PROTEINS 💪

Question 1

Elements of proteins

Answer 1

Hydrogen, carbon, oxygen, nitrogen and sometimes sulfur

Question 2

Definition of a polypeptide

Answer 2

linear sequence of amino acids covalently joined together by peptide bonds

Question 3

Function of a protein determined by

Answer 3

1. nature of amino acids present in the protein, based on the R-groups of the amino acid
2. **3D conformation **of protein molecule

Question 4

2 classes of protein based on shape

Answer 4

Globuar and fibrous

Question 5

Fibrous VS Globular protein

8 points in total

Answer 5

Shape:
Fibrous: Elongated and wound around each other to form rope-like structure
Globular: folded, bent, twisted to form a compact and spheroidal structure

Sequence of amino acids:
Fibrous: repetitive sequence
Globular: specific, non-repetitive sequence

Variety of amino acids:
Fibrous: small, specific variety of amino acids
Globular: wide variety of amino acids

Consistency of sequence:
Fibrous: sequence of amino acids may vary slightly between 2 samples of the same fibrous protein
Globular: amino acid sequence never varies between 2 samples of the same globular protein

Consistency in length:
Fibrous: length of polypeptide chain may vary in two samples of the same fibrous protein
Globular: length of polypeptide is always identical in two samples of the same globular protein

Stability:
Fibrous: stable structures due to the numerous intra- and inter- molecular hydrogen and and covalent bonds
Globular: relatively unstable due to the numerous intra- and inter-molecular non-covalent bnds, such as hydrogen bonds, ionic bonds and hydrophobic interactions

Solubility:
Fibrous: generally insoluble in water(forms colloid)
Globular: more solublar in water than fibrous proteins, due to
- non-covalent bonds are polar, and are thus able to form hydrogen bonds with water
- folded such that hydrophilic/charged R groups are facing outward to aqueous exterior and hydrophobic R groups face inwards to form hydrophobic core

Functions:
Fibrous: structural functions
Globular: metabolic functions

Examples:
Fibrous: collagen, myosin, fibroin, actin, keratin, elastin
Globular: enzymes, hormones, antibodies, haemoglobin

Question 6

Classes of protein based on function

Answer 6

Enzymatic, defensive, storage, transport, hormonal, receptor, contractile, motor, structural

Question 7

Cofactor

Answer 7

non-protein component that is combined with a protein

Cofactor organic in nature tightly bound to a protein is known as a prosthetic group

Question 8

Classes of composition

Answer 8

Simple proteins: only formed by amino acids

Conjugate protein: protein combined with a non-protein component known as cofactor

Question 9

No diff for plants: able to synthesise all the amino acids they need

Essential and non-essential amino acids, derivatives

But they are EQUALLY important

Answer 9

Essential amino acids: amino acids obtained by animals through their diet
Non-essential amino acids: can be synthesised by the body
Derivatives: rare amino acids made from fundamental amino acids

Question 10

Structure of amino acid

Answer 10

basic amine group + acidic carboxyl group + hydrogen atom + variable R group

Question 11

Definition of a zwitterion(ref to page 9 on drawing)

Answer 11

Zwitterion: electrically neutral, dipolar ion

Question 12

Definition of a buffer

Answer 12

Substance that can resist changes in pH in a solution when a small amount of alkali or acid is added to it

Question 13

Properties of amino acids

Answer 13

Colourless, crystalline, relatively high melting points

Insoluble in organic solvents but soluble in water where they form ions

Ability to form zwitterions:
1. Formed by loss of H+ from -COOH, making it negatively charged(COO-)
2. H+ loss associates with amine group(-NH2), making it positively charged(-NH3+)

Ability to act as buffer to maintain pH of blood plasma/intersial fluid, small changes in pH can affect function of enzymes and other proteins:
1. Amino acids amphoteric due to having both acidic and basic properties in aqueous solution
2. When acid is added, amino acid +H3N-RCH-COO- takes up a hydrogen ion and becomes +H3N-RCH-COOH
3. When alkali is added, amino acid +H3N-RCH-COO- loses a hydrogen ion and becomes H2N-RCH-COO-

