Studied by 7 peopleDefine dipeptide
A molecule containing two amino acids joined by a single peptide bond
Define oligopeptide
consists of two to twenty amino acids and can include dipeptides, tripeptides, tetrapeptides, and pentapeptides
Define polypeptide
chains of amino acids that are made by linking together amino acids by condensation reactions
State where in the cell polypeptide formation occurs.
Ribosomes
Compare the source of amino acids by plant and animal cells.
Animals :
Animals can synthesise up to 11 amino acids from other amino acids in the body
The remaining nine must be acquired via the diet and the food one ingests
Plants
Plants synthesize their own amino acids from inorganic nitrogen taken up by the roots through active transport
Define essential amino acids
Amino acids that need to be taken in by the body via the diet because the body cannot synthesis them by itself
Define non-essential amino acids
Amino acids that can be synthesised by the body via other amino acids and do not to be taken in by the body
Outline why vegan diets require attention to food combinations to ensure essential amino acids are consumed.
Most essential amino acids are already present in a lot of proteins sources, but for a vegan or vegetarian diet, one needs to make sure they’re eating enough of a variety of foods to make sure they’re getting all necessary amino acids into the body
Outline why there is a limitless diversity of DNA base sequences.
DNA has four bases that can vary in length and arrangement-they can be arranged in virtually any order which gives DNA the ability to store as much information as possible
Because DNA codes for proteins and because proteins can be made up of 20 amino acids, it means that there is a large diversity in proteins as well
Define denaturation.
Denaturation is a structural change in a protein that results in the loss (usually permanent) of its biological properties
Explain the effect of pH on temperature on protein structure and function.
Each protein has its own specific optimum pH or temperature in which they work the best
If the pH or temp is below that, it will work slowly, however if it above that than the proteins will denature and lose their shape, which essentially renders them useless
Outline the effect of R-group structure on the properties of an amino acid with reference to hydrophilic, hydrophobic, polar and charged.
hydrophobic R groups :
form proteins with that are structural and stationary
found in center to stabalise
active site of enzymes like lipase
in contact with membrane localised to surface
hydrophilic :
surface membrane cuz interact with H2O
form channel proteins
found outside enzymes to increase solubility
Charged :
form ionic bonds with other charged r groups in tertiary structure
Define “confirmation” as related to protein structure.
"conformation" related to protein structure refers to the three-dimensional shape or arrangement of a protein molecule. This shape is crucial because it determines the protein's function.
Changes in protein conformation, whether by genetic mutation or environmental factors, can lead to a loss or alteration of function
Describe the primary structure of a protein, including the type of bonding involved.
the sequence of amino acids bonded by peptide bonds
this is determined by the genetic code and is specific to every protein
mutation may arise to incorrect amino acid being ordered and this causes polypeptides with different functions
Outline how a DNA sequence codes for a polypeptide that will repeatedly fold into the same precise, predictable protein confirmation.
Transcription:
DNA to mRNA: The DNA sequence of a gene is transcribed into messenger RNA (mRNA) in the nucleus. The enzyme RNA polymerase reads the DNA template strand and synthesizes a complementary strand of mRNA.
Translation:
mRNA to Polypeptide: The mRNA is then translated into a polypeptide chain in the ribosome. Transfer RNA (tRNA) molecules bring amino acids to the ribosome, where the mRNA codons are read in sets of three nucleotides (codons) that correspond to specific amino acids.
Amino Acid Sequence:
The sequence of codons in the mRNA determines the sequence of amino acids in the polypeptide chain. This sequence is known as the primary structure of the protein and is crucial because it dictates how the polypeptide will fold.
Protein Folding:
Secondary Structure: The polypeptide chain folds into local structures such as alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds between the backbone atoms.
Tertiary Structure: Further folding results in the overall three-dimensional shape of a single polypeptide chain, driven by interactions among the side chains (R groups) of the amino acids, including hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.
Quaternary Structure: For proteins with more than one polypeptide chain, the quaternary structure is formed by the assembly of these subunits.
Predictability of Folding:
The specific sequence of amino acids (primary structure) ensures that the protein will fold in a precise and predictable manner. This is because the chemical properties and interactions of the amino acid side chains lead to the formation of the secondary, tertiary, and quaternary structures.
Chaperone proteins sometimes assist in the proper folding of polypeptides to ensure they reach their correct conformation.
Functional Protein:
The correctly folded protein achieves its functional conformation, which is necessary for its biological activity. The precise folding is critical because the three-dimensional shape of the protein determines its specific function, whether it be enzymatic activity, structural support, transport, or signaling.
