BIS2A SS1 Week 1

requirements of living

growth, development, energy utilization (photosynthesis and/or cellular respiration), respond to surroundings, homeostasis, evolve, high level of structural organization

fundamental unit of life

cell

prokaryote vs eukaryotes

eukaryotes - many membrane-bound organelles, larger, eukarya domain, uni/multicellular
prokarya - no membrane bound DNA, no nucleus, few/no membrane-bound organelles, unicellular

organelles common in eukaryotic cells

cell membrane, nucleus, nucleolus, smooth and rough ER, golgi apparatus, ribosomes, lysosomes, peroxisomes, vacuoles, vescicles, chloroplast (plant cell, endosymbiont), centrioles (animal cell), cell wall (plants), mitochondria (endosymbiont)

nucleoid

region in the cell of a prokaryote that contains genetic information (not membrane bound)

nucleolus

produces ribosomes subunits and rRNA —

found in the nucleus (separated by a membrane)

nucleus

membrane bound strcture containing genetic material in eukaryotes (contains the nucleolus as well); surrounded by nuclear envelope

cytoplasm

substance between cell membrane and nucleus

cytosol

only the fluid portion of cytoplasm (no organelles)

plasma membrane

selectively permeable phospholipid bilayer that controls traffic in and out of cell + responsible for cell communication

internal membrane

membrane that surrounds organelles that partitions cells into compartments (not present in prokaryotes) — made of phospholipid bilayer

inner membrane (mitochondria)

allows for the transfer of H+ ions into intermembrane space for cellular respiration/electron transport chain +chemiosmosis (has cristae)

outer membrane (mitochondria)

prevents the escape of H+ ions

cell wall

surrounds plasma membrane of cells and provides protection, shape, and prevents excess water uptake — is rigid (found in plant, fungi, bacterial cells)

cytoskeleton

provides framework, support, and movement (made of microtubules, intermediate filaments, and microfilaments)

flagella

helical appendages that protrude through the cell membrane and are long and whip-like — used for movement

pili

hollow filamentous extensions that emerge from the cell's surface — used for attachment and sometimes movement — also the sex pili which exchanges genetic information between bacteria

ribosomes

made of protein and rRNA; site of protein synthesis; can be bound to ER (rough ER) for proteins in endomembrane system OR free — suspended in cytosol (make protein for non-membrane bound organelles/cytosol)

endomembrane system

group of membranes and organelles that modify, package, and transport lipids and proteins (made of nucleus, ER, Golgi apparatus, lysosomes, vacuoles) — exchange membrane via vesicles

ER (synthesis) —> golgi (sorts, modifies, redirects) —> plasma membrane, lysosomes, vacuoles, ER, nucleus, etc.

rough ER

involved in protein synthesis — post translational modification, folding, and sorting of proteins (protein is produced by ribosome not rough ER); products shipped to golgi by vesicles

smooth ER

lipid production (phospholipids, hormones, etc.), calcium ion regulation, detoxification, carb metabolism

golgi apparatus

transport, sort, and modify proteins and lipids from ER; contains vesicles to secrete and transport

makes lysosomes

primary lysosome

non-functioning lysosomes; contain inactive enzymes + newly formed from golgi

secondary lysosome

active primary lysosome, produced in golgi apparatus

lysosomes act as the recycling centers of the cell; contain hydrolytic enzymes to do intracellular digestion, recycling of excess/worn out parts, programmed cell destruction

mitochondria

site of cellular respiration (ATP production); contains DNA

cristae

folds of inner mitochondrial membrane that increase surface area for ATP production

matrix

space within the inner mitochondrial membrane that carries out a portion of cellular respiration

plastid

manufactures and stores food in plants — contains photosynthetic pigments (ex. chloroplasts)

chloroplast

the organelle that is the site of photosynthesis; contains DNA (thought to be endosymbiotic cyanobac)

