Amino acids are the building blocks of ______. As described below, amino acids contain differing _____ _____ with varying _______ and ______ properties. The large number of possible _______ of amino acids with different properties allows different types of proteins to have a wide variety of _______, contributing to the multitude of _______ that proteins carry out in the body.
- side groups
- physical and chemical properties
A single protein is built from a chain of _____ _____ linked together by ______ bonds; thus proteins are sometimes referred to as ______ (Greek: polys ~ many).
- amino acids
It is important to be able to recognize the general structure of an amino acid and a polypeptide. A peptide bond creates the functional group known as an _____, an _____ connected to a ______ ______. It is formed via a ______ reaction of _____ _____ ______. The reverse reaction is the ______ of a ______ bond.
- carbonyl carbon
- two amino acids
- peptide bond
Since nitrogen is most stable with ____ bonds and oxygen attracts _____ ______, resulting in a partial ______ charge, electrons _______ to give the peptide bond a partial ______ ______ character. This double bond character prevents the bond from _______ freely and affects the ________ and, to some extent, the ______ structure of the polypeptide
- double bond
Nearly all proteins in all species are built from the same ____ _____ _____.
20 α-amino acids
Why are they called alpha amino acids?
They are called amino acids because the amine is attached to the carbon in the alpha position to the carbonyl.
In humans, _____ of the amino acids are essential, meaning that they cannot be _______ by the body and thus must be ______ directly. Digested proteins reach the cells of the human body as single _____ _____.
- amino acids
Notice the R group on each amino acid. The R group is called the ____ ____ of the amino acid. Each amino acid differs only in its ____ ____. Like the amino group, the side chain is attached to the _______.
- side chain
- R group
The R groups have different chemical properties, which can be divided into four categories: (Name them)
- 1. acidic
- 2. basic
- 3. polar
- 4. nonpolar.
All acidic and basic R groups are also _____. Generally, if the side chain contains ______ _____, then it is acidic; if it contains _____, then it is basic. These properties of the side chains affect the overall ______ of the protein.
- carboxylic acids
The amino acid structures typically depicted are artificial representations. Amino acids in solution, such as in the biological environment, will always carry one or more ______. The position and nature of the ______will depend upon the ___ of the solution.
List and draw the 20 common amino acids
The structure of a protein is described according to several levels of organization. The ______ and ______ of amino acids in a polypeptide is called the primary structure. Once the primary structure is formed, the single chain can form into distinct ______ known as the secondary structure of the protein. The polypeptide can twist into an ______, or lie alongside itself and form a _______ _____.
- number and sequence
- β-pleated sheet
With β-pleated sheets, which directions can the connecting segments of the two strands lie?
the same direction or in opposite directions.
Both a-helices and β-pleated sheets are reinforced by ______ bonds between the ______ ______ of one amino acid and the ______ on the amino group of another. A single protein usually contains both structures at various locations along its chain. These areas of ______ structure contribute to the _______, or overall shape, of the protein.
- carbonyl oxygen
All proteins have a ______ structure and most have areas of ______ structure. ______ proteins can have a tertiary and quaternary structure.
The tertiary structure refers to the three dimensional shape formed by curls and folds of the peptide chain. Five forces contribute to the tertiary structure: (Name them)
- 1. covalent disulfide bonds between two cysteine amino acids on different parts of the chain, creating the dimer cystine
- 2. electrostatic (ionic) interactions, mostly between acidic and basic side chains
- 3. hydrogen bonds
- 4. van der Waals forces
- 5. hydrophobic side chains pushed away from water toward the center of the protein (hydrophobic bonding).
- *In addition to these forces, turns that disrupt both a helix and β-pleated sheet formation are induced by the amino acid proline due to its physical structure
Turns that disrupt both a helix and β-pleated sheet formation are induced by the amino acid proline due to its physical structure (explain)
The R group binds to the amine group, causing proline to be more rigid than a typical amino acid and creating a kink in the structure of the protein
When two or more _______ _____ bind together, they form the quaternary structure of the protein. The same five forces at work in the tertiary structure can also act to form the quaternary structure.
Although many different _______ are possible for any one protein, it will generally exist in one of a few possible conformations that have the highest _______ and allow the protein to carry out its necessary _______.
The water surrounding proteins in the biological environment helps stabilize these ______ conformations. Due to the presence of ________ R groups on the protein, surrounding molecules assemble into an organized structure known as a _______ ______ that forces these hydrophobic groups towards the _____ area of the protein.
- solvation layer
Why is the gathering of hydrophobic R groups away from the surrounding water highly favorable?
Simply because it allows a decrease in the size of the highly ordered solvation layer, increasing the entropy of the system (see the Thermodynamics Lecture of the Chemistry Manual for more on entropy).
When the native conformation is disrupted, the protein is said to be _______. A denatured protein has lost most of its _______, _______ and _______ structure.
- secondary, tertiary, and quaternary
Some denaturing agents and the forces that they disrupt are given in Table 1.1. Very often, once the denaturing agent is removed, the protein will spontaneously _____ to its _____ ______. This suggests that the amino acid _______ plays a key role in the conformation of a protein.
