molecular components of cells Flashcards
how many elements are found in living cells, and how are they distributed?
27
C N O H -> 96%
S K P Cl Ca Mg -> 4%
B F Mn Fe Co Cu Zn I -> <1%
what are the four classes of organic compounds?
carbohydrates, lipids, proteins, nucleic acids
what are the properties of water?
- most abundant (70%, 80%, 65%)
- differs among diff cell types (least in bones)
- electrically neutral
- polar
- forms hydrogen bonds
what do the properties of water mediate?
- solubilisation of molecules (by negative poles of oxygen)
- hydrolysis
- photosynthesis
- thermal regulation
- providing aqueous medium for metabolism
- lubrication function that permits diffusion of cell components
define hydration
it’s when mineral salts are dissolved in water and ionised, and each ion entity is surrounded by water molecules
what three conditions are essential for most physiological phenomena?
balance of concentration of diverse ions + acid-base equilibrium + osmotic pressure
what are some examples of physiological phenomena that adhere to the three conditions?
- membrane permeability
- cell division
- muscle contraction
- enzymatic activity
- intracellular signaling
- generation & propagation of nerve impulses
how is the activity of certain enzymes/proteins attributed to certain metal ions?
- calcium aids in the release of neurotransmitters into the synaptic cleft, and allows for muscle contraction
- iron is crucial for oxygen transport by hemoglobin and oxidation-reduction reactions catalysed by cytochromes
give examples of insoluble mineral salts. where are they found?
calcium carbonate, calcium phosphate, and silicium. they are mostly found in rigid structures like skeletons and animal shells.
define a metabolite
an intermediate or end product of metabolism
define a metabolome
a set of metabolites
are vitamins considered a fifth class? why or why not?
vitamins are not considered a fifth class since they do not form a homogenous independent class; i.e., some vitames (A, E, D) are derived from lipids, while others (C) from carbohydrates. the only common thing between them is that they are needed at low concentrations.
what percentage of dry weight do proteins make up?
proteins are the most abundant compound found in cells (they range from 55-85% of dry weight)
define a protein
proteins are unbranched amino acid polymers whose sequences are determined by genetic information carried by genes
what are the functions of a protein?
- determine cell structure and shape (ex. proteins of cytoskeleton)
- perform almost all physiological functions
- responsible for molecular identity of cells (ex. HLA, blood types)
- responsible for morphology of organisms (ex. skin colour, hair colour, size)
- all crucial physiological processes (expression of genetic information, DNA replication)
- involved in storage and transportation of:
- ions and molecules (pumps and channels in membrane)
- macromolecules (cytoskeleton and nuclear pore proteins)
- electrons (proteins in mitochondria/chloroplast)
- intercellular communication (many hormones)
- immunity (antibodies are proteins)
- progression of cell cycle and mitosis
- convert chemical energy (ATP) into mechanical energy in muscles for movement
- necessary for senses
how do we calculate the different possible variations of a polypeptide chain based on its length?
20^n, n=length in aa
what are the properties of amino acids?
- amphoteric
- composed of C, H, N, O (+sometimes S in 2 cases)
- made up of an amino group, carboxyl group, R-side chain, chiral C alpha
- only L-stereoisomers
- all soluble in water
there are 20 amino acids. how many are synthesised by our body? what about the other ones?
11 by our body, 9 supplied by our diet
what are the groups amino acids are divided into?
- hydrophobic side chains (methyl, propyl, ethyl, C6H6)
- hydrophilic uncharged side chains (OH, CO, NH2)
- polar basic positively charged side chains (NH3+)
- polar acidic negatively charged side chains (COO-)
what is the formation of peptide bonds catalysed by?
enzymes of the ribosome
what is the chemical name of a peptide bond?
amide bond -NH-CO-
explain how peptide bonds are formed
it results from a reaction between amino group of an aa (position n) and carboxylic group of the previous one (position n-1). this reaction leads to the elimination of one H2O and the formation of the peptide bond (chemically known as an amide bond -CO-NH-).
why does a polypeptide chain have two distinct poles?
since the backbone of a polypeptide chain is made up of a repetition of N-Calpha-C
what are the two termina of a polypeptide chain?
- N-terminus or amino terminus, H2N
- C-terminus or carboxy terminus, COOH
what do polypeptides owe their flexibility to?
the three dihedral / torsion angles that are formed between the planes that intersect at the covalent bonds of:
- NH and CO
- NH and Calpha
- CO and Calpha
such rotation confers flexibility which is necessary to chain folding back and adoption of precise 3-D conformations of proteins.
how is the geometrical structure of proteins analysed?
using crystals of the pure protein and by electron microscopy or x-ray diffraction
what is the primary structure of a protein stabilised by?
covalent peptide bonds between consecutive amino acids
for secondary structure of proteins, where are the side chains exposed in helices and beta-pleated sheets respectively?
- helices: outwards
- beta-pleated sheets: downwards or upwards
what are helices sustained by?
hydrogen bonds between CO and NH and between side chains
how are the side chains oriented in tertiary structure of proteins?
hydrophobic aa side chains are hidden in the core, charged ones are exposed outwards
how are active domains created?
in tertiary structure, the folding of the protein brings together distant segments that work together
what do active proteins consist of?
two or more domains that perform specific functions
what does each domain consist of?
helices and/or beta-pleated sheets grouped together
give some examples of domains
- substrate binding domain
- catalytic domain
- dimerisation/polymerisation
- DNA-binding domain
what is the tertiary structure sustained by?
- ionic bonds
- salt bridges
- hydrogen bonds
- hydrophobic interactions
- disulfide bridges
describe disulfide bridges
they are the strongest covalent bond. they involve two cysteine molecules forming a di-sulfide bridge through sulfhydryl side chains (SH)
define protein denaturation
the unfolding and loss of tertiary and secondary structures.
what causes protein denaturation?
- physical agents (low pH, high temperatures)
- chemical agents (detergents, urea)
is it reversible?
usually it is irreversible, unless it is mild (urea)
what are induced reversible confirmational changes?
many proteins have allosteric binding sites for specific ligands such as ions, aa, and monosaccharides. the binding of a ligand to the allosteric site temporarily alters the 3-D structure of the protein, temporarily inactivating it.
how do we classify proteins?
- solubility in water
- heteroproteins
- function
- 3D structure
give examples of soluble and insoluble proteins
-soluble: albumin, globulin, histones
- insoluble: collagen, keratin
define heteroproteins
holoproteins/apoproteins (purely aa) + prosthetic group (non aa)
give examples of heteroproteins
- lipoproteins
- nucleoproteins
- glycoproteins
- hemoproteins
what are the six different functions of specific proteins?
- structural
- regulatory
- catalytic
- defence
- transporter
- contraction
how are proteins classified based on 3-D structure? give examples
- fibrous (structural role, mechanically strong, insoluble): keratin, collagen
- globular (spherical, compact, soluble): albumin, globulins, histones
