?
primarily in the cytosol, however, the conversionoof pyruvate to oxaloacetate to malate (1st step) occurs in the mitochondria, malate crosses the mitochondrial membrane to the cytosol where it is converted back to oxaloacetate then to PEP by PEP carboxykinase
What hormones effect gluconeogenesis?
stimulated by glucagon and cortisol, inhibited by insulin
What are the primary precursors for gluconeogenesis?
- glycerol - from breakdown of triglycerides, travels to liver and is converted to glucose or enters the glycolytic pathway
- lactate - from anaerobic conditions, converted to pyruvate then glucose as part of the cori cycle
- amino acids - converted to either pyruvate or TCA cycle intermediates via transamination reactions then to glucose
What transamination reactions give gluconeogenic precursors?
- All require pyridoxine (B6)
- Alanine --> pyruvate (glucose-alanine cycle)
- Aspartate --> oxaloacetate (aspartate transaminase AST)
- Glutamate --> alpha=ketoglutarate (glutamate-oxaloacetate transaminase GOT)
What are the gluconeogenic enzymes?
- pyruvate carboxylase: pyruvate + CO2 + ATP --> oxaloacetate + ADP, carboxylation reaction (biotin is required), occurs in the mitochondria
- PEP carboxykinase: oxaloacetate + GTP --> PEP + GDP + CO2, bypasses pyruvate kinase
- Fructose 1,6 bisphosphatase: fructose 1,6 bisphosphate --> fructose 6 phosphate + Pi, bypasses PFK in glycolysis
- Glucose 6 phosphatase: glucose 6 phosphate --> glucose + Pi, present in liver but not in muscle, allows liver to generate free glucose from glycogen breakdown and gluconeogenesis, bypasses glucokinase in glycolysis
Where is glycogen stored?
cytoplasm of the liver and muscle
What regulates glycogen synthesis?
glycogen synthase catalyzes: UDP-glucose addition to glycogen, stimulated by insulin, inhibited by glucagon
What regulates glycogen degradation?
glycogen phosphorylase catalyzes: release of glucose-1-phosphate from glycogen, stimulated by glucagon, inhibited by insulin
What is the HMP shunt?
hexose monophosphate shunt (pentose phosphate pathway, phosphogluconate pathway), occurs in cytosol, glucose-6-phosphate dehydrogenase is major regulatory enzyme
What are the functions of the HMP shunt?
production of NADPH for both fatty acid synthesis and steroid hormone synthesis, production of ribose-5-phosphate for nucleotide (DNA/RNA) synthesis, there is no net gain or loss of ATP in this pathway
Where does fatty acid synthesis (lipogenesis) occur? When? Regulation? Coenzymes?
cytosol, lipogenesis, low fat diet stimulates, acetyl CoA carboxylase (acetyl-CoA + CO2 + ATP --> malonyl-CoA + ADP, 1st step) regulates, stimulated by insulin, inhibited by glucagon, NADPH is used, reductive process, acetyl-CoA is transported from the mitochondria to the cytosol by citrate
Where does fatty acid degradation (lipolysis) occur? Regulation?
beta-oxidation occurs in mitochondria, hormone senstive lipase cleaves off triacylglycerides that are stored in the adipose tissue, stimulated by epinephrine, inhibited by insulin, carnitine transports fatty acids from the cytosol into the mitochondria
Where does the urea cycle take place? Regulation?
urea = 90% of nitrogen containing compounds, 1st cycle that Kreb discovered, takes place in mitochondria (steps 1 and 2) and the cytosol (steps 3-5), urea contains two nitrogen atoms and a single carbon, both nitrogens come from the amino acid glutamate (or alanine), carbamoyl phosphate synthase (CO2 + NH4 + 2ATP --> carbamoyl phosphate) - present in the mitochondria,
What are the important intermediates of urea cycle?
ARginine, Citrulline,Ornithine "ARCO", urea is made by the liver and excreted by kidney
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