bio 1 test

amylose

a plant starch that is unbranched

glyceral

a small molecule with three hydroxyl groups

integrin

a transmembrane protein that often mediates the attachment of epithelial cells to extracellular matrix. they bind to both extracellular matrix but also to actin which are part of the cytoskeleton, so it plays a role in maintaining cell structure as well as adhesion

glycogen

a water insoluble, highly branched polymer of glucose. it's used to store glucose in teh liver and muscles and is thus an energy storage compound for animals, as starch is for plants. both glycogen and starch are readly hydrolyzed into glucose, which in turn can be broken down to liberate their stored energy. it's not stored as glucose bc of hte energy it would take to expel water from cells

amino acids with nonpolar hydrophobic side chains

alanine, isoleucine, leucine, methionine, phenylalanine, tryptophan, valine

saturated fatty acids

all the bonds are single bonds. the bonds are all saturated with H atoms. they're relatively straight, pack together tightly

secondary structure of protein

alpha helix and beta pleated sheet

optical isomers

are mirror images of each other in structure

amino acids with electrically charged side chains at pH of living cells

arginine, histidine, lysine, aspartic acid, glutamic acid

cellulose

as the predominant component of plant cell walls, it's by far the most abundant organic compound on earth. it's a polysaccharide of glucose, but its individual monosaccharides are connected by beta rather than alpha glycosidic bonds. ceullulose is chemically more stable bc of this. it's an excellent structural material that can withstand harsch evnironmental conditions without substantial change.

amino acids in cells

at pH in cells of 7-7.4, both the carboxyl and amino groups of amino acids are ionized: the carboxyl group has lost a hydrogen ion and amino group has gained a hydrogen ion

ester linkages

The bonds that join the glycerol to the fatty acids

homotypic

The same molecule sticks out from both cells and forms a bond

gap junctions

channels that run between membrane pores in adjacent cells, allowing substances to pass between cells. in the heart, for exmaple, gap junections allow the rapid spread of electric current so the heart muscle cells beat in unison.

glycosidic bond

condensation reactions happen to form glycosidic bonds which link disaccharids, oligosaccharides and polysaccharieds. a sing glycosidic bond between two monosaccharieds forsm disaccharide

cell junctions

connections between cells that hold the cells together as a unit

glyoclipid

consists of a carbohydrate covalently bonded to a lipid. extending out from cell surface, the carbohydrate may serve as a recognition signal for inerctions between cells. ex: the carbohydrates on some glycolipids change when cells become cancerous. this change may allow white blood cells to target cancer cells for destruction

glycoprotein

consists of one or more short carbohydrate chains covalently bonded to a protein. the bound carbohydrates are oligosaccharides, usually not exceeding 20 monosaccharide units in length. a proteoglycan is a more heavily glycosylated protein: it has more carbohydrate molecules attached to it, and the carbohydrate chains are often longer than they are in glycoproteins.

oligosaccharides

contain several monosaccharides bound together by glycosidic linkages. they are often covalently bonded to proteins and lipids on outer cell surface where they serve as recognition signals. the diff human blood groups get their specificities from oligosaccharides chains

unsaturated fatty acids

contains one or more double bonds. kinks prevent fat molecules from packing together tightly. plants store unsaturated fats, such as in corn oil and soy oil. the kinks are important in determining the fluidity and melting points of lipids. when they're more packed together they have a higher melting point and are typically soild at room temperature

light reactions

convert light energy into chemical energy in form of ATP and the reduced electron carrier NADPH. this molecule is similar to coenzyme NADH but with an additional phosphate attached to sugar of its adenosine. in general, NADPH acts as a reducing agent in photosynthesis and other anabolic reactions

special case amino acids

cysteine, glycine, proline

native v denatured proteins

denatured proteins take up more volume, native are compact native exist in one, preferred shape. denatured can take many shapes native proteins have hydrogen bonds that stabilize the structure internally, denatured proteins have H bonds on the exterior, to water