- original conformation
There are two types of proteins: _____ and ____. There are more types of _____ proteins than there are types of ______ proteins. Name 6 functions of globular proteins
- globular and structural
- 7 functions:
- enzymes (e .g. pepsin)
- hormones (e.g. insulin)
- membrane pumps and channels (e.g. Na+ / K+ pump and voltage gated sodium channels)
- membrane receptors (e.g. nicotinic receptors on a post synaptic neuron)
- intercellular and intracellular transport and storage (e.g. hemoglobin and myoglobin)
- osmotic regulators (e .g. albumin)
- in the immune response (e.g. antibodies)
- *and more
Structural proteins are made from long polymers. They maintain and add strength to _____ and ______ structure. Collagen, a structural protein made from a unique type of _____, is the most ______ protein in the body. Collagen fibers add great strength to _____, ______, _______ and _____, among other structures.
- cellular and matrix structure
- skin, tendons, ligaments, and bone
Microtubules, which make up ______ _____ and _____, are made from ______ _____, which polymerizes under the right conditions to become a structural ______.
- eukaryotic flagella and cilia
- globular tubulin
Glycoproteins are proteins with ______ groups attached. These are a component of cellular ______ ______. Proteoglycans are also a mixture of ______ and ______, but they generally consist of more than ___% carbohydrates. Proteoglycans are the major component of the ______ _____.
- plasma membranes
- proteins and carbohydrates
- 50% carbs
- extracellular matrix
Cytochromes (Greek: kytos ~ cell, chroma ~ color or pigment) are proteins which require a _______ (_______) _____ (Greek: haima ~ blood) group in order to function. Cytochromes get their name from the _____ that they add to the cell.
- prosthetic (nonproteinaceous) heme
Two examples of cytochromes
What are proteins containing nonproteinaceous components called?
Hemoglobin and the cytochromes of the electron transport chain in the inner membrane of mitochondria
By creating ______ _____ across membranes, they assist in the transport of substances entering and exiting the cell. They can combine and solidify to give strength to a _____, such as ________ in bone. Minerals also act as ______ (discussed later in this lecture) assisting enzyme or protein function. For instance, iron is a mineral found in _____, the prosthetic group of cytochromes.
- Minerals are the dissolved inorganic ions inside and outside the cell.
- electrochemical gradients
Virtually all biological reactions are regulated and made possible by _______. Enzymes are typically ______ proteins, although there are a few _____ ____ that act as enzymes. Just as the _______ in structure of proteins makes them well-suited for many different biological functions, this variability also facilitates their action as ______. The differing characteristics of enzymatic ____ ______ accounts for the specificity of enzymes for certain substrates, as will be described below.
- globular proteins
- nucleic acids
- R groups
The function of any enzyme is to act as a catalyst (explain)
lowering the energy of activation for a biological reaction and thus increasing the rate of that reaction.
How much can enzymes increase reaction rates?
This is a much ______ increase than typical lab catalysts. *Such extreme control over reaction rates gives enzymes the ability to pick and choose which reactions will or will not occur inside a cell.
- By magnitudes of as much as thousands of trillions.
Without the catalytic effect of enzymes, the energy of activation of essential biological reactions would be ______ high. Thus, enzymes have a regulatory ability (explain)
- Making the body's chemical reactions possible, but ensuring that they occur only when needed.
State 3 characteristics of enzymes
- Enzymes, like any catalysts, are neither consumed nor permanently altered by the reactions which they catalyze.
- Only a small amount of catalyst is required for any reaction.
- Also like other catalysts, enzymes do not alter the equilibrium of a reaction; in other words, they do not alter the relative amount of reactants and products at equilibrium.
The reactant or reactants upon which an enzyme works are called the ______. _______ are generally _____ than the enzyme. The substrate binds to the enzyme at a particular location called the _____ _____, usually with numerous _______ bonds. The enzyme and substrate bind together to form the _____ ______ complex.
- active site
- enzyme substrate complex
Normally, enzymes are designed to work only on a specific substrate or group of closely related substrates. This is called ______ _______. There are two models explaining how this works, state and describe both
- The lock and key model is an example of enzyme specificity. In this theory, the active site of the enzyme has a specific shape like a lock that only fits a specific substrate, the key. The lock and key model explains some but not all enzymes.
- A second theory called the induced fit model says that the shapes of both the enzyme and the substrate are altered upon binding. Besides increasing specificity, the alteration actually helps the reaction to proceed by destabilizing the substrate. In reactions with more than one substrate, the enzyme may also orient the substrates relative to each other, creating optimal conditions for a reaction to take place.
Enzymes exhibit saturation kinetics (explain)
As the relative concentration of substrate increases, the rate of the reaction also increases, but to a lesser and lesser degree until a maximum rate, the Vmax has been achieved.
Why do enzymes exhibit saturation kinetics?
Define Turnover number
This occurs because as more substrate is added, individual substrates must begin to wait in line for an unoccupied enzyme. Thus, Vmax is proportional to enzyme concentration.
Turnover number: the number of substrate molecules one active site can convert to product in a given unit of time when an enzyme solution is saturated with substrate.
