Unit 1 Flashcards
Hydrocarbons
Hydrogens bonded to carbons
Nonpolar and form straight or branched chains and ring shaped structures
Saturated hydrocarbon
Single bonds between carbons
Do not react with H
Unsaturated hydrocarbon
Double or triple bonds between carbons
React with H
Alcohol
Contains hydroxyl group
-ol
Used in alcoholic beverages, gas-line, anti-freeze or as bacteriocidal agent
Aldehyde
Carbonyl group on the end of hydrocarbon
-al
Found in living systems in the form of sugars and hormones
Ketones
Carbonyl group in the middle of hydrocarbon
-one
Found in living systems in the form of sugars and hormones
Amine
N bonded to three other atoms- H, C, or combo
-amine
Found in many proteins and nucleic acids. Adrenaline stimulates nervous system. Can be extracted from plants as decongestants
Functional groups
Site of chemical reactivity in a molecule
Include Pi bonds (double or triple bonds) or an electronegative/electropositive atom
Reactive clusters of atoms attached to C backbone
Thiol
Sulfhydryl group
-Thiol
Amino acids
Carboxylic acid
Carboxyl group made of carbonyl + hydroxyl
-oic acid
Phosphate
PO4-
Organic chemistry
The study of carbon compounds
Macromolecules and subunit
Carbohydrates - simple sugars
Lipids - glycerol & fatty acids
Proteins - amino acids
Nucleic acids - nucleotides
Carbohydrates
Produced through plants and algae through process of photosynthesis
Used for energy, building materials, and for cell identification and communication
Contain carbon, hydrogen and oxygen in a 1:2:1 ratio - (CH2O)n
3 classifications of carbs
Monosaccharides
Oligosaccharides
Polysaccharides
Monosaccharides
Simple sugars ex. Glucose, galactose, fructose
5 or more carbons - linear in dry state, form ring structure when dissolved in water
Glucose
Found in fruits and vegetables
Alpha or beta 50% chance
Fructose
Found in fruits
Isomer of glucose, different chemical properties (ex. Sweeter)
Galactose
Picture
Dehydration reaction (condensation)
To link subunits, a covalent bond is formed between a hydroxyl group and hydrogen to remove water
Hydrolysis
Water is added to separate the linkage group and the macromolecule is broken
Oligosaccharides
Commonly known as disaccharides
2 or 3 simple sugars attached by covalent glycosidic linkages, formed by condensation reactions
Ex. Maltose and sucrose
Properties of mono- and disaccharides
White crystalline compounds that are solid at room temperature and dissolve readily in water
Are all sweet to or taste but each sugar has its own level of sweetness
Oligosaccharide reactions
Glucose + glucose = maltose + water
Glucose + fructose = sucrose + water
Glucose + galactose = lactose + water
polysaccharides
100s-1000s of monosaccharides held together by glycosidic linkages
starch
energy storage for plants
white, powdery, insoluble in water, not sweet (compared to sugar)
a mixture of two polysaccharides:
-amylose (20%) small not branching, all glucose
-amylopectin (80%) large, branched, all glucose
glycogen
polymer of glucose produced by animals
stores excess glucose in muscle and liver cells
hydrolyzed when glucose levels are low in blood
pectin
complex mixture of polysaccharides
used mostly in foods as a gelling agents (ex. jam and jelly)
when pectin is mixed with water, it swells and the various polysaccharides interlock to form a meshwork which traps water
to work it needs a pH of less than 3.5 and a sugar content of about 50%
cellulose
also called dietary fibre
found in the cell walls of plant cells
linear chain of alternating flipped beta-glucose which most organisms find difficult to break
enzyme CELLULASE can digest in (found in termite and ruminant guts)
chitin
polymer of special glucose molecules that have nitrogen groups attached to C2
makes up arthropod exoskeletons (ex. insects, spiders, crustaceans) and mushrooms
2nd most abundant organic compound naturally occurring
gums
complex polysaccharides which are hydrophilic and which combine with water to form thick solutions
ex. plant seeds, plant secretions, seaweed, microorganisms
lipids
includes fats, phospholipids, steroids, and waxes
like carbs but less Os and more C-H bonds
nonpolar, insoluble in water
not really a polymer, two parts
lipid function
long term energy storage (stores more than 2x amt of chemical energy per gram than carbs or proteins)
building membranes
hormones
insulation layers
carb linkage vs lipid linkage
glycosidic linkage vs ester linkage
saturated fats
come from animals
solid at room temperature
single bonds between C atoms
unsaturated fats
comes from plant oils
liquid at room temp
one or more double bonds between C
rigid kinks due to double bonds
phospholipids
one glycerol, two fatty acids, highly polar phosphate
form cellular membranes (phospholipid bilayer)
steroids
composed of 4 fused hydrocarbon rings & functional groups
have diff functional groups attached to these rings
ex. cholesterol, testosterone, estrogen
waxes
long chain fatty acids linked to alcohols or carbon ring
firm, pliable consistency, used as a waterproof coating
ex. cutin on leaves, earwax
protein functions
structural (keratin in hair) storage (casein in mother's milk) transport (hemoglobin) hormonal (insulin) receptors (taste buds) contractile (actin in muscles) defensive (fibrin for clotting) enzymatic (lactase)
amino acids
amphiprotic (acidic and basic)
may be polar, nonpolar, or charged depending on the R group
20 different R groups, 8 are essential
amino acids are joined together by
