Biology Semester 1

hydroxyl

OH - alcohol - alcoholic beverages

carbonyl

COH - aldehyde/ketone - end/middle - sugars, ketose, and aldose`\

carboxyl

COOH - carboxylic acid/organiz acid - acetic acid (vinegar)

sulfhydryl

SH - thiol - cross links stabilize protein structure (hair)

amino

NH2 - amine - glycine/amino acids

methyl

CH3 - methylated compound - affects expression of genes/sex hormones

phosphate

OPO32- - organic phosphate - DNA backbone/chemical reactions

polymerization

process by which cells make polymers and enzymes

structural isomer

different arrangement of atoms

cis-trans (geometric) isomer

different spatial arrangement because the double bond is inflexible - functional groups in different orientations

enantiomer

mirror image because of asymmetric carbon

carbohydrates

CHO - 2:0 H to O ratio

ribose, glucose

lipids

CHO; insoluble in water, fats solid + oils solid at room temp

• sterouds, waxes, fatty acids, triglycerides, oleic acid, testosterone

proteins (amino acid chains)

CHON(S); amino acid chains

• amine group, carboxyl group, hydrogen atom, r group

nucleic acids

CHONP; nucleotide chains - RNA, DNA

metabolism

sum of all reactions that occur in an organism

metabolic pahtways

chain reactions and cycles

anabolism

make big from small - synthesis of complex molecules from simpler molecules

• needs energy (atp)

• condensation rxns and dehydration sysnthesis

ex: protein synthesis w/ ribosomes, dna synth during replication, photosynth, formation of macromlc from monomers

catabolism

make small from large - breakdown of complex molecules into simpler molecules

• hydrolysis releases energy (atp)

ex: dugestion, cell resp, macromolecule to monomer

hydrogen bonds

unique bc of polar covalent bonds within water mlc

• H bonds are weak but abundant in water

cohesion

hydrogen bonds, 2 water mlc

• transport of water undertension in xylem

• use of water surfaces bc of surface tension

adhesion

materials that are polar and charged

• capillary action in soil and plant cell walls

• keep cell walls moist and water droplets

specific heat capacity of water

very high; hear needed to raise water temp is a lot → water temp suitable for living things

water - latent heat of vaporization

heat needed to go from liquid to vapor → creates a coolant effect in evaporation and makes for a good coolant

boiling point of water

high boiling point

water vs methane (methanogenic proaryotes in swamps)

sweat cooling: the heat needed to evaporate water in sweat is taen from skin tissue

water as a solvent

water = medium for metabolism and transport in animals (cytoplasm)

• hydrophilic mlc dissolve in water (H bonds with polar mlc)

• enzyes catalyze in aq solution

  • fuctions of some molecules depend on them being hydrophobic and insoluble

physical properties of water

buiyancy, viscosity, thermal conductivity, specific heat capacity

transport in blood plasma

• NaCl - dissolve, carried in blood plasma

• amino acid: soluble enough to carry in blood plasma (varies by R)

• glcose: dissolve, carried in blood plasma

• oxygen: nonpolar but dissolves bc small, hemoglobin in RBC

• fats: nonpolar/insoluble, carried by lipoprotein complexes

• cholesterol: hydrophobic, carried in lipoprotein phospholipid monolayer (hydrophilic region phases outwards)

hemoglobin

binding sites for oxygen - increases capacity

catbohydrates

macromolecules produced by condensation rxns that link monomers to forn a polymer

monosaccharides

glucose, fructose, galactose

pentoses

fructose, ribose (dna backbone)

hexoses

glucose, galactose (milk)

disaccharide

maltose, sucrose (table sugar), lactose

disaccharide

maltose, sucrose (table sugar), lactose

polysaccharide

energy storage compound - starch, glycogen, cellulose

starch

in plants; alpha glucose molecules, only made by plant cells

amylose

unbranched, forms a helix (all oriented in the same direction)

think bc ose sounds circular

amylopectin

branched; globular shape

• does not affect osmotic balance

• temporary store in lead cells + energy storage

glycogen

in animals and fungi

• branched (compact molecule)

