Proteins SL and HL

proteins

fiberous proteins

offer strength and support structurally, Fibrous proteins consist of elongated polypeptide chains that lack typical tertiary structures. Instead, their quaternary structure involves linking polypeptides into long fibres or filaments, stabilized by hydrogen bonds.

globular proteins

Globular proteins are compact, spherical proteins that are typically soluble in water. Their structure results from the folding of the polypeptide chain into a tightly packed three-dimensional shape. Globular proteins have a rounded shape, formed by the folding of polypeptides into intricate structures. These shapes are stabilized by bonds between R-groups.

example of globular protein

• Conformation: Insulin’s specific three-dimensional shape allows it to bind precisely to insulin receptors on cells.

• Function: This precise binding triggers intracellular signals for glucose absorption, essential for maintaining blood sugar levels.

Functionality
The precise arrangement of atoms, known as conformation, is critical for the function of globular proteins. Examples include:

• Enzymes: Their active sites rely on the precise folding of R-groups to catalyze reactions.

• Receptors: Ligand-binding sites depend on specific protein conformations to transmit signals.

genetic code connection

it’s universal so the 20 amino acids are encoded by the same genetic code across all species, the code is read as three-nucleotide mRNA codons, each coding for one specifc amino acid

amino acids

monomer of proteins

oligopeptides

Short chains of 3-20 amino acids

basic structure of amino acid

amine group, alpha carbon(backbone sturcture in polypeptides), hydrogen atom, variable side chain, carboxyl group

non-essential amino acids

5 types of amino acids we can get fromfood and make ourselves

dipeptide

two amino acids joined via a condensation reaction removing one molecule of water and forming a peptide bond(C-N)

conditionally essential amino acids

6 amino acids our body can make if healthy eg. can’t make when starving or with inborn error of metabolism

variety in amino acids

The R-groups are the functional gorups makeing the 20 amino acids different(some polar, non polar, charged and uncharged, acidic or basic, some ringed structured and variety of elements) and this composition is going to affect how amino acids in a polypeptide interact with each other, affecting the folding, and the particular sequence of amino acids is determined by the DNA.

protium

set of proteins we can make in an organism, we can make and infiite number of possible coded for by our DNA

condensation reactions/ dehydration synthesis

builds complex molecules by joining two or more molecules together, removing a molecule of water, it’s an anabolic process requiring enrgy to occur and catalyzed by enzymes, forms a peptide bond between carboxylic group and amine gorup of two amino acids.

location of polypeptide synthesis

occurs in the ribosomes which are repsonsible for translating mRNA into popylpeptides

hydrolysis

amylase

Enzyme in saliva that breaks down starch, Composed of a single polypeptide chain with 496 amino acids§§§

collagen

• Quaternary Structure: Composed of three polypeptides twisted into a triple helix.

• Primary Structure: Features a repeating sequence of three amino acids, proline, glycine, and X (variable).

  • Glycine, with its small R-group (a single hydrogen atom), faces inward, allowing the tight triple helix structure.

  • Proline or hydroxyproline prevents the formation of alpha-helices, facilitating the triple helix.

Functionality

• Tensile Strength: Collagen’s rope-like triple helix provides structural integrity to tissues such as skin, tendons, ligaments, and cartilage.

• Variability: The R-group of the third amino acid is flexible, enabling different types of collagen for various functions (e.g., forming the basement membranes of epithelia and the outer layer of the eye).

haemoglobin

denaturation

• process by which a protein unfolds from its functional structure due to the disruption of the interactions that stabilise protein structure,

• including hydrogen bonds, ionic and hydrophobic interactions which when overcome by environmental stresses the protein unfolds into a more random and extended conformation losing its 3D arrangement of amino acids required for biological activity is destroyed.

• It’s often a permanent chnage but sometimes can renature. eg. render a protein that used to be soluble into insoluble

temperature effect on proteins

• kinetic energy and molecular motion increases with temperature, causing greater and faster vibration and movement of atoms within protein molecules.

• metabolic protein function increases with small increases in temperature because the greater molecular motion leads to more frequent and energetic collisions between proteins involved in biochemcial reactions

pH effect on proteins

• Each protein has an optimal pH range within which it functions, and if it is placed in environments outside of this range, the protein can break bonds/interactions, unfolding its shape and shifting its function. 

• As pH chnages the charge of amino acid R-groups can change altering the pattern of electrostatic interactions in the tertiary structure and causing protein denaturation

• at low pH, negatively charged amino acid R groups become protonated changing their negative charge to neutral 

• as pH increases and the solution becomes more basic positively charged amino acid R groups(HIS, LYS and ARG) can lose a proton(N- becomes N) changing their positive charge to neutral. These electrostatic interactions between charged R-groups contribites significantly to protein stability, and can influence protein to protein interactiosn and enzyme-substrate binding.

protein conformation

the specific 3D shape of a protein molecule, the native conformation is it’s most stable and natural shape 

insulin

Hormone that regulates blood sugar levels and Made of two polypeptide chains, one with 21 amino acids and the other with 30.

polar interactions in tertiary structure

polar- partially positive and partial negative charge due to unequal electron sharing between atoms in the R groups, easily form hydrogen bonds with other polar molecules, such interactions are crucial for protein folding, enzyme specificity and protein-protein interactions that drive cellular processes.

hydrophobic and hydrophylic interactions

• hydrophobic- amino acids with R groups composed of primarily of carbon and hydrogen atoms are nonpolar and hydrophobic, these tend to minimize their contact with wayer typically clustering together in the interior of globular proteins , away from the aqueous environment

• hyrdophylic- interact favourably with water through hydrogen bonding or electrostatic interactions, often appear on protein surfaces interact with the aqueos envirnoment which enables proteins to maintain solubility in cellular environments and facilitates interactiosn with other polar molecules including proteins and nucleic acids.