Describe the secondary structure of a protein, including the type and location of the bonds involved.
forming of complex shapes from the primary structure, which are just chains of polypeptides
these are caused by weak H bonds between non-adjacent amino acids which change their linear shape
they can form either alpha helices or beta-plated-sheats
Describe the tertiary structure of a protein, including the types of R-group interactions involved.
tertiary structure refers to the forming of complex 3d shape from alpha helices and beta-plated-sheets
very specific shape for each function
Interactions with R groups :
H bonds between polar R groups
hydrophobic interactions between R group of nonpolar AA with protein interior to avoid contact with water
covalent bonds between R group of cytesine AA to form disulfide bridges
Ionic bonds between positive and negative R groups by dissociation or binding of H ions
Explain the effect of polar and non-polar R-groups of amino acids on tertiary structure of proteins.
Hydrogen Bonds:
Polar R-groups contain atoms that can form hydrogen bonds with other polar groups, including other R-groups, the backbone of the protein, and water molecules. These hydrogen bonds help stabilize the folded structure of the protein.
Interactions with Water (Hydrophilic):
Polar R-groups are hydrophilic, meaning they are attracted to water. In aqueous environments, these R-groups tend to be located on the exterior of the protein, interacting with the surrounding water molecules. This helps make the protein soluble in water.
Ionic Bonds:
Some polar R-groups are charged (acidic or basic amino acids). These charged R-groups can form ionic bonds (salt bridges) with oppositely charged R-groups, further stabilizing the protein’s structure.
Hydrophobic Interactions:
Non-polar R-groups are hydrophobic, meaning they repel water. In aqueous environments, these R-groups tend to cluster together in the interior of the protein, away from water. This clustering is driven by hydrophobic interactions, which significantly contribute to the folding and stability of the protein’s core.
Van der Waals Interactions:
Non-polar R-groups can also participate in van der Waals interactions, which are weak attractions between non-polar molecules or parts of molecules. These interactions help pack the non-polar R-groups tightly together in the protein core, contributing to the protein’s overall stability.
Folding Pattern:
The distribution of polar and non-polar R-groups influences the folding pattern of the protein. Polar R-groups generally face the aqueous environment, forming hydrogen bonds and ionic interactions, while non-polar R-groups cluster inside, driven by hydrophobic interactions.
Stability:
The specific interactions among R-groups (hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces) collectively stabilize the protein’s tertiary structure.
Functional Conformation:
The precise arrangement of polar and non-polar R-groups is crucial for the protein to achieve its functional conformation. Any changes in the sequence of amino acids (mutations) can disrupt these interactions, potentially leading to misfolding and loss of function.
Explain the effect of positively and negatively charged amino acid R-groups on the tertiary structure of proteins.
Electrostatic (Ionic) Interactions:
Positively charged R-groups, such as those of lysine (Lys) and arginine (Arg), can form ionic bonds with negatively charged R-groups. These electrostatic interactions are also known as salt bridges or ion pairs.
These interactions help stabilize the folded structure of the protein by bringing together different parts of the polypeptide chain.
Interaction with Negatively Charged Groups:
Positively charged R-groups can interact with negatively charged groups on other molecules, such as DNA or the phosphate groups of ATP, which can be crucial for the protein’s function.
Hydrophilicity:
Positively charged R-groups are hydrophilic, meaning they are attracted to water. These groups tend to be located on the exterior of the protein, interacting with the aqueous environment, which helps make the protein soluble.
Electrostatic (Ionic) Interactions:
Negatively charged R-groups, such as those of aspartic acid (Asp) and glutamic acid (Glu), can form ionic bonds with positively charged R-groups. These salt bridges contribute to the stabilization of the protein’s tertiary structure.
They can also repel each other if they are too close together, which helps in maintaining the proper folding and conformation of the protein.
Interaction with Positively Charged Groups:
Negatively charged R-groups can interact with positively charged groups on other molecules, such as metal ions or other proteins, which can be critical for the protein’s biological activity.
Hydrophilicity:
Like positively charged R-groups, negatively charged R-groups are also hydrophilic. They tend to be found on the surface of proteins, interacting with the surrounding water molecules.
Stabilization through Ionic Bonds:
The formation of ionic bonds between positively and negatively charged R-groups (salt bridges) is a major stabilizing force in the tertiary structure of proteins. These interactions help maintain the specific three-dimensional shape necessary for the protein’s function.
Surface Localization:
Charged R-groups are typically found on the protein’s surface, where they interact with the aqueous environment. This positioning not only stabilizes the protein but also facilitates interactions with other molecules, such as substrates, inhibitors, and other proteins.
Influence on Folding:
The distribution and interaction of charged R-groups influence the way the protein folds. Proper folding is essential for achieving the functional conformation of the protein. Misfolding, often due to disrupted ionic interactions, can lead to loss of function or diseases.
