Proteins Flashcards
what elements make up proteins?
carbon, hydrogen, oxygen, nitrogen
maybe sulfur
what are proteins? (type of molecule, type and number of types of monomer)
polymers
made up of a set of 20 different amino acids, as encoded by our DNA
what is the difference between a polypeptide and a protein?
polypeptides are linear sequences of amino acids covalently bonded by peptide bonds, proteins are one or more polypeptides in a specific 3D conformation
what are the features of fibrous proteins?
polypeptide chains are elongated and wound around each other in a rope-like structure
repeated amino acid sequence, small number of specific amino acids used
different samples of the same fibrous protein may vary slightly in length or amino acid sequence
stable structures due to numerous intra/intermolecular hydrogen and covalent bonds
generally insoluble in water
structural functions
what are the features of globular proteins?
polypeptide chains are folded, bent, twisted to form compact and spheroidal structure
each chain has specific and non-repetitive amino acid sequence, wide variety of amino acids
amino acid sequence and length never varies between two samples of same protein
relatively unstable structures due to numerous intra/intermolecular non-covalent bonds (eg. hydrogen bonds, ionic bonds, hydrophobic interactions)
more soluble in water than fibrous
metabolic functions
give the functions and examples of fibrous and globular proteins
fibrous: structural (collagen, myosin, fibroin in silk, actin, keratin, elastin)
globular: metabolic (enzymes, hormones, antibodies, haemoglobin)
what type of proteins are there as classified by functions?
enzymatic storage (casein) hormonal (insulin) contractile and motor (actin and myosin) defensive (antibodies) transport (haemoglobin) receptor (cell-to-cell signalling) structural (keratin)
what are the types of simple proteins?
albumins (egg white)
globulins (antibodies, fibrinogen)
histones (associated with nucleic acids in nucleoproteins of cell, DNA wraps around it to form chromosomes)
what are conjugated proteins and cofactors and prosthetic groups?
proteins combined with a non-protein component, known as a cofactor (aids protein function, can be organic or inorganic)
if an organic cofactor is tightly bound to a protein, it is a prosthetic group
what are examples of conjugated proteins?
glycoproteins (+ carbohydrate) in blood plasma, cell membrane, mucin (saliva component)
chromoprotein (+ pigment) in haemoglobin’s iron-containing haem, plant’s phytochrome, respiratory’s cytochrome
lipoprotein (+ lipid) in membrane structure and transported in blood
flavoprotein (+ flavin adenine dinucleotide) important in electron transport chain respiration
nucleoprotein (+ nucleic acid) in viruses, chromosomes, ribosomes
how many amino acids are there in a cell? how many are fundamental, and what are essential / non-essential / rare amino acids?
60 in cell, 20 fundamental
essential aa obtained directly from diet
non-essential aa can be synthesised in the body
rare aa are derivatives made from fundamental aa, not coded for by DNA (eg. hydroxyproline in collagen from proline, hydroxylysine in collagen from lysine, modified after incorporation into pp chain)
describe the basic structure of an amino acid
central carbon covalently bonded to: a basic amine group (NH2) an acidic carboxyl group (COOH) hydrogen atom variable R group / side chain (that determines which aa it is)
what are the properties of amino acids?
colourless and crystalline solids with relatively high melting points
insoluble in organic solvents but soluble in water
what are the three features of amino acids?
- ability to form zwitterions (when dissolved in water) by the loss of H+ from COOH, making COO-, to the NH2 amine group, making NH3+. electrically neutral, dipolar ion formed
- ability to act as a buffer. zwitterions are amphoteric and can resist changes in pH
- unique properties of the R group
what are the three types of R groups an amino acid can have, and what are their respective properties?
non-polar: hydrophobic, hydrocarbon in nature (many C-C and C-H), unreactive
polar: hydrophilic, no net charge
charged: hydrophilic, acidic with net negative charge, basic with net positive charge
how is a peptide bond formed?
a CN bond, formed between the amine group (-NH2) of one aa and the carboxyl group (-COOH) of another, in a condensation / dehydration reaction (with the elimination of one water molecule)
what are the ends of a polypeptide chain known as?