thylakoid

flattened sacs where the light dependent reactions of photosynthesis take place

grana

stacks of thylakoids

stroma

fluid within the chloroplast that surrounds the grana/thylakoids

peroxisomes

produce hydrogen peroxide and carry out oxidative processes with oxygen and detoxification

glyoxysomes

a type of plant peroxisomes that converts lipids to sugar during plant germination

vacuole

acts as a storage area for waste, food, and other nutrients

vesicles

used to transport substances inside and out of a cell

centrioles

cylindrical organelle near the nucleus in animal cells only that produces spindle fibers during mitosis

electronegativity (abbreviated as EN in flashcards)

tendency of an atom to attract electrons to itself

what drives bond formation?

electrons want to fulfill the octet rule (8 valence electrons) in their s and p orbitals in order to be stable

ionic bonds

electrons are transferred from one less electronegative atom to another more electronegative atom; attraction between oppositely charged ions (like Na+ and Cl- in NaCl)
EN diff: greater than 2

covalent bonds

bonds where the electrons are shared by the two atoms

nonpolar covalent bonds

electrons are shared equally between the two atoms, no dipoles exist
EN difference: 0-0.4

polar covalent bonds

electrons are shared unequally between the two atoms, dipoles do exist
more electronegative atom has a partial negative charge, less electronegative atom has a partial positive charge

EN difference: 0.5-1.9

hydrogen bonds

weak electrostatic attraction (NOT A BOND) between a partially positive hydrogen and a partially negative atom in another molecule (usually O or N)

why is water liquid at room temperature?

due to the strength of the hydrogen bonds (attractive forces aka H bonds holds together the water molecules)

hydrogen bond donor/acceptor

donor donates the partially positive H
acceptor is the partially negative atom that accepts the H

hydrophobic interactions

nonpolar substances tend to stick together in the presence of polar substances, especially water (which is why like dissolves like)

van der Waals interactions

interactions of electrons in nonpolar substances (creates instantanous dipoles resulting in induced dipoles)

rate strength of bonds/interactions from strongest to weakest

covalent —> ionic = hydrogen —> hydrophobic interactions —> van der Waals

functional groups often found in proteins

amides; carboxylic acid and amine at the ends

functional groups found in nucleic acids

phosphates, ether (in ribose sugar)

functional groups found often in carbohydrates

hydroxyl/alcohol (which is why carbs are so hydrophilic!)
ketones OR aldehydes (not both) — aka carbonyls

aldehyde when first carbon has double bond O, ketone if not

lipids

they have polar heads and long nonpolar hydrocarbon tails, mostly made of CHO

lipid functions

store/gather energy (fats to burn/photosynthetic pigments)

structure (plasma membrane)

insulation

signaling molecules

how to identify lipids

look for a nonpolar body and a polar head, lots of hydrocarbons in the nonpolar “body” (remember C-H is nonpolar covalent)

what molecule do lipids start off as? what is the fate of those molecules

start off from acetyl-CoA
end up as fatty acids or sterols

fatty acids

building blocks for membranes

effects of double bonds/desaturation on membrane fluidity and melting point

double bonds create kinks in the fatty acid, which increases membrane fluidity

it can also decrease the melting point of lipids

at high temps, prefer saturated lipids

effect of hydrocarbon chain length on membrane fluidity

longer HC chains = stronger bonds = less fluidity (also higher melting point)

carbohydrates

monomer: monosaccharide

formula: (CH2O)n

have many hydroxyl/alcohol groups making carbs very hydrophilic (can H bond)

spontaneously arrange into a ring in water/aqueous solutions and can be chemically modified by functional groups

functional groups involved in carbohydrate ring formation

ketone OR aldehyde AND hydroxyl

key aspects of carbohydrate function

quick energy (starch, glycogen)

protection/structure - chitin, cellulose

signaling molecules

how to identify carbohydrates

look for lots of oxygens; remember that CHO in carbs has a ratio of 1:2:1

proteins

monomer: amino acid
made of CHON; have NCC backbone
mostly have R groups with sulfur or ring structure (not all the time)