peptide bonds (amide bonds) condensation reaction
four levels of protein folding
primary - linear sequence of amino acids
secondary - folding and coiling of chain into helix or pleated sheet (parallel bonding)
tertiary - additional folding into 3d shape due to R group/side chain interactions hydrophobic interactions, hydrogen bonds, ionic bonds, or disulphide bridges
quaternary - two or more polypeptide chains come together
denaturing
when temp or pH changes cause a protein to unravel. a denatured protein is unable to carry out its biological function
uses for protein denaturing
meats cured by denaturing spoilage bacteria
blanching fruits denatures browning enzymes
curl/straighten hair temporarily w/ heat
meats easier to chew when heat is used to denature fibrous proteins
nucleic acids
found in DNA (stores hereditary info)
nucleotides
monomers
consist of nitrogenous base, a five-carbon sugar and a phosphate group
nucleic acid structure
C, T, and U are single-ringed pyramidines
A and G are double ringed purines
A bonds with T with 2 hydrogen bonds, and G bonds with C with 3 hydrogen bonds
the two strands in DNA are antiparallel
enzyme
specialized proteins that act as catalysts, lower activation energy
not used up during a reaction
are specific to a particular substrate (reactant)
active site
where the substrate binds to the enzyme
induced fit
protein changes shape to accomodate substrate
enzyme-substrate complex
substrate attached to enzyme
factors that can affect the rate of enzyme activity
temperature
pH
concentration
cofactors
inorganic substances that aid in enzyme activity
ex. Zn2+, Mn2+
coenzymes
organic substances that aid in enzyme activity
ex. NAD+
competitive inhibitors
compete with substrate for enzymes active site
block active site
reversible, overcome by increasing substrate concentration
ex. drugs, CO, cyanide
non-competitive inhibitors
bind to the enzyme at an allosteric site (not the active site) and cause a conformation change in the enzyme, preventing the normal substrate from binding
loss of enzyme activity
ex. DDT
allosteric regulation
cells control enzyme activity to coordinate cellular activities
allosteric sites
receptor sites that bind substances that inhibit or stimulate enzyme activity
activators
may bind to allosterically controlled enzymes to stabilize its shape and keep all active sites available
allosteric inhibitors
binds to allosteric site and stabilizes inactive form of the enzyme
feedback inhibition
a method used by cells to control metabolic pathways involving a series of reactions
a product formed later in a sequence of reactions allosterically inhibits an enzyme that catalyzes the reaction earlier on
nucleus
contains DNA, which stores and replicates the genetic info of the cell
cytoplasm
consists of everything outside the nucleus but within the cell membrane
cytosol
fluid in the cell
nucleolus
a non-membrane-bound, denser region within the nucleus containing RNA, proteins, and chromatin
nucleoplasm
thick fluid filling the nucleus
nuclear matrix
network of protein fibres in the nucleus that provides internal structure and support
nuclear envelope
a double membrane consisting of two phospholipid bilayers surrounding the nucleus
lumen
narrow space between bilayers
nuclear pore complexes
groups of proteins studded on the nuclear envelope that form openings in the nuclear envelope
endoplasmic reticulum
a complex system of channels and sacs composed of membranes enclosing a lumen; made up of two parts, the rough ER and the smooth ER
ribosomes
structures composed of RNA and proteins, and responsible for synthesis of polypeptides in the cytosol and on the surface of the rough ER
rough ER
ribosomes attached
produce proteins
smooth ER
no ribosomes
synthesizes lipids and lipid-containing molecules such as phospholipids that make up membranes
endomembrane system
the system within the cell that acts to synthesize, modify, and transport proteins and other cell products; includes the endoplasmic reticulum, nuclear envelope, Golgi apparatus, and vesicles
vesicle
a membrane-enclosed sac used for transport and storage
Golgi apparatus
a stack of curved membrane sacs that packages, processes, sorts, and distributes proteins, lipids, and other substances within the cell; acts like a “post office” for the cell
lysosome
produced by the Golgi apparatus by animal cells
membrane-bound vesicle/sac that contain digestive enzymes and catalyze hydrolysis reactions, breaking down macromolecules
catalyze hydrolysis reactions
peroxisome
membrane-bound sac containing oxidative enzymes that break down excess fatty acids and hydrogen peroxide, and participate in the synthesis of bile acids and cholesterol
break down biological and toxic molecules
form by budding off from the ER
catalyze redox reactions
vacuole
single large central vesicle in plants
stores water, ions, sugars, and cell wastes
quantity of water determines turgor pressure
a full vacuole increases turgor pressure and causes plant cell to be rigid
chloroplasts
an organelle in the cells of photosynthetic organisms in which light energy from the sun is captured and stored in the form of high-energy organic molecules such as glucose
mitochondria
an organelle in eukaryotic cells in which high-energy organic molecules are broken down and oxidized to convert stored energy into usable energy
cell wall
a rigid layer surrounding plant, algae, fungal, bacterial, and some archaea cells, composed of proteins and/or carbs; gives the cell its shape and structural support
