Proteins & Enzymes Flashcards
T or F: almost every function of living beings depends on proteins
TRUE
Define proteins
Proteins are a biologically functional molecule that are made up of one or more polypeptides folded into a specific 3D structure.
T or F: humans only have a few different types of proteins
FALSE. humans have thousands of different types of proteins
How many sets of amino acids are ALL proteins constructed from?
the same set of 20 amino acids
Define amino acids
Unbranched polymers linked by a peptide bond
What is a polymer of amino acids called?
a polypeptide
What is a peptide?
a compound consisting of two or more amino acids linked in a chain
What is a dipeptide?
two amino acids linked by a covalent bond (peptide bond)
What is a polypeptide?
unbranched polymers made from any of the 20 amino acids (can be all the same or all different)
Describe peptide bonds
The covalent bond that links amino acid POLYMERS together to form polypeptides.
The carboxyl group of one amino acid will bond with the amino group of another during a DEHYDRATION reaction.
What is a very important kind of protein?
Enzymes (though not all enzymes are proteins, some are RNA-based)
Define catalyst and give an example
a catalyst is a chemical agent that selectively speeds up a chemical reaction without being consumed in the reaction and can be used over and over again
enzymes are catalysts
Describe the two main shapes of proteins and give examples of each
- Globular: roughly spherical
- ex. lactase and amylase enzymes - Fibrous: long, linear fibres
- ex. keratin, collagen
What are the 8 major functions of proteins and give examples
- enzymes CATALYZE specific chemical rxns
- ex. amylase and lactase are digestive enzymes - DEFENSIVE proteins protect organisms from disease
- ex. antibodies - STORAGE proteins store amino acids
- ex. casein, ovalbumin - TRANSPORT proteins move substances throughout an organism or across membranes
- ex. hemoglobin, aquaporin - HORMONAL proteins help coordinate the body’s activities
- ex. prolactin, insulin - RECEPTOR proteins receive chemical signals from outside the cell
- ex. receptors that bind hormones, neurotransmitters, and peptides - CONTRACTILE/MOTOR proteins function in cell movement
- ex. actin and myosin in muscles - STRUCTURAL proteins function in support
- ex. keratin, collagen, silk, elastin
T or F: all amino acids share a common structure
TRUE
Describe what an amino acid is
An organic molecule containing a CARBOXYL group and an AMINO group
In an amino acid, is the central carbon symmetrical or asymmetrical?
ASYMMETRICAL
What are the other terms for an asymmetrical carbon and what does it mean to be asymmetrical?
AKA chiral or alpha
Means the carbon has 4 bonds with 4 different atoms or groups
T or F: If a molecule has an asymmetrical carbon, it can form enantiomers
TRUE
Which 4 things bond to the central carbon of amino acids?
- an amino group
- a carboxyl group
- a hydrogen atom
- a variable R group
Explain how R groups effect amino acids
R groups are different and specific to each kind of amino acid.
R groups determine the different functions and characteristics of different amino acids
T or F: each of the 20 amino acids has a unique R group
TRUE
What is the chemical formula for an amino group?
-NH2
What is the chemical formula for a carboxyl group?
-COOH
What are the four kinds of side chains/R groups that can attach to an amino acid?
- Nonpolar = hydrophobic
- Polar = hydrophilic
- Negatively charged = acidic and hydrophilic
- Positively charged = basic and hydrophilic
How can you tell the R group is nonpolar and hydrophobic?
The R group will consist of nonpolar molecules such as hydrocarbons (H, CH3, etc.)
How can you tell the R group is polar and hydrophilic?
The R group will consist of polar molecules such as CH2-OH; HO-CH-CH3)
How can you tell the R group is charged and hydrophilic?
The R group will have ions.
Negative charge = ACIDIC
Positive charge = BASIC
If an R group has a negative charge, is it acidic or basic?
ACIDIC
If an R group has a positive charge, is it acidic or basic?
BASIC
What type of reaction causes a peptide bond to form?
Dehydration
the OH of the carboxyl group at the C-terminus will bond with the H of the amino group at the N-terminus of another amino acid to form water which will be removed so that a peptide bond can form between the C - N
A functional protein is
one or more polypeptides specifically twisted, folded and coiled into a molecule of unique shape
What determines the unique structure of a protein?
the amino acid sequencing
What determines the sequence of amino acids in proteins?
This information is encoded by genes in the DNA
T or F: A protein’s specific structure directly correlates with how it functions
TRUE
What does a protein’s function depend on?
It’s ability to recognize and bind to another molecule
What are the 4 levels of protein structure?
- Primary
- Secondary
- Tertiary
- Quaternary
Describe the primary protein structure
the linked LINEAR sequence of amino acids connected by peptide bonds that determines all other levels of structure
Describe secondary protein structure. Name the two kinds of secondary structures.
proteins that have segments of their POLYPEPTIDE CHAINS repeatedly coiled or folded in patterns that contribute to the overall shape
These folds and coils are a result of hydrogen bonds between atoms in the N-C POLYPEPTIDE BACKBONE
- Alpha helix
- Beta sheets
Describe the two kinds of secondary structures
- ALPHA HELIX: a delicate coil held together by hydrogen bonding between every FOUR amino acids
- side chains are on the outside - BETA SHEETS: 2 or more strands lie side by side and are connected by hydrogen bonds to form a zig-zag
- many sheets can form and sheets can stack together
Describe tertiary protein structure
the complete 3D structure of a polypeptide chain with irregular folding that is stabilized by interactions between SIDE CHAINS
This structure occurs within a SINGLE polypeptide
What are the five kinds of bonds that can occur in tertiary and quaternary protein structures?
