Chapter 2: Molecular Interactions Flashcards
What are the four major groups of macromolecules?
carbohydrates
lipids
proteins
nucleotides
what can macromolecules combine to form?
glycoproteins, glycolipids, lipoproteins
*are biomolecules made mostly of carbon and hydrogen
*lipids have a backbone of
glycerol and 1–3 fatty acids
*are nonpolar and
therefore not very soluble in water
lipids
what are the two categories of lipids?
fats
oils
are long chains of carbon atoms bound to hydrogens, with a carboxyl (–COOH) or “acid” group at one end of the chain
fatty acids
*have no double bonds between carbons, so they
are “saturated” with hydrogens
*solid at room temp
saturated fatty acids
*have one double bond between two of
the carbons in the chain
*For each double bond, the molecule has two
fewer hydrogen atoms attached to the carbon chain
monounsaturated fatty acids
have two or more double bonds
between carbons in the chain.
polyunsaturated fatty acid
what are 3 types of lipid related molecules?
eicosanoids
steroids
phsopholipids
modified 20-carbon fatty acids with a
complete or partial carbon ring at one
end and two long carbon chain “tails.”
eicosanoids
lipid-related molecules whose structure
includes four linked carbon rings
steroids
- *have 2 fatty acids and a phosphate group (–H2PO4)
* *important component of cell membrane
phospholipids
- the most abundant biomolecule
* that for each carbon there are two hydrogens and one oxygen
carbohydrates
what are the 3 categories of carbohydrates?
monosaccharides
disaccharides
polysaccharides
- simple sugars
- building blocks of complex carbohydratess
- examples are ribose and glucose
monosaccharides
- consist of glucose plus another monosaccharide
* examples are sucrose, maltose, lactose
disaccharides
- glucose polymers
- glucose is stored in this form for energy
- animals (chitin & glycogen)
- plants (cellulose & starch)
- yeast/bacteria (dextran)
polysaccharide
polymers of smaller building block molecules called amino acids
proteins
- have a carboxyl group (–COOH), an amino group (–NH2), and a hydrogen attached to the same carbon
- The fourth bond of the carbon attaches to a variable “R” group
amino acids
bond in which the amino group of one amino acid joins the carboxyl group of the other, with the loss of water.
peptide bond
what are the different structures of proteins?
primary
secondary
tertiary
quaternary
*The sequence of amino acids in a peptide chain
primary structure
- Covalent bond angles between amino acids determine secondary structure
- alpha helix or beta pleated sheets
secondary structure
- protein’s 3D shape
- fibrous proteins (collagen)
- globular proteins
tertiary structure
- Multiple subunits combine with noncovalent bonds
* Hemoglobin molecules are made from four globular protein subunits
quaternary structure
*biomolecules that play an important role in energy and information transfer
*consists of (1) one or more phosphate
groups, (2) a 5-carbon sugar, and (3) a carbon-nitrogen ring structure called a
nitrogenous base
nucleotide
- nucleotide polymers
- RNA and DNA
- store and transmit genetic information
nucleic acids
include energy transferring compounds such as ATP, ADP, cyclic AMP
single nucleotides
- have a double ring structure
- nitrogenous base
- include adenine and guanine
purines
- have a single ring structure
- nitrogenous base
- includes cytosine, thymine, uracil
pyrimidines
what are the 2 functions of single nucleotides?
- capture and transfer energy in high energy electrons or phosphate bonds
- aid in cell-cell communication
what is the function of ATP, ADP, NAD, FAD?
energy capture and transfer
what is the function of cAMP?
cell-cell communication
- smallest particle of any element
- link by sharing electrons to form molecules
- consist of protons, neutrons, and electrons
atom
what are the three elements that make up 90% of our body mass?
oxygen
carbon
hydrogen
simplest type of matter
elements
determine the element (atomic #)
protons
determine the isotope
neutrons
- form covalent bonds
- create ions when gained or lost
- capture and store energy
- create free radicals
electrons
an atom that gains or loses neutrons becomes….
an isotope of the same element
an atom that gains or loses electrons becomes an…..
ion of the same elements
lipids + proteins
lipoproteins
proteins + carbohydrates
glycoproteins
carbohydrates + lipids
glycolipids
the units formed when two or more atoms link by sharing electrons
molecules
the links between atoms, which are formed by transferring/sharing of electrons
bonds
what are the main two types of bonds?
