lect 2: chemical components of cells Flashcards
what is the definition of an acid?
a molecule that releases a proton when dissolved in water; this dissociation generates hydronium (H3O+) ions, thereby lowering the pH
what is the definition of an amino acid?
small organic molecule containing both an amino group and a carboxyl group; it serves as the building blocks of proteins
what is the definition of base?
molecules that accepts a proton when dissolved in water
-also used to refer to the nitrogen-containing purines or pyrimidines in DNA and RNA
what is the definition of buffer?
-mixture of weak acids and bases that maintains the pH of a solution by releasing and taking up protons
what is the definition of chemical group?
a combination of atoms, such as hydroxyl group (-OH) or an amino group (-NH2) with distinct chemical and physical properties that influence the behavior of the molecule in which it resides
what is the definition of a condensation reaction?
chemical reaction in which a covalent bond is formed between two molecules as water is expelled
-used to build polymers, such as proteins, polysaccharides and nucleic acids
what is the definition of DNA?
double-stranded polynucleotide formed from two separate chains of covalently linked deoxyribonucleotides
-it serves as the cell’s store of genetic information that is transmitted from generation to generation
what is the definition of a fatty acid?
molecule that consists of a carboxylic acid attached to a long hydrocarbon chain
-used as a major source of energy during metabolism and as a starting point for the synthesis of phospholipids
what is the definition of hydrolysis?
chemical reaction that involves cleavage of a covalent bond with the accompanying consumption of water (its -H being added to one product of the cleavage and its -OH to the other)
-the reverse of a condensation reaction
what is the definition of hydrophobic force?
a noncovalent interaction that forces together the hydrophobic portions of dissolved molecules to minimize their disruption of the hydrogen-bonded network of water
-causes membrane phospholipids to self-assemble into a bilayer and helps to fold proteins into a compact, globular shape
what is the definition of a lipid?
an organic molecule that is insoluble in water but dissolves readily in nonpolar organic solvents; typically contains long hydrocarbon chains or multiple rings
-one class, the phospholipids, forms the structural basis for biological membranes
what is the definition of a lipid bilayer?
thin pair of closely juxtaposed sheets, composed mainly of phospholipid molecules, that forms the structural basis for all cell membranes
what is the definition of a macromolecules?
polymer built from covalently linked subunits
-includes proteins, nucleic acids and polysaccharides with a molecular mass greater than a few thousand daltons
what is the definition of a molecule?
group of atoms joined together by covalent bonds
what is the definition of a monomer?
small molecule that can be linked to others of a similar type to form a larger molecule (polymer)
what is the definition of a nucleotide?
basic building block of the nucleic acids, DNA and RNA; a nucleoside linked to a phosphate
what is the definition of a polymer?
long molecule made by covalently linking multiple identical or similar subunits (monomers)
what is the definition of a protein?
macromolecule build from amino acids that provides cells with their shape and structure and performs most of their activities
what is the definition of RNA?
molecule produced by the transcription of DNA; usually single-stranded, it is a polynucleotide composed of covalently linked ribonucleotide subunits
-serves a variety of informational, structural, catalytic and regulatory functions in cells
what is the definition of a sequence?
the linear order of monomers in a large molecule
-for example, amino acids in a protein or nucleotides in DNA; encodes information that specifies a macromolecule’s precise biological function
what is the definition of a subunit?
a monomer that forms part of a larger molecule, such as an amino acid in a protein or a nucleotide in a nucleic acid
-can also refer to a complete molecule that forms part of a larger molecules
-many proteins, for example, are composed of multiple polypeptide chains, each of which is called a protein subunti
what is the definition of a sugar?
a substance made of carbon, hydrogen, and oxygen with the general formula (CH2O)n
-a carbohydrate or saccharide
-the sugar of everyday use is sucrose, a sweet-tasting disaccharide made of glucose and fructose
cells are made of relatively few ______________
types of atoms
what are the types of bonds found in important biomolecules?
covalent bonds (formed by the actual sharing of electrons)
-polar
-nonpolar
noncovalent bonds
-ionic bonds
-hydrogen bonds
-hydrophobic interactions
-van der waals forces
what determines how atoms interact?
the outermost (valence electrons)
when are covalent bonds formed?
by sharing electrons
-fairly strong
how are covalent bonds characterized?
by particular geometries
-bond angles
-bond lengths
three dimensionality is very important in biochemistry
-structure dictates function
what happens when some covalent bonds involve more than one electron pair?
double bonds and triple bonds
-less flexibility to move around (less mobility)
-changes to planar structure instead of tetrahedral
-need more energy to break these bonds
what is it called when electrons in covalent bonds are often shared unequally?