how to identify proteins

look for the repeating NCC backbone; can also check for amine and carboxylic acid groups at each end

nucleic acid

monomer: nucleotide; polymer: DNA/RNA
can hydrogen bond
CHONP
used for information storage

nucleotide components

up to 3 phosphate groups attached to a sugar
sugar is ribose (RNA) or deoxyribose (DNA)
nitrogenous bases: adenine, thymine, guanine, cytosine, uracil

features of pentose sugar of DNA

at carbon 1: nitrogenous base attached
at carbon 2: has a hydroxyl group for RNA; hydrogen for DNA
at carbon 3: has a hydroxyl group used to create bonds between nucleotide

at carbon 5: phosphate group attached

H bonds and nitrogenous bases

many strong hydrogen bonds between nitrogenous bases hold together the antiparallel DNA strands

amino groups of nitrogenous bases are the H bond donors
carbonyl groups of nitrogenous bases are the H bond acceptors

phosphate groups of nucleic acids

bonds between phosphates store energy (ATP); can be up to 3 phosphates

how to identify nucleic acids

look for phosphate group, sugar, and nitrogenous base monomer

pH

measure of proton (H+) concentration

acids and bases

acids donate protons; bases accept protons

pH and acidity/basicity

lower pH = more acidic = greater H+ concentration

acidic functional groups

carboxylic acid (give up protons/can become deprotonated from their protonated form)

basic functional groups

amine (accept proton to become protonated from its deprotonated form)

pKa

the pH at which a functional group is 50% protonated and 50% deprotonated

pH and pKa

pH = pKa —> A- = HA
pH < pKa —> HA dominates (A- will become protonated)
pH > pKa —> A- dominates (HA will become deprotonated)

why is pH and pKa important?

determines whether the R group on the amino acid will be protonated or deprotonated and provides a charge on the amino acid

alpha carbon

the central carbon attached to the hydrogen, R group, and carboxylic/amine group

backbone - protein

amine group and carboxylic acid attached to the alpha carbon

variable (R) group

determines what type of amino acid the protein is

how many amino acids? how many are essential/what does essential mean?

20 amino acids - 9 essential (cannot be synthesized by human body/must be consumed)

peptide bond

the bond between two amino acids, which results in the formation of an amide group due to the condensation reaction that occurs — is endergonic and anabolic

no free rotation around peptide bond due to electron sharing between C, O, N

condensation reaction

a reaction that results in the release of a water molecule (in proteins, OH from carboxylic acid and H from amine group is released)

N-terminus

the end with the “free” amine group; the first amino acid in the chain is attached part of N-terminus

C-terminus

the end with the “free” carboxylic acid group

primary structure

sequence of amino acids held together by peptide bonds (order of AAs matter)

secondary structure

interactions (H bonds) between the backbone form two types of secondary structures: alpha helix, beta pleated sheet (parallel or antiparallel), unstructured

this is a spontaneous process — can be disrupted by pH change

tertiary structure, what interactions can be found in tertiary structure

interactions between the R groups twist the secondary structure into a 3D shape; all proteins have tertiary structure

interactions: H bonds, ionic bonds, disulfide bridges, covalent bonds, hydrophobic interaction

H bonds and ionic bonds can be disrupted by pH and salt concentrations

quaternary structure, what interactions?

2+ subunits (polypeptides) combine to form the final active protein; not all proteins have quaternary structure

allosteric site

a second site where compounds can bind, besides the active site (can increase/decrease activity of enzyme)

enzyme substrate complex

held together by hydrogen bonds (mostly), electrical attraction, or covalent bonds

enzyme always returns to original form after catalyzing a reaction

4 ways that an enzyme works

1) orients substrate molecules
2) stretch bonds in substrate to make it unstable
3) temporarily add chemical groups to substrates to get better rxns

4) provide a suitable environment for the reaction to get catalyzed