D amino acid

dextro

structural isomers

differ in how their atoms are joined together. consider two simple molecules, each composed fo four carbon and ten H atoms bonded covalanetly, boht with formula C4H10. these atoms can be linked in two diff ways, resulting in diff molecules

Maltose and Cellobiose

disaccharieds made from two glucose molecules. they're structuer isomers with the formula C12H22O11. they have different chemical properties and are recognized by diff enzymes in biological tissues. maltose can be hydrolyzed into its monosaccharides in the human body while cellobiose cannot

carbon fixation reactions

do not use light directly, but instead use ATP, NADPH and CO2 to produce carbohydrate. these pathways take place in chlorophlats

secondary active transport

does not use ATP directly, instead its energy is supplied by an ion concentration gradient established by primary active transport

fermentation

doesn't inve O2 its anerobic. wiht the exception of maby microorganisms fermetation converts pyruvate into lactic acid or ethyl alchol. both of which are still relatively energy rich molecules. bc the breakdown of glucose is incomplete, much less energy is released when glycolysis is coupled to fermentation than when coupled to respiration

trans fat

h atoms are on opposite sides of the plan of the molecule. in these, there are no kinks and the fat containing them packs tightly. these cause higher levels of low densitiy lipoproteins LDLs. which may result in accumulation of lipids on inner walls of arteries, leading to heart disease and stroke.

alpha carbon of amino acid

has four available electrons for covalent bonding. it's asymmetircal bc it's bonded to four atoms or groups of atoms. therefore amino acids can exist as optical isomers called D amino acids and L amino acids.

anchored membrane proteins

have lipid components that anchor them in the bilayer

desmosomes

hold neighboring cells firmly together, acting like spot welds or rivets. materials can still mvoe around in the extracellular matrix. this provides mechanical stability for tissues such as skin that receive physical stress

lipids (fats)

hydrocarbons that are insoluble in water bc of their many nonpolar covalent bonds. the huge macromolecular aggregations that can form are not polymers in a strict chemical sense, bc the individual lipid molecules are not covalently bonded

In an α helix, the coiling is stabilized by

hydrogen bonding of the N-H groups on one amino acid and the C=O groups on another.

interactions involved in formation of a proteins tertiary structure

hydrogen bonds, van der waals interactions, disulfide bridges, salt bridges

when they need energy, cells bread down glycogen and starch into glucose using

hydrolysis

primary active transpor

involves the direct hydrolysis of ATP which provides the energy required for transport

Starch and glycogen, which are both polysaccharides, differ in that starch _______, while glycogen _______.

is the principal energy storage compound of plants; is the main energy storage in animals

oxygen bound to carbon - carbonyl oxygen

it carries a slight negative charge, whereas the H bound to the N in teh amino group is slightly positive. this asymmetry favors H bonding within the protein molecule itself and between molecules. these bonds contribute to structure and funciton of many proteins.

starch and water

it readily binds water. however, when water is emoved, hydrogen bonds form between the unbranched polysaccharide chains, which then aggregate. large starch aggregates called starch grains can be observed in teh storage tissues of plant seeds. these aggregates are broken up when starch is heated, breaking the hydrogen bonds. the starch becomes less solid and crystalline and water is absorbed, making the starch even more amorphous. this is what happens in baking with wheat flour, and what gives bread its texture

polypeptide chain is sometimes in danger of binding the wrong susbtance

just after a protein is made when a protein has not yet folded completely, it can present a surface that binds the wrong molecule. following denaturation, certain conditions, such as moderate heat, can cause some proteins to denature without killing the organisms. before the protein can refold, it may present a surface that binds the wrong molecule. the inappropriate binding may be irreversible

coenzyme NAD+

key electron carrier in redox reactions. it exists in two forms NAD+ - oxidized and NADH - reduced. both participate in redox. the electrons dont remain wtht he coenzyme. oxygen is highly electronegative and accepts electrons from NADH. the oxidation of NADH by o2 is exergonic.

peripheral membrane proteins

lack exposed hydrophobic groups and are not embedded in bilayer. instead they have polar or charged regions that interact with exposed parts of integral proteins or white ht polar heads of phospholipids.

