B1.2: Proteins

Question 1

What are proteins?

Answer 1

Complex macromolecules composed of one or more amino acid chains

Essential role in many biological processes (support, catalyst, signaling pathways…)

Ex: enzymes, cell membrane protein, hormones, immunoproteins, transport proteins…

All genes code for protein -> all life reactions dependent on function of protein

Question 2

What are amino acids?

Answer 2

Monomers used to make protein
20 unique amino acids
- each has different R group
-> R group can be polar or non-polar
-> ringed or linear
—> distinct chemical properties

Sequence+type+number of amino acids -> shape and function of protein

Question 3

Formation of proteins

Answer 3

Amino acid joined by condensation reaction

-> peptide bond (carboxyl group of one + amino group of other)
-> water byproduct
-> type of covalent -> stable
-> N-terminal and C-terminal -> unbound amino/carboxyl groups

More AA can be added to dipeptide through condensation
-> polypeptide

(Hydrolysis -> add water -> break)

Question 4

What is a non-essential amino acid?

Answer 4

AA that our body can produce (11/20)

From other AA or the breakdown of protein

Not required in diet

Important functions in the body

Question 5

What is an essential amino acid?

Answer 5

Need to be consumed (9/20)

Necessary for proper growth, maintenance, repair of tissue and muscle

-> need for balanced diet

Question 6

What is genetic code?

Answer 6

Set of rules that specifics how information stored in DNA is translated into the sequence of amino acids that make up proteins -> universal language

Protein synthesis -> transcription (DNA-mRNA) and translation (mRNA-amino acids)
-> ribosome -> polypeptide

Genetic code + diverse AA combination -> complexity and diversity of life

Question 7

What are codons and their function?

Answer 7

Genetic code composed of codons (3 nucleotides that specify type of AA/stop)

U, C, A, G -> table used to deduce AA

64 codons in total, 20 AA -> multiple codons code for the same amino acid
- allow for silent mutations -> change in DNA results I n no change in AA

Question 8

How does the number of amino acids effect the number of possible proteins?

Answer 8

allows for the creation of an almost limitless number of unique proteins with different structures and functions

given that the average length of a protein is300 amino acids, the number of possible combinations is so large, we can consider it to beinfinite

Question 9

What are some roles of protein?

Answer 9

• speeding up cellular reactions, orcatalysis, is performed byenzymes
• blood clotting, where blood proteins interact with oxygen to form a gel-like scab across a wound
• strengtheningfibres in skin, hair, tendons, blood vessels e.g.collagen, keratin
• transportof vital metabolites e.g. oxygen which is carried byhaemoglobin
• formation of thecytoskeleton, a network of tubules within a cell that cause chromosomes to move during the cell cycle
• cell adhesion, where cells in the same tissue stick together
• hormones, chemical messengers that are secreted in one part of the body to have an effect elsewhere
• compaction of DNAin chromosomes for storage, caused byhistoneproteins
• the immune response producesantibodies, the most diverse group of proteins
• membrane transportchannel and carrier proteinsthat determine which substances can pass across a membrane
• cell receptors, which are binding sites for hormones, chemical stimuli such as tastes, and for other stimuli such as light and sound

TLDR: versatile and many uses

Question 10

Examples of polypeptides/proteins (PT.1)

Answer 10

• lysozymeis an enzyme that is composed of 129 amino acids and is present in tears and saliva
  
  • it has antimicrobial properties, disrupting the cell walls of certain bacteria thereby providing a defence mechanism against microbial infections
• alpha-neurotoxinsrepresent a group of polypeptides that are present in snake venom which specifically target and disrupt the nervous system
  
  • these polypeptides range from 60 to 75 amino acids in length and can bind to and inhibit specific receptors, inducing neurotoxic effects, paralysis and possibly death
• glucagonis a hormone composed of 29 amino acid residues
  
  • this hormone is crucial for regulating blood sugar levels
  • glucagon is secreted from the pancreas when glucose levels in the blood are low, stimulating the liver to release stored glucose into the bloodstream, thereby raising blood sugar levels
• myoglobinis an oxygen-binding protein, mainly found in muscle tissues, which is composed of 153 amino acid residues
  