free amine group (beginning): N terminus
free carboxyl group (ending): C terminus
R groups of each aa project from the backbone of the pp
discuss the properties of polypeptides (buffering ability and diversity)
the presence of free amine (N terminus) and carboxyl (C terminus) groups, but not as great as the aa’s ability
R groups of some amino acids can also ionise, additional buffering capacity
variations in length and aa sequence of pp contributes to diversity in shape and biological functions of proteins
describe the protein biuret test (principle, method, observation)
principle: detects peptide bonds and thus all proteins (not amino acids), nitrogen atoms in peptide bonds complexes with Cu2+ ions to give purple colouration
method: add an equal volume of 5% KOH solution to test solution, add 1% copper sulfate solution dropwise, shake to mix
observation: a purple/violet colour indicates presence of proteins, but blue is the absence (colour of CuSO4 solution)
what are the four hierarchical levels of organisation for proteins (for their functioning)?
primary, secondary, tertiary, quaternary (specific 3D conformation)
what is the definition and influence of the primary structure of a protein?
the unique number and linear sequence of amino acids that constitute the polypeptide chain
the three other higher levels of protein organisation are direct consequences of the primary structure, since the aa R groups and its size, charge, polarity, hydrophobicity affects the ultimate specific 3D conformation
what is the definition of the secondary structure of a protein, what is it caused by, and what are the two most common types?
the regular coiling and folding of regions of the pp chains to give repeated patterns caused by hydrogen bonds at regular intervals along the pp backbone
alpha-helix and beta-pleated sheet
in proteins, where are the hydrogen bonds formed?
between the N-H group of one amino acid and the C=O group of another amino acid (not involving R groups)
individually weak, collectively serve to stabilise the structure
what is an alpha-helix, its type of bonding and characteristics?
extended spiral spring, stabilised by intrachain hydrogen bonds between O atom of C=O group of the nth aa residue and H atom of the N-H group of (n + 4)th aa
hydrogen bonds are parallel to the main axis of helix, all C=O and N-H groups can participate in hydrogen bonding for maximum stability
one complete turn every 3.6 amino acids
R groups of aa residues project outside the helix, perpendicular to main axis, preventing steric interference with pp backbone and eo
R group’s chemical properties influence alpha-helix interactions
proline and hydroxyproline insert a kink or bulky R groups disrupt formation
what is a beta-pleated sheet, its type of bonding, characteristics, and two varieties?
extended zigzag, sheet-like conformation
stabilised by hydrogen bonds between O of C=O and H of N-H within same pp chain (intrachain) or neighbouring pp chains (interchain)
neighbouring hydrogen-bonded pp segments can run in the same or opposite N-terminus to C-terminus directions
how do amino acids with bulky R groups interfere with protein structure?
steric hindrance, interferes with formation of beta-pleated sheet (so beta-pleated sheets usually have aa with small R groups)
what is the definition of tertiary structure in proteins, and its bonding?
tertiary structure refers to the further bending, twisting, and folding of pp chain with secondary structures to give an overall specific 3D conformation
four types of R group interactions formed between aa residues some distance apart on same pp chain (intrachain)
non-covalent (relatively weak): ionic bonds, hydrogen bonds, hydrophobic interactions
covalent (strong): disulfide bonds
tertiary is the final structure for some proteins (only made of one pp chain)
describe a disulfide bond / linkage (R group interaction)
covalent bond, formed by oxidation of sulfhydryl groups (-SH) of any two cysteine residues in same or diff (interchain disulfide bridge) pp chain
breakage via reduction reaction
what are hydrogen bonds and ionic bonds in protein structure?
both relatively weak
formed between electropositive H atom that is attached to N or O, and another electronegative atom (N or O) within the pp chain
(no F bc it is not present in proteins)
ionic bonds between oppositely charged R groups (eg. NH3+ and COO-), may be broken by changes in pH, leads to denaturation
what are hydrophobic interactions in protein structure?
the pp folds so as to shield hydrophobic R groups from the aqueous environment, interactions between hydrophobic R groups of aa residues
what are protein domains?
