IB Biology HL: Proteins

Proteins

Large, complex molecules consisting of amino acid residues joined by peptide bonds. account for 50% of the dry weight of most cells.

Structural

Type of protein used for support (collagen, keratin).

Storage

Type of protein used for storing amino acids (casein, plant seeds).

Transport

Type of protein used for moving other substances (hemoglobin).

Hormonal

Type of protein used for the coordination of an organism's activities (insulin).

Receptor

Type of protein used for the response of cell to chemical stimuli.

Contractile

Type of protein used for movement (actin, myosin).

Defensive

Type of protein used for protection against disease (antibodies).

Enzymatic

Type of protein used to accelerate chemical reactions (enzymes).

Amino Acids

Building blocks of proteins.

Essential Amino acids

Amino acids required in the human diet and cannot be synthesised from other metabolites

R-group

A functional group that defines a particular amino acid and gives it special properties.

Polypeptides

Polymers of amino acids. Joined together by peptide bonds.

Explain how the amino acid sequence detremines the 3D conformation of apolypeptide?

• Bonds between amino acids’ R-groups hold the final conformation

• Hydrophilic amino acids end up on the edges

• the sequence of amino acids influence folding

Peptide Bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid.
Forms dipeptide and water

What kind of reaction is breaking down polypeptides into amino acids ?

Hydrolysis - it requires water

There is an ______ variety of polypeptide chains

Infinite

Dipeptide

Two amino acids bonded together.

Carboxyl Group

Part of an animo acid that reacts with another amino acid's amine group.

N and C

Elements between which a peptide bond is formed.

Covalent

Type of bond a peptide bond is.

Ribosomes

Site of protein synthesis- facilitate the formation of peptide bonds

DNA

Provides information for construction of polypeptides.

1

Proteins are made up of at least ___ polypeptide.

Protein _______ determines function

shape

Primary Structure

Unique sequence of amino acids in a protein- determined by DNA
- Specific order will determine how the protein folds. Amino acids in a chain bonded to each other with peptide bonds.
- To avoid tangling and breaking parts of the chain are stabilised as they are made (Hydrogen bonds, ionic bonds, hydrophic interactions and disulfide bonds)

Sickle Cell Anemia

Genetic disorder resulting from a single change in the amino acid sequence of a cell.

Secondary Structure

• Alpha helix = hydrogen bonds formed between coiling chain

• Beta pleated sheets= parallel hydrogen bonds between folded chain

• Hydrogen bonds between C=O and N-H

Sidechain

The portion of amino acids not included in the backbone of a protein.

Alpha-Helix

A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.

Beta-Pleated Sheet

the polypeptide chain folds back and forth and the fold are held together by parallel hydrogen bonds.

In an alpha-helix, hydrogen bonds exist between every _____ amino acid.

4th

In a beta-pleated sheet, hydrogen bonds form between parts of the backbone in __________ regions.

parallel

Teritary Structure

• folding of a polypeptide chain into a 3d conformation

• hydrogen bonds between polar r-groups

• hydrophobic interaction between non-polar R-groups

• covalent bonds/ dissulfide bridges between R-groups of cysteine amino acids

• Ionic bonds between R-groups with opposite charges

• This gives protein specific shape - function

Hydrophobic Interactions

Clustering of hydrophobic R-groups away from water

Hydrogen Bonds

• Very weak bonds;

• Between R-groups

• H- - -O

Ionic Bonds

Formed when one or more electrons are transferred from one atom to another.

Disulfide bridge

Covalent bond between two cysteine amino acids.

Quarternary Structure

• has 2 or more polypeptide chains

• has prosthetic groups

• forms conjugated proteins

conjugated proteins

protein molecules combined with another kind of biomolecule (prosthetic group) in the final molecule e.g. Haemoglobin

Non-conjugated protein

A protein that is made up of only amino acids/ polypeptide chains

Fibrous Protein

• only has a secondary structure;

• generally insoluble;

• long, narrow, coiled,

• repetitive amino acid sequences

• collagens, elastins, and keratins.