  • it facilitates the storage and release of oxygen to muscle fibres, particularly during periods of low oxygen availability, such as strenuous physical activity
• rubisco - ribulosebisphosphatecarboxylase
  
  • an enzyme that catalyses thefixing of CO2from the atmosphereduring photosynthesis
  • composed of16 polypeptide chainsas aglobularprotein
  • this isthe source of all organic carbon, so Rubisco is arguably the most important enzyme in nature!
  • themost abundant enzyme on Earthas it’s present in all leaves
  • rubisco isa very slow catalyst, but it’s the most effective to have evolved so far to fulfil this vital function
• insulin - ahormoneproduced and secreted by β-cells in thepancreas
  
  • binds to insulin receptors (on liver, fat and muscle cells) reversibly, causingabsorption of glucose from the blood
  • composed of2 polypeptide chainsas ashort, globular protein

Question 11

Examples of polypeptides/proteins (PT. 2)

Answer 11

• immunoglobulins - also known asantibodies
  
  • they have ageneric ‘Y’ shape, with specific binding sites at the two tips of the ‘Y’
  • they bind to specificantigens
  • the binding areas of immunoglobulins arehighly variable, meaning that antibodies can be producedagainst millions of different antigens
  • immunoglobulins (as the name suggests) areglobularand are themost diverse range of proteins
• rhodopsin - apigment in the retinaof the eye
  
  • amembrane proteinthat is expressed in rod cells
  • contains a light-sensitive part,retinal, which is derived fromVitamin A
  • a photon oflight causes a conformational changein rhodopsin, which sends a nerve impulse along the optic nerve to thecentral nervous system
• collagen - a fibrous proteinmade ofthree separate polypeptide chains
  
  • themost abundant protein in the human body- approximately 25%
  • fibresform a networkin skin, blood vessel walls and connective tissue that canresist tearing forces
  • plays a role inteethandbones, helping toreduce their brittleness
• spider silk - silk used by spiders to suspend themselves and create the spokes of their webs is asstrong as steel wirethough considerably lighter
  
  • containsrope-like, fibrous partsbut alsocoiled partsthat stretch when under tension, helping tocause extensionandresist breaking
  • does not denature easily at extremes of temperature
  • has many attractive aspects forengineeringandtextile product designthanks to itsstrengthandlow weight
  • can begenetically engineeredto beexpressed in goats’ milkas spiders can’t be farmed on a large enough scale
  • other kinds of spider silk protein aretougherthough lack the tensile strength, e.g. the silk they use to encase their prey after capture

Question 12

What is denaturation?

Answer 12

Structure of a protein is altered causing it to lose function, usually permanently
-> cause by pH and temp

Bonds between r-groups -> relatively weak -> broken easily -> structure of protein change -> dénaturation

Proteins have optimal range for optimal activity -> efficiency
pH -> affect protein solubility and shape by altering charge
Temp -> break weak hydrogen bonds -> unfold -> no function

Question 13

Why is structure so important in proteins?

Answer 13

3D Structure -> vital for function -> change in structure -> no function
-> theprecise structureof a protein is dependent on the ionic interactions, hydrogen bonds and other intermolecular forces between polypeptide chains being intact

Different structures -> allow WIDE variety of function
-> viewed using AI tech
-> 500 AA found in nature, only 20 commonly found in protein

Question 14

What is an example of denaturation?

