Proteins

Question 1

what elements make up proteins?

Answer 1

carbon, hydrogen, oxygen, nitrogen

maybe sulfur

Question 2

what are proteins? (type of molecule, type and number of types of monomer)

Answer 2

polymers

made up of a set of 20 different amino acids, as encoded by our DNA

Question 3

what is the difference between a polypeptide and a protein?

Answer 3

polypeptides are linear sequences of amino acids covalently bonded by peptide bonds, proteins are one or more polypeptides in a specific 3D conformation

Question 4

what are the features of fibrous proteins?

Answer 4

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

Question 5

what are the features of globular proteins?

Answer 5

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

Question 6

give the functions and examples of fibrous and globular proteins

Answer 6

fibrous: structural (collagen, myosin, fibroin in silk, actin, keratin, elastin)
globular: metabolic (enzymes, hormones, antibodies, haemoglobin)

Question 7

what type of proteins are there as classified by functions?

Answer 7

enzymatic
storage (casein)
hormonal (insulin)
contractile and motor (actin and myosin)
defensive (antibodies)
transport (haemoglobin)
receptor (cell-to-cell signalling)
structural (keratin)

Question 8

what are the types of simple proteins?

Answer 8

albumins (egg white)
globulins (antibodies, fibrinogen)
histones (associated with nucleic acids in nucleoproteins of cell, DNA wraps around it to form chromosomes)

Question 9

what are conjugated proteins and cofactors and prosthetic groups?

Answer 9

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

Question 10

what are examples of conjugated proteins?

Answer 10

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

Question 11

how many amino acids are there in a cell? how many are fundamental, and what are essential / non-essential / rare amino acids?

Answer 11

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)

Question 12

describe the basic structure of an amino acid

Answer 12

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)

Question 13

what are the properties of amino acids?

Answer 13

colourless and crystalline solids with relatively high melting points
insoluble in organic solvents but soluble in water

Question 14

what are the three features of amino acids?

Answer 14

1. 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
2. ability to act as a buffer. zwitterions are amphoteric and can resist changes in pH
3. unique properties of the R group

Question 15

what are the three types of R groups an amino acid can have, and what are their respective properties?

Answer 15

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

Question 16

how is a peptide bond formed?

Answer 16

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)

Question 17

what are the ends of a polypeptide chain known as?

Answer 17

free amine group (beginning): N terminus
free carboxyl group (ending): C terminus
R groups of each aa project from the backbone of the pp

Question 18

discuss the properties of polypeptides (buffering ability and diversity)

Answer 18

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

Question 19

describe the protein biuret test (principle, method, observation)

Answer 19

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)

Question 20

what are the four hierarchical levels of organisation for proteins (for their functioning)?

Answer 20

primary, secondary, tertiary, quaternary (specific 3D conformation)

Question 21

what is the definition and influence of the primary structure of a protein?

Answer 21

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

Question 22

what is the definition of the secondary structure of a protein, what is it caused by, and what are the two most common types?

Answer 22

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

Question 23

in proteins, where are the hydrogen bonds formed?

Answer 23

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

Question 24

what is an alpha-helix, its type of bonding and characteristics?

Answer 24

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

Question 25

what is a beta-pleated sheet, its type of bonding, characteristics, and two varieties?

Answer 25

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

Question 26

how do amino acids with bulky R groups interfere with protein structure?

Answer 26

steric hindrance, interferes with formation of beta-pleated sheet (so beta-pleated sheets usually have aa with small R groups)

Question 27

what is the definition of tertiary structure in proteins, and its bonding?

Answer 27

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)

Question 28

describe a disulfide bond / linkage (R group interaction)

Answer 28

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

Question 29

what are hydrogen bonds and ionic bonds in protein structure?

Answer 29

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

Question 30

what are hydrophobic interactions in protein structure?

Answer 30

the pp folds so as to shield hydrophobic R groups from the aqueous environment, interactions between hydrophobic R groups of aa residues

Question 31

what are protein domains?

Answer 31

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

Question 32

define quaternary structure in protein structure and the bonding involved

Answer 32

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

Question 33

what is the function of haemoglobin, and its structure?

Answer 33

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

Question 34

describe the structure of haemoglobin

Answer 34

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

Question 35

describe the structure of haemoglobin's haem prosthetic groups

Answer 35

Fe2+ held in a porphyrin ring | iron ion binds one of the oxygen atoms in an oxygen molecule reversibly

Question 36

explain haemoglobin's cooperative binding as an allosteric protein

Answer 36

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)

Question 37

explain the sigmoidal shape of the haemoglobin's oxygen-dissociation curve and its function

Answer 37

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

Question 38

what is the function and structure of the collagen protein?

Answer 38

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

Question 39

describe the structure of tropocollagen

Answer 39

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)

Question 40

what is denaturation of proteins, and what bonds does it disrupt?

Answer 40

``` 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 ```

Question 41

how do different denaturants cause denaturation?

Answer 41

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

Question 42

what types of interactions hold polypeptide chains together in a (quaternary structure) protein?

Answer 42

R-group interactions: - hydrogen bonds - ionic bonds - hydrophobic interactions - disulfide bonds