CHAPTER 3 Flashcards
what are the molecules that make up organisms?
-proteins
-carbohydrates
-lipids
-nucleic acids
all but lipids are polymers of smaller molecules called monomers
define monomers. define polymers
-monomers: A small molecule, two or more of which can be combined to form polymers
-polymers: A large molecule made up of similar or identical subunits called monomers.
define macromolecules
-polymers containing thousands of more atoms. (large lipids are also treated as macromolecules)
-macromolecules function depends on the properties of functional groups; each group has a specific property (like polarity)
-a single macromolecule may contain many different functional groups
define functional groups
- A characteristic combination of atoms that contributes specific properties when attached to larger molecules. A group of species that function in similar ways, whether or not they use the same resources.
define isomers and name the three types
-molecules with the same chemical formula, but the atoms are arranged differently
-structural isomers , cis-trans isomer , and optical isomers
define structural isomers
-differ in how atoms are joined
define cis-trans isomers
-centered around a double bond with a toms on either side in different orientations with respect to each other
-cis:
-trans:
define optical isomers
-mirror images
define condensation reactions
-energy is used to make covalent bonds between monomers to make a polymer; a water molecule is removed
-also known as dehydration reaction
define hydrolysis reactions
-polymers are broken down into monomers; energy is realized and water is consumed (added)
what chains do proteins consist of? how are the chains folded?
-they consist of one or more polypeptide chains
-the chains are folded into specific 3D shapes as defined by the sequence of amino acids
-proteins have diverse functions
define polypeptide chains
a single, unbranched chain of amino acids
what are the 10 types if proteins?
-enzymes
-structural proteins
-defensive proteins
-signaling proteins
-receptor proteins
-membrane transporters
-storage proteins
-transport proteins
-gene regulatory proteins
-motor proteins
enzymes function
catalyze (speed up) biochemical reactions
structural proteins function
provide physical stability and movement
defensive proteins function
recognize and respond to non self substances (ex: antibodies)
signaling proteins function
control physiological processes (ex: hormones)
receptor proteins function
receive and respond to chemical signals
membrane transporters function
regulate passage of substances across cellular membranes
storage proteins function
store amino acids for alter use
transport proteins function
bind and carry substances within the organism
gene regulatory proteins function
determine the rate of expression of a gene
motor proteins function
causes movement of structures in the cell
amino acids
-they have carboxyl and amino groups which allows them to function both as an acid and base
-amino acids are grouped based on the side chains
-the alpha carbon (central atom) is asymmetrical
-amino acids can be optical isomers: D-amino and L-amino acids
define side chains and R-groups
The distinguishing group of atoms of a particular amino acid. Also called a side chain.
amino acids with electrically charged hydrophilic side chains
positive charge: arginine (Arg; R), histidine (His; H), lysine (Lys; K)
negative charge: aspartic acid (Asp; D), glutamic acid (Glucose; E)
amino acids with polar but uncharged side chains (hydrophilic)
serine (Ser; S)
threonine (Thr; T)
asparagine (Asn; N)
glutamine (Gln; Q)
tyrosine (Tyr; Y)
special cases of amino acids
cysteine (Cys; C)
glycine (Gly; G)
proline (Pro; P)
amino acids with non polar hydrophobic side chains
alanine (Ala; A)
isoleucine (Ile; I)
leucine (Leu; L)
methionine (Met; M)
phenylalanine (Phe; F)
tryptophan (Trp; W)
valine (Val; V)
disulfide bridge
the cysteine amino acid
-SH group can react with another cysteine side chain to form a disulfide bridge, or disulfide bond (-s-s-) in this reaction the 2 H atoms are taken out
-these are important in protein folding but most cysteines in a protein are not involved in disulfide bridges
oligopeptides, or peptides
short polymers of 20 or fewer amino acids
polypeptide
longer polymer
peptide linkages/ bonds
amino acids bond together covalently in a condensation reaction (water being taken out) and are linked together with peptide bonds
the four levels of protein structures
-primary
-secondary
-tertiary
-quaternary
primary structure of a protein
-the sequence of amino acids
-the properties of side chain functional groups determine h ow the protein can twist and fold which determines the secondary and tertiary structure
secondary structure
α helix: right-handed coil resulting from hydrogen bonding between N-H groups and C=O groups
β pleated sheet: two or more polypeptide chains are aligned; hydrogen bonds form between the chains
tertiary structure
-folding results in the specific 3D shape. which is determined by interactions between R-groups
-the outer surfaces present functional groups that can interact with other molecules
denatured
-if a protein is heated, secondary and tertiary structures break and the protein is said to be denatured
-when cooled some proteins return to normal tertiary structures; which means information to specify protein shape is in the primary structure
quaternary structure
these results from interaction of subunits by hydrophobic interactions, van Der Waals forces, ionic attractions and hydrogen bonds
-each subunit has its own unique tertiary structure
proteins bind non-covalently with specific molecules, the specificity is determined by?
