IMS1 TBL2 (remake for AKT)

What are proteins

Long chains of amino acids (contain carbon, hydrogen, oxygen and nitrogen)

What does the R group determine?

The chemical characteristics and interactions of each amino acid

How many amino acids are there?

20

Nonpolar (hydrophobic)

Tend to avoid water (eg. alanine and valine)

Polar (hydrophilic)

Interact with water and contains hydroxyl groups (eg. serine, threonine, tyrosine)

How many Non-Polar Amino Acids are there?

10

How many Polar Amino Acids are there?

5

How many + charged amino acids are there?

3

How many - charged amino acids are there?

2

What are the three + charge amino acids?

Lysine, Arginine, Histidine

What are the two - charge amino acids?

Aspartic acid, Glutamic acid

What is an essential amino acid?

Amino acids that cannot be synthesised by the body and must come from the diet

How many essential amino acids are there?

9

What are the 9 Essential Amino Acids

Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Lysine, Leucine (PVT TIM HLL)

What happens if there is essential amino acid deficiency?

leads to issues such as poor growth, weakened immunity, reduced fertility and depression

What is proline becoming hydroxyproline an example of?

Amino acid modification (amino acids can be chemically modified) (addition of a hydroxyl group)

What is required for the synthesis of hydroxyrpoline?

Vitamin C

What does hydroxyproline do?

Stabilise collagen structure

What does a deficiency in hydroxyproline cause?

weak collagen and leads to scurvy

What are the four functions of amino acids?

Protein synthesis, source of energy, source of glucose, precursors of other biomolecules (such as neurotransmitters)

What bond forms polypeptides?

peptide bonds

What is the N terminus (amino acids joining to make polypeptides)

Amino end of the polypeptide chain

What is the C terminus (amino acids joining to make polypeptides)

Carboxyl end of the polypeptide chain

Which way do proteins grow in the polypeptide chain?

from the N terminus to the C terminus

Primary structure of protein

The linear sequence of amino acids in a polypeptide chain

What does primary structure of protein determine?

folding and function of the polypeptide chain

Secondary structure of protein

Alpha helices and Beta sheets

Alpha helices (secondary structure)

Coiled structures

Beta sheets (secondary structure)

strand like structures aligned side by side (zig zag)

Examples where alpha helix motifs are important for proteins

connective tissue (collagen), DNA binding proteins (transcription factors), Membrane proteins (such as ion channels and receptors)

Examples where beta sheet motifs are important for proteins

antibodies, cell surface proteins, enzymes, transport proteins

What bond forms secondary structure of proteins?

Hydrogen bonds form between oxygen in a carboxyl group and the hydrogen in an amine group

What is a hydrogen bond?

A weaker attraction involving hydrogen and electronegative atoms

Tertiary structure

Three dimensional arrangement of the secondary structure of the polypeptide chain, mainly determined by different types of interactions between amino acid side chains

What bonds/interactions are in the side chain reactions that make the Tertiary structure of protein?

Covalent bonds, ionic bonds, hydrogen bonds, hydrophobic interaction

What is a covalent bond?

The mutual sharing of one or more pairs of electrons between two atoms

What is a ionic bond?

Interaction between oppositely charged side chains

What are hydrophobic interactions?

nonpolar side chains aggregate inward to avoid water (the positioning of hydrophilic and hydrophobic residues determines the folding pattern)

Quaternary structure

Formed when multiple polypeptide subunits assemble into a functional protein

What bond types stabilise quaternary protein structure?

Disulphide bridges, hydrogen bonds, ionic bonds and hydrophobic interactions

Protein denaturation

Proteins can lose their structure and function due to pH or temperature changes

What layers of protein structure does denaturation disrupt?

Secondary, tertiary, quaternary

What do chaperone proteins do?

assist in folding new proteins, refolding misfolded proteins, and preventing proteins from clumping together

Alzheimer’s Disease (clinical relevance of protein folding)

Misfolded Tau protein aggregates in neurons

What is the Tau protein (Alzheimer’s)

A protein that primarily exists in neurons and helps stabilise the internal structure of cells by binding to and stabilising microtubules

Parkinson’s Disease (clinical relevance of protein folding)

Misfolded alpha-synuclein forms Lewy bodies

What is alpha-synuclein (Parkinson’s)

a protein found primarily in neurons, where it plays a role in presynaptic terminals, the communication hubs between nerve cells

Creutzfeldt-Jakob Disease (clinical relevance of protein folding)

Infectious prions cause normal proteins to misfold

What are signal sequences

Short peptide segments in amino acid sequences that act as an address tag

What is Protein Sorting?

The process by which proteins are transported to their appropriate destination

What are Post-Translational Modifications?

Covalent modifications of proteins after synthesis

What do Post-Translational Modifications do?

They increase the functional diversity of proteins and help with protein sorting

What is Cotranslational Translocation?

Proteins are synthesised at the same time they are translocated to the endoplasmic reticulum

What are the two primary protein synthesis pathways?

Free ribosomes in cytosol and membrane-bound ribosomes on endoplasmic reticulum

Where do free ribosomes in cytosol make proteins for?

mitochondria, peroxisomes, nucleus

Where do membrane-bound ribosomes on the er make proteins for?

plasma membrane, secretory vesicles, endosomes, lysosomes

What are peroxins?

Proteins which transport other proteins that are targeted into peroxisomes into or across the peroxisomal membrane

What is co-translational translocation?

the process by which a protein is inserted into or transported across a membrane while it is still being synthesized by a ribosome

What is the hydrophobic leader sequence?

