Unit1:Biomolecules Flashcards
> 90% of the body’s mass consists of:
a. Oxygen
b. Carbon
c. Hydrogen
Cations
(lost an electron, positively charged)
: Sodium (Na+);
Potassium (K+); Calcium (Ca2+); Magnesium (Mg2+); Hydrogen (H+
Anions
(gained an electron, negatively charged): Chloride (Cl-);bicarbonate (HCO3-); Phosphate (PO42-), Sulfate (SO42-)
List Other major elements:
Nitrogen (N); Phosphorus (P); Sulfur (S)
list minor elements
: Iron (Fe); Iodine (I); Copper (Cu); Zinc (Zn), etc.
molecules
Atoms join together to form…..
Covalent Bonds
atoms share electrons
Ø Strong bonds that require energy to make or break
Ø Can form single, double and triple bonds depending on how many
electrons are shared.
- non polar, polar
Non-Polar Covalent Molecules
shared electrons are distributed evenly amongst
atoms, leading to all regions of the molecule having a neutral charge
are not very soluble in water (i.e. are hydrophobic not hydrophilic).
Ø E.g. O2, CO2, fatty acids, cholesterol (or any molecule composed mostly of
carbon and hydrogen atoms).
Polar Covalent Molecules
shared electrons are distributed unevenly (spend more time around a particular atom or part of the molecule)
Result: one region of the molecule has a partial negative charge (d-) and another region has a partial positive charge (d+).
Ø Molecules with polar covalent bonds are
soluble in water (i.e. are hydrophilic)
Ø E.g. water (H2O), glucose (C6H12O6)
Non-Covalent bonds
facilitate reversible reactions
- ionic
-VDWS
- h bonds
Ionic Bonds
atom to atom transfer of electron(s).
Ø The most polar bond (making them very soluble in water, i.e. hydrophilic)
Ø Transfer of electrons forms anions & cations.
Ø The two oppositely charged ions are attracted to one another (electrostatic attraction - like magnets, opposite charges attract and like charges repel).
Ø E.g. NaCl
Hydrogen Bonds
weak bond between hydrogen atom
and nearby oxygen, nitrogen or fluorine atom.
Ø E.g. attractive forces between individual water
molecules leading to surface tension.
Van der Waals Forces
– weak bond involving attraction
between electrons of one atom and the nucleus
(protons) of another atom.
Inorganic Molecules
usually lack carbon atoms
Ø E.g. water (H2O), salt (NaCl), hydrochloric acid (HCl)
List the exceptions of organic molecules
Ø There are some exceptions. The following are
inorganic molecules that contain carbon: carbonic
acid (H2CO3); Bicarbonate (HCO3), Carbon dioxide
(CO2), Carbon monoxide (CO).
Organic Molecules
molecules that contains
covalently bonded carbon atoms (often combined with H, O, N, P, or S). Includes all of the biomolecules
List the biomolecules
a. Carbohydrates
b. Lipids
c. Nucleic acids
d. Proteins
Carbohydrates
a. Consist of C, H, and O
b. General formula of CnH2nOn
Ø E.g.1: glucose (n=6); C6H12O6
Ø E.g.2: ribose found in RNA (n=5); C5H10O5
Ø Some exceptions: E.g.3: deoxyribose found in DNA = C5H10O
List some of the properties of carbs
i. Most are polar and therefore hydrophilic (soluble in water)
ii. Most abundant biomolecule in nature. Found in both plants
(cellulose & starch) and animals (chitin & glycogen)
Monomer
basic unit of structure
monosaccharides
1 sugar
- monomers of carbs
(glucose, fructose, galactose, ribose, deoxyribose)
Polymers
(formed by joining monomers together
disaccharides
are polymers
sucrose, maltose, lactose
polysaccharides
starch & glycogen)
What two monosaccharides form sucrose (table sugar)?
fructose and glc
What are some of the functions of carbs?
i. Energy for cells
Ø Glucose metabolism forms ATP (adenosinetriphosphate)
ii. Structural component of other biomolecules (DNA & RNA)
Ø E.g.1: DNA contains deoxyribose
Ø E.g.2: RNA contains ribose
iii. Structural component of cells – e.g. can be bound to lipids and proteins to form glycolipids and glycoproteins which have important roles in the structure and function of cell membranes.
Lipids
Consist of C, H, and O, but in a different ratio than carbohydrates (less oxygen); some have N and P
List some of the properties of lipids
Hydrophobic (insoluble in water)
list the different groups of lipids
- FA
- glycerides
- phospholipids
-sphingolipids - steroids
- eicosanoids
Fatty acids
Ø Long hydrocarbon chains with 8-28.carbon
Ø Has a carboxyl (-COOH) functional group (= acidic)
- can be saturated or unsaturated
Saturated
no double bonds between carbon atoms so forms a straight chain
Solid at room temperature.
