Lecture 2 Terms/Questions Flashcards
Osmolarity
concentration expressed in osmoles per liter
Isoosmolar
isosmotic?
if 2 solutions contain the same # of solute particles per unit volume
Hypoosmolar
hyposmotic?
solution B, with fewer osmoles per unit volume, is hyposmotic to solution A
Hyperosmolar
hyperosmotic?
if solution A has a higher osmolarity (contains more particles per unit volume, is more concentrated) than solution B, we say that solution A is hyperosmotic to solution B
Allosteric
act to block a competitive agonist by binding to the protein away from the binding site & inactivate the binding site
- agonists & antagonists may be ____
Affinity
the degree to which a protein is attracted to its ligand
- a protein binds a ligand with “_____”
- high ____ means it binds strongly
- weak ____ means weak binding
Phosphatase
removes phosphates
Biomolecule
organic molecule that is commonly associated with life
- carbohydrates
- lipids
- nucleic acids
- proteins
General Formula of a Carbohydrate
CnH2nOn
Eicosanoid
are a subset of oxylipins
- polyunsaturated fatty acid, having a length of 20 carbon atoms
Subunit
a distinct component of something
- ex: in the quaternary structure their are multiple of these for ex, fibrous proteins and globular proteins
Regulatory Subunit
will facilitate or inhibit the activity?
Phosphorylation
an enzyme activity that transfers a phosphate onto another protein - a biological reaction
- AKA addition of a phosphate group to a molecule (to one of the amino acid side chains of a protein)
- phosphates are (-)ly charges so that their addition to a protein will change the characteristic of the protein
- this change is often a conformational one, causing the protein to change how it is structured
Dephosphorylation
- the reaction is reversible by this process
- the protein switches back to its original conformation when the phosphorus is removed
- AKA removal of a phosphate group
Kinase
enzymes that covalently add phosphate
- AKA an enzyme that adds a phosphate group to the substrate
Phosphatase
enzymes that catalyze the hydrolysis of phosphates ??
Sphingolipid
a type of lipid
- analogous to a phospholipid structurally
- contains a phosphate, variable “R” group, sphingosine (contains a N molecule) and a fatty acid ???
Amino Acid
have a carboxyl group (-COOH), an amino group (-NH2), and a hydrogen attached to the same carbon
- the 4th bond of the carbon attaches to a variable “R” group
- the building blocks of proteins
Fibrous Protein
are generally insoluble
- can be Beta-strands or long chains of alpha-helices
Globular Protein
are usually soluble
- can be a mix of alpha-helices, beta-sheets, & amino acid chains that fold back on themselves
Protein Binding
in order for a protein to DO SOMETHING, it must INTERACT WITH OR BIND TO other proteins, molecules or ions
- binding site
- “activity”
protein binding is SPECIFIC
- a molecule that binds to a protein binding site is called a ligand
Whats the difference between an organic molecule and a biomolecule?
organic molecule - contains carbon
biomolecule - organic molecule that is commonly associated with life (carbohydrates, lipids, nucleic acids, proteins)
Schematically, show the difference between a monosaccharide and a polysaccharide
monosaccharides are simple sugars (have either 5 carbons or 6 carbons)
polysaccharides are complex carbohydrates composed of glucose polymers
Why would a cell store glucose as glycogen?
polysaccharides are glucose polymers
- all living cells store glucose for energy in the form a polysaccharide
- digestion of starch or glycogen yields maltose
- glycogen is a typical storage material for mammals
- glycogen is the polymerized version of glucose stored in organs like the liver or muscle for example
In animal cells, glucose is generally stored in the form of glycogen. This is done to not upset the osmotic balances in the cell. Glucose molecules are soluble in water and thus can cause the cell to become hypertonic. … On the other hand, glycogen is insoluble in water and therefore stays inert. ?
Schematically show the difference between a fatty acid, a phospholipid and a
sphingolipid
fatty acid - long unbranched hydrocarbon chain with 8-28 carbons
- has carboxyl (=acidic) functional group
phospholipid - 2 fatty acids, a phosphate group (-H2PO4) & a variable “R” group attached to the glycerol
sphingolipid - 1 fatty acid, a phosphate group (-H2PO4) & a variable “R” group attached to the sphingosine
Why are some fatty acids considered saturated? Unsaturated?
saturated fatty acids (no double bonds) form a straight chain
- can stack quite closely & neatly
unsaturated fatty acids (double bonds) have a “kink”
- the more double bonds, the less likely it will be solid at room temp
- won’t like to stack so instead will pack loosely
What is an R-group? What is the significance of different R- groups
some kind of amino acid like molecule (small additions to a basic structure)
- different function groups (“R” groups”) confer different functions
Describe the difference between primary, secondary, tertiary and quaternary structure
of a protein
primary - the sequence of amino acids in a peptide chain (linear)
secondary - created primarily by hydrogen bonds b/t adjacent chains or loops (determined by pattern of hydrogen bonds b/t the amino hydrogen & carboxyl oxygen atoms in the peptide backbone)
- alpha-helix & beta-pleated sheets
tertiary - protein’s 3-D shape
- fibrous proteins & globular proteins
quaternary - multiple subunits combine with noncovalent bonds
T or F: all amino acids are considered acidic
F - some amino acids are acidic, basic, polar, non-polar
Define the functional categories of proteins (not necessary to memorize the list)
primary - the sequence of amino acids in the peptide chain
secondary - spatial arrangement of amino acids in the chain
tertiary - protein’s 3-D shape
quaternary - arrangement of a protein with multiple peptide bonds
What does adding an antagonist do to reaction velocity?
they inhibit or block the area so that the agonist reduces its action, so I can imagine it would cause no biological response so nothing would occur?