Question 14

3 categories of R groups

determined by their physical and chemical properties

Answer 14

Non-polar
Polar
Charged

Question 15

Properties of non-polar amino acids

Number of amino acids: 9

Answer 15

1. R-group hydrocarbon in nature(R group has many C-C and C-H bonds)
2. hydrophobic and unreactive
3. Tend to be localised in the interior of the protein: shielded from aqueous medium of polypeptide as it folds into its 3D conformation

Question 16

Properties of polar amino acids

Number of amino acids: 6

Answer 16

1. polar R-group(-OH and -NH) with no net charge
2. hydrophilic in nature

Question 17

Charged amino acids

Number of amino acids: 5

Answer 17

1. charged R-groups, hence hydrophilic
2. acidic amino acids: net negative charge when ionised in water due to presense of **carboxyl ** group in R group(carboxyl group ionises to release a H+ ion)
3. basic amino acids: net positive charge when ionised in water due to presense of amine group in R group(amine group gains H+ ion)

Question 18

Definition of a peptide bond

same chemical properties as an amide bond but between amino acids

Answer 18

covalent bond formed between amine group of one amino acid and caroxyl group of the other

Question 19

Peptide bond formation + draw it out(ref pg13)

Answer 19

1. via condensation reaction
2. with loss of a water molecule

Question 20

Structure of polypeptide

Answer 20

1. consists of many amino acids joined together by peptide bonds in a specific linear amino acid sequence
2. neighbouring amino acid residues joined together in head to tail fashion -> linear and not branched
3. Amino acid member in polypeptide known as amino acid residue
4. N terminus: a free amine group, which marks the beginning of the polypeptide
5. C terminus: a free carboxyl group, which marks the end of the polypeptide
6. R group of each amino acid residue projects from backbone of polypeptide

Question 21

Properties of polypeptides

Answer 21

1. Buffer solutions, additonal buffering capacity(maintain pH of blood plasma/intersial fluid, small changes in pH can affect function of enzymes and other proteins): free amine and carboxyl group + ability of some R groups to ionise
2. variations in length and amino acid sequence of polypeptides contribute to the diversity in shape and biological functions of proteins
   
   • molecules made up of one or more polypeptide chains that attain stable, specific 3D conformation is biologically functional

Question 22

Biuret test: principle + method + observation

Answer 22

Principle:
1. detects peptide bonds(amino acids will give a negative result)
2. nitrgoen atoms in peptide bonds complexes with Cu2+ ions to give purple colouration

Method:
1. Add equal volume of 5% KOH solution to test solution(necessary to create alkaline pH which is needed for Cu2+ ions to bind to polypeptide)
2. Add 1% copper sulfate solution dropwise
3. Mix contents by shaking and **leave for 3 minutes **

Analysis:
1. Purple/violet: presence of peptide bonds
2. Blue: no peptide bonds present

Question 23

Levels of protein structure and its importance

Answer 23

3D shape maintained by 4 different type of bonds between R groups of amino acids in the chain

Primary, secondary, tetiary, quatenary

Question 24

Define Primary structure and bonds present

Answer 24

Definition:** unique number **and **linear sequence **of amino acids that constitute the polypeptide chain

Synthesis: proteins synthesised in vivo by stepwise polymersiation of amino acids in order specified by sequence of nucleotides in a gene

Bonds:
1. peptide bonds between amine group of one amino cid and carboxyl group of another

Question 25

Properties of polypeptides and effect on protein formed

Answer 25

Characteristic of protein affected by** sequence of amino acids,** not composition **Amino acid R group** determines type and location of bonds present at higher level of protein **Size, charge, polarity and hydrophobicity of R groups** affect the ultimate 3D conformation, and therefore the function of the protein

Question 26

Formation of secondary structure

Answer 26

Regular coiling and folding from **hydrogen bonds **of polypeptide chains giving rise to repeated patterns Coils and folds result from** hydrogen bonds ** between N-H group and C=O group of another amino acid(`note: hydrogen bonds do NOT involve the R groups` Hydrogen bonds weak individually but collectively serve to stabilise the structure

Question 27

Types of secondary structure

Answer 27

α-helix and β-pleated

Question 28

α-helix structure shape and nautre of bonds(+ their function) | Shape, nature of bonds