E.g. palmitic acid (palm oil, butter, animal fats); stearic acid (butter, chocolate, lard); lauric acid (coconut oil).
Unsaturated
has double bonds between carbon atoms
monounsaturated
One double bond
e.g. oleic acid (most common in nature, part of triglycerides and phospholipids that make cell membranes; olive oil).
polyunsaturated.
Two or more double bonds
e.g. linoleic acid (found in canola oil, sunflower oil, nuts, seeds); arachidonic acid
The more double bonds, the less likely the fat is to be soluble at room temp
Glycerides
Formed from fatty acids and glycerol via dehydration synthesis (glycerol gives up the hydrogen atoms from its hydroxyl group, which combine with the -OH of the fatty acid carboxyl group to form water)
monoglyceride
Ø Glycerol + 1 fatty acid
diglyceride
Glycerol + 2 fatty acids
triglyceride
Glycerol + 3 fatty acids
are an important form of stored energy in
the body (adipose/fat tissue).
Phospholipids
Ø Derived from glycerides. Essentially a diglyceride to which a phosphate group (PO 4) and a variable R
group have been added.
Ø Glycerol + 2 fatty acids + PO 4 + variable R group
Ø R group
– Allows the formation of of different types
of phospholipids.
e.g
-group = serine, forms
phosphatidylserine, if R
-group = choline, forms
phosphatidylcholine.
List some of the properties of phospholipids
Are amphipathic molecules – have both
hydrophilic and hydrophobic regions. Polar heads
(phosphate + R-group) are hydrophilic, and non-
polar fatty acid tails are hydrophobic.
Ø Phospholipids can arrange themselves into
bilayers, micelles and liposomes. Polar heads face
the ECF or ICF, non-polar tails towards each other
Sphingolipids
Ø Modified phospholipids.
Ø Sphingolipids incorporate a sphingosine molecule
instead of glycerol and have only 1 fatty acid.
Ø form lipid rafts on cell membranes that may help
to protect the cell surface.
Glycophospholipids
a phospholipid with a
carbohydrate group attached (usually a
polysaccharide)
Glycosphingolipids
a sphingolipid with a
carbohydrate group attached
Steroids
Basic structure consists of three 6-carbon rings plus
one 5 carbon ring (17 carbons total).
Ø Many derived from cholesterol.
Ø Different functional groups (R-groups) give steroids
their different functions.
Ø Play roles in communication (hormones) and cell
structure
Ø E.g.1: Cholesterol (stabilizes cell membranes)
Ø E.g.2: Cortisol (stress hormone)
Ø E.g.3: Testosterone & Estrogen (reproductive
hormones)
Eicosanoids
Ø Polyunsaturated fatty acids with a length of 20 carbons
(“eicos-” = Greek for 20) attached to a complete or partial carbon ring. Contains oxygen atoms.
Ø Many derived from arachidonic acid or other unsaturated fatty acids.
Ø Synthesized as needed (not stored)
Ø Unlike most lipids, Eicosanoids are often able to cross cell membranes.
Ø They Function in communication within and between cells.
Ø E.g.1: Prostaglandins (help mediate inflammation and pain
response during injury/infection among other roles)
Ø E.g.2: thromboxane (important for blood clotting –
specifically platelet aggregation
List the general functions of lipids
i. Cell structure – important components of cell membranes and organelles.
ii. Energy source – e.g. triglycerides in adipose tissue of the human body is a large store of energy.
iii. Communication (within and between cells
Describe the general structure of nucleotides
i. a 5-carbon sugar (ribose, deoxyribose)
ii. a phosphate (PO4) group
iii. A nitrogenous base (carbon-nitrogen ring structure)
Ø Nitrogenous bases are either purines (2 rings) or
pyrimidines (single ring).
Ø Purines = adenine + guanine
Ø Pyrimidines = Cytosine, Thymine, Uraci
Nucleosides
re nucleotides minus the phosphate
group.
Proteins
Macromolecules that consist of C, H, O, N (and sometimes S (polymers of aa’s )
amino acids
monomers
basic units of protein structure
Describe the structure of proteins
central carbon atom to which is attached:
Ø Carboxyl group (-COOH)
Ø Amino group (-NH2)
Ø R-group (functional group – determines the structure of the
amino acid
How many aa’s are there?
Ø 9 are essential and we need to consume them in the foods we eat
(e.g. leucine, tryptophan, valine, etc.)