example of polar interactiosn in enzymes 3D structure

Enzymes’ active sites are typically located in pockets on the protein surface and the active site containes a mixture of polar and nonpolar amino acids that create a chemical environment that is specific to the particular enzyme substrate whiche nsures that only chemcially complementery substrates are able to bind to the enzyme.

ionic bonds in 3D structure

positively charged R groups: have a nitrogen atom that can gain a hydrogen to become N+ and negatively charged R groups: have a carboxyl group that can lose an H atom to become COO-, they for ionic bonds with oppositely charged amino acids.

amphipathic

hydrophobic and hydrophylic regions

integral membrane protein

integral membrane proteins permanently embedded withina  plasma membrane with roles in transporting molecules, transmiting chemcial signals, and facilitating cell adhesion, integral membrane proteins are amphipathic. Nonpolar hydrophobic amino acids willa rrange themselves within the hydrophobic core of the bilayer  with the fatty acid chains of phospholipids.

quaternary structure

disulfide bridges

disulfide covalent bonds between cysteine amino acids that are close together in the primary sequence or between cysteine close together in the folded structure to cause further folding, they are the most stronf bonds in tertiary structure emhancing stability in proteins exposed to harsh conditions.

polar

has a positive and negative charged region, hydrophylic and struggle to difuse across cell membrane

non polar

electrical charged evenly distributed(no negative or positive region), nydrophobic and easily diffuses acrss cell membrane.

essential amino acids

our bodies can’t produce them and thus we msut get them from food, 9 types - histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine

complete proteins

Contain all nine essential amino acids in proportions similar to what the human body needs. eg. eggs, meat, fish

incomplete

Lack one or more essential amino acids but contain some of them, in different proportions, eg. Cereals (e.g., wheat): Low in lysine and Legumes (e.g., beans and peas): Low in methionine. Combining lots of different plant foods can profide a compelte amino acid profile.

vegan diet concerns

must be very purposeful and mindful about what protein sources confirmed as they all containe some essential amino acids but not in the same proportions  as the body needs them and lack some, thus by combining plant foods with complimenting amino acid profiles form very varied sources vegans can still meet the needs. 

eg. meal that is complimentary for vegans

• rice- Low in lysine but high in methionine.

• beans-Low in methionine but high in lysine.

• Rice and beans create a meal that provides all essential amino acids in sufficient quantities.

risks of deficiencies in certain amino acids

muscle wasting: skeletal muscles are digested to release amino acids for more critical organs and functions, decrease in muscle mass

stubnted growth in children

reduced immune function making one suseptible to illness and slowing recovery and healing process

Feeling more tired and lethargy

Deficiencies in certain amino acis can affect certain neurotransmitter production and potentially contrute to depression, anxiety and iritability.

Hair loss, thininning of hear and skin problems as they are heavily dependent on protein production.

why protein consumption matters

Proteins are essential for nearly every biological process in your body, from building muscle to producing enzymes and hormones. A deficiency in essential amino acids can disrupt these processes, leading to a cascade of health issues. Understanding amino acid requirements helps maintain overall health and biological functions.

number of possible combinations with “n” amino acids

Tripeptide (3 amino acids): 20 to the power of “n”

20 to the power of 3= 8,000 possible combinations.

non-conjugated

• Made entirely of polypeptide subunits

• Examples include insulin (two chains linked by disulfide bonds) and collagen (three chains in triple helix) 1

• Function depends only on the arrangement and interactions of polypeptide chains_

conjugated

• Contain polypeptide chains plus non-polypeptide components called prosthetic groups

• Example: hemoglobin has four polypeptide chains, each with a heme group containing iron (Fe²⁺) 2

• The non-polypeptide components are essential for biological function (heme groups bind oxygen)

conjugated

diversity in proteins

While natural constraints exist, there is an infinite length and combinations of amino acids theoretically. Changing just one amino acid in a sequence can dramatically alter the protein folding and thus stability and function.

sickel cell anemia

example of how chang in one amino acid can alter conformation of a protein, it’s caused by a single nucleotide mutation in the haemoglobin HBB gene and this adenine to thymine substiution chnages an amino acids of haemoglobin protein from glutanine to a valine and this valine amino acid is hydrophobic and causes the molecule to form long, inflexible chnages that lead to stiffening of the red blood cell causing it to have the sickle shpae

primary structure

• linear sequence of amino acids joined together by peptide bonds, these covalent bonds are relatively stable under typical physiological conditions

• provide the permanent structural framework of a protein and the sequence is determined by the genetic code.

• The primary structure of a protein determines the final confromation of a protein

secondary structure

regular repating alpha helices and beta pleats that form in polypeptide chains through hydrogen bonding between atoms in the polypeptide backbone(nitrogen, alpha-carbon, and carbonyl atoms formed when the amino acids link by peptide bonds).

• alpha helix is a spiral where the polypeptide backbone coils around an imaginary central axis, hydrogen bonds form between atoms od the polypeptide backbone roughly every 4 amino acids.

• beta pleated sheets structure forms hen a polypeptide chain folds back on itself and amino acids align side-by-side and form hydrogen bonds between their backbones.

tertiary

the overall 3D folding pattern of a complete polypeptide chain determined by interactions between amino acid R-groups of the polypeptide chian, deciding it’s function. Molecular forces between R groups include:

• hydrogen bonds between polar R groups

• ionic bonds between charged R gorups

• disulfide covalent bonds/bridges between cyteine amino acids

• hydrophobic interactions between nonpolar R-groups

quaternary

• Multiple polypeptide chains assembled together

• Each chain is called a subunit

• Example: Insulin consists of two chains (21 and 30 amino acids