cytoskeleton
a network of protein fibres that extends throughout the cytosol, providing structure, shape, support, and motility
anchors cell membrane and organelles in place
used as travelling tracks
cilia
short appendages
flagella
long appendages
cell membrane
separates contents of the cell from extracellular fluid that surrounds all cells
controls traffic in and out of the cell (selectively permeable)
made of phospholipids, proteins & other macromolecules
cells will die if membrane does not function properly
fluid mosaic model
phospholipids act as a scaffold
proteins and other macromolecules are embedded (mosaic)
molecules in membrane can move about freely (fluid)
fluidity of phospholipid bilayer
membrane must be fluid and flexible (viscosity similar to vegetable oil)
if too fluid, bilayer permits too many substances in/out of cell
if not fluid enough, bilayer prevents too many substances from crossing
factors that affect fluidity
temperature (increase temp, increase fluidity)
double bonds in fatty acids (kinks less tightly packed)
length of fatty acids (more intermolecular attractions, held tighter)
cholesterol (increase fluidity at low temp & vice versa)
membrane proteins
determine membrane’s specific functions
peripheral proteins
loosely/temporarily bound to surface of membrane or to integral proteins
integral proteins
penetrate lipid bilayer, usually across whole membrane
help stabilize membrane, link with cytoskeleton of cell
transport proteins
membrane proteins determine the function of the membrane by performing the following functions:
transport - transporting substances across the cell membrane
reaction catalysis - carry out chemical reactions
cell recognition - carb chains that protrude from glycoproteins enable cells to recognize each other and identify harmful intruders
signal reception and transduction - receptor proteins bind to signal molecules such as hormones and change shape, initiate cellular response to signal
functions of membrane proteins
transporter, enzyme activity, cell surface receptor, cell surface identity marker, cell adhesion, attachment to the cytoskeleton
membrane carbohydrates
play a key role in cell-cell recognition (ability of a cell to distinguish one cell from another)
basis for rejection of foreign cells by immune system
important in organ and tissue development
substrate
the reactant that an enzyme works on. it binds to a particular site (active site) on the enzyme
types of protein fibres
microtubules
intermediate filaments
microfilaments
microtubules
thickest fibres
proteins that form hollow tubes
maintain cell shape
facilitate movement of organelles
assist in cell division (spindle formation)
intermediate filaments
intermediate thickness
proteins coiled together into cables
maintain cell shape
anchor some organelles
form the internal scaffolding of the nucleus
microfilaments
thinnest fibres
two strands of actin wound together
maintain cell shape
involved in muscle contractions
assist in cell division (cleavage furrow)
passive transport
movement of ions or molecules from a region of higher concentration to a region of lower concentration, without input of energy
concentration gradient
difference in concentration between sides of membrane
3 forms of passive transport
diffusion
osmosis
facilitated diffusion
diffusion
net movement of ions or molecules from area of higher concentration to an area of lower concentration
osmosis
diffusion of water
movement of water from high concentration of water to low concentration of water
hypertonic
more solute less water
hypotonic
less solute more water
isotonic
equal solute, equal water
managing water balance in isotonic solution
not net diffusion of water
flows across membrane equally, in both directions
volume of cell is stable
managing water balance in hypotonic solution
gains water, swells, and can burst
managing water balance in hypertonic solution
lose water and die
need to take up water or pump out salt
what molecules can get directly through the phospholipid bilyar
fats and other lipids small molecules (H2O, O2, and CO2)
what molecules can NOT get through directly
polar molecules
ions
large molecules
facilitated diffusion
diffusion through protein channels
channels move specific molecules across cell membrane
no energy needed
carrier proteins
bind to specific molecules, transport across the membrane, release on other side
change shape while transporting molecules
ability to transport larger molecules such as glucose and amino acids
lower diffusion rate, only bind to a few molecules at a time
channel proteins
channels move specific molecules across cell membrane (ions or polar molecules)
active transport
transport of substances across a membrane against their concentration gradient
requires energy
uses hydrolysis of ATP for energy
all carrier proteins
secondary active transport
involves use of existing gradient to actively transport another substance (electrochemical gradient)
membrane-assisted transport
transport method for macromolecules that are too large to cross cell membrane through a channel or carrier protein
requires energy
two types - endocytosis and exocytosis
endocytosis
cell membrane engulfs extracellular material to bring it inside cell
pinches off to form vesicle inside cell
phagocytosis (solid), pinocytosis (liquid), receptor-mediated (receptor proteins bind to specific molecules)
exocytosis
vesicles fuse with cell membrane and empty contents into extracellular environment