Functional Sites:
Charged R-groups are often involved in the active or binding sites of enzymes and other proteins. Their ability to form ionic interactions can be crucial for substrate binding, catalysis, and interactions with other biomolecules.
Where does a strong disulfide bond occur?
between R groups of cysteine amino acids
Discuss the arrangement of amino acids in soluble globular proteins.
Non-polar oriented towards the center
polar R-groups oriented outside
This allows them to still be soluble and take part in metabolic reactions
Discuss the arrangement of amino acids in integral membrane bound proteins.
Hydrophobic Core Interaction:
The regions of integral membrane proteins that span the lipid bilayer are rich in hydrophobic (non-polar) amino acids. These hydrophobic amino acids, such as valine, leucine, isoleucine, phenylalanine, and methionine, interact favorably with the hydrophobic fatty acid tails of the phospholipids.
These hydrophobic regions typically form alpha-helices or beta-barrels, which are secondary structures that can traverse the hydrophobic core of the membrane. Alpha-helices are more common and usually consist of about 20-25 amino acids that can span the membrane's thickness.
Transmembrane Domains:
The segments of the protein that pass through the membrane are known as transmembrane domains. These domains are usually alpha-helices with hydrophobic amino acids facing outward, interacting with the lipid bilayer, and sometimes with hydrophilic amino acids facing inward, forming a pore or channel.
In beta-barrel structures, the outer surface is hydrophobic to interact with the lipid bilayer, while the inner surface is often hydrophilic to allow passage of polar molecules or ions.
Extracellular and Cytoplasmic Interactions:
The portions of the protein that extend into the aqueous environments on either side of the membrane (extracellular and cytoplasmic regions) are typically rich in hydrophilic (polar) amino acids. These regions interact with the aqueous surroundings and often contain sites for signal transduction, ligand binding, or interaction with other cellular components.
These regions often have charged amino acids (e.g., lysine, arginine, aspartic acid, glutamic acid) and polar amino acids (e.g., serine, threonine, tyrosine) that help stabilize the protein's conformation through interactions with the aqueous environment.
Selective Transport:
The arrangement of hydrophobic and hydrophilic amino acids in transmembrane proteins is critical for their function as channels or transporters. The hydrophobic regions anchor the protein in the membrane, while the hydrophilic regions form channels or pores that allow specific molecules to pass through the membrane.
Signal Transduction:
Integral membrane proteins often function as receptors. The extracellular domain binds to signaling molecules (ligands), while the intracellular domain transmits the signal into the cell, often initiating a cascade of intracellular events. The specific arrangement of amino acids facilitates these interactions and ensures proper signaling.
Structural Support:
Some integral membrane proteins serve as anchors, connecting the cell membrane to the cytoskeleton or extracellular matrix. The arrangement of amino acids in these proteins ensures they can form strong interactions with both the membrane and structural elements inside or outside the cell.
Enzymatic Activity:
Certain integral membrane proteins have enzymatic functions. Their active sites, often located in the extracellular or cytoplasmic regions, are composed of specific amino acids arranged to catalyze reactions effectively.
Discuss the arrangement of amino acids in channel proteins in membranes.
Transmembrane Domains:
Channel proteins typically have multiple transmembrane domains composed of alpha-helices. These helices span the lipid bilayer and are rich in hydrophobic (non-polar) amino acids, such as leucine, isoleucine, valine, and phenylalanine, which interact favorably with the hydrophobic core of the membrane.
The hydrophobic amino acids face the lipid bilayer, anchoring the protein within the membrane.
Pore Formation:
The transmembrane domains are arranged in a way that creates a central pore or channel. The inner lining of this pore is formed by the hydrophilic (polar) amino acids, creating a pathway that can interact with water and polar molecules or ions.
The specific arrangement of these polar amino acids determines the selectivity of the channel, allowing only certain ions or molecules to pass through based on size, charge, and other properties.
Selectivity Filter:
Many channel proteins have a selectivity filter, a region within the pore that determines which ions or molecules can pass through. This filter is composed of specific amino acids arranged to create a highly selective environment. For example, in potassium channels, the selectivity filter allows potassium ions to pass while excluding smaller sodium ions due to differences in ionic radius and hydration energy.
Gating Mechanisms:
Channel proteins often have gating mechanisms that control the opening and closing of the channel. These gates are influenced by changes in voltage (voltage-gated channels), binding of ligands (ligand-gated channels), or mechanical stress (mechanically-gated channels).
The amino acids involved in the gating regions are critical for sensing these signals and inducing conformational changes that open or close the channel.
Ion Transport:
The arrangement of amino acids in the channel's pore allows for selective ion transport, which is crucial for maintaining cellular homeostasis, generating electrical signals in neurons, and various other physiological processes.
For example, in the sodium-potassium pump, specific amino acids bind to sodium and potassium ions, allowing their selective transport across the membrane.
