Flashcards in TBR 6 - Structure and Function in Cells and Viruses Deck (70):
What is collagen?
Collagen is the main structural protein in the extracellular space in the various connective tissues in animal bodies
What is an amino acid composed of?
A basic amino group (NH2), an acidic carboxyl group (COOH), a hydrogen atom (H), and a side chain which is characteristic to each amino acid.
Amino acids can exist in either D or L configuration. What is one exception and what configuration is found in proteins?
Glycine is the exception. Only the L configuration of amino acids are found in proteins.
Ampholytes are amphoteric molecules that contain both acidic and basic groups and will exist mostly as zwitterions in a certain range of pH.
What's a zwitterion.
In chemistry, a zwitterion, formerly called a dipolar ion, is a neutral molecule with both positive and negative electrical charges.
Average pka for α-amino terminal and α- carboxyl terminal.
pka = 9.4 and 2.2.
What are two major components of collagen?
Hydroxyproline and hydroxylysine.
What is the most abundant protein in mammals?
What does a small pKa say abut the acid?
Strong ass acid.
What does a large pka say about the acid?
Weak ass acid.
What's the Hendersen Hasselbach equation?
pH = pka + log [A-]/[HA]. This can be used to determine the fraction of either the α-amino, α-carboxyl, or side chain groups that are ionized at a particular pH. A - = conjugate base and AH is the conjugate acid.
What is the isoelectric point (pI)? This is also known as the equivalence point.
The pH at which an amino acid ( or molecule) carries no net electrical charge. pI = (pKa 1 + pKa 2) /2
If we were to place an AA with a PI of 10 in an electric field, any PH above their IP would result in migration toward the anode (+ electrode)
What is a buffer?
The ability of a solution to resist a change in pH when either an acid or a base is added. If a weak acid is within 1 pH unit of its pka value, it resides in a good buffering range.
Difference between polypeptide, oligopeptide, and protein?
Polypeptide is a convenient term for any length of polymer of AA. Oligopeptides is simple 10 or so AA. A protein is generally described by 100 or more AA linked together.
What is unique about peptide bonds ( O-C-N-H)?
The peptide unit is planar is rigid due to the partial double bond character of CN bond. However, there can be rotation about the bonds between the α carbon and the carbonyl carbon and nitrogen.
Proteins with cysteine residues can form ___ bonds.
When two cysteine residues are oxidized, they form a disulfide called ______.
The α-helix is stabilized by...?
Hydrogen bonding between the CO and NH groups. See page 10, TBR.
The α-heix has how many AA per turn?
3.6 amino acids per turn. 3.5 for beta sheet turns.
The side chains of the AA residues of α - helices extend ( inward, outward, up).
Outward and away from the helical axis.
The beta sheet is stabilized by...?
Hydrogen bonding between CO and NH groups. With B turns, hydrogen bonding occurs between the CO group of one AA and the NH group of an AA 3 residues away.
Define the primary structure of AA.
The sequence of AA in a protein.
Define the secondary structure of AA.
The spatial arrangement of AA that are close to one another.
Define the tertiary structure of AA.
The spatial arrangement of AA that are far from one another. A protein with a tertiary structure can be referred to as a subunit.
Define the quaternary structure of AA.
The association of various subunits with one another. Interactions could be hydrophobic, ionic, hydrogen bonding, or polar interactions.
Which protein structure determines the way in which a protein will fold?
Primary structure. This was proven by a scientist who used b-mercaptoethanol and urea to cleave disulfide bonds. Enzyme activity was restored to the protein after SH groups on the cysteine residues were oxidized, and b + urea was removed via dialysis.
Protein folding is ( random, specific)?
Specific. It would take too long to try out all conformations.
What is the empirical formula for carbohydrates?
In order for a molecule to be classified as a carb, it must have:
Aldehyde or ketone functional group; two or more alcohol functional groups.
Name the two simplest carbohydrates ( n = 3)?
Glyceraldehyde and dihydroxyacetone.
If a molecule has 2 chiral centers, it will have how many stereoisomers?
4. 2^n.....where n is the number of chiral centers.
Most of the naturally occurring sugars are found in their D/L form?
D form. Opposite of AA. In order to tell if a monosacc drawn in the Fisher projection is in the D or L isomeric form, we look at the chiral carbon furthest from the carbonyl carbon ( reference carbon). If the hydroxyl group is to the left, the molecule is the L isomer.
Which sugars prefer the cyclic form?
5 or more atoms in their backbone prefer to be in the cyclic form.
A six-membered ring.
A 5 membered ring.
Anomers are diastereoisomers of cyclic forms of sugars or similar molecules differing in the configuration at the anomeric carbon. The cyclic forms of carbohydrates can exist in two forms, α- and β- based on the position of the substituent at the anomeric center.
A hemiacetal involves a reaction with ____ and ___. It has _,_, _, _ attached to the carbon in the center.
Aldehyde + alcohol; RO, OH, H, R1
A hemiketal involves a reaction with ___ and ___. It has _,_, _, _ attached to the carbon in the center.
Ketone + alcohol; R3O, OH, R1, R2
How do we identify ketone and aldehyde funtional groups in carbs?
Using Tollens or Benedict's agent (oxidizing agents), we can identify aldoses or ketoses AND thus reducing sugars. Carbs that contain a hemiacetal or a hemiketal group give + tests with Tol or Benedict.