covalent bonds
noncovalent bonds
- result when atoms share electrons
- these bonds require the most energy to make or break
- include nonpolar molecules and polar molecules
covalent bonds
- have an even distribution of electrons
* molecules made of mostly carbon and hydrogen are usually this
nonpolar molecules
- have regions of partial charge
* example is water
polar molecules
includes ionic bonds, hydrogen bonds, and Van der Waals Forces
noncovalent bonds
- electrostatic attractions between ions
* example is NaCl
ionic bonds
- forms between a hydrogen atom and a nearby oxygen, nitrogen, or fluorine atom
- responsible for surface tensions
hydrogen bonds
weak, nonspecific attractions between atoms
Van der Waals Forces
*Molecules that have polar regions or ionic bonds readily interact with the polar regions of water. *This enables them to dissolve easily in water
hydrophilic
- Water molecules interact with ions or other polar molecules to form hydration shells around the ions.
- This disrupts the hydrogen bonding between water molecules, thereby lowering the freezing temperature of water
hydrophilic interactions
have polar heads and nonpolar tails
phospholipid molecules
**Because they have an even distribution of electrons and no positive or negative poles, nonpolar molecules have no regions of partial charge, and therefore tend to repel water molecules
**Molecules like
these do not dissolve readily
in water
hydrophobic interactions
What are the categories of proteins?
- enzymes
- membrane transporters
- signal molecules
- receptors
- binding proteins
- immunoglobulins
- regulatory proteins
biological catalysts
enzymes
found in the ECF and transport molecules within the body
binding proteins
- antibodies
* help protect the body from foreign invaders
immunoglobulins
turn cell processes on and off or up and down
regulatory proteins
Any molecule or ion that binds to another molecule
ligand
how can proteins bind to other molecules?
noncovalent interactions on binding sites
model of protein binding where the binding site shape is not an exact match to the ligands’ (L) shape
Induced fit model of protein-ligand binding
the degree to which a protein is attracted to a ligand
affinity
are protein binding reactions reversible
yes
- states that when a reaction is at equilibrium, the ratio of the products to the substrates is always the same
- binding reactions obey this law
law of mass action
what does a higher affinity for a ligand mean?
a larger Keq
equation of the equilibrium for a reaction
Keq= [PL]/[P][L]
reciprocal of the equilibrium equation
- is the dissociation constant
* Kd= [P][L]/[PL]
what does a lower affinity for a ligand mean?
a larger Kd
what happens during a reaction at equilibrium?
rate of reaction in forward direction (r1) = the rate of reaction in the reverse direction (r2)
what is the ratio of bound to unbound at equilibrium?
it is always the same
- closely related proteins whose function is similar but whose affinity for ligand differs
- alters protein binding
isoforms
has increased affinity for oxygen
fetal isoform of hemoglobin
- alters protein binding
* synthesized in an inactive form and must become activated
activation protein
how do the activation proteins become activated?
- enzymes remove portions of the protein
* may require cofactors that must attach to the protein before the binding site becomes active
how are inactive forms of proteins identified?
prefix pro- or suffix -ogen added to the name of the active enzyme
- protein is inactive until peptide fragments are removed
* essential for binding activity
proteolytic activation
- essential for binding activity
* required for ligand binding at the binding site
cofactors
- alters protein binding
* a factor that influences either protein binding or protein activity
modulation
what are the 2 mechanisms of modulation?
- The modulator changes the proteins ability to bind the ligand
- The modulator changes the proteins ability to create a response.
a modulator that binds to protein
away from binding site and turns it on
allosteric activator
a modulator that binds to protein away
from binding site and inactivates the binding site
allosteric inhibitor
blocks ligand binding at the binding site
competitive inhibitor
- alters proteins binding
* the programmed production of new proteins (enzymes, receptors, membrane transport proteins)
up-regulation
- alters protein binding
* the programmed removal of proteins
down-regulation
How do temperature and pH affect proteins?
- may disrupt protein structure and cause loss of function
* can be irreversible if the protein becomes denatured
What happens if the protein concentration in the cell is constant?
the magnitude of the response is determined by the concentration of the ligand.
what does increased ligands result in?
increase in response
occurs when all the protein binding sites are occupied
saturation
