Lec 9/10 Flashcards
Atoms most abundant in biomolecules
H,O,S,N,P,C
what are basic organic compounds?
alcohol, aldehyde, ketone,carboxylic acid, sulfhydryl group, A disulfide, Amino group,Phosphoester, Amide
characteristics of noncovalent bonds
- weak attractive forces
- ionic interaction
- form H-bonds
- hydrophobic effect
characteristics of covalent bonds
- strong attractive forces
- can make single, double, triple bonds
properties of water
- polar
- cohesive: H-bonds
- Solvent(H-bonds, ionic interactions)
Basic biological compounds
aa, nucleotides, sugars, lipids, proteins, DNA, RNA, starch, cellulose, biomembranes
what is a common theme for all biological compounds?
loss of water in formation of covalent polymers
characteristics of aa
- alpha C, R group, contain both acidic(carboxyl) and basic (amino)
- at pH 7-double ionized form(amino accepted a proton–>+, carboxyl lost a proton–>-)
- Zwitterion form of aa(equal nunber of positive and negative ions)–> net charge=0–>neutral
is polar molecule water soluble?
yes
is nonpolar molecule water soluble?
no
what does Amphipathic mean?
having both polar and non-polar properties
what does Aliphatic mean?
having a straight or branched chain structure
what aa are hydrophobic?
Alanine-A, Valine-V, Leucine-L, Isoleucine-I, Proline-P, Methionine-M, Phenylalanine-F, Tryptophan-W
what aa are hydrophyllic?
Glycine-G, Serine-S, Threonine-T, Cysteine-C, Asparagine-N, Glutamine-Q, Tyrosine-Y
what are aa hydrophyllic and negative charge?
Aspartic acid-D, Glutamic acid-E
what are aa hydrophyllic and positive charge?
Lysine-K, Arginine-R, Histidine-H
what are characteristics of polypeptide chains?
- aa linked by peptide bonds
- a-carboxyl group joined to a-amino group
- peptide bond=amide bond: covalent bond
- loss of a water molecule
- require an input of free energy
- stable, >1000 years in absence of catalyst
what is another name for aa unit?
residue
does polypeptide chain have polarity?
- amino-terminal (N-terminal)
- carboxyl-terminal(C-terminal)
what type of bond mainly found in backbone of polypeptide chains?
H-bonds
what are characteristics of proteins?
- 50% of dry weight of cell
- catalysts
- transport+store other molecules. EX: O2
- mechanical support, immune protection, generate movement, transmit nerve impulses, control growth and differentiation
what gives function of a protein?
chemical reactivity of functional groups give function
what categories of proteins?
Fibrous proteins and globular proteins
what is fibrous protein?
contributes to structure of cell
what is globular proteins?
contributes to function of cell
what are characteristics of fibrous protein?
- fibrous-like and insoluble in H2O
- unaffected by changes in temp and pH
what are examples of fibrous proteins?
- collagen&elastins
- keratins
- fibrin
what are collagen and elastin?
proteins of CT(tendon and ligament)
what is keratin?
protein that is major component of skin and hair
what is fibrin?
protein formed when blood clots
what is structure of collagen?
- Glycine every 3rd aa
- Gly-Pro-Hyp frequent
- Superhelical cable is formed by H-bonds and Hyp participated
what is hyproxylation?
process of putting OH into Prolin to make hyproxyprolin
what is Prolylhydroxylae?
required for Hyp formation
what are effect of Scurvy?
bleeding gums, loss of teeth, periodontal disease
what are characteristics of globular proteins?
- interior nonpolar residues
- polar, charged on surface
- regulatory, maintenance and catalytic roles
- either dissolve or form colloidal suspensions in water
- sensitive to temp and pH change
what are EX of globular proteins?
hormones, antibodies, and enzymes
what are characteristics of enzymes?
- mediate energy conversion
- catalytic power and specificity
- proteins that have single polypeptide, multiple subunits, multienzyme complex
- sometimes is RNA
biological catalytic features of enzymes
-dont change equilibrium, not consumed; present at low []; reactants are present at low []; function in mild condition of temp, pH, and pressure; RXN would not normally proceed w/o enzymes;accelerate RXN rates 106to1012; activity depends on structural integrity; high degree of specificity; activity can be precisely regulated
Are enzymes regulatory elements?
yes
How can enzyme control rates of physiological processes?
- by amount of enzymes available
- enzymatic activity- allosteric control(modulation of activity by changes in [S], activators and inhibitors), isozymes or multiple forms of enzyme, covalent modifications
what is isozyme?
- different forms that catalize same RXN
- different genes-different aa sequence
- different kinetics
- regulated differently
what are EX of isozyme?
lactate dehydrogenase, heart isoform, muscle isoform
how to modify enzymes post-translationally?
- cleavage of peptide bond
- chemical modification
cleavage of peptide bond
- irreversible
- activates enzyme from inactive precursor.EX: activation of zymogens
chemical modification
- phosphotylation of a hydroxyl-containing residue(Ser,Thr, Tyr)
- acetylation
- hydroxylation(Proline, Lysine residues in collagen)
- glycosylation
- methylation(Histidine)
phosphorylation
- reversible
- bidirectional-can acitvate enzyme by adding phosphate (phosphatase) or inhibit by removing phosphate(kinase`)
glycosylation
- attachment of linear and branched carbohydrate chains
- atteched at side chain of Asparagine, Serine, Threonine
gama-carboxylation
of Glutamate in prothrombin, an essential blood-clotting factor, vitamin K required
what is role of carbohydates in living organisms?