-polarity of a covalent bond depends on the relative electronegativities of the participating atoms
-electronegativity: tendency to attract electrons
what is polarity of covalent bonds?
polar covalent bond
-electrons shared unequally (e.g. water)
nonpolar covalent bon
-electrons shared equally
-polar vs nonpolar molecule
-strongly polarized bonds increase reactivity of molecule (require less energy to break bond)
what does polarity of covalent bonds have to do with biological molecules?
biologically important polarized molecules have 1 or more electronegative atoms
-oxygen
-nitrogen
-sulfur (disulfide bonds are very important)
biological nonpolar molecules do not have electronegative atoms
-carbon, hydrogen
-e.g. waxes, fats
-relatively inert (less reactive)
some biological molecules have both polar and nonpolar regions
-proteins
-phospholipids
__________ are strong enough to survive the conditions inside cells
COVALENT BONDS
bond strength
-amount of energy required to break a bond
-units: kcal/mol or kJ/mol
-1 kcal= amount of energy required to increase temperature of 1L of H2O by 1 degrees celcius
thermal energy
-average energies of impacts molecules undergo
-collisions create certain amount of heat, which is less energy than is needed to break covalent bond
bond strength»»> thermal energy of the cell
-more stable and long lasting
when are ionic bonds formed?
gain and loss of electrons
-attraction between charged atoms
e.g. NaCl (table salt)
-chlorine is way more electronegative, so pulls electron away from sodium
-Cl gains electron=anion
-Na loses electron= cation
what is strong in ionic bonds?
-ionic bond in crystal form= strong
-in solution, ions surrounded by H2O which disrupts the bond. The oxygen interacts with the positively charged sodium
what ionic characteristic is important in biomolecules?
-weak attraction between oppositely charged (or opposite polarity) groups in large biomolecules are important
-ionic bonds may be disrupted in H2O
-but… deep within core of protein may still be intact
what are electrostatic interactions?
attraction between charged atoms
-despite being weakened by water and inorganic ions, electrostatic attractions are very important in biological systems
-for example, an enzyme that binds a positively charged substrate will often have a negatively charged amino acid side chain at the appropriate place
what are hydrogen bonds?
noncovalent bond
-hydrogen covalently bound to an electronegative atom (esp O and N)->partial+charge
-partial + charge H can interact with a second electronegative atom->hydrogen bon
what is the graph of hydrogen bonds?
-hydrogen bonds are important noncovalent bonds for many biological molecules
-for ex: hydrogen bonding can occur between amino acids in the same chain which forms a 3-D shape
-for ex: hydrogen bonding between the nitrogenous bases in the different nucleotides which gives the helix stability
what are hydrophobic interactions?
polar molecules=hydrophilic
-form H-bonds with H2O
-philic=loving
nonpolar molecules=hydrophobic
-aggregate to decrease exposure to H2O
-phobic=fearing
-phospholipids have both, so will innately form structures to eliminate water in the tails which are hydrophobic
what are van der waals forces?
weak force
hold together neutral molecules
-transitory dipole in “A”
-induces dipole in “B”
-weak dipole interaction between “A” and “B”
-in all molecules, including polar and non polar. It is the constant movement of electron clouds
when do van der waals forces occur?
-operate at optimum distances
-maximized by complimentary surfaces
too close=force is very strong
too far=force is very weak
chemical properties of ______ are important to biological systems
WATER
-so much of our bodies are made up of water
what are some unique properties of water?
-highly asymmetric
-polarized covalent bonds
-all 3 atoms can H-bond
what are the life-supporting properties of water?