Water Transport:
Aquaporins are a type of channel protein specifically for water transport. The arrangement of amino acids in aquaporins creates a highly selective pore that allows water molecules to pass through while excluding ions and other solutes.
Signal Transduction:
Ligand-gated ion channels play a role in signal transduction by opening in response to the binding of a signaling molecule (ligand). The specific arrangement of amino acids in the ligand-binding site and the pore allows these channels to convert chemical signals into electrical signals.
Cellular Communication:
Gap junctions are channel proteins that form direct connections between adjacent cells, allowing ions and small molecules to pass directly from one cell to another. The amino acid arrangement in these channels ensures selective permeability and communication between cells.
Describe the quaternary structure of a protein.
for more than one polypeptide chain which can be referred to as subunits
sometimes they have prosthetic groups and are then referred to as conjugated proteins
Compare the structure of conjugated and non-conjugated proteins.
Definition: Non-conjugated proteins, also known as simple proteins, are composed solely of amino acids. They do not contain any non-protein components.
Structure:
Primary Structure: The linear sequence of amino acids linked by peptide bonds, determined by the gene encoding the protein.
Secondary Structure: Localized folding into alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds between the backbone atoms.
Tertiary Structure: The overall three-dimensional shape formed by further folding and interactions among the side chains (R groups) of the amino acids. This includes hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.
Quaternary Structure: Some non-conjugated proteins have quaternary structures formed by the assembly of multiple polypeptide chains (subunits), held together by the same types of interactions as in the tertiary structure.
Examples:
Myoglobin: A simple globular protein involved in oxygen storage in muscles.
Keratin: A fibrous protein providing structural support in hair, nails, and the outer layer of skin.
Definition: Conjugated proteins consist of a protein component combined with one or more non-protein components, known as prosthetic groups, which are essential for the protein's function.
Structure:
Primary Structure: Similar to non-conjugated proteins, composed of a linear sequence of amino acids.
Secondary Structure: Alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds.
Tertiary Structure: The three-dimensional folding pattern involving interactions among amino acid side chains and the incorporation of the prosthetic group.
Quaternary Structure: In some conjugated proteins, multiple polypeptide chains and their associated prosthetic groups form a functional complex.
Prosthetic Groups:
These are non-protein components that can be organic molecules (e.g., vitamins) or metal ions. They are tightly bound to the protein and are crucial for its biological activity.
Examples:
Hemoglobin: A globular protein with four polypeptide subunits, each containing a heme group (iron-containing prosthetic group) essential for oxygen transport in the blood.
Cytochromes: Proteins involved in electron transport in cellular respiration and photosynthesis, containing heme groups as prosthetic groups.
Glycoproteins: Proteins with carbohydrate prosthetic groups, important in cell-cell recognition and signaling.
Lipoproteins: Proteins with lipid prosthetic groups, crucial for lipid transport in the bloodstream.
Composition:
Non-Conjugated Proteins: Composed only of amino acids.
Conjugated Proteins: Composed of amino acids and one or more prosthetic groups.
Functionality:
Non-Conjugated Proteins: Functions are determined solely by the amino acid sequence and resulting structure.
Conjugated Proteins: Functions are significantly influenced by the prosthetic groups, which are essential for the protein's biological activity.
Examples:
Non-Conjugated Proteins: Myoglobin, keratin.
Conjugated Proteins: Hemoglobin (with heme groups), cytochromes (with heme groups), glycoproteins (with carbohydrate groups), lipoproteins (with lipid groups).
Role of Prosthetic Groups:
Non-Conjugated Proteins: Lack prosthetic groups, with function arising from the polypeptide chain alone.
Conjugated Proteins: Prosthetic groups are integral to the protein's function, often involved in binding sites, catalytic activity, or structural stability.
State an example of a conjugated and non-conjugated protein.
Haemoglobin is conjugated and insulin is non-conjugated
Describe, with reference to collagen, the structure and function of fibrous proteins.
Fibrous proteins are long strands with crosslinks with H bonds
They are hydrophobic and have limited number of AA, so sequences are repetitive
used for structural things, strong and organized
Collagen is used to build connective tissues like tendons, cartilage, skin, cornea of the eye and etc
It is a triple helix held by H bonds
100 AA
glycine, proline, hydroxyproline
covalent crosslinks R groups in interacting triple helices which form fibrils
They have staggered ends that provide strength
firbrils turn into fibres, positioned to line up with forces to withstand
Describe, with reference to insulin, the structure and specificity of globular proteins.
They are compact and spherical in the tertiary structure
they are also hydrophilic
Insulin is made of two chains, one 21 length and the other 30, connected by disulfide bridges
Form dimers and hexamers for storage
Note
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