• Is less sensitive to changes in heat and pH than globular proteins

• STRUCTURAL

Globular Proteins

• compact,circular

• soluble

• irregular amino acid sequences,

• catalase, hemoglobin, insulin.

• FUNCTIONAL / PHYSIOLOGICAL

RNA

A single-stranded nucleic acid that passes along genetic messages. Moves to the ribosome to bond together amino acids.

Transcription

The organic process whereby the DNA sequence in a gene is copied into mRNA.

Translation

Movement of mRNA to ribosomes to bond together amino acids.

Rubisco

• Enzyme with an active site

• fixes carbon during photosyntheis

Insulin

• Hormone

• soluble in bloods

• converts glucose into glycogen

• Type 1 diabetics- pancreas does not produce enough insulin

• Non-conjugated - 2 polypeptide chains

Immunoglobulins

• Antibodies that bind to antigens and pathogens.

• Allows specific immunity against many different diseases : very variable

Rhodopsin

• Pigment that makes the rod cells of retina light

• sensitive. Rod cells send nerve impulses to the brain.

Collagen

• Structural protein

• 3 polypeptides (non-conjugated)

• rope-like conformation/ used

• prevent tearing, in bones to prevent fractures, and in tendons to give tensile strength.

• Fibrous

Why is Collagen a strong structural protein?

• forms a triple helix

• triple helix contains both covalent + hydrogen bonds

• many collagen finrils join to make collagen fibre

Spider Silk

• fibrous

• tensile strength

• beta-pleated sheets

• Becomes stronger when stretched resisting breakage.

Denaturation

• high temperatures cause protein denaturing

• deviation of pH from te optimum causes protein denaturing

• Bonds within protein between R-groups break

• 3d conformation of protein changes

Why is denaturation of proteins fairly easy ?

The 3D structure of proteins are stabilised by bonds or interactions between R- groups of amino acids within the molecule - most of there are relatively weak and can be disrupted and broken by pH + temp

causes denaturation of proteins

• heat- vibrations cause intermolecular bonds to break

• pH, chemicals, salt concentrations
  Charges of R groups of amino acids changing - break ionic bonds and form new ones

Thermophiles

• Archaea that thrive in very hot environments, such as volcanic springs

• Their proteins are stable at much higher temperatures (100 degrees)

What are the nutritional benefits of cooking protein rich foods before injesting them?

• heat denaturation starts the process of digestion of proteins to amino acids

• in the stomach, pH further denatures

• amino acids readily absorbed in small intesine

• can be used for synthesis fo human proteins

Proteomes

The complete complement of proteins that a cell or organism can make.

Genome

All the genetic information in an organism; all of an organism's chromosomes.

Explain why the genome of an organism is fixed but not the proteome?

• all cells carry the same genome

• not all cells make the same proteins

• the range of proteins made in a cell can vary during its lifetime

Why does every organism have a unique proteome?

• every organism has unique genome due to mutations

• genes code for amino acid that code for proteins that code for

• the range of proteins produced thus the proteome

When amino acids bond to form peptide bonds what kind of reaction is it ?

Condensation reaction - water removed

Polymerisation of amino acids

Amino acids can be combined by condensation polymerisation. The products of this reaction are a polypeptide and water.

Word equation for the polymerisation of amino acids

Amino acid 1 + Amino acid 2 = Dipeptide + water (H20)

Effect of pH on protein structure

The charges on R groups are changed- breaking the ionic bonds within the protein or causing New Ionic bonds to form

Effect of temperature on protein structure

- Can cause denaturation - vibrations within the molecule break the intermolecular bonds or interactions

why are some amino acids polar and some are non-polar ?

- Amino acids with hydrophobic R-groups are non-polar (like leucine)
- Amino acids with hydrophilic R-groups are polar (threonine)

Why are cellular enzymes mainly made up of proteins? (5 marks)

• Enzyme function is detremined by shape of active site

• shape of protein is determined by amino acid sequence- very variable

• primary → secondary with a helix abd b pleated regions

• secondary structure held by hydrogen bonds

• secondary → tertiary (3d)

• folding of primary = bonds between amino acids

• hydrogen, ionic and disulfide