15-30 amino acids that the emerging polypeptide from membrane bound ribosomes contain

What recognises the hydrophobic leader sequence?

Signal Recognition Particle (SRP) (The hydrophobic property makes it easy to recognise)

What does the Signal Recognition Particle do?

Halts translation temporarily and directs the ribosome to the translocon channel on the ER membrane

What is the role of the Endoplasmic Reticulum in protein modification?

imports and processes newly synthesised proteins, aiding the growth of the nucleus, golgi apparatus, lysosomes and plasma membrane

What do post-translational modifications (PTMs) do?

increase protein diversity, influence function and localisation, play essential roles in cell signalling and cell regulation

Phosphorylation (PTMs)

Addition of a phosphate group to serine, threonine or tyrosine residues catalysed by protein kinases and reversed by phosphatases

Example of phosphorylation

Golgi apparatus phosphorylation marks proteins for lysosomal transport (proteins not phosphorylated this way are secreted instead)

Hydroxylation (PTMs)

Addition of a hydroxyl group (-OH) hence increasing amino acid reactivity

Example of hydroxylation

collagen hydroxylation is necessary for proper collagen maturation in the extracellular matrix

Ubiquitination (PTMs)

Addition of a ubiquitin molecule and functions primarily to target proteins for degradation via the proteasome

What is a ubiquitin molecule

a 76 amino acid protein

Acetylation (PTMs)

Alters the charge of histone proteins involved in DNA packaging and modifies chromatin structure thereby influencing gene expression and epigenetic regulation

Proteolysis (PTMs)

Cleavage of amino acids or peptide segments from a polypeptide chain and is a common activation mechanism for enzymes and hormones

Example of proteolysis

preproinsulin contains a single peptide that directs it to the ER where disulphide bridges form between cystein residues creating proinsulin, subsequent cleavage yields active insulin composed of two peptide chains connected by disulphide bonds

Disulphide bond formation (PTMs)

Covalent bonds formed between cysteine residues which provide structural stability for secreted and membrane bound proteins

How do membrane proteins play a role in signal transduction?

Act as receptors for peptide hormones, neurotransmitters and other molecules

How do membrane proteins play a role in transport?

Facilitate movement of nutrients, ions and molecules using facilitated and active transport

How do membrane proteins play a role in cell-cell communication/intracellular connections?

Maintaining contact between adjacent cells

How do membrane proteins play a role in cell identification/cell-cell recognition?

Act as markers distinguishing different cell types

How do membrane proteins play a role in anchorage/cell attachement?

Provide attachment points for the cytoskeleton and extracellular matrix

How do membrane proteins play a role in enzymatic activity?

Function as biological catalysts that speed up reactions in metabolic pathways.

Signal Transduction

Transmission of signals from a cell’s exterior to its interior to trigger a response

What is the basic process of signal transduction?

A ligand binds to a membrane receptor and the signal is passed through intermediate molecules to activate a response in the cytoplasm or nucleus

Describe the structure of G Protein Coupled Receptors (GPCRs)

Seven transmembrane a-helices, extracellular region is the ligand binding site and intracellular region is the G protein binding site

What is cAMP cascade activated by?

Triggered by low blood glucose

Explain the cAMP Cascade pathway

Glucagon (ligand) binds to GPCR on liver cells, a subunit activates adenylyl cyclase (AC). Adenylyl cyclase converts ATP into cyclic AMP, which activates Protein Kinase A. Protein Kinase A phosphorylates enzymes leading to glycogen being broken down into glucose hence blood glucose increases

Cyclic AMP Cascade pathway amplification?

Adenylyl cyclase produces many cAMP molecules

What is the phosphoinositide pathway triggered by?

Low blood pressure

Explain the Phosphoinositide pathway?

Angiotensin II binds a-adrenergic GPCR, a subunit activates phospholipase, phospholipase hydrolyses PIP2 into IP3 and DAG (second messengers). IP3 and DAG activate Pritein Kinase C which phosphorylates target proteins leading to vasoconstriction and increased blood pressure

Phosphoinositide pathway amplification

Phospholipase C acts on many PIP2 molecules

Physiological roles of GPCRs Sensory functions

vision, taste, smell

Physiological roles of GPCRs Neural regulation

pain, behaviour, mood (ligands include serotonin and dopamine)

Physiological roles of GPCRs Immune and Inflammatory regulation

Regulation of immune system, including through inflammation

Physiological roles of GPCRs autonomic control

Heart rate, blood pressure, digestion

Physiological roles of GPCRs Endocrine function

Glucagon regulation of glucose

Physiological roles of GPCRs cell proliferation

Can cause cancer if signaling is abnormal

Pertusis Toxin (GPCR Malfunctions and Disease)

Inhibits G-protein receptor interaction leading to G protein stuck in inactive GDP bound form

Rhodopsin Mutation (GPCR Malfunctions and Disease)

Causes continuous activation leading to congenital night blindness

Cholera toxin (GPCR Malfunctions and Disease)

prevents GTP hydrolysis leading to prolonged GTP bound active a subunit hence excess cAMP leading to severe diarrhoea (excess water/salt secretion)

Acquired Mutations (GPCR Malfunctions and Disease)

Overactive receptors or overexpression leading to cancer

What are Receptor Tyrosine Kinases (RTKs)

Another major class of receptors responsible for signal transduction which activate MAP kinase and Phosphatidylinositol pathway

What are the three main structure parts that RTKs consist of?

Extracellular N-terminal domain, Transmembrane a-helix, cystolic C-terminal domain