Bio HL1 Test 2 - Kim

carbon can form up to ______ covalent bonds

four

carbon can single, double, and triple bond with

carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus (6 most common elements in life)

carbon forms tetrahedrons with 4 single bonds, and form _______ chains and single or multiple ______.

branched or unbranched; rings

anabolism

joining of a monomer to form a more complex molecule (polymer)

anabolism is done by which reaction

condensation reaction; removal of H2O—removal of -OH (hydroxyl) from one and -H from another; it is endergonic, meaning it requires energy

catabolism

breaking of polymers into monomers—done by hydrolysis, addition of H2O, releases energy

carbohydrate monomer

monosaccharide—typically glucose

monosaccharides are linked by condensation reactions to form

disaccharides and polysaccharides

bond between carb monomers

glycosidic linkage (C-O-C covalent bond)

glucose exists in two forms:

linear and ring

pentose contains carbons, hexose contains _

5 (deoxy/ribose); 6 (glucose)

glucose as energy storage

highly soluble, easily transported in mediums like blood, chemically stable, circulates without breaking down, yields large amnts of ATP when oxidized

polysaccharide

large carb molecules formed by linking many monosaccharides (1,000)

starch

short term plant energy storagge; e.g. amylose—unbranched, helical, preferred form (1-4 bonds); amylopectin—branched (1-4, 1-6 bonds)

1-4 linkages vs 1-6 linkages

linear vs branched

glycogen

short term energy storage in animals; unbranched (1-4 linkages) and branched (1-6 linkages)—found in animal liver, similar to amylopectin but more branched

polysaccharides as energy storage

compact; coiling of chains and branching during polymerization makes it compact, less soluble than glucose due to size—doesn’t interfere with osmotic gradient of cell, easy to add and remove alpha-glucose monomers via condensation and hydrolysis

cellulose

polysaccharide made of beta-glucose, forms plant cell walls, unbranched (1-4 bonds), indigestible for most—fiber—ruminants (cows) can due to bacteria in their specialized stomachs

alpha vs. beta glucose

structural isomers; position of hydroxyl (-OH) on C1 is different—for condensation rxn to occur between two B-glucoses, newly added one must be rotated 180 degrees

alternating beta-glucoses produce

a straight chain, aligning parallel to one another with the ability to group in bundles—regularly spaced -OH groups allow for additional H-bonds to form between adjacent strands—allows for structural support to resist osmotic pressures

lipids

nonpolar molecules that include fats, oils, waxes, steroids; hydrophobic, do not consist of monomers/polymers

triglycerides

condensation joins one glycerol and three fatty acids— -OH (hydroxyl) of glycerol and -COOH (carboxyl) form ester bonds: O-C=O

this produces 3 H2O

phospholipids

joining of a glycerol to one phosphate group and two fatty acids—amphipathic; hydrophilic (water-loving) and lipophilic (fat-loving)

fatty acids

long hydrocarbons that have -COOH groups on one end—varying in number of carbons and double bonds

saturated fatty acids

no double bonds, linear, coming from animal fats (butter, lard), high melting point—solid at room temp.

unsaturated fatty acids

contains double bonds (mono/polyunsaturated), bent, comes from plant oils (olive oil), low melting point—typically liquid at room temp., as double bonds increase, melting point decreases

cis unsaturated fatty acids vs trans unsaturated fatty acids

cis—2 H atoms adjacent to double bonds are on the same side, hydrogens repel one another—liquid at room temp

trans—2 H atoms adjacent to double bond are on different sides, produced through industrial process hydrogenation (banned), makes fats spreadable (margarine), linear and solid at room temp despite double bonds

endotherms store energy with

saturated fats for compact long-term storage

plants store energy with

unsaturated oils that remain fluid for transport and enzyme function

triglycerides—long-term energy storage’s function

carry twice as much energy as carbohydrates, stored in adipose tissue (specialized connective tissue), immiscible with H2O, allowing for compact storage w/o affecting osmotic gradient

triglycerides—thermal insulation’s function

adipose tissue found under skin, reduces heat loss, low thermal conductivity slows heat transfer from body to ENV, important in arctic life (blubber in marine mammals)

amino acids (monomers) build…

polypeptides

amino acid structural components

alpha-carbon—central carbon where all others are attached

-NH2 (amine group)

-COOH (carboxyl group)

hydrogen

R-group (sidem chain)

amino acids are amphiprotic, meaning

-COOH can donate H+ (acid), and -NH2 can accept H+ (base)