-shape: there must be a general “fit” between the protein and the other molecule
-chemistry: surface R groups interact with other molecules via ionic, hydrophobic, or hydrogen bonds
conditions that affect secondary and tertiary structures
-high temperatures
-pH changes
-high concentrations of polar molecules
-non-polar substances, via hydrophobic interactions
protein shape can change as a result of?
-interaction with other molecules (EX: an enzyme changes shape when it comes into contact with a reactant )
-covalent modification: addition of a chemical group, such as a phosphate, to an amino acid
Chaperones
proteins can bind to the wrong molecules after denaturation or when they are newly made and still unfolding; chaperones are proteins that help prevent this by surround a denatured protein and allowing it to refold
carbohydrates
(C1H2O1)n
-sources of stored energy
-used to transport stored energy
-carbon skeletons for many other molecules
-form extracellular structures such as cell walls
monosaccharide? disaccharide? oligosaccharide? polysaccharide?
-simple sugar (just one)
-two simple sugars linked by covalent bonds
-3 to 20 monosaccharides
-hundreds or thousands of monosaccharides
glucose
-all cells use glucose as an energy source
-exists as a straight chain or ing form
-ring is more stable if there dis a ring there are two different types of glucose ( α- or β-glucose), that can interconvert
types of monosaccharides
-pentoses
-hexoses
pentoses
five-carbon sugars; includes ribose (RNA; has an oxygen) and deoxyribose (DNA; takes away oxygen)
hexoses
six-carbon sugars; some are structural isomers
α-mannose, α-glucose, fructose
glycosidic bonds
monosaccharides bind together in condensation reaction to form glycosidic bonds to form disaccharides
oligosaccharides
several monosaccharides linked by glycosidic bonds; often covalently bonded to proteins and lipids on cell surfaces, where they serve as recognition signals
examples of glycosidic bonds
sucrose
maltose
cellobiose
polysaccharides
large polymers of monosaccharides connected by glycosidic bonds; some are branched.
what are the 3 types of polysaccharides
-starch: storage of glucose in plants
-glycogen: storage of glucose in animals
-cellulose: very stable, good for structural components; only found in plant; often make up cell walls in plants (humans cannot digest)
carbohydrates can be modified by the addition of functional groups to form?
-sugar phospahtes
-amino sugars
-chitin
lipids
non-polar hydrocarbons; insoluble in water; if close together, weak but additive van Der Waals forces hold them together in aggregates
types of lipids?
-fats and oils: store energy
-phospholipids: structural role in cell membranes
-carotenoids and chlorophylls: capture light energy in plants
-steroids and modified fatty acids: hormones and vitamins
-animal fat: thermal insulation
-lipid coating around nerves: provides electrical insulation
-oil and wax on skin, fur, and feathers: repel water and slows evaporation
triglycerides
fats and oils made of three fatty acids and a glycerol
fatty acid
non polar hydrocarbon chain with a polar carboxyl group
ester linkages
carboxyl bond with hydroxyls in glycerol through ester linkages; from condensation reactions
saturated fatty acid
no double bonds between carbons: it is matured with H atoms so they tightly pack together (animal fats; solid at rom temperature)
unsaturated fatty acid
-one or more double bonds in the carbon chain result in kinks that prevent packing (plant oils; liquid at room temperature)
-double bonds in naturally occurring unsaturated fats are sis (H atoms are on the same side)
trans fats
-H atoms are on opposite sides of the C=C bond (trans)
-may contribute to heart disease and stroke
hydrogenation
-the process by which hydrogen atoms are added to unsaturated fats and oils.
-trans fats result from hydrogenation of vegetable oils to produce a saturated fat (EX margerine), but some of the cis bonds convert to trans
omega-3 fatty acids
-protect against heart disease and stroke
-the first C=C bond is at position 3 in the fatty acid chain
phospholipids
-fatty acids bound to glycerol; a phosphate group replaces one fatty acid
-they are amphipathic
phospholipids are amphipathic which means?
-“head” is a phosphate group which is hydrophilic
-“tails” are fatty acid chains which is hydrophobic
bilayer
in water, phospholipids line up with the hydrophobic tails together and the phosphate heads facing outwards
phospholipid bilayer
biological membranes have this kind of structure
lipoproteins
in animals, phospholipids and proteins form lipoproteins which transport lipids such as cholesterol in the blood
carotenoids
light-absorbing pigment EX:β-carotene traps light energy for photosynthesis and in humans it breaks down into vitamin A
steroids
multiple rings share carbons. cholesterol is important in membranes; other steroids are hormones
waxes
long-chain alcohol bound to an unsaturated fatty acid