L amino acid

levo. only L amino acids are foudn in teh proteins of most organisms and their presence is an important chemical "signature" of life

amyloids

long fibrillary insoluble protein aggregates with extensive beta pleated structures. this can happen if a protein has changes in amino acid sequence such that regions ordinarily on the inside of protein are now on outside.

fatty acid

made up of a long nonpaolar hydrocarbon chain and an acidic polar carboxyl group

environmental conditions affect protein structure

temperature, changes in pH, high concentration of polar substances, nonpolar substances

C-N bond of peptide bond

the adjacent alpha carbons are not free to rotate fully, which limits the folding of polypeptide chains

cell membranes adhere to extracellular matrix

the attachment of a cell to the extracellular matrix is important in maintaining the integrity of a tissue. in addition, some cells can detach from their neighbors, move, and attach to other cells; this is often mediated by interactions with the extracellular matrix

energy

the capacity to do work, which occurs when a force operates on an object over a distance. the capacity for change.

ester linkage

the carboxy group of a fatty acid bonds with the hydroxyl group of glycerol resulting in thise covalent bond and the release of a water molecule

cell adhesion

the connection between two cells is strengthened

n terminus

the end of a polypeptide or protein that has a free amino group - the beginning

c terminus

the end of a polypeptide or protein that has a free carboxyl group - the end of the chain

potential energy

the energy of state or position-stored energy. it can be sotred in many forms: covalent bonds, a concentration gradient, or even as electric charge imbalance

turgor pressure

the pressure within the cell. it keeps plants upright and is the driving force for the enlargement of plant cells.

water potential

the tendency of water molecules to move in response to forces such as pressure and solute concentration gradients. it determines teh direction of water movement from cell to cell. water tends to mvoe away from regions of high pressure and toward regions of high solute concentration. measured in megapascals MPa, a unit of pressure. 1 atm is about 0.1 MPa or 14.7 pounds per sq inch

phosphodiester bond

the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide

polysaccharides store energy and provide structural materials

they are large polymers of monosaccharides connected by glycosidic bonds. in contrast to polypeptides, polysaccharides are not necessarily linear chains of monomers. each monomer has seveeral sites that are capable of forming glycosidic bonds, and thus branched molecules are possible

starch

they make up a family of large molecules with similar structures. while all starches are polysaccharides of glucose with alpha glycosidic bonds, the different starches can be dstinguished by the amount of branching that occurs between carbons 1 and 6. it's the principal energy source of plants

experiemnts with isotopes show that O2 comes from water in oxygenic photosynthesis

they used 16 and 18 . results showed that all teh oxygen gas produced during photosynthesis comes from water. this led to an understanding of photosynthesis in terms of redox. the oxygen atoms are oxidized and the carbon get reduced to carboxydrate

cis trans isomers

typically involve a double bond between two carbon atoms, where the carbons cshare two pairs of elections. when remaining two bonds of each of these carbons are to two different atoms or groups of atoms, these can be oriented on the same or different sides of hte double bonded molecule. if the diff atoms or groups of atoms are on the same side, the double bond is cis. if they are on opposite sides, it's trans. these molecules can have very diff properties

omega-3 fatty acids

unsaturated fatty acids identified by position of the carbon atom of the first double bond, witht he first carbom atom (omega) being at the opposite end of the chain from teh carboxylic acid group. when the first double bond is at position 3, it's an omega 3

cellular respiration

uses oxygen from the envirionment and thus is aerobic. each pyruvate moleucle is completely converted into three moelcules of CO2 thru a set of catabolic pathways including pyruvate oxidation, the citric acid cycle, and an electron transport chain. in the process a great deal of energy stored in the covalent bonds of pyruvate is captured to form ATP

triglycerides

when they're solid at room temp they're fats, when liquid they're oils.