- supply biological energy via glycolysis and TCA cycle
- energy stores, metabolic intermediates (structural components of cell membrane and extracellular matrix)
- framework for DNA,RNA(ribose, deoxyribose)
- linked to proteins(mediating activity)
what is structure of carbohydrate?
polyhydroxylated hydrocarbons up to 7C that have carbonyl groups
types of Carb?
- monosaccharide (glucose, galactose, fructose)
- disaccharide (sucrose, lactose)
- oligosaccharide(3-6 monosaccharides)
- polysaccharide(>6monosaccharides)- starch, glycogen, cellulose
triose?
monosaccharide that has 3C
tetrose?
monosaccharide that has 4C
EX of aldohexoses
galactose, mannose, glucose
what are characteristics of smallest Carb?
- 3C, C2 is chiral
- has D & L form, naturally occurs in D form
what are characteristics of erythrose?
-4C, naturally occurs in D isomer cuz configuration around penultimate C same as in glyceraldehyde (not from direction rotates polarized light, not from R/S configuration)
How does glucose create anomers?
- hydroxyl group reacts w/ aldehyde or ketone to form ring–> 2 form of glucose
- C1 is asymmetric C=anomeric C
what are characteristics of glucose ring structure?
- C1 is anomeric, ring is an intramolecular hemiacetal
- 6-member ring is related to ring found in pyran(glucosepyranose)
- 5-member ring forms furanose sugars
- straight chain and cyclic structures in equilibrium whcih lies to side of ring structures
what are characteristics of fructose ring structure?
- 6C w/ ketone group
- reducing sugar
- C2 is anomeric carbon
how to test reducing sugar?
- place sugar in either Benedict’s or Fehling’s solution and heated
- positive result: sugar reduces Cu++ to Cu+ and red precipitate forms
- negative result: sugar is not interconverted w/a form that contains a free aldehyde group
what are characteristics of Maltose?
- 2 glucose
- linked by alpha-1,4-glycosidic
- reducing sugar cuz one glucose has a potentially free aldehyde group
what are characteristics of sucrose?
- glucose+fructose
- alpha,beta-1,2- linkage
- not reducing sugar cuz either glucose or fructose has a potentially free aldehyde
what are characteristics of lactose?
- abundant in milk
- D-galactose+D-glucose=alpha-lactose
- beta-1,4-linkage
- reducing sugar
what are characteristics of ribose and deoxyribose?
- 5C aldose, component of nucleic acids
- C1 and C4 are connected by an O brigde to form to form Furanose ring
- ribose is converted to deoxyribose by removing OH at C2
what is polysaccharide?
monosaccharides joined together. EX: starch, glycogen, cellulose
what is starch?
- polymers of >200 glucoses
- amylases(like ptyalin in saliva) digest starch to form maltose
what is glycogen?
- same as amylopectin
- alpha-1,4 linked chains of glucose, alpha-1,6 branches
- higher density of branches
- in tissus, glucose is converted to glycogen for storage in liver and muscle
what is cellulose?
- polymer of >3000 glucoses
- beta-1,4 linkage
- indigestable
- structural component of green (plant cell wall)
what is glycosaminoglycans (GAG)?
- alternating copolymers of uronic acid and amino sugar derivative(glucosamine or galactosamine)
- has sulfate groups
- if attached to proteins called proteoglycans
- found in CT and teeth
- cushioning effect in joint
lipids
- soluble in fat solvents
- insoluble in water
- polar and non-polar
- energy storage, structural components of membranes, hormones, vitamin, bile salts, cellular messengers
fatty acids
- metabolic fuel, building blocks for other lipids
- long chain hydrocarbons represented by R-COOH
- can be saturated, monounsaturated, polyunsaturated
- most have even # C(14-22, 16-18)
acylglycerols
- fatty acid storage and transport, metabolic intermediates and regulation
- ester formed from FA and glycerol
- glycerol may be exterified to different extents
- triacylglycerol- most abundant, fat storage, hydrolyzed by lipases
phospholipids
- membrane structurem membrane signal transduction, storage of arachidonic acid
- has glyceride backbone, 2 FA at C1 and C2
- alcohol component esterified to phosphoric acid group to form phosphodiester
aphingolipids
membrane structure, surface antigens
ketone bodies
metabolic fuel
phosphoglycerides
- families differ by C1 uusually saturated and C2 unsaturated
- 50% of membrane lipids are phosphatidyl choline and phosphatidyl ethanolamine
steroids
- derivative of perhydrocyclopentanophenanthrene ring system
- contain a hydroxyl group at C3 and hydrocarbon chain attached to C17
- cholesterol is most abundant in animal tissue
nucleotides
- cell signaling
- protein synthesis
- energy generation
cell signaling
- cAMP(cyclic adenosine monophosphate)
- cGMP(cyclic guanosine monophosphate)
protein synthesis
- DNA(deoxyribosenucleic acid)
- mRNA(messenger ribonucleic acid)
- rRNA(ribosomal ribonucleic acid)
- tRNA(transfer ribonucleic acid)
energy generation
- GDP,GTP(guanosine di, triphosphate)
- ADP, ATP(adenosine di, triphosphate)
nucleic acids
- consists of 4 kinds of bases linked to sugar phosphate backbone
- joined by phosphodiester bond
purine
adenine, guanine
pyrimidine
cytosine, thymine, uracil