• does not affect osmotic balance - used in cells where large stores of dissolved glucose would cause osmotic problems

  • glycoproteins in cell-cell recognition (ABO antigens)

cellulose

structure related to function as a structural polysaccharide in plants

• alternating orientation of beta glucose monomers = straight chains that can be grouped in bundles and cross-linked with H bonds

  • cross links: cellulose microfibrils

  • high tensile strength - prevents plant cells from bursting

  • vertebrates cannot digest cellulose. grazing animals have host bacteria in their guts that have enzymes to break down cellulose

MEMORIZE THIS CHART!!

functions of lipids

• long term energy storage (triglyc)

• hormonal roles (steroids

• insulation (thermal - triglyc and electrical - sphingolipids)

• protection of internal organs

• structural components (plips and cholestrol)

types of lipids

tryglycerides (long term energy), phospholipids (structure), wax (protection against water loss), cartenoids (absorb light), glycolipids (cell receptor), steroids (hormones)

hydrophobic fat

dissolve in nonpolar; fats, oils, waxes, and steroids

triglyceride

forms from one glycerol and 3 fatty acids

phospholipid

forms from 2 fatty acids and 1 phosphate group (head and 2 tails)

fat structure

ester bonds; four fused rings in sterouds

sat vs monosat vs polyunsat fatty acid

• number of double carbons affects melting point

• diff types of fatty acids in oils and fats used tfor energy storage in plants and endotherms respectively

sat (oils, palmitic acid), polyunsat (cis-linolenic acid), monounsat cis (palmitoleix acid), trans fat and saturated (CHD correlation)

Depiction - sat vs monosat vs polyunsat fatty acid

cis isomers

• very common in nature

• h atoms on the same side of the 2 C atoms

• double ond —> bend in chain —> loosely paced

• have melting points — usually liquid @ room temp

trans-isomers

• rare in nature - usually artificially produced for margarine from veg oils

• h atoms on dif sides of the 2 C atoms

• double bond = no bend → closely packed

• solid @ room temp

triglycerides in adipose tissue

for energy storage and thermal insulation

amphipathic

phospholipid bilayer - having both hydrophibic and phillic parts

ostradiol and testosterone

both can pass through the plip bilayer - tetracyclic skeleton - 4 ringsb

bmi calculation

(mass in Kg)/(height in m)²

other lipid info

• the amount of energy released in cell resp per gram of lipid is double that for carbs and proteins

• lipids add 1/6 as much to body mass as carbs

• fats stored as droplets but carbs are stored with water

  • lipids have a higher hydrogen to oxygen ratio (are more reduced and release more energy

polypeptide

amino acid chain linked by peptide bond through condensation (amine and carboxyl group)

• on ribosome during translation

• oligopeptide: chains of <20 amino acis

aino acid

20 dif diverse ones; hydrophillic/hydrophobic or acid/base; evolved from one single species with 20 a

amino acids + genes

amino acid sequence is coded by genes

• 20^n possible sequences

• 3 bases of a gene = 1 amino acid

  • dna in the nucleus, polypeptide made in the cytoplasm on ribosomes (mRNA)

collagen

structural protein in tendon, liganment, skin, blood vessel walls - high tensile strength - limited stretching

protein denaturation

change in conformation of a protein by heat or pH extremes

• conformations stabilized by R groups interactions are weak

• usually permanent e.g. hydrophobic r group exposed to water

• heat causes vibrations and break bonds

• pH changes R group charge — ionnic bonds break and new ones form

conformations of proteins

1. fibrous (collagen) = elongated

2. elongated

3. globular = helical/sheet like —polypeptides fold up as they are made

• r groups sabilize structure

• hydrophobic/hydrophillic amino acid on surface determines solubility

fibrous proteins

long, narrow, structural, usually insoluble, repetetive sequence, less sensitive to pH and heat