How to determine alpha and beta when naming carbs?
Locate the anomeric carbon and note the OH group. If if the hydroxyl group is on the opp side of the ring from the CH2OH that is attached to the reference carbon.
How do we make an acetal? And does it react with Tollen's reagent?
Hemiacetal + alcohol; no it does not.
Imagine the structure of lactose. Is it a reducing sugar?
Lactose is composed of galactose and glucose. Glucose can be reduced. Galactose is locked up in a glycosidic linkage. Lactose is a reducing sugar.
Name two important storage molecules and what stores them.
Starch and amylopectin is a food reserve n plants. Glycogen is the storage polysaccharide common to all animals.
What is starch composed of? Is it branched or unbranched? If so, number of branch points?
α- amylose, a linear polymer of unbranced D-glucose residues linked together in an α1-->4 linkages .
What is amylopectin composed of? Is it branched or unbrached? If so, number of branch points?
A branched polymer of D-glucose residues linked together primarily α1-->4 linkages but include branch points in α1-->6 linkages. The branch points occur roughly every 24 - 30 glucose residues
Digestion of starches begins in the...
Mouth with α-amylase.
What is glycogen composed of? Is it branched or unbranched? If so, number of branch points?
Glycogen is a branched polymer of D-glucose residues. Branch points are more frequent than amylopectin. About every 8 - 12 glucose residues.
What are fatty acids composed of?
Carboxylic acids with a hydrocarbon side chain.
In nature, FA are rarely free. Rather, they are esterified to a glycerol backbone to form a ____________.
Triacylglycerol. In animals, these compounds are stored in adipocytes ( fat cells)
Triacylglycerols that have a high degree of saturated fatty acids pack have a ( low, high) melting point? And why this melting point?
Triacylglycerols with many saturated FAs have a high MP. They pack together well. This high MP is mainly due to the high Van Der Waals attractions between methylene groups in the FA chains.
Increase in molecular weight (decreases, increases) the MP of fatty acids.
As the MW of a saturated FA increases, so does the MP.
How does one lower the MP of fats?
Introducing an unsaturated cis double bond.
What is the predominant lipid component of all biological membranes? Describe the structure of them
Glycerophospholipids. They have two FA residues esterified to the C1 and C2 carbons of glycerol. Esterified to the C3 carbon of glycerol is a phosphate group which bears a negative charge at pH 7. Glycerophospholipids are amphiphillic ( nonpolar tails + polar heads).
Name the hydrophobic amino acids with nonpolar R groups.
Glycine, alanine, valine, leucine, isoleucine, proline, methionine, phenylalanine, tryptophan
Name the polar, uncharged R groups.
Tyrosine, serine, threonine, cysteine, asparagine, glutamine,
Name the charged R groups.
Aspartate, glutamate, arginine, histidine, lysine.
True or false. All hydrolysis reactions are favorable.
TRUE. See page 9. Hydrolysis of a peptide bond is more favorable than its synthesis.
What are the best AAs to make alpha helices?
A protein with an allosteric regulatory site can control the binding of various substrates or modulate molecule. Explain hemoglobin and how it acts as an allosteric protein.
Hgb is an allosteric protein. Hgb has four polypeptide subunits for a 4 structure, each having a heme group that has the capability of binding O2. When one O2 molecule binds to the heme group of one subunit, that binding facilitates others subunits to change conformation and bind to O2.
is sucrose a reducing sugar?
No, it is not. It's composed of glucose and fructose, but the OH group of fructose is locked in an o-glycosidic linkage.
How are sphingolipids different from glycerophospholipids?
The sphingolipids are based on derivatives of amino alcohols for their backbones. See page 19. Ceramide is the simplest structural residue. Sphingomyelin is important in the myelin sheaths; cerebrosides and gangliosides are sphingolipids with sugars attached.
Where is cholesterol synthesized?
Name 3 - 4 properties of cholesterol.
It generally exists as cholesterol ester - a major component in animal plasma MB. They're an intermediate to ALL steroids. It's composed of 4 rigid rings and a polar OH group, which makes it slightly amphiphilic.
Where are steroids synthesized?
The five major classes of steroids (progesterone, glucocorticoids, mineralocorticoids, androgens, estrogens) are synthesized in the mitochondrion.
The function of progesterone?
Prepares the uterus for implantation of an ovum. If implantation occurs, it maintains the endometrial lining of the uterus and hence maintains pregnancy. Stimulates mammary tissue growth for parturition.
The function of cortisol?
Secreted from adrenal cortex. In the liver, it ^glycogen synthesis and gluconeogenesis. In skeletal muscle, it decreases glucose uptake and protein syn, and ^protein catabolism. In adipose, it ^lipid mobilization and decreases glucose uptake.
The function of Aldosterone?
Secreted from the adrenal cortex. It acts to increase Na+ reabsroption at the level of the kidney, intestines, salivary and sweat glands. Net result is increase Na+ in the EC fluid, thereby increasing ECF volume. Leads to ^blood volume, pressure, and flow.
The function of testosterone?
Made by Leydig cells in male testes and aids in sperm maturation. ALso reach blood, circulates throughout body and promotes secondary sex characteristics.
The function estradiol?
Synthesized in the theca cells of the ovarian follicles. Development of secondary sex characgteristics, regulates ovarian cycle, conrol of certain metabolic processes.