R-groups determine

chemical properties and behavior of AAs

R-groups are mainly divided into

hydrophilic or hydrophobic—of hydrophilic they are polar, with some having charges (behaving as acids or bases)—this causes polypeptides to fold and function based on R-group’s position in chain

synthesis of polypeptides

condensation reaction joins two AAs, -NH2 of one AA bonds with another’s -COOH, forming a peptide bond (C-N) (produces 1 H2O), and is catalyzed by ribosomes

polypeptides have a direction; the reaction that takes place is

NH2 losing an H and COOH losing an OH to form H2O, N-terminus is NH2 end and C-terminus is COOH end; repeated sequences of N-C-C-N-C-C creates backbone

essential versus non-essential AAs

essential cannot be made by the body and must be consumed through food—insufficient intake can limit protein production and affect growth, repair, and enzyme function

animal-based foods have similar AA balances as that of humans

non-essential AAs can be made from other AAs or nitrogen-containing compounds

genetic code specifically codes for __ AAs

20

proteome

total amount of protein synthesized in an organism—every organism’s DNA is unique—so is its proteome

polypeptides can contain any # of AAs, arranged in

any order—meaning there are 20^n possibilies (n=# in chain)

examples of polypeptides

insulin—regulates blood glucose levels

hemoglobin—transports oxygen

titin—elastic protein found in striated muscle

primary structure of protein

specific sequence of AAs in a polypeptide—determined by genetic code within DNA, composed of only peptide bonds

precise position of AAs in primary structure determines

3-D shape and function of proteins—structure is precise, predictable, and repeatable despite their complexity

example of one wrong AA

sickle cell anemia

secondary structure of proteins

local folding of polypeptide into shapes, stabilized by H-bonds; C=O and N-H are polar

alpha-helices

a spiral arrangement with H-bonds every 4th AA

beta-pleated sheets

sheet-like arrangement with H-bonds between parallel or antiparallel strands

tertiary structure of proteins and its bonds

specific 3D conformation of a polypeptide—determined by affinity or repulsion between R-groups

bonds: disulfide covalent (S-S)—between two cysteine AAs (strongest, provides stability)

ionic—COOH can donate H+ and NH2 can accept them, becoming negatively and positively charged respectively

hydrogen bonds

hydrophobic interactions—found between nonpolar groups that cluster together away from H2O

quatenary structure of proteins and its bonds

arrangement and interaction of multiple polypeptides

conjugated proteins

contain one or more non-proteins (prosthetic groups); e.g. hemoglobin—4 polypeptides, each with an iron-containing heme group

non-conjugated proteins

composed only of polypeptides; e.g. insulin—2 polypeptides, linked by disulfide bonds; collagen—3 polypeptides, wound together to form a triple helix

proteins’ specific 3D structures determine

their biological functions:

specific DNA sequence → specific AA sequence → unique R-group interaction → 3D shape → function—STRUCTURE DETERMINES FUNCTION

fibrous proteins and example

long, narrow insoluble proteins that have structural roles, e.g. collagen (3 polypeptides in a triple helix)—contains repeating sequences of 3 AAs, one of which preventing alpha-helices from forming, provides high tensile strength (skin, tendons, eyes) to prevent tissue tearing under stress.

globular proteins and example

compact, spherical water-soluble proteins that have metabolic roles, e.g. insulin—has a specific shape that allows it to bind to its receptor (like substrate and enzyme’s active site)—allows specific and unambiguous signals to be sent, like when blood sugar is too high

all living organisms have which genetic material

DNA

DNA stores

hereditary (genetic) information

DNA is made of individual

nucleotides

DNA is passed on from

cell to cell and parent to offspring

some viruses carry ___ as their genetic material

RNA, but this doesn’t negate that all living things have DNA since viruses are nonliving since they can’t reproduce

nucleotides components for drawing

5-carbon pentose sugar (deoxyribose or ribose), nitrogenous base attached to 1’ carbon, phosphate group

sugar-phosphate backbone

forms covalent bond between phosphate of one nucleotide and pentose sugar of next nucleotide—called phosphodiester bond—always added in same direction, chain of repeating C,O, and P—alternating sugar and phosphate

all DNA and RNA bases contain which element

nitrogen

any two bases can be

linked covalently, creating infinite possibilities

purine

A and G, two rings

pyrimidine

C and T, one ring

each base pair contains

one purine and one pyrimidine, equal in width and length, allows DNA to be stable and have variety in sequence

