Unit 1 - Biochemistry Flashcards
cell (plasma) membrane
- phospholipid bilayer with embedded protein and carbohydrate molecules that surround the cell
- is a semi-permeable membrane that allows only certain substances to enter (e.g. nutrients) and exit (e.g. metabolic wastes)
cell wall
- found in plant cells only
- made of cellulose
- provides structural support
nucleus
- separated from the cytoplasm by a double membrane called the nuclear envelope
- spherical
- “control center” of the cell
- contains DNA
- contains the nucleolus, which produces ribosomes
cytoplasm
- consists of cytosol, an aqueous solution, and organelles
- contains various chemicals and molecules (ions, amino acids, enzymes, ATP, carbohydrates, etc.)
vacuole
- membrane-bound sac
- much larger in plant cells
- stores starch, molecules, water, and wastes
- provides structural support to plants
ribosome
- dense-looking, spherical granule
- free-floating in cytoplasm or attaches to RER
- synthesizes proteins (where amino acids are assembled into proteins)
endoplasmic reticulum (ER)
- RER (rough endoplasmic reticulum): have ribosomes; are the site of protein synthesis
- SER (smooth endoplasmic reticulum): don’t have ribosomes; manufacture lipids
golgi apparatus
- flattened stack of membranes
- receives and modifies fats and proteins produced by the ER
- packages fats and proteins into vesicles for transport out of the cell (exocytosis)
lysosome
- found in animal cells only
- is a membrane-bound sac (vesicles) produced by the golgi apparatus and ER
- contains hydrolytic enzymes
- are like mini-stomachs
- breaks down molecules and old organelles/cells, digests food particles, and destroys microorganisms
mitochondrion
- rod-shaped
- site of cellular respiration
- glucose molecules are broken down to produce ATP
chloroplast
- found in plant cells only
- double-membrane
- contains chlorophyll
- site of photosynthesis
- enables plants to convert sunlight, CO2 and H2O into glucose (C6H12O6)
molecular polarity
- symmetrical arrangement of polar covalent bonds = non-polar molecule (e.g. CCl4)
- asymmetrical arrangement of non-polar bonds = non-polar molecule (e.g. O3)
- asymmetrical arrangement of polar bonds = polar molecule (e.g. NH3)
electronegativity
a measure of an atom’s ability to attract electrons of a covalent bond (fluorine (F) is the most electronegative, francium (Fr) is the most electropositive)
molecular shapes
- tetrahedral (e.g. CH4)
- pyramidal (e.g. NH3)
- angular (e.g. H2O)
- linear (e.g. HCl)
applications of radioisotopes
1. radiometric dating; measuring the carbon-12/carbon-14 ratio of dead organism or fossil
2. radioactive tracers in biological research; radioisotopes which flag various molecules and trace their path in vivo
3. radioactive tracers in nuclear medicine; diagnosis and treatment of various diseases
- iodine-125 for bone density measurements
- iodine-131 for thyroid monitoring
- technetium-99
isotopes
- atoms of an element with the same atomic number, but a different atomic mass (e.g. carbon-12 and carbon-14
EXAMPLE OF USEFULNESS: sulfur-33 used in human genome research
isomers
- molecules that have the same atomic mass, but different atomic rearrangement (e.g. glucose and fructose (C6H12O6))
EXAMPLE OF USEFULNESS: used in clinical pharmacology, due to difference in properties
intermolecular forces of attraction
- a.k.a. “van der Waals” forces
- bonds amongst molecules
London forces
- weakest intermolecular force of attraction
- is between all molecules
- e.g. methane (CH4(g))
- number of associations determine the state of matter (more forces = g→s; and vice versa)
dipole-dipole attractions
- “average-strengthed” intermolecular force of attraction
- between polar molecules
- e.g. between hydrogen chloride (HCL) molecules
hydrogen bonds
- strongest intermolecular force of attraction
- between polar molecules containing nitrogen, oxygen, or fluorine (H-N, H-O, or H-F)
- e.g. between water (H2O) and ammonia (NH3) molecules
intramolecular forces of attraction
bonds within molecules
ionic bond
- type of intramolecular bond
- electrostatic attraction between oppositely charged ions
- electrons are transferred
- e.g. between sodium (Na) and chlorine (Cl) in sodium chloride (NaCl)
covalent bond
- type of intramolecular bond
- electrostatic attraction between nuclei and valence electrons of natural atoms
- electrons are shared
- e.g. between nitrogen atoms (N) in nitrogen gas (N2)
polar covalent bond
- type of intramolecular bond
- covalent bond with an electronegativity difference (EN) of 0-1.7
