Lecture 2- Biomolecules Flashcards
what are the properties of ions and molecules that are essential for life? (4)
carbohydrates
nucleotides, nucleosides and nucleic acids
lipids
proteins
what is an organic molecule?
a molecule that contains carbon
what is a biomolecule?
organic molecule that is commonly associated with life (carbohydrates, nucleic acids, lipids, proteins)
what is the general formula for carbohydrates?
CnH2n0n
what are examples of carbohydrates?
glucose C6H12O6
ribose C5H10O5
cellulose
chitin
what are 3 characteristics of carbohydrates?
most are hydrophilic
very abundant in nature
used for structure and energy
what biomolecule can be added to a molecule to modify it?
carbohydrates
how many carbons do glucose have?
6
how many carbons does ribose have?
5
how does the different number of carbons alter the molecule?
the number of structural monomers increases rapidly with the increase in carbons
are carbohydrates monomers or polymers?
Carbohydrates are a biological polymer made of monomers called monosaccharides
why are monosaccharides considered to be simple sugars?
because they are the building blocks for large complex carbohydrates or sugars
why are we interested in nucleotides/ nucleosides?
because of their involvement in energy metabolism and signaling
what does a nucleotide contain?
one or more phosphate groups
5- carbon sugar
carbon- nitrogen ring structure (nitrogenous base/ nucleobase)
what is DNA made up of?
nitrogenous bases
what are the 5 nitrogenous bases?
adenine
cytosine
guanine
thymine
uracil
how is the nitrogenous base determined?
based on the structure
what are examples of nucleotides?
adenosine
adenosine triphosphate
cyclic AMP
guanosine triphosphate
cyclic GMP
what is adenosine?
a neurotransmitter
what is adenosine triphosphate?
(ATP) basic molecule of energy storage in most organisms
what is the function of cyclic AMP and cyclic GMP?
important signaling molecule within cells
what is the function of guanosine triphosphate?
energy source in many physiological chemical reactions
are lipids hydrophilic or hydrophobic?
hydrophobic molecules
what do lipids contain?
mostly carbon and hydrogen
few oxygen
nitrogen
phosphorus
what are examples of lipids? (5)
fatty acids
glycerides
phospholipids and sphingolipids
steroids
oxylipins
what are the 3 roles of lipids?
structure of cells
energy source
communication (within cells and between cells)
what is meant by lipids having a role in structure of cells?
lipids are in cell membrane (phospholipids) and membrane bound organelles
why is it good that lipids are hydrophobic?
waterproof and thus keeps insides in and outsides out
what do fatty acids consist of?
long unbranched hydrocarbon chain (8-28 carbons)
has carboxyl functional group (ACIDIC)
what is the difference between saturated fatty acids and unsaturated fatty acids?
saturated fatty acids have no double bonds and form a straight chain
unsaturated fatty acids have double bonds and have a kink
what does it mean if a fatty acid has more double bonds
its unsaturated and is less likely to be a solid at room temperature (it will remain an oil)
what does a glyceride consist of?
fatty acid + glycerol (3 carbons)
when a fatty acid and a glycerol make glyceride what happens?
looses a water (H2O) molecule
what is the difference between a monoglyceride, diglyceride and triglyceride?
monoglyceride: glycerol + 1 fatty acid
diglyceride: glycerol + 2 fatty acids
triglyceride: glycerol + 3 fatty acids
what does a phospholipid consist of?
diglyceride (glycerol + 2 fatty acids)
phosphate
variable “R” group
is the variable “R” group in a phospholipid polar or non-polar?
polar group
phospholipids are amphipathic, what does that mean?
hydrophilic and hydrophobic
hydrophilic head
hydrophobic tail
is hydrophilic polar or nonpolar?
polar
is hydrophobic polar or nonpolar?
nonpolar
what are the 3 arrangements of phospholipids?
phospholipid bilayer
micelles
aqueous center
(lecture 2, slide 22)
what is the difference between a phospholipid and a sphingolipid?
sphingolipids have sphingosine
phospholipids have glycerol
(other than that this is the only difference)
what is the difference between a phospholipid and a glycolipid/ glycophospholipid?
glycolipids have a carbohydrate attached to the “R” group
phospholipids dont have a carbohydrate
what does a glycosphingolipid consist of?
fatty acid
sphingosine
carbohydrate
what is the basic structure of steroids?