DNA drawing

two strands of nucleotides joined at bases via H-bonds, pairs of complimentary bases

DNA in antiparallel form

two DNA strands run parallel in opposite directions—one strand runs 5’—3’, and one runs 3’—5’

double helix

results in a structure that looks like a twisted ladder, consistent diameter of 2nm—very efficient

semi-conservative replication

each strand serves as a template—added bases are complimentary to bases on template—results in DNA consisting of one original (parent) and one new (daughter) strand

nucleosome

DNA wrapped ~ twice around 8 histone proteins (octamer)—two copies of four different histones form disc-shape

H1 histone

linker histone that assists in bonding of DNA to octamer—all plant and animal DNA have nucleosomes—bacterial DNA doesn’t

DNA vs RNA: strands, sugar type, nitrogenous bases

2 vs 1; deoxyribose vs ribose; AGCT vs AGCU

RNA

single stranded polymer of nucleotides (monomer)—always linked by condensation reaction—removal of H2O— -OH from phosphate and -H from sugar

-O on sugar forms phosphodiester bond

DNA is read

with codons—64 diff. triplet bases—considered to be universal—transferable between species—one codon codes for one AA—AUG codes for start, UAA, UGA, UAG signal stop

at 3’ end, ___ is unbound

at 5’ end, ___ is unbound

pentose sugar; phosphate

tetranucleotide hypothesis

DNA was thought to have consisted of four repeating bases in equal numbers, which wouldn’t account for genetic difference—this is why the 20 AAs to be the genetic material

plant storage / structure

starch-alpha; cellulose-beta

animal storage / structure

glycogen-alpha; chitin-modified/beta

cell membrane and its properties

bilayer of phospholipids that forms a continuous battier, separating the cell from its environment and controls passage of its particles

phospholipid structure

amphipathic, both hydrophilic and lipophilic, polar head consisting of glycerol and phosphate, two nonpolar taios composed of fatty acids, in aqueous environments spontaneously arrange into a bilayer, hydrophobic tails attracted to each other, hydrophilic heads H-bond with cytosolic and extracellular fluids

fluid-mosaic model

phospholipid bilayer with embedded proteins

fluid: phospholipids are free and move laterally

mosaic: different types of proteins (like tiles in a mosaic)

phospholipid bilayer is sustained by hydrophobic interactions, so they drift ______, but not _______.

laterally; transversely

saturated fatty acid structure

straight, packed tightly, increased density and decreased fluidity and permeability for diffusion

unsaturated fatty acid structure

bent, packed loosely, decreased density and increased fluidity and permeability

ratio of saturated and unsaturated fatty acids must be regulated because the membranes must be:

fluid but intact, permeable but not perforated

arctic animals have a ______ proportion of unsaturated fatty acids than saturated

greater

steroid

four fused carbon rings, 3 cyclohexanic rings, 1 cyclopentane ring, 17 carbons total

Cholesterol’s role/location in animal cell membrane fluidity

maintains membrane fluidity and stability in animal cells, steroid rings aligning with fatty acid tails, hydroxyl groups aligning with phosphate heads; commonly located btwn saturated fatty acids

cholesterol properties

controls membrane fluidity by seperating phospholipid tails, too fluid (increased kinetic energy) means increased permeability and increased diffusion, buffers against temperature changes, in high temperatures maintains impermeability and in low temperatures stops crystallization, anchors peripheral proteins

glycoproteins

involved in cell-to-cell recognition, proteins covalently bonded to short, branched monosaccharides, e.g. ABO blood groups

glycolipids

lipid’s polar heads bound to carbohydrate chains, e.g. antigens and antibodies

carbohydrate chains project to the extracellular side, forming

glycocalyx

glycocalyx

carb-rich layer providing protection and allowingg for communication btwn cells

glycoproteins and glycolipid function in cell adhesion

glycoproteins: help cells bind to each other or to ECM

glycolipids: promote membrane stability

glycoproteins and glycolipid function in cell recognition

carb chains serve as identification markers used by immune and signalling systems, seperates “self” from “non-self” cells

cell-adhesion molecules

specialized proteins on cell surface that enables cells to recognize, bind, and communicate with other cells, binds to complimentary molecules on adjacent cells or components of the ECM, allowing cells to organize into tissue, coordinates communication and function, prevents cells from detaching under mechanical stress

different types of CAMs create

junctions (tight, gap)