principals of metabolic pathway

1. a complex chemcial transformation occurs in a series of separate reactions that form a metabolic pathway 2. each reaction is catalyzed by a specific enzyme 3. many metabolic pathways are similar in all organisms, from bacteria to humans 4. in eukaryotes, many metabolic pathways are compartmentalized, with certain reactions occurring inside specific organelles, or even specific regions of an organelle 5. some key enzymes in each pathway can be inhibited or activiated to alter the rate of the pathway

carbohydrates have 4 major roles

1. source of stored energy that can be released in a form usable by organisms 2. they are use dot transport stored energy within complex organisms 3. they served as carbon skeletons that can be rearranged to form new molecules 4. they form extraceull

molecular chaperones

A protein that helps other proteins fold or refold from a partially denatured state. typically it has a cage like structure that pulls in a polypeptide, causes it to fold into the correct shape, and then releases it

quaternary structure

Results from two or more polypeptide subunits. hydrophobic interactions, VDWs, H bonds and ionic bonds all hold subunits together.

disulfid bridges

SH group can react with another cysteine side chain in an oxidation reaction to form covalent bond. this helps determine how a polypeptide chain folds.

glycolysis

begins glucose catabolism. through a series of chemcial rearrangements, glucose is converted to two molecules of the three carbon product pyruvate, and a small amount of energy is captured in usable forms. glycolysis is anaerobic

heterotypic

binding between different molecules on different cells

waxes

birds and mammals have glands in their skin that secrete waxy coatings onto their feather or hair. these repel water and help keep the heair and feathers pliable. waxes are substances that are hydrophobic and platic, or malleable at room temp. each wax moleucle consists of a saturated, long chain fatty acid and a satruated, long chain alcohol joined by an ester linkage.

kinetic energy

energy of movement-type of energy that does work, makes things change. heat causes molecular motions and can even break chemical bonds

catabolic and anabolic reactions often linked

energy released in catabolic reactions often used to drive anabolic reactions. ex: the energy released by breakdown of glucose is used to drive anabolic reactions such as the synthesis of triglycerides

role of lipids

energy storage, phospholipids in cell membranes, carotenoids and chlorophylls help plants capture light energy, steroids and modified fatty acids play regulatory roles as hormones and vitamins, fat in animal bodies serves as thermal insulation, a lipid coating around nerves provides electrical insulation, oil or wax on the surfaces of skin, fur, feathers, and leaves repels water and prevents excessive evaporation of water from terrestrial animals and plants

carotenoids

family of light absorbing pigments found in plants and animals. beta carotene is one of the pigments that traps light energy in leaves. in humans, a molecule of beta carotene can be broken down into two vitamin A molecules. vitamin A is used to make the pigment cis retinal, which is required for vision. they are responisble for the colors of carrots, tomatoes, pumpkins, egg yolks and butter

steroids

family of organic compounds whose multiple rings are linked thru shared carbons. the steroid cholesterol is an imortant constiutent of membranes, helping maintain membrane integrity. others can function as hormones. cholesterol is synthesized in the liver and is the starting material for making steroid hormones like testosterone and estrogen

tertiary structure

formed by bending a nd folding. it's a molecules definitive 3D shape. covalent disulfid bridges, H bonds between side chains stabilize folds in protein, hydrophobic side chains can aggregate together in the interior of the protein, away from water, folding the polypeptide in the process. close interactions between hydrophonic side chains are staibilized by van der waals, ionic bonds can form between positively and negatively charged side chains

beta sheet

formed from two or more polypeptide chains that are almost completely extended and aligned side by side. the sheet is stabilized by H bonds between the N-H groups on one chain and the carbonyl groups on the other. a beta sheet may form between separate polypeptide chains or between different regions of a single polypeptide chainthat is bent back on itself.