Answer 28

Shape: extended, spiral spring Nature of bonds: 1. interchain hydrogen bonds between O atom of C=O group of (nth) an amino acid and H atom of N-H group of amino acid situated 4 amino acid residues ahead in linear sequence(n+4) - C=O and N-H group found on peptide backbone 2. **hydrogen bonds paralell** to **main axis** of helix + **All** C=O and N-H groups of peptide backbone **can participate in hydrogen bondin**g to bring **maximum stability** to α-helix structure 3. α-helix makes one complete turn every 3.6 amino acids 4. R groups **project** outside the helix, **perpendicular** to the main axis, preventing **steric interference** with polypeptide backbone and with each other (side chain being bulky and large main intefere with space for folding) 5. **Proline** and **hydroxyproline** insert a **kink** and disrupts formation of α-helix 6. Amino acids with bulky R-groups if present in large numbers can intefere with formation of α-helix

Question 29

β-pleated sheets shape + nature of bonds(+function)

Answer 29

Shape: extended zigzag, sheet-like conformation Nature of bonds: 1. stabilised by hydrogen bonds between C=O and N-H groups of polypeptide backbone 2. Hydrogen bonds can occur between C=O and N-H groups within same polypeptide chain or between C=O and N-H groups of neighbouring polypeptide chains 3. Hydrogen bonding in same polypeptide chain = intrachain sheets(will form a u-turn) 4. Hydrogen bonding between different polypeptide chains = interchain sheets(2 chains side by side that are antiparallel) 5. Amino acid residues in β-pleated sheets usually have small R groups: amino acids with bulky R groups interfere with formation of β-pleated sheets by causing stearic hinderance

Question 30

Variations of β-pleated sheets(ref to pg22 for diagram)

Answer 30

Antiparallel β-pleated sheet: neighbouring hydrogen-bonded polypeptide segments run in oppostive N-terminus to C-terminus directions Parallel β-pleated sheet: hydrogen-bonded segments run in same N-terminus to C-terminus direction

Question 31

Defintion of tetiary structure

Answer 31

further bending, twisting and folding of polypeptide chain with secondary structures to given an overall 3D conformation of a protein

Question 32

Nature of bonds in tetiary structure | contains only ONE polypeptide chain only some teriary protein functional

Answer 32

3D conformation determined by four types of** R group interactions **between **amino acid residues some distance aprat on same polypeptide chain ** HIHIS bonds: hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bonds - first three are**non-covalent bonds and are therefore weak** - disulfide bond is a covalent bond and is therefore strong

Question 33

R-group interactions maintaining 3D conformation + formation + breakage | draw the formation and breakage process out

Answer 33

Disulfide bonds/linkages: 1. covalent bond 2. Formation: oxidation of **sulfhydryl groups(-SH) **of any 2 **cysteine** residues in same polypeptide chain or in different chains by removal of 2 hydrogens 3. Breakage: via reduction using reducing agent such as DTT Hydrogen bonds: 1. between **electropositive hydrogen atom** and another** electronegative atom** within the** same polypeptide chain ** 2. Hydrogen atoms have **partial postive charge** while nitrogen, oxygen atoms have **partial negative charge**, oppositely charged atoms attracted to each other to form a hydrogen bond 3. Each bond is weak 4. large number of hydrogen bonds confers stability to protein Ionic bonds: 1. Amino acid with postively charged R group and amino acid with negatively charged R group form ionic bond 2. Ionic bonds relatively weak in aqueous cellular environment 3. Breakage: changes in pH of surrounding medium Hydrophobic interactions: 1. formed by folding of polypeptide to shield hydrophobic R groups from aqueous environment 2. interactions between hydrophobic R groups 3. Breakage: excessive heat increases KE, increasing vibration of atoms, distrupting hydrophobic interactions

Question 34

Definition of a quatenary structure

Answer 34

oveall protein structure that results from **association of two or more polypeptide chains** to form a **functional** protein

Question 35

Formation + bonds present

Answer 35

Each individual polypeptide adopts a tetiary structure and is called a protein subunit Multimeric: proteins with more than one polypeptide/subunit(subunits may or may not be identical) Nature of bonds: HIHIS bonds between **R groups of different protein subunits**