Answer 14

• denaturation can be seen most easily by looking at thechanges in an egg whiteas the egg is fried or poached
  
  • egg white is mainly the proteinalbumin
  • thehydrophobic amino acidsin albumin are at the centre of the molecule in its normal state, so albumin is soluble
  • heating causes the hydrophobic amino acids to appearat the edges, where they cause the protein to becomeinsoluble
  • a harder, solid layer forms, which is thecooked white
  • similar events occur in the proteins of theegg yolkas it cooks

(More example in kasia notes)

Question 15

R groups role

Answer 15

R group -> great variance -> high chemical diversity between AA

R groups give each AA/polypeptide unique characteristics

Can be hydrophobic/philic

Question 16

Four levels of protein structure

Answer 16

• primary structure
• secondary structure
• tertiary structure
• quaternary structure
• first three levels are structural aspects of a single polypeptide chain
• fourth level relates to a protein that has more than one polypeptide chain

Question 17

Primary structure of protein

Answer 17

The specific sequence of AA that are joined to form a polypeptide chain

DNA determines primary structure

the unique sequence of amino acids determines how the polypeptide chain will fold, ultimately leading to the three-dimensional structure of the protein

-> position of each AA -> critical in determining shape
Change in sequence -> change in structure+function

Question 18

Secondary structure of proteins (general)

Answer 18

Formation of complex shapes within polypeptide
Local folding patterns that occur within the polypeptide chain -> affects 3D structure/function
-> can occur due to weak hydrogen bonds

2 common types: alpha helix and beta-pleated sheets
Formation facilitated by the ability of the polypeptide chain to fold into coils/pleats
- hydrogen bonding between carboxyl + amino in different parts of polypeptide
- hydrogen bonds -> regular -> stabilize + aid in formation of 2nd structure

• hydrogen bond alone -> weak
• many H-bonds -> strong

Question 19

Secondary structure of protein (alpha helix)

Answer 19

H bond formed between amine hydrogen + carboxyl oxygen that is 4 residues away

-> repeated -> coil -> helical structure

Question 20

Secondary structure of protein (beta pleated sheet)

Answer 20

Form when sections of the polypeptide chain run parallel to each other, h-bonds dormant between adjacent strand

H-bond -> pleated structure -> individual strand = flat surface of sheet

Question 21

Tertiary structure of protein

Answer 21

Further folding of polypeptide
-> dependent on the interaction between R groups which may include the formation of hydrogen bonds, ionic bonds, disulfide covalent bonds and hydrophobic interactions

Stabilize structure
Tertiary structure -> rise to overall 3D shape
Very specific shape -> key to function

Question 22

Tertiary structure of protein (H-bonds)

Answer 22

Hydrogen bonds

Between polar R-groups
Stabilize 3D shape by holding distant regions together
Critical for maintaining functional integrity -> deviation can impair activity of protein

Question 23

Tertiary structure of protein (ionic bonds)

Answer 23

Type of chemical bond between oppositely charged ions

Proteins -> R-groups undergo binding/dissociation of H-ions -> pos or neg charged state -> Charged r-groups -> interact with oppositely charge atoms in other molecules -> ionic bond

• contribute to stability and function

Question 24

Tertiary structure of protein (disulfide covalent bonds)

Answer 24

Between pairs of cysteine amino acid residues (contains sulphur atoms)

Critical for stability the 3 and 4 structures by forming covalent bonds that help maintain 3D shape -> stability + function

Question 25

Tertiary structure of protein (hydrophobic interactions)

Answer 25

Occur between non-polar amino acids

this occurs as water is a polar molecule and forms hydrogen bonds with polar amino acids, as the non-polar amino acids are unable to interact with water, they tend to clump together into hydrophobic clusters in the interior of the protein, to minimise contact with the surrounding water molecules

-> stabilize 3 + 4 structure

Question 26

How does polarity affect amino acids?

Answer 26

Non-polar:
Less soluble -> structural and stationary
Center of protein -> stabilize
Active sites of lipase enzyme to allow interaction with lipid substrate

Polar:
Soluble
Surface -> interact with water
Interior pores - hydrophilic channels for transport of polar molecules into and out of cell
Outside of enzymes -> soluble in aqueous environments

Question 27

Polar and non-polar amino acids - position in amino acids
(+ examples)