- dissolving power
-facilitates chemical reaction necessary for life (universal solvent) - H-bonding
-self: cohesive, adhesive environment
-polar molecules (e.g. amino acids, sugars)
-provides stability - temperature regulation
-high specific heat capacity
-high heat of vaporization - versatility in physical states
-solid, liquid, gas (normal terrestrial conditions)
-solvent for biological processes
what are acids, bases and buffers?
-some polar molecules-> acids or bases in H2O
-hydrogen looses shared electron-> proton (H+)
-acids: release H+
-bases: accept H+
-atmospheric molecules: act as either acids or bases
-buffers in living systems resist changes in pH
-acidity measures with pH scale [H+]
what is the nature of biological molecules?
-chemistry of life centers around chemistry of carbon atom
-compounds produced by living organisms=biochemicals
-long chains of carbon atoms: linear, cyclic, branched
what are functional groups? (KNOW STRUCTURE)
-found in many biologically important organic molecules
-act as a unit (predictable chemistry)
-sources of molecule’s physical properties, chemical reactivity, solubility
electronegative atoms (N, P, O, S): increase polarity, H2O solubility, reactivity
-possibility for ionization->charged molecule
-hydroxyls are found in things like sugars
-carboxyl amino groups are found in amino acids
-phosphates and carbonyls are important in lipids
-sulfhydryl is important in stabilizing protein structures (disulfide bridges)
what are macromolecules?
organic molecules within cell
-four main types that have particular cell structure and facilitate different cellular activities
-are huge polymers
formed by linking smaller building blocks (monomers)
-polymerization is the process of linking monomers to form a polymer
-hydrolysis is the reverse process of hydrolysis (addition of water and catalyst)
what are the four types of biological molecules?
carbohydrates
lipids
nucleic acids
proteins
structure and function similar in all organisms (conservation across species)
what are carbohydrates?
AKA polysaccharides or glycans
function
-energy stores (readily available)
-building material biological construction
-simple sugars are monosaccharides
-complex sugars are polysaccharides
what is the structure of sugars?
-general formula: (CH2O)n
-backbone of C atoms linked by linear fashion via single bonds
-highly water soluble due to their hydroxyl group (-OH)
what is the linking of sugars together?
glycosidic bond
-covalent bond linking sugars (-C-O-C-) (esters)
disaccharide linkage example
-molecules with 2 linked sugars
-readily available energy source
-e.g. sucrose (plant sap to table sugar)
-e.g. lactose (mammalian milk)
oligosaccharides: oligo=few
polysaccharides: polymer of many sugar monomers
what are nutritional polysaccharides?
act as energy stores in two main forms
glycogen
-primary animal product
-branched glucose polymers
starch
-plant product
-both branched and unbranched glucose polymers but structure is very different
-same monomer but different chemical and physical properties
what are structural polysaccharides?
more for things like protection
-tough and durable structural materials
linked glucose monomers
-cellulose in plant cell walls
-chitin in outer skeleton of insects
-glycosaminoglycans (GAGs): extracellular space and connective tissue
what are lipids?
diverse group of nonpolar biological molecules
-soluble in organic solvent (chloroform, benzene)
-do not dissolve in water
-hydrophobic interactions dictate structure
important cellular lipids are fats, steroids and phospholipids
-different structures
what is a fat?
fat: glycerol + 3 fatty acids
-triacylglycerol or triglyceride
-ester linkage (-C-O-C-)
-main component of body fat in humans (energy reserve)
fatty acid
-long unbranched hydrocarbon chain
-carboxyl group at one end (-COOH) which allows it to bond with glycerol
what is the structure of fats?
amphipathic
-tails (fatty acid) are hydrophobic
-head (glycerol) is hydrophilic (negatively charged)
what can fatty acids differ?
what is the structure of steroids?
usually synthesized from cholesterol
-just changing functional groups to create different molecules
what are phospholipids?
-resembles fat (has glycerol head)
-only has two fatty acid chains
-third OH of glycerol bonded to a phosphate group
major cellular function!