pp with >200 residues fold into two or more globular clusters known as domains
each domain is a distinct structural unit, each with its own specific function, connected by only one or two pp segments, but there may be extensive interactions between domains
define quaternary structure in protein structure and the bonding involved
it is the overall protein structure that results from the association of two or more pp chains to form a functional protein (eg. haemoglobin and collagen), multimeric proteins
each individual pp has tertiary structure, is a protein subunit
bonds: ionic, hydrogen, hydrophobic interactions, disulfide bonds between R groups of different protein subunits
what is the function of haemoglobin, and its structure?
it is an oxygen-binding protein, transports oxygen, in erythrocytes (red blood cells)
globular multimeric protein with quaternary structure (4 pp chains, 2 alpha and 2 beta), tetramer made up of two identical dimers
describe the structure of haemoglobin
two types of subunits: alpha chain with 141 aa, beta chain with 146 aa
each pp chain has eight alpha-helices (named letters A to H, starting from N-terminus with amine group)
each pp chain is folded such that hydrophilic residues at surface, hydrophobic buried, making haemoglobin soluble and good transport protein in blood
folding of pp chain forms a hydrophobic cleft (lined with hydrophobic aa residues) to allow binding of haem prosthetic group, 4 haem prosthetic groups = 4 oxygen molecules per haemoglobin
quaternary: hydrophobic interactions, ionic and hydrogen bonds in globular molecule held by multiple non-covalent interactions
describe the structure of haemoglobin’s haem prosthetic groups
Fe2+ held in a porphyrin ring
iron ion binds one of the oxygen atoms in an oxygen molecule reversibly
explain haemoglobin’s cooperative binding as an allosteric protein
as the first haem group binds 1 oxygen molecule, the F helix (third closest to C terminus in that pp chain) is pulled closer to haem group, creating strain on other subunits, revealing other previously obscured groups, changing their 3D conformation slightly for remaining groups to bind oxygen more readily (increasing subunits’ affinities for oxygen)
explain the sigmoidal shape of the haemoglobin’s oxygen-dissociation curve and its function
oxygen is loaded onto haemoglobin in the lungs where partial pressure is high (higher oxygen concentration), unloaded in rest of the body where partial pressure is low (lower oxygen concentration)
LOWER AFFINITY BINDING (SIGMOIDAL) to oxygen than myoglobin (one pp, hyperbolic curve), less saturated with oxygen at same partial pressure)
efficient oxygen carrier bc of subunit cooperativity
what is the function and structure of the collagen protein?
strong, insoluble fibres, great tensile strength, structural support
primary: amino acid sequence is repeating tripeptide sequence of glycine and X (often proline) and Y (often hydroxyproline or hydroxylysine, both rare aa)
each of the three pp chains (called an alpha-chain) around 1000 aa residues long
secondary: each pp has left-handed helical conformation, 3 residues per turn known as collagen helix, regular repeated structure indicative of fibrous protein
each pp chain is an alpha-chain
quaternary: three parallel alpha-chains in right-handed, rope-like twist (right-handed triple helix) known as tropocollagen, well-packed and rigid for tensile strength
describe the structure of tropocollagen
every third residue passes through centre of helix, must be glycine with the smallest R group, so three alpha-chains can pack tightly for high tensile strength
proline in X position with ring structure stabilises helix, and X and Y are outside the helix
extensive network of hydrogen bonds and covalent cross-links between amine end and carboxyl end to make a fibril (rigid and brittle)
staggered manner, stabilised by hydrophobic interactions for greater strength)
what is denaturation of proteins, and what bonds does it disrupt?
the loss of the specific 3D conformation primary structure of the protein remains unaffected bonds disrupted (secondary, tertiary, quaternary): R group interactions like disulfide, ionic, hydrogen, hydrophobic interactions and hydrogen bonds
how do different denaturants cause denaturation?
heat: increases atom vibrations, disrupting bonds
pH changes: changes charges in acidic and basic R groups, disruption of ionic and hydrogen bonds
organic solvents: disrupt hydrophobic interactions that make up stable core of globular proteins, turns inside out so hydrophobic and hydrophilic regions change places
urea detergents: chemicals disrupt ionic and hydrogen bonds
what types of interactions hold polypeptide chains together in a (quaternary structure) protein?
R-group interactions:
- hydrogen bonds
- ionic bonds
- hydrophobic interactions
- disulfide bonds