Define the term isoform and describe how isoforms can have an effect on protein binding.
isoform - closely related proteins whose function is similar but whose affinity for ligands differs
for ex: the oxygen-transporting protein hemoglobin has multiple isoforms
- 1 hemoglobin molecule has a quaternary structure consisting of 4 subunits
- in the developing fetus, the hemoglobin isoform has 2 alpha chains & 2 gamma chains that make up the 4 subunits
- shortly after birth, fetal hemoglobin molecules are broken down & replaced by adult hemoglobin
- the adult hemoglobin isoform retains the 2 alpha chain isoforms but has 2 beta chains in place of the gamma chains
- both adult & fetal isoforms of hemoglobin bind oxygen,, but the fetal isoform has a higher affinity for oxygen
- this makes it more efficient at picking up oxygen across the placenta
Describe protein activation. What role do cofactors play in activation?
protein activation: some proteins are inactive when they are synthesized in the cell
- the activation of some proteins requires the presense of a COFACTOR, which is an ion or small organic functional group
- cofactors must attach to the protein before the binding site will become active & bind to ligand
- ionic cofactors include Ca2+, Mg2+, and Fe2+
- MANY ENZYMES WILL NOT FUNCTION WITHOUT THE COFACTORS
- cofactors are essential for binding activity
- required for ligand binding at binding site
Identify the basic mechanisms by which a modulator can affect protein interactions.
a factor that influences either protein binding or protein activity is called a modulator
- there are 2 basic mechanisms by which modulation takes place
- the modulator either:
(1) changes the protein’s ability to create a response
(2) changes the protein’s activity or its ability to create a response
Briefly describe the actions of the following modulators. (Tbl. 2.3)
Chemical modulators
are molecules that bind covalently or noncovalently to proteins & alter their binding ability or their activity
- may activate or enhance ligand binding, decrease binding ability, or completely inactivate the protein so that it is unable to bind any ligand
- inactivation may be either reversible or irreversible
Briefly describe the actions of the following modulators. (Tbl. 2.3)
Antagonists
a ligand that REDUCES the action of an agonist (i.e. binds but causes NO biological response)
- also called inhibitors, blockers
- may be competitive or allosteric
- they are like the guy who slips into the front of the movie ticket line to chat with his girlfriend, the cashier
- he has no interest in buying a ticket, but he prevents the people in line behind him from getting their tickets for the movie
Briefly describe the actions of the following modulators. (Tbl. 2.3) Competitive inhibitors (Fig. 2.12d)
are reversible antagonists that compete with the customary ligand for the binding site
Briefly describe the actions of the following modulators. (Tbl. 2.3)
Irreversible antagonists
bind tightly to the protein & cannot be displaced by competition
Briefly describe the actions of the following modulators. (Tbl. 2.3) Allosteric modulators (Fig. 2.12c, e)
bind reversibly to a protein at the regulatory site away from the binding site, & by doing so change the shape of the binding site; may be inhibitors or activators
allosteric inhibitors: are antagonists that decrease the affinity of the binding site for the ligand & inhibit protein activation
allosteric activators: increase the probability of protein-ligand binding, & enhance protein activity
Briefly describe the actions of the following modulators. (Tbl. 2.3)
Covalent modulators
are atoms or functional groups that bind covalently to proteins & alter the proteins’ properties
- like allosteric modulators, they may either increase or decrease a protein’s binding ability or its activity
ex: phosphate groups b/c many proteins in the cell can be activated or inactivated when a phosphate group forms a covalent bond with them, the process known as PHOSPHORYLATION
Physical Factors
Describe how temperature and pH affect protein structure and function. (Fig.
2.13a)
- small changes in pH or temp act as modulators to increase or decrease activity
- however, once these factors exceed some critical value, they disrupt the noncovalent bonds holding the protein in its tertiary conformation
- these can cause structural changes
- protein may become denatured (when the protein loses its conformation)
The Body Regulates the Amount of Protein in Cells
Define and distinguish between the processes of up-regulation and downregulation. (Fig. 2.13b)
- the body has mechanisms that enable it to monitor whether it needs more or less of certain proteins
- complex signaling pathways, many of which themselves involve proteins, direct particular cells to make new proteins or to break down (degrade) existing proteins
- this programmed production of new proteins (receptors, enzymes, & membrane transporters, in particular) is called UP-REGULATION
- conversely, the programmed removal of proteins is called DOWN-REGULATION
- in both instances, the cell is directed to make or remove proteins to alter its response
Reaction Rate Can Reach a Maximum
Define saturation and describe how proteins can reach the point of saturation. (Fig. 2.13c)
saturation: all active sites on a given amount of protein are filled with substrate & reaction rate is maximal
a good analogy from the show I Love Lucy:
- Lucille Ball’s character was working at the conveyor belt of a candy factory, loading chocolates into the little paper cups of a candy box
- initially, the belt moved slowly, & she had no difficulty picking up the candy & putting it into the box
- gradually, the belt brought candy to her more rapidly, & she had to increase her packing speed to keep up
- finally, the belt brought candy to her so fast that she could not pack it all in the boxes b/c she was working at her maximum rate
- that was Lucy’s saturation point