- e.g. water (H2O); ΔEN = 1.24
acids
- substances that release H+ ions in solution (proton donors)
- e.g. HCL
bases
- substances that accept H+ ions (proton acceptors), and sometimes produce OH- (hydroxide donors) in solution
- e.g. NaOH
pH
- the unit of measurement that describes the acidity or basicity of a solution
- as [H+] concentration increases, acidity increases, and pH decreases
buffers
- chemical systems that resist significant changes in pH; releasing H+ in solutions too basic, and absorbing H+ in solutions too acidic
- usually consist of specific conjugate acid-base pairs (HCO3-(aq))
- proteins may also act as buffers (e.g. hemoglobin)
- e.g. carbonic acid/bicarbonate buffer system found in kidneys to resist significant changes of pH in bloodstream:
H2O(ℓ) + CO2(aq) ⇄ H2CO3(aq) ⇄ HCO-3(aq) + H+(aq)
ionization
the strength of an acid or base is relative to their ionization (breakdown)
Examples:
- HCl → H+ + Cl-; ∴ strong acid (complete ionization)
- CH3 → H+ + CH3COO-; ∴ weak acid (partial ionization)
neutralization
- when an acid and a base react, a neutralization reaction occurs: the acid and base lose their acidic and basic properties respectively, producing water and a salt
- e.g. HCL(aq) + KOH(aq) → H2O(ℓ) + KOH(aq)
oxidation-reduction reactions
- a.k.a. REDOX reactions
- the process in which electrons are transferred from one substance to another; the molecule which accepts electrons is “oxidized” (oxidation = loss of electrons), and the molecule which gives away electrons is “reduced” (reduction = gain of electrons)
functional groups
- groups of elements that contribute to the formation of products in biochemical reactions
- allow the interaction between biomolecules
hydroxyl
⎯ OH
carboxyl
⎯ COOH
amino
⎯ NH2
sulfhydryl
⎯ SH
phosphate
⎯ PO4
aldehyde
⎯ COH
ketone
⎯ CO ⎯
dehydration synthesis
the formation of a covalent bond between two molecules with the production of a water molecule
hydrolysis
the breakdown of a covalent bond, due to the addition of a water molecule
carbohydrates
- macromolecules composed of carbon, hydrogen, and oxygen atoms
- simplest and quickest sources of energy
- either simple (mono/disaccharides), or complex (polysaccharides)
monosaccharides
- simple carbohydrates
- ratio of C:H:O = 1:2:1
- e.g. glucose
monosaccharide classification
classified according to the number of carbons or the functional group
number of carbons:
- triose sugars; have 3 carbons
- pentose sugars; have 5 carbons
- hexose sugars; have 6 carbons
functional group:
- aldoses; have an aldehyde (⎯ COH)
- ketoses; have a ketone (⎯ CO⎯)
disaccharides
- simple carbohydrates composed of two monosaccharadies, combined via α 1-4 glycosidic linkages (dehydration synthesis)
- formula for disaccharides = C12H22O11
MUST-KNOW EXAMPLES:
α-glucose + α-glucose = maltose
α-glucose + fructose = sucrose
α-glucose + galactose = lactose
polysaccharides
- complex carbohydrates (carbohydrate polymers) composed of many monosaccharides via α 1-4 glycosidic linkages, and sometimes α 1-6 glycosidic linkages
- number of particles - 1 = number of linkages
MUST-KNOW EXAMPLES:
many α-glucoses = starch (amylopectin)
many β-glucoses = cellulose
examples of polysaccharides in biology
- glycogen is used for temporary storage in the liver
- cellulose gives structure and form to plants
- chitin is found in the exoskeleton of insects
lipids
- macromolecules composed of carbon, hydrogen, and oxygen atoms, with a high proportion of non-polar carbon–hydrogen bonds
- store energy and regulate hormones
4 main types:
1. triglycerols/triglycerides
2. phospholipids
3. steroids
4. waxes (only one not made up of fatty acids)
fatty acids
- made of a carboxylic acid as the head, and a hydrocarbon tail
- max amount of H’s = saturated; solid at room temperature (e.g. butter)
- not the max amount of H’s = unsaturated; carbon-carbon double bonds, and “kink” (bend) in the tail; liquids at room temperature (e.g. olive oil)
triglycerides
lipids composed of a glycerol molecule (C3H8O3) and three fatty acids linked by ester bonds via esterification (dehydration synthesis)
phospholipids
- lipids composed of a glycerol molecule (C3H8O3), two fatty acids, and a phosphate group with a R group; linked by ester bonds via esterification (dehydration synthesis)
- made of a hydrophilic head (phosphate and glycerol), and hydrophobic tails (fatty acids); are polar molecules
lipid bilayers
- made up of hydrophilic heads directed towards aqueous solutions, and hydrophobic tails tucked away from aqueous solutions, interacting with each other