But what is the difference between the bonds in tertiary vs quaternary?
- Hydrogen bonds
- ionic bonds
- covalent bonds
- Disulphide bridges
- Van der Waals interactions
In tertiary structures, these bonds occur between SIDE CHAINS of a single polypeptide
In quaternary structures, these bonds occur between different POLYPEPTIDES
Describe disulphide bridges
Covalent bonds between two sulfhydryl groups
Describe Van der Waals interactions
a weak, temporary asymmetric distributions of orbiting electrons –> the constantly changing regions of + and - cause them to stick together
this only occurs in atoms that form NON-POLAR bonds and when they are very close together
HYDROPHOBIC interactions
How do Van der Waals interactions stabilize tertiary structures?
By giving a force of attraction between + and -
Describe quaternary protein structure
Similar to tertiary, but the interactions are between different POLYPEPTIDES
Only SOME proteins form quaternary structure because the protein must be composed of at least 2 polypeptide chains aggregated into one functional macromolecule
ex. collagen
What happens when a protein is denatured? How does this happen? Give examples
Changes in conditions in the surrounding environment can cause the weak chemical bonds and interactions to be destroyed causing a protein to unravel and lose its shape –> become biologically inactive
Changes in
- pH
- salt concentration
- temperature
Define enzymes
Biological catalysts that are mostly proteins (some are RNA-based ribozymes)
Define cofactors and give examples
Non-protein, inorganic helpers that are required for enzymes to catalyze reactions
ex. Zn, Fe, Cu ions
Define coenzymes and give examples
Cofactors that are organic molecules
ex. NADH, FADH2, CoA
Define activation energy
the energy that a reaction requires for it to occur
How do enzymes effect activation energy?
Enzymes lower the activation energy barrier of a specific reaction so that the state at which it can occur is conducive to life. This also speeds up the reaction because it allows it to happen with less energy.
Why is activation energy important?
Without it, proteins, DNA and other macromolecules would spontaneously break down
What are the two kinds of reactions?
- Exergonic/Exothermic: spontaneous reactions that release energy
- Endergonic/Endothermic: non-spontaneous reactions that require an input of external energy
Describe metabolic pathway and list the two kinds
A metabolic pathway is a series of enzyme-catalyzed reactions
- anabolic pathways
- catabolic pathways
Define anabolic pathways and give an example
CONSUME energy to synthesize complex molecules from simple ones
- endergonic/endothermic
ex. protein synthesis
Define catabolic pathways and give an example
RELEASE energy by breaking down complex molecules into simpler compounds
- exergonic/exothermic
ex. cellular respiration
Define a substrate and substrate specificity
Substrates are the reactants of a reaction that enzymes act on
Each enzyme can only catalyze a specific reaction which means it can only work on a specific substrate
How do enzymes form substrate complexes?
enzymes use weak interactions to bind to its substrate and while joined, the reactant(s) are converted into the product(s)
What is specificity based on?
The shape on an enzyme which is determined by the amino acid sequencing (determined by genetic) code
Describe the active site
The specific spot on the enzyme where the substrate binds
It is usually very small and composed of just a few amino acids
Where does enzyme specificity come from?
the compatible fit between the active site and substrate
Describe induced fit. What is the point of it?
When the enzyme binds the substrate, the enzyme will change shape slightly to hold the substrate tighter
This enhances the ability to catalyze a reaction
What is it called when the enzymes and substrates are bound together?
An enzyme-substrate complex
In what was does an enzyme lower activation energy?
- by correctly orientating substrates
- straining substrate molecules towards a transition state (stresses their bonds)
- providing favourable microenvironment (ex. pH, salinity)
What occurs while the enzyme-substrate complex exists?
The enzyme catalyzes the reaction to convert the reactants (substrates) into products and then releases them to make an available active site
What does the rate by which an enzyme converts a substrate to a product depend on?
- initial concentration of substrate
- shape of enzyme: if their shape changes or is impaired, they cannot accept the same substrates
- temperature and pH
When denaturation of enzymes/proteins occurs, which protein structures are affected?
Structures 2-4 because they have the weakest bonds
Describe inhibition of enzymes. Give examples
an IRREVERSIBLE inhibition that permanently destroys enzyme activity
This usually involves an inhibitor that covalently bonds with the enzyme
ex. cyanide and other poisons
Describe reversible inhibition of enzymes. List the two kinds
A temporary inhibition that stops enzyme activity but can be reversed
This occurs when an inhibitor is weakly bonded to an enzyme (by hydrogen bonds, ionic bonds, hydrophobic bonds, etc.)
- Competitive inhibitors
- Noncompetitive inhibitors
What are the two kinds of reversible inhibitors?
- Competitive: inhibitors with similar shapes to substrates that compete for active sites
- Noncompetitive: inhibitors that bind to an enzyme somewhere other than the active site so that it changes the shape of the active site and prevents substrates from binding
Describe allosteric regulation of enzymes
A protein’s function at one site is affected by binding of a regulatory molecule to a separate site
Describe allosteric enzymes
Enzymes with quaternary structure (composed of 2 or more polypeptides each with its own active site)
the entire enzyme can be in an active or inactive shape
Why is regulation of enzyme activity important?
Metabolic pathways cannot operate all the time otherwise cells would make excess or break down things too readily
Describe feedback inhibition
A metabolic pathway that is switched off by an end product binding as an allosteric inhibitor to an enzyme that acts earlier in the pathway
Stops cells from wasting chemicals
using up the product will remove the inhibitor and allow the pathway to continue