chemically modified carbohydrates contain addnl fxnl groups

glucosamine and calactosamine are important in the extracellular matrix where they form parts of glycoproteins. galactosamine is a major component of cartilage

cell membrane carbohydrates are recognition sites

glycolipid or glyocprotein

cell recognition and adhesion involve proteins and carbohydrates on the cell surface

molecules responsible for cell recognition and adhesion in sponges are proteoglycans that carry two kinds of carbs. one is relatively small, binds to membrane compoenents, keeping it attached to cell. the other kind is a larger sulfated polysaccharide. if the sufated polysaccharide from a particular species of sponge is purified and attached ot cellulose beads, the beads will aggregate together or with sponge cells, but only cells of hte same species fromw hciht he polysacc was purified.

optical isomer

occur when a carbon atom has four different atoms or groups of atoms attached to it. it allows for two different ways of making hte attachments, each the mirror image of each other. such a carbon atom is called an asymmetric carbon, and the two resulting molecules are optical isomers of each other.

what interaction is not involved in the formation of a protein's tertiary structure?

peptide bonds

condensation reactions

polyers are formed from monomers by a series of condensation reactions (dehyradtion - loss of water) they result in the formation of covalent bonds between monomers. a molecule of water is released with each covalent bond fromed. the condenstiaon reactions that produce the different kinds of polymers idffer in detail, but in all cases polymers form only if water molecules are removed and energy is added to the system.

tight junctions

prevent substances from moving thru the spaces between cells. ex: cells lining the bladder have tight junctions so urine cannot leak out into the body cavity. another important function is to maintain distinct faces of a cell within a tissue by restricting the mirgration of membrane proteins over the cell surface from one face to the other.

polypeptide chains

proteins consist of one or more - they are unbranched linear polymers of covalently bonded amino acids

proteins

range in size - small ones like insulin, which has 51 amino acids and a molecular weight of 5,733, to huge molecules like the muscle protein titin, with 24,000-36,000 amino acids

hydrolysis reaction

result in breakdown of polymers in to their component monomers. water reacts with the covalent bonds that link the polymer together. for each covalent bond that is broken, a water molecule splits into two ions each of which bcomes part of one of the products

alpha helix

right handed coil that runs in same clockwise directionas a standar wood screw. The R groups extend outward from teh peptide backbone of hte helix. the coiling results form H bonds that form between the positive H of the amino group and carbonyl of another.

all the following contribute to the 3D shape of a protein

salt bridges, van der waals forces, hydrophobic interactions, hydrogen bonds

polar amino acid side chains

serine, threonine, asparagine, glutamine, cysteine

oligopeptides

short polymers of 20 or fewer amino acids. these include hormones and other molecules involved in signaling between parts of an organism.

hypertonic

solution has a higher solute concentration than the other solution which it's being compared

hypotonic

solution has a lower solute concentration than the other solution with which it's being compared.

isotonic

solutions have equal solute concentrations

digitalis

strengthens the contraction of the heart muscle, slows the heart rate, and helps eliminate fluid from body tissues. it blocks release of phosphate inons from protein whic freezes shape of the sodium potassium pump. it can then no longer bind sodium. so sodium accumulates inside heart cells. this leads to a greater force of contraction of the heart muscle, whcih aids a patient whose heart is not pumping well

how does a high solute concentration affect tendency of water to move across membrane?

while water molecules are able to diffuse across a semipermable mebrane in both directions, solute molecules cannot cross the membrane. as a result, teh movement of solute molecules that contact a semipermable membrane is redirected away fromt eh membrane, much as a ball bounces off a wall. this morevement of the solute particles away from the membrane impacts the solvent as well, with the result that the solvent (water) is also directed away from the membrane. therefore a higher solute concentration decreases the effective pressure of free water ont eh membrane, allowing more water to enter