- found in micelles and the cell membrane
steroids
- lipids composed of four attached carbon-based rings
- are chemical messengers
- aid in cell-to-cell communication
- a lot of them are hormones
EXAMPLES:
- cholesterol (pre-cursor steroid)
- estradiol (an estrogen)
- testosterone (an androgen; mostly in males)
- progesterone (a progestin; mostly in females)
proteins
- macromolecules composed of amino acid monomers linked by covalent bonds
- are folded and functional polypeptides (peptide bonds link amino acids together)
- serve many functions: including acting as enzymes, providing structural support, regulating passage of substances across the cell membrane, and maintaining pH levels
denaturation
the process in which proteins can potentially unfold
amino acids
- an organic molecule composed of an amino group (amino), a central carbon atom, an R group, and a carboxyl group (acid)
- humans have 20 amino acids (proteins are made of up to 20 different types of amino acids
- can be ionized (H3N+ amino group), or crystalline (H2N amino group)
4 levels of protein structural organization
1. primary structure
- linear sequence of amino acids
2. secondary structure
- hydrogen bonding between amino acids result in a coil-like shape (α-helix) or a fan-like shape (β-pleated sheet)
3. tertiary structure
- composed of one folded polypeptide
- e.g. myoglobin
4. quaternary structure
- composed of many polypetides
- found in bigger proteins
- e.g. hemoglobin (composed of 4 subunits (polypeptides))
types of amino acids
nonpolar
- composed of H or CH3, and aliphatic (open-chained) R-groups
- hydrophobic
polar
- composed of O, NH2, or SH
- hydrophilic
electrically charged
- acidic (negative charge) or basic (positive charge) composed of a negative or positive change in the R-group respectively
protein synthesis
amino acids are joined together via peptide bonds and dehydration synthesis; DNA specifies the order in which the amino acids follow one another
protein shape
- either globular (e.g. hemoglobin) or fibrous (e.g. keratin)
- polypeptide forming occurs in the Golgi bodies
things that affect the shape of a polypeptide:
- hydrogen bonds: between two polar amino acids (can be broken with high temperature)
- proline kink: formation of a bend in a proline amino acid, as it folds in on itself
- hydrophobic and van der Waals interactions: hydrophobic association between two non-polar amino acids (can be broken with high temperature)
- disulfide bridge: covalent linkage between two cysteine amino acids (very strong; needs a REDOX agent to break it)
- ionic bonds: associations between two oppositely charged amino acids (can be broken with high temperature)
nucleic acids
- macromolecules composed of nucleotide monomers
- DNA or RNA
- are acidic; H+ donors
- carry genetic information
nucleotides
organic molecules composed of a phosphate group, a pentase sugar, and a nitrogenous base
DNA
- contains deoxyribonucleotide monomers; A, G, T, C
- contains deoxyribose
- serves as a guide to make proteins
- homes the genetic code of an organism
RNA
- contains ribonucleotide monomers; A, G, U, C
- contains the sugar ribose
- many functions and forms (mRNA, tRNA, mtRNA, rRNA, gRNA, etc.)
Benedict’s reagent
an indicator used to identify the presence of monosaccharides and some disaccharides; turns a different colour depending on the sugar concentration
- blue colour: nil
- light green colour: 0.5%-1.0% concentration
- green to yellow colour: 1.0%-1.5% concentration
- orange colour: 1.5%-2.0% concentration
- red to red brown colour: 2.0%< concentration
Lugol’s solution
an indicator used to identify the presence of complex carbohydrates; turns from a brown to a blue-black colour in the presence of starch (complex carbohydrates)
Sudan IV solution
an indicator used to identify the presence of lipids; turns from a pink to a red colour in the presence of lipids
Biuret reagent
an indicator used to identify the presence of proteins; turns a different colour depending on the relative amounts of peptide bonds (from “-“ (none) to “+++”)
- blue: -
- pink: +
- violet: ++
- purple: +++
The Fluid Mosaic Model of Cell Membranes
- the accepted model of the cell membrane
- “Fluid”: parts move around (dynamic nature; not static)
- “Mosaic”; made up of many different components
features of the model:
- carbohydrate chains: make up glycoproteins, which can recognize harmful cells
- protein chains: can act as receptors
- phospholipid bilayer: separates the extracellular fluid (E.C.F) and the intracellular fluid (I.C.F.)