Answer 27

• hydrophilic polar amino acids orient to the outside towards the aqueous environment
• hydrophobic non-polar amino acids are protected in the core, minimising unfavourable interactions between hydrophobic side chains and water molecules
• compact, folded conformation exposes hydrophilic surfaces to the solvent and buries hydrophobic residues in the protein’s interior -> stability and function

myoglobin: a protein found in muscle tissue that binds and stores oxygen
haemoglobin: a protein responsible for transporting oxygen throughout the body
-> both examples of globular proteins with hydrophobic cores

rhodopsin, a protein found in the cell membrane of retinal cells responsible for absorbing light, is an example of an integral membrane protein that has hydrophobic regions

Question 28

Quaternary structure of protein

Answer 28

• Arrangement and interaction of two or more polypeptide chain to form a functional protein
• how polypeptides and other components are arranged

Essential for biological functions
Highlights complexity and importance of protein structure

Question 29

Quaternary structure of protein (example: haemoglobin)

Answer 29

4 individual polypeptide chains, 2 a-chain and 2 b-chains (both globins)

conjugate proteins -> associated with a non-protein component (haem)
-> complex molecule with iron in center
-> responsible for binding to oxygen + facilitate transport

4 subunits held together by non-covalent bonds + interaction between subunits -> conformational changes needed to carry out function

Question 30

What is a non-conjugated protein?

Answer 30

A protein with only polypeptide subunits

Ex: collagen -> 3 polypeptide units
-> fibrous protein
-> helix shape
—> arrangement of helix -> quaternary structure

Ex: insulin -> 2 polypeptide units
-> consists of two chains of amino acids, one being 21 amino acids long, the other 30 amino acids in length; the chains are joined by three disulfide bridges
-> it forms two quaternary different structures called dimers and hexamers which act as storage molecules of insulin

Question 31

What is a conjugated protein?

Answer 31

• polypeptide subunits and non-protein components (metal ions or carbohydrates)
  -> increases the protein’s diversity and functionality

-> e.g: non-protein components play a crucial role in many enzymes, helping them perform their catalytic functions
-> e.g: haemoglobin

Question 32

What is globular protein?

Answer 32

Complex proteins that are usually spherical in shape with irregular folds, compacts

Irregular and wide range of R-groups

Soluble in water

Spherical (when folding into their 3 structure) because:
Non-polar R groups -> center of protein + polar R groups -> outside of protein

Folding due to interactions between R-groups -> globular proteins have specific shapes
-> helps globular to play physiological/functional role

Ex: enzymes, transporters, regulators

Question 33

What is fibrous proteins?

Answer 33

Long strand of polypeptide chains that have cross-linkages (due to H-bonds)

Insoluble

Usually composed of repeating structures (limited number of AA/R-groups ) -> designed for structure

Insoluble in water (large number of non-polar R groups)

Little to no tertiary structure

Ex: collagen, keratin, myosin, actin, fibrin

Question 34

Example of globular proteins

Answer 34

Insulin (two polypeptide chains a and b)
Hormone -> regulates blood glucose
-> produced in pancreas and released when blood sugar too high
-> binds to specific receptor cells -> glucose enter cell -> energy

Arranged in a specific 3D shape held by h-bonds, hydrophobic interactions, disulfide bonds

overall structure: compact and globular with a hydrophilic exterior and a hydrophobic interior
Hydrophilic exterior-> insulin interact with hydrophilic molecules in blood (important bc it travels via blood)
Hydrophobic interior -> stable and shape -> help bind to receptor

Question 35

Example of fibrous protein

Answer 35

Collagen -> most abundant protein in the body
Main component of connective tissue in animals (skin, bone, tendons, ligaments, etc.)

Insoluble

3 polypeptide chains (1000ish AAs) -> twisted into triple helix
Each chain rich in AA glycine -> has proline and hydroxyproline residues

-> residues allow twisting into tight helix -> held together by H-bonds, van der waals force (+covalent bonds)

Triple helix structure -> long and thin -> give collagen fibrous shape -> strong and flexible -> structural support to tissues (shape and integrity)

Covalent bonds -> cross links between R-groups in different helices when parallel to each other -> fibrils

Fibrils -> staggered ends -> strength
Many fibrils -> collagen fibers -> positioned so they line up with the forces they are withstanding