Question 36

Function of haemoglobin + general structure of one molecule

Answer 36

oxygen-binding protein functioning to transport oxygen in blood from lungs to other tissues in the body to supply cells with oxyegn required for aerobic respiration found in blood in RBC **mulitmeric** protein comprising **4 polypeptide chain**s, **2 α-chains** and** 2 β-chains** **tetramer**(α2β2) and **2 identical dimers**(αβ)

Question 37

Structure of individual haemoglobin subunits

Answer 37

Primary structure: 1. α-chain, containing 141 amino acids 2. β-chain containing 146 amino acids Secondary structure: 1. each polypeptide chain consists of eight α-helices(named by letters a to H, starting from N-terminus) connected by non-helical segments 2. hydrogen bonds stabilise the eight α-helices Tetiary structure: 1. each polypeptide chain folded such that amino acid residues located at **surface** of subunit are generally **hydrophilic** while those **buried in interior** of molecule mostly **hydrophobic** 2. folding allows for formation of a **hydrophobic cleft**(lined with hydrophobic amino acid residues) for **haem prosthetic group to bind** Quatenary structure: 1. **2 subunits** in each dimer held together primarily by **hydrophobic interactions, with ionic and hydrogen bonds also occuring** 2. 4 subunits form a **globular molecule** held together by **multiple non-covalent interactions**(HIHI bonds, no disulfide bonds)

Question 38

Structure of haem prosthetic group + function

Answer 38

iron ion(**Fe2+**) held in **porphyrin ring** Fe2+ binds one of the oxygen atoms in a molecule of O2 reversibly, enhancing the release of O2 in metobolically active tisses such as muscles

Question 39

Structure of haemoglobin in relation to its structure

Answer 39

**Tetiary structure: ** 1. polypeptide chain folded such that hydrophobic amino acid residues buried in interior of molecule while hydrophilic amino acid residues located at surface of subunit `->` haemoglobin soluble** an aqueous medium**, hence a **good transport protein** for oxygen in blood 2. folding of polypeptide chain allows for formation of hydrophobic cleft(lined with hydrophobic amino acid residues) to allow for haem prosthetic group to bind + haem prosthetic group consists of an iron ion(Fe2+) and a porphyrin ring `->` each haemoglobin molecule will bind to 4 molecules of O2 **Quatenary molecule: ** Structure: 1. 2 subunits in each dimer held together by hydrophobic interactions with ionic and hydrogen bonds occuring 2. 4 subunits form globular protein that is held together by multiple non-covalent interactions Function: binding of oxygen to haemoglobin, step by step process of cooperative binding 1. Fe2+ in first haemoglobin subunit binds to 1 molecule of O2 2. **F helix pulled closer** to the haem group 2. Pull creates a **strain on other haemoglobin subunits**, such that the **previously obscured haem groups** of other subunits are **revealed** 3. **Remain subunits changed their 3D conformation slightly**, allowing respective haem groups to bind O2 more readily 4. Remaining **subunits' affinities for O2 molecues increases** Therefore, haeomoglobin is an **allosteric protein**

Question 40

Deinfition of an allosteric protein

Answer 40

Binding of a ligand to one site affects the binding properties of another site on the same protein. it has other conformaiton induced by binding of activators or inhibitors

Question 41

Subunit cooperativity, shape of graph and significance in binding of oxygen haemoglobin

Answer 41

Haemoglobin's oxygen-dissocation curve: sigmoidal shape, as the four polypeptides of haemoglobin displays subunit cooperativity: 1. steep part of curve: when one binds, binding affinity of other subunits increases, thus saturation increases quickly and O2 can be **loaded onto haemoglobin quickly**, coversely when one oxygen releases, binding affinity of other subunits decreases, thus saturation decreases quickly and **oxygen can be unloaded efficiently ** 2. hence, subunit cooperativity allows haemoglobin to be an **efficient oxygen carrier**, since haemoglobin loses oxygen quickly in an environment with low oxygen concentration and vice versa 1. oxygen loaded in lungs where partial pressure is high, and unloaded from haemoglobin in rest of body tissues where partial pressure is low 2. when partial pressure is high, more haemoglobin subunits bound to O2 and haemoglobin more saturated with O2, reverse occurs when PO2 is low