Ø 11 are non-essential, the body synthesizes them (e.g. tyrosine,
glycine, etc.
Peptide bonds
joins aa’s together thru a dehydration reaction
Peptides
short chains of amino acids (oligopeptides = 2-9 amino
acids; polypeptides = 10-100 amino acids)
Proteins
long chains of amino acids (>100 aa
Primary
the sequence of amino acids in the chain
Secondary
hydrogen bonds between adjacent amino acid chains
or loops within the same chain create b-sheets and a-helices (helix
= singular) respectively
Tertiary
a-helices and b-sheets combine to form globular or
fibrous proteins. Globular proteins are usually soluble, while fibrous proteins are not.
Quaternary
multiple tertiary structures combine to form the
finished protein (e.g. hemoglobin has 4 globular protein subunits)
Protein Interactions
n order for a protein to do something, it must interact with or bind to other
proteins, molecules or ions
binding site
where the ligand binds
Ligand
also known as substrate
- Molecules that bind to protein binding sites.
endogenous ligand
ligands naturally present in
body (e.g. hormones and neurotransmitters)
non- endogenous ligand
enter the body from the external environment and include
drugs/toxins
Agonist
a ligand that binds to a protein binding site and alters the state of the protein resulting in a biological response.
E.g. a hormone, neurotransmitter, or drug
Antagonist
a ligand that reduces the action of an agonist (i.e. binds to the protein but causes no biological responses)
Also called inhibitors, blockers
List the types of antagonist
Ø Antagonists may be competitive: bind to the same binding site as the agonist.
Ø Antagonists may be allosteric: bind to to a different site than the agonist, but this interaction inactivates the binding site.
Affinity
– refers to strength of the binding between the protein and the ligand.
Ø High affinity = protein binds the ligand strongly
Ø Low affinity = protein binds the ligand weakly
List factors that affect protein binding or alter the rate of
protein binding/activity
isoforms – proteins whose structure and functions are
similar, but that have different affinities for the same
ligand.
E.g. fetal hemoglobin has a higher affinity for
oxygen than adult hemoglobin
Activation/protein processing
protein must be
converted into its active form before any binding/activity
can take place. Proteolytic activation
Ø E.g. Pepsinogen in the stomach undergoes proteolytic
activation by HCl, which converts it into its active form pepsin
(pepsin is an enzyme involved in protein digestion)
Cofactors
ions (e.g. Ca++) or molecules that must
attach to the protein in order for the binding site to
become active. If no cofactor is present, binding/activity
stops.
Modulation
Changes ability of protein to bind to the ligand or
changes the response of the protein to the binding of
the ligand
Physical factors, like pH and temperature
Irreversible inhibition
antagonist binds to
binding site and cannot be removed (even if the
concentration of agonist increases)
Competitive inhibition
antagonist binds
reversibly to binding site. Level of activity/binding
of agonist depends on relative concentrations of
agonist and antagonist. More antagonist = more
inhibition, less activity. More agonist = less
inhibition, more activit
Allosteric modulation
modulator binds to site
other than agonist binding site. May cause
inhibition or activation of agonist binding site.
Covalent modulation
atoms or functional
groups (like phosphates) bond covalently to the
protein altering its structure and changing its
activity (increase or decrease)
a) Phosphorylation and Dephosphorylation –
addition or removal of a phosphate group
changes the protein’s activity. Common action
of protein kinases.
b) Addition of a lipid or carbohydrate
Saturation
Protein/enzyme activity depends on the amount of ligand present and
the amount of protein present.
Ø When concentration of ligand is higher than available protein binding
sites can handle, binding sites are completely filled and saturation is
reached.
Ø Enzymes, membrane transporters, receptors, binding proteins, etc can
all reach a saturation point (the point where addition of more ligand
will not make any difference in activity because all binding sites on the
proteins involved in the process are occupied).
Figure 2.13
solute
any substance dissolved in solvent
solvent
liquid into which solute dissolves
Solubility
Ability of a solute to dissolve a solve
Acids
Ø dissociate in water releasing H+
ØHigher [H+] = lower pH
ØE.g. hydrochloric acid (as produced by the stomach) has
a pH of 2
bases
Ø substances that bind free H+ ions in solution and so
decrese [H+] in solution..
Ø Lower [H+] = higher pH
pH scale
measure of the free H+ ion concentration in a solution.
Ø pH = -log [H+] or pH = log (1/[H+])
ØpH >7 = alkaline (basic); pH < 7 = acidic
Ø Log scale, so every time the pH sacel goes up or down
by 1, this represents a 10X increase or decrease in the
[H+].
