Kaplan Gre Biology Part 1

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Macromolecules (Biomolecule, Monomer, Major Elements)

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Proteins (Amino Acids [20 naturally occurring], C, H, N, O, [S])

Carbohydrates (Simple sugars [glucose, fructose, etc], C, H, O)

Lipids (Glycerol & Fatty Acids), C, H, O

Nucleic Acids (Nucleotides [phosphate, sugar, base], C, H, N, O, P)

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Amino Acids

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called amino acids b/c of amino (NH2) group on one end of the molecule, and carboxyl COOH group on the other end

R variable group in central carbon which varies between amino acids

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Amino Acid ph buffering

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since amino acids are zwitterions, they can attract positive and negative ions (+ charged NH2 attracts excess OH-, Carboxyl picks up excess H+), thereby maintaining neutral ph levels

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Dehydration Synthesis

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Carboxyl carbon of one amino acid binds to the amino nitrogen of the other (H is removed from the amino group to form water)

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Polypeptides (proteins)

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formed when several hundred to several thousand amino acids bond together via dehydration synthesis

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Primary Structure

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The linear order of the amino acid chain. Dictatges the secondary and tertiary structures which give the polypeptide its overall shape & function

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Secondary Structure

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Formed between amino acids close enough in primary structure, add 3-D structure to Proteins

Alpha Helices - tightly wound coils (like a single strand of DNA)

Beta pleated-sheets - straight chains of amino acids held above or below each other in parallel arrangement due to H-bonding.

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Tertiary Structure

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Bonding & interactions between amino acids that are further apart than secondary structure interactions. Includes disulfide bridges & patterns like bunched up hydrophilic amino acids on the outside of a hydrophobic core in an aqueous environment. Provide overall 3-D structure which is essential for function

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Quaternary Structure

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Multi-subunit structures with other proteins which create distinct attributes from the subunits in isolation. Ex- hemoglobin tetramer (4 units of 2 identical alpha chain proteins and two identical beta chain proteins) Ex- collagen a trimer (3 units) used to build connective tissue

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Lipids

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nonpolar, insoluble in water, & used in membrane formation, energy storage, protective barriers, vitamins, hormones

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Forms of lipids

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fatty acids, glycerides, complex lipids, nonglycerides [some lipids combine two or more forms]

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Fatty Acids (definition/chemical formula)

"fatty" = due to extreme nonpolarity, acid due to COOH end

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long chains of carbon & hydrogen one end is COOH carboxylic acid

Ch3(CH2)nCOOH where n is an even number between 12 & 24

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Saturated/ unsaturated fatty acids

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saturated fatty acids have only single bonds within their hydrocarbon chains,

unsaturated fatty acids have one or more double bonds that create bends in structure. The bends push away other lipids, helping to create the keep temperatures cool & membranes fluid

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Glycerides (aka fats) triglycerides store energy in adipose tissue

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Esters made of glycerol plus one to 3 fatty acid chains.

one fatty acid chain = monoglyceride, 2=diglyceride

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Phospholipids (predominant class of lipids in cell membranes)

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glycerol + 2 fatty acid chains (create non polar tails)+ a phosphate group attached to a variable R group (phosphate group makes one end polar & hydrophilic)

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Amphipathic

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Having two poles, ex phospholipids

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Emulsification

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when ampipathic lipids surround a fat droplet & break it down into smaller particles, ex detergents

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Lipid complexes/ aggregates (useful for transporting substances around the body by enclosing them in a lipid/ protein barrier which allows them to flow through the bloodstream easier)

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Lipids grouped with proteins or other molecules

ex plasma membrane, steroids such as cholesterol, proteins, triglycerides

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Examples of Lipid complexes/ aggregates

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chylomicrons - surround & transport triglycerides from intestines & transport it around the body

High-density lipoproteins (HDL) / low density lipoproteins (LDL) - which carry cholesterol from the intestines around the body

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Non-glycerides

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Steroids, sphingolipids examples of steroids, cholesterol, estrogen, testosterone

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Steroid Structure

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a common core of 4 fused carbon rings. Differ from one another by the groups that attach to the fused rings. Since they are lipids, steroids can move straight through cell membranes & act directly on cell DNA

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Carbohydrates (simple sugars like monosaccharides)

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Contain C, H, O in a specific ratio. Formula is typically (CH2O)n , where n is the # of C atoms in the sugar ring or chain.

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Forms of carbohydrates

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linear or cyclic caused by when the aldehyde or ketone group bonds to the terminal hydroxyl group to form a ring w/ O in it.

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Oligosaccharides

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a carbohydrate consisting of 2-10 simple sugars attached to each other in a row

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Polysaccharides

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a carbohydrate consisting of more than 10 simple sugars

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glycosidic bonds

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Bonds that bridge sugars across an atom of Oxygen

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Alpha Linkage (found in energy storage carbohydrates such as starch or glycogen)/ Beta Linkage (found in structural carbohydrates such as cellulose)

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bonds between carbohydrates which result in winding & twisting configurations

Beta linkages create straight chains of sugars

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Chitin

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A polysaccharide of amino sugars, similar to cellulose in structure (monosaccharides via eta glycosidic linkages) found in exoskeletons of insects & crustaceans

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Nucleic Acids

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Information storage molecules, which also form the structures that build proteins for all cells. Basic unit is the nucleotide.

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Nucleotide

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A phosphate group, a sugar group (always deoxyribose in DNA, ribose in RNA), & a nitrogenous base (ATP can also be used as an RNA nucleotide)

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DNA structure

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double-stranded molecule bonded together w/ H bonds between base pairs in an antiparallel fashion (G-C, A-T).

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Enzymes (makes molecules smaller by breaking them down, can act on thousands to millions of particles per second) Most enzymes are inactive most of the time

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Proteins which bind to very particular molecules (called Substrate molecules) to increase the rate of reactions. Do not change free energy, decrease activation energy. substrates bind to enzymes in active sites.

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Maximum reaction Rate

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vmax, the point in which enzymes become saturated with substrate

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Lock & Key / Induced fit models of Enzyme-Substrate Interaction

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enzyme & substrate are an exact fit together/ the induced fit model enables the enzyme to shift to accommodate the incoming substrate molecule

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Enzyme Cofactors (most enzymes work best in 98.6 F & 7.4 pH)

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Vitamins allow certain enzymes to work. Low concentrations enable enzymatic regulation

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Active Site components

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binding site - consists of amino acids which the substrate temporarily bonds to, & the catalytic site where the reaction occurs. Enzyme & substrate separate once the product is formed.

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Transition State

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when the substrate molecule is neither the original substrate molecule nor the product. Ends when the product is formed & enzyme/substrate separate.

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Feedback Inhibition

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End-product of an enzyme-catalzyed reaction works to block the original enzymes that started the reaction.

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Competitive Inhibition

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Reduces the productivity to enzymes by introducing competing molecules for substrates for the same active sites on enzymes.

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Irreversible Inhibitors

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Competitive inhibitors that chemically & covalently bind to an enzyme's active site, rendering the enzyme permanently inactive.

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Noncompetitive inhibitors

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Instead of acting on the active site, bind elsewhere to the enzyme to change its shape, thus decreasing its affinity for substrates.

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pseudoirreversible inhibitors

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competitive inhibitors w/ extremely high affinities for enzyme active sites. Not permanent, but hard to displace