Question 42

hyperbolic curve of myoglobin's oxygen-dissociation curve

Answer 42

Myoglobin is made up to only one polypeptide, and thus cannot undergo subunit cooperativity Hyperbolic: as partial pressure increase, saturation with oxygen of myoglobin inreases at decreasing rate as myoglobin becomes increasingly saturated, cannot uptake as much oxygen But in general, myoglobin has higher binding affinity to oxygen than haemoglobin at the same partial pressure

Question 43

Function of collagen

Answer 43

- strong insoluble fibres - has great tensile strength, acts as major stress-bearing components of connective tissues - provides bones with requried structure, flexibility and strength - provides tendons with strength to transmit muscular contraction - provides blood vessels with strength, structure and flexibility to withstand blood pressure

Question 44

Structure of collagen molecule

Answer 44

Primary structure: 3 polypeptide chains 1. has repeating **tripeptide** sequence of **Glycine-X-Y ** 2. X is often **proline** 3. Y is often **hydroxyproline** or **hydroxylysine** 4. Each chain is ~1000 amino acid residues long Secondary structre: 1. each collagen assumes left-handed(goes clockwise) helical conformation with about 3 resiudes per turn, known as **collagen helix** 2. regular repeated structure indicative of a fibrous protein 3. each polypeptide chain know as **α-chain ** Quatenary structure: 1. **3 parallel α-chains** wind around each other with a gentle right-handed, rope-like twist to form **right-handed triple helix** 2. forms basic structural unit of collagen known as **tropocollagen**

Question 45

Function in relation to structure of tropocollagen

Answer 45

Quatenary structure: winding of the 3 α-chains around each other to form right-handed triple helix 1. triple helix structure is **well-packed** and **rigid** -> **tensile** strength 2. twist in helix cannot be pulled out under tension as component polyppetide chains are **supertwisted** about each other Tight packing, allowing for high tensile strength due to: 1. **every third resiude** of each polypeptide **passes through centre of triple helix**, which is very crowded -> **every third resiude must be Glycine with small R group** as it is the only one that can fit into the crowded centre of the triple helix 2. residues in X and Y positions located outside of triple-helix where there is room for bulky R groups of proline, hydroxyproline, hydroxylysine and other resiudes Rigidness -> high tensile strength: 1. Proline's ring structure stabilises helix 2. Tropocollagen held togehter by extensive network of hydrogen bonds - **hydrogen bonds** formed between **N-H group of glycine residue** in one α-chain and **C=O group of another amino acid** resiude in a neighbouring α-chain - **hydroxyl group** of **hydroxyproline** and **hydroxylysine** residues can participate in **interchain hydrogen bonding ** 3. presence of covalent cross-links present **within** tropocollagen molecules

Question 46

Formation of collagen fibrils and fibre

Answer 46

- tropocollagen molecules lie side by side, linked to each other by covalent cross-links between carbonyl end of one molecule and the amino end of another - increasingly rigid and brittle character of ageing connective tissue results from accumulated covalent cross-links in collagen fibrils - tropocollagen molecules are arranged in staggered manner with each other, stabilised by hydrophobic interactions between tropocollagen molecules -> greater strength - aggregation of collagen fibrils form a collagen fibre

Question 47

Denaturation and renaturation of proteins

Answer 47

Definition of denaturation: loss of specific 3D conformation - bonds maintaining conformation broken and protein unfolds - primary structure unaffected Disruption of secondary, tertiary and quaternary structure(R group HIHIS interactions, hydrogen bonds between N-H and C=O groups of polypeptide backbone): Heat: excessive heat, increase KE, increase vibration of atoms, disruption of HIHI bonds Changes in pH: changers charges in acidic and basic R groups, disruption of ionic and hydrogen bonds Organic solvents: transfer of protein from aqueous environment to organic solvent, disrupting hydrophobic interactions making up stable core of globular protein -> proteins turn inside out, hydrophobic regions changes place with hydrophilic interactions making Urea detergent: addition of chemicals disrupt ionic and hydrogen bonds