- cholesterol: stabilizes the cell membrane
- globular proteins: can act as transport channels
micelles
- non-specific vehicles which can carry hydrophobic substances - even nucleic acid - for gene therapy and vaccination administration
- made of phospholipids
permeability factors of the cell membrane
- phospolipids are not static; they move laterally, or - rarely - flip flop
The degree of fatty acid tail hydrogen saturation will dictate cell membrane permeability:
* unsatured hydrocarbon tails with kinks are more porous, and therefore more permeable
* saturated hydrocarbon tails with no kinks are less permeable
The amount of cholesterol within the phospholipids will also dictate cell membrane permeability:
* more cholesterol means more permeability
* less cholesterol means less permeability
functions of integral proteins
- transport channel: can transport substances into the cell
- enzyme: acts as a biological catalyst to speed up reactions
- receptor site: ligands bind to receptors (e.g. hormones) and change shape; the causes a cascade of reactions called “signal transduction”
- cell identity marker: carbohydrate chains that protude from glycoproteins enable cells to recognize each other, and therefore identify “intruders”; can be used to detect various cancers and infections
- cell adhesion: used for tissue formation
- attachment of cytoskeleton: maintain cell shape and form (proteins, microfilaments, microtubules and spindle fibers, etc.)
The Genetic Dogma
the process of which DNA is USED (not TRANSFORMED) to create proteins
1. DNA replication: DNA is replicated during the S phase of the cell cycle within the nucleus
2. DNA transcription: a strand of DNA is copied into a molecule of messenger RNA (mRNA) within the nucleus
3. DNA translation: mRNA is used in the process of protein synthesis within the RER, and polypeptide folding (packaging and modifying of proteins) within the Golgi bodies; the new protein is then excreted outside of the cell membrane via exocytosis and vesicles
enzymes
- organic substances that speed up biochemical reactions; is mostly proteins
- are specific to substrates
- e.g. amylase
substrates
- the reactant that an enzyme acts on
- e.g. amylose
enzymatic action
- follows the “induced-fit model” (a.k.a. the “hand in glove model”), NOT the “lock and key model”; the enzyme/substrate changes shape to fit the other
EXAMPLE: (maltose → glucose + galactose)
1. Maltase (the enzyme) binds with maltose (the substrate) at the active site.
2. Hydrolysis takes place, and there is a conformation change of the enzyme.
3. The enzyme recycles (reverts to it’s original shape), and the glucoses (the products) are released.
factors that affect enzyme activity
pH
- enzymes tend to have an optimal pH level in which they work
temperature
- increase in temperature means the enzyme denatures and theres a loss of activity
- decrease in temperature means the activity is reduced, but is restored when the temperature is raised (is reversible)
concentration
presence of co-factors and co-enzymes
- co-factors are inorganic non-proteins (e.g. ions; Zn2+, Mg2+)
- co-enzymes are organic non-proteins (e.g. vitamins; Vitamin B3, NAD+, NADP)
characteristics of enzymatic action
1. optimal conditions: each enzyme operate at optimal conditions
- e.g. pepsin (in stomach; digests proteins) will operate best at pH3
- e.g. trypsin (in duodenum; digests proteins) will operate best at pH8
2. specificity: every enzyme is specific for it’s substrate
- e.g. amylase breaks down amylose
3. sensitivity: refers to an enzyme’s binding affinity (degree of attraction) to it’s substrate
enzymatic regulation
1. Competitive inhibitors: the active site of the enzyme is blocked directly by the competitive inhibitor; prohibiting the substrating from binding with the enzyme
2. Non-competitive inhibitors: the non-competitive inhibitor binds allosterically (not in the active site; causing a change in the shape of the active site, and prohibiting the substrate from binding with the enzyme
3. Allosteric activators and inhibitors
* allosteric activators bind to the active site of an enzyme and keep an enzyme active, or cause an increase in activity (ACTIVE FORM)
* allosteric inhibitors bind to the active site of an enyzme and causes the enzyme to be inactive, or cause a decrease in activity (INACTIVE FORM)
biochemical pathways
A –(Ase)-> B –(Base)-> C –(Case)-> D
(If there’s too much/not enough product (D), it can act as an allosteric activator/inhibitor to produce less/more activity at A.)
enzymes in society
1. food industry; e.g. lactase in dairy/cheese
2. sanitation; e.g. enzymes in detergents (doesn’t work in higher temperatures), lipases
3. ethanol production; e.g. maltases
diffusion
the net movement of substances from an area of higher to lower concentration
osmosis
the movement of water from an area of higher to lower concentration, across a semipermeable membrane
passive transport
the movement of substances from an area of higher to lower concentration, without the input of energy
active transport
the transport of a solute across a membrane against the concentration gradient
endocytosis
process where the cell membrane ingulfs extracellular material to bring it inside the cell
phagocytosis
endocytosis of solid particles
pinocytosis
endocytosis of liquid particles
exocytosis
process in which a vacuole fuses with the cell membrane, and releases its contents outside of the cell
isotonic solution
- equal osmotic pressure
- no net movement of water
hypotonic solution
- lower osmotic pressure
- water enters the cell; the cell grows
hypertonic solution
- higher osmotic pressure
- water leaves the cell; the cell shrinks
hydrogenation
adding more hydrogen atoms to unsaturated fats