• collagen, myosin, fibrin, actin

globular proteins

spherical, functional (catalytic, transport etc), soluble, irregular sequence, sensitive to pH change

• catalase, hemoglob, insulin

muscle contraction

actin + myosin = locomotion, transport

tensile strengthning

fibrous protein = tensil strength — collagen = rope like mesh with skin and blood vessel fibers

histones

proteins that help chromosomes condense during mitosis

spider silk

extensible and veyry resistant to breaking

proteome

all of the proteins made by a cell, tissue, or organism

• genome: al of the genes of a cell, tissue, or organism

• gel electrophoresis: separates protein mixtures

  • vairiable bc diff cells in an organism make dif proteins

primary structure

sequance of amino acids in a polypeptide (count starts @ amino end)

PEPTIDE BONDS

secondary structure

alpha helices/beta pleated sheets stabilized by hydrogen bonds

• HB between carboxyl and amine groups

tertiary structure

further folding stabilized by R group interactions

• + r groups interact with -r groups, polar interactions

• hydrophbic oriented towards the center

• disulphide bridge: cysteine r-groups

quaternary structure

exits in proteins withmore than one polypeptide chain

enzymes

globular protein that speeds up chemical reactions

enzyme substrate specificity

collusion

substrate mlc and active site coming together

temperature

increase in temp = more colluision s—> denaturation becuse bonds break (pH = ionic)

pH & enzymes

pH differences have a bell curve effect on enzyme activity

induced fit model

enzyme can change shape to fit the substrate

competitive inhibition

often irreversible if binding has covaleent bondsno

non-competitive inhibition

changes shape of enzyme; reversible inhibition part of metaolism

binds @ allosteric site

feedback inhibition

pathway turned off by its end effect

enzyme factors graphs

immobilized enzymes

attachment of enzymes to another material/into aggregations to restrict enzyme movement via glass surface, alginate gel, bodn with enzyme aggregate

cell theory

1. all things are composed of cells

2. cell = smallest unit of life

   1. cells only come from prior cellsc

cell theory discrepancies

• striated muscle fibers: not an autonomous unit

• aseptate fungal hyphae: not discrete cells

• giant algae: not microscopic cells (unicellular algae may grow very large)

light microscopes

lenses bend light and magnify; chemical stain/fluorescent labeling

• magnification = image size/actual size (according to scale bar)

unicellular organisms

nutrition, metabolism, growth, response, excretion, homeostasis, reproduction

1. paramecium

2. Scenedesmus

3. Chlamydomonas

sa to volume ratio

specialized: villi or microvilli (alveoli in lungs)

cell division

efficiency, growth, cell differentiation, development of embryos, replace dead/damaged/infected cells, asexual reproduction

prophase

DNA supercoils, nuclear membrane breaks down, centrosomes move to opposite polesm

metaphase

fibers attatch to centromeres, contraction of fiber = chromatids line up

anaphase

sister chromatids are separated

telophase

chromosomes deconsdense, nuclear membranes reform

cytokinesis

division of cell cytoplasm

animal vs plant cytokinesis

• animal: ring of contractile protein produces a cleaage furrow

• plant: vesicles from golgi move to the center of the cell , fuse as tubular structures

  • tubular structures merge to form 2 layers of p membrane

  • cell plate develops until it connects with membrane

  • vesicles deposit pectins, lumen, etc → forms middle lamella

diploid cells

somatic cells; temporarily 4n before cell replication

• gametes (sex cells) are haploid

• humans have 23 sets = 46 chromosomes

gap 1

increase volume of cytoplasm, organelles produced, proteins synthesized

• needs external stimulus

• restriction point (point of no return)

gap 0

resting phase where cell has left the cycle and stopped dividing

• G0 = nonregrowing state (quiescence)

synthesis phase

dna replicated; checkpoint before s phase (cell size + dna damage)