-found in membranes
-gives membrane its properties
what are proteins?
carry out cellular activities
-have wide range of differing functions
what is the structure of proteins?
-polymers of amino acids (polypeptide chains)
-20 different amino acids which different chemical properties
all amino acids contain
-carboxyl group
-amino group
-differ at R site
-alpha-carbon single C atom in between
linked via peptide bonds (i.e. amide bond)
what are the properties of side chains?
-all polypeptides have a common backbone
variability exists in the side chain or R group
-gives proteins their diverse structures and activities:
-nonpolar
-polar
-ionic (positive or negative)
what is the properties of side chains example of cysteine?
cysteine has a thiol group (SH), important because they can undergo oxidation which forms disulfide bonds
disulfide bond formed by:
-oxidation (loss of electron) of sulfur to create a covalent bond between two cysteine residues (-S-S-)
cysteine residue locations
-distant
-entirely different polypeptide chain
-disulfide bridges help stabilize the shapes of proteins
what are the four levels of structure organization in proteins?
primary
secondary
tertiary
quaternary
2,3,4=higher-level organization
what is the primary structure of proteins?
sequence of amino acids which is encoded in the genome
-sequence contains 3D structure information, hence function
-all levels of structure are ultimately determined by the primary structure
-changes in sequence (mutations) may or may not be tolerated depending on location or specific amino acids
what is the influence of amino acid side chains on protein folding?
character of side chains is very important to structure/function
-ionic
-polar
-nonpolar
driving force for protein folding is hydrophobic interactions
-contribute to overall stability of the protein
what is sickle cell anemia?
how mutations in amino acid sequence can affect 3D structure of protein
-normal red blood cell shape=biconcave shape
-sickle cell anemia=crescent or sickle shaped
-single change amino acid change within hemoglobin molecule
-glutamic acid-> valine
-dont flow through veins the same way
what is the secondary structure of protein?
-conformation of portions of the polypeptide chain
-preferred conformation maximizes hydrogen bonding (formed by H-bonds)
-2 shape: alpha helix and beta pleated sheet
what is the tertiary structure of protein?
-3D conformation of the entire polypeptide
-impacts protein properties
-3D structure is not entirely fixed (discovered through prions which are misfolded proteins)
categorization based on shape
-fibrous=elongated
-globular=compact
what may tertiary structures reveal?
unexpected similarities in proteins
-primary sequence similarity to identify proteins with similar structure/function
-tertiary structure to predict protein interactions and enzymatic activity
-interestingly, proteins with different primary sequence has been found to have similar tertiary structure
what is important in tertiary structures?
domains
-structural unit of tertiary structure
-hydrophobic cores connected by loop regions
-fold independently
-eukaryotic proteins have equal to or more than 2 domains
-often have specific function
what is the quaternary structure of proteins?
not every protein has quaternary structure, only the ones with many polypeptide chains will
-protein with single polypeptide chain: only 3 levels of structure
-protein with multiple polypeptide chains or subunits have quaternary structure
what are molecular chaperones?
-“helper proteins”
-not all proteins can assume their final tertiary structure by self-assembly
-bind to short stretches of hydrophobic amino acids to help unfolded proteins achieve their proper 3D conformation
what are some examples of how protein misfolding can have deadly consequences?
-alzheimer’s disease: 10% of individuals above the age of 65
-AD patients exhibit memory loss, confusion and loss of reasoning ability
brain of a person with AD
-amyloid plaques (amyloid aggregated of A-peptide)
-neurofibrillary tangles (misfolded tau protein)
what are nucleic acids?
stores and transmit genetic information
-DNA=info storage
-RNA=info transfer
polymers of nucleotides. nucleotides have 3 parts:
1. sugar (5 carbon)
2. nitrogenous base
3. phosphate group
what are the differences in structures of RNA and DNA?
what are the nitrogenous bases?
where do DNA and RNA differ?
what is the structure of DNA?
what is the structure of RNA?
what do noncovalent bonds specify?
the precise shape of a macromolecule
what do noncovalent bonds also allow a macromolecule to do?
to bind other selected molecules?
what are the learning objectives of this lecture?