3 six- carbon rings
1 five- carbon ring
in steroids what do different “R” groups cause?
different function
what do steroids do? what do they play a role in?
communication and cell structure
what are oxylipins?
oxygenated metabolites of fatty acids
where do eicosanoids originate from?
oxylipins (eicosanoids are a subset of oxylipins)
what are eicosanoids?
polyunsaturated fatty acids
have 20 carbon atoms!
where are many oxylipins derived from?
fatty acid
arachidonic acid (type of fatty acid)
other unsaturated fatty acids
are oxylipins stored?
not generally, but they are synthesized as needed
what is the main function of oxylipins?
communication within cells and between cells
what type of molecules are proteins?
macromolecules
what are macromolecules?
Macromolecules are made up of single units known as monomers that are joined by covalent bonds to form larger polymers
what are proteins made up of?
linear chains of amino acids
how many amino acids are there?
20
how many amino acids are essential?
9
how do we gain these essential amino acids?
consume them
why are 11 amino acids not essential?
we can synthesize them
are amino acids diverse? why/
yes, because theres a lot of them and because some are acidic, basic, polar, non-polar, bulky or small
what is a short chain of amino acids called?
a peptide
what is a long chain of amino acids called?
proteins
proteins have complex structures, what are the 4 structures?
primary
secondary
tertiary
quaternary
how is the structure of the amino acid determined?
by the sequence of amino acids that make them up (sequence is encoded in the genome)
what is a primary structure?
sequence of amino acids
what are two forms of the secondary structure?
alpha helix
beta pleated sheets
proteins are the tools of cells and are very versatile, in a given mammalian cell how many different proteins might be expressed?
10,000 - 15,000
what is the difference between fibrous proteins and globular proteins?
fibrous proteins are insoluble
globular proteins are soluble
there are 7 categories of soluble proteins, what are they?
enzymes
membrane transporters
signal molecules
receptors
binding proteins
regulatory proteins
immunoglobulins
function of enzymes
help speed up metabolism, or the chemical reactions in our bodies
function of membrane transporters
catalyzes the translocation of solutes
function of signal molecules
transmit information between cells
function of receptors
detect the signals and then send them to the brain in the form of electrical signals
function of binding proteins
regulate many cellular processes
function of regulatory proteins
regulates other biological processes
function of immunoglobulins
protecting against bacteria, viruses, and fungi (recognize parts inside our bodies that arent supposed to be there
in order for a protein to do something, what does it need to interact with?
other proteins, molecules or ions by binding or interacting
what is a molecule that binds to a protein binding site called?
ligand
what is an endogenous ligand?
something natural in your body, example is hormone or neurotransmitter
what would non- endogenous be?
a drug or toxin
a protein binds a ligand with affinity, what would high and weak affinity mean?
high: binds strongly
weak: weak binding
what would the agonist (good guy) be in light of a ligand?
a ligand that binds to a protein binding site and alters the state of the protein
ex. hormone or drug
what would an antagonist (bad guy) be in light of a ligand?
a ligand that reduces the action of an agonist
also called inhibitors or blockers
agonists and antagonists may be competitive, what does that mean?
acts to block the agonist (good) at its normal binding site
agonists and antagonists may be allosteric, what does that mean?
acts to block a competitive agonist by binding to the protein away from the binding site and inactivate the binding site
what 5 factors alter protein binding?
isoforms
cofactors
activation/ protein processing
physical factors (pH, temperature)
modulation
what are examples of covalent modification or modulation?
phosphorylation and dephosphorylation
addition of lipid or carbohydrate
agonist/ antagonist
what is phosphorylation?
enzyme transfers (adds) a phosphate onto one of the amino acid side chains of a protein
how was glycogen metabolism regulated?
by the addition or removal of a phosphate
how many proteins in a mammalian cell are covalently bound to phosphate?
one third
what charge do phosphates have?
negative
what do phosphates being negatively charged have to do with their addition to a protein?
the negative phosphate will change the characteristics of the protein (causes the protein to change how it is structured)
how can the transfer of phosphates onto proteins be catalyzed?
by a variety of enzymes called protein kinases
what enzymes are responsible for the reverse reaction in which phosphates are removed from a protein?
protein phosphatases
what are the 3 advantages of phosphorylation/ dephosphorylation of a protein as a control mechanism/
it is rapid
does not require new proteins to be made or degraded
easily reversible
what does the reception of a signal on the surface of a cell result in?
the activation of kinases and phosphatases
does phosphorylation cause activation or inhibition?
can cause both
who won the nobel prize for discovering phosphorylation and dephosphorylation? (2)
edwin krebs and edmond fisher 1992