Related to Vmax is the Michaelis constant, also known as the ____ (define).
Km (Michaelis constant): the substrate concentration at which the reaction rate is equal to 1/2Vmax.
The value of the Michaelis constant indicates how _____ ______ the substrate must be to speed up the reaction. If a higher concentration of substrate is needed, the enzyme must have a ______ affinity for the substrate. Thus Km is ______ ______ to enzyme-substrate affinity.
- highly concentrated
- inversely proportional
Unlike Vmax, Km does not vary when the _______ ______ is changed; in other words, it is a characteristic of the _____ fit between the enzyme and substrate, rather than reflecting the amount of ______ present. However, the value of Km can be altered by certain types of ______ ______.
- enzyme concentration
- enzyme inhibition
Michaelis-Menten curves plot reaction velocity as a function of ____ _____ and show an enzyme's ____ and ____ (Figure 1.14). They are valuable tools for recalling and understanding the types of _____ _____, as will be discussed further in this lecture
- substrate concentration
- Vmax and Km
- enzyme inhibition
_____ and ____ also affect the rates of enzymatic reactions. At first, as the temperature increases, the reaction rate _______. However, since enzymes are generally proteins, at some point the enzyme _______ and the rate of the reaction _______ precipitously. For enzymes in the human body, the optimal temperature is most often around __°C.
- Temperature and pH
- 37° C
Enzymes also function within specific pH ranges. The optimal pH varies depending upon the enzyme. For instance, pepsin, which is active in the stomach, prefers a pH below ___, while trypsin, which is active in the mall intestine, works best at a pH between ___ and ___.
In order to reach their optimal activity, many enzymes require a non-protein component called a ____ (Latin: co- ~ with or together). Cofactors can be ______ or ____ _____.
- coenzymes or metal ions
What are the two types of coenzymes
- Coenzymes are cofactors that are organic molecules. Many types of water soluble vitamins serve as coenzymes or their precursors.
- Coenzymes are divided into two types: cosubstrates and prosthetic groups.
Cosubstrates ______ bind to a specific enzyme, and transfer some chemical group to another substrate. The cosubstrate then reverts to its original form via another -______ reaction . This reversion to original form is what distinguishes a cosubstrate from ______ substrates. _____ is an example of the cosubstrate type of coenzyme.
Prosthetic groups remain ______ bound to the enzyme throughout the reaction, and, like the enzyme, emerge from the reaction _______. As mentioned previously, _____ is a prosthetic group. It binds with catalase in peroxisomes to degrade _____ _____.
- hydrogen peroxide
Metal ions are the second type of cofactor. They can act _____ or with a _____ group. Typical metal ions that function as cofactors in the human body are _____, _____, _____, ____, _____ and _____.
- prosthetic group
- iron, copper, manganese, magnesium, calcium, and zinc
An enzyme without its cofactor is called an ______ (Greek: apo- ~ away from) and is completely nonfunctional. An enzyme with its cofactor is called a _____ (Greek: holos ~ whole, entire, complete).
Enzymes select which _____ take place within a cell, so the cell must regulate _____ activity. Regulation of enzymes ensures that they are activated when needed by the cell, and that the amount of product created in the reactions that are catalyzed is at the level required for cellular functions. Enzymes are regulated by _____ primary means
What are the four primary means of enzyme regulation. Explain each
- 1. Proteolytic cleavage (irreversible covalent modification)-Many enzymes are released into their environment in an inactive form called a zymogen or proenzyme (Greek: pro ~ before). When specific peptide bonds on zymogens are cleaved, the zymogens become irreversibly activated. Activation of zymogens may be instigated by other enzymes, or by a change in environment. For instance, pepsinogen (notice the "-ogen" at the end indicating zymogen status) is the zymogen of pepsin and is activated by low pH.
- 2. Reversible covalent modification-Some enzymes are activated or deactivated by phosphorylation or the addition of some other modifier such as AMP (adenosine monophosphate). The removal of the modifier is almost always accomplished by hydrolysis. Phosphorylation typically occurs in the presence of a protein kinase, a type of catalytic enzyme.
- 3. Control proteins-Control proteins are protein subunits that associate with certain enzymes to activate or inhibit their activity. Calmodulin and C -proteins are typical examples of control proteins.
- 4. Allosteric interactions-Allosteric regulation is the modification of an enzyme's configuration through the binding of an activator or inhibitor at a specific binding site on the enzyme.
Normally, an enzyme governs just one reaction in a series of reactions. In a phenomenon called ____ ____ or _____ ____, one of the products downstream in a reaction series comes back and inhibits the enzymatic activity of an earlier reaction.
negative feedback or feedback inhibition
When does negative feedback provide a shut down mechanism for a series of enzymatic reactions?
When that series has produced a sufficient amount of product. Most enzymes work within some type of negative feedback cycle.
When does positive feedback occur?
True or False: Positive feedback occurs more often than negative feedback.
When the product returns to an earlier step to activate the associated enzyme.
False: less often
Positive and negative feedback work in a _______ fashion to ensure that a reaction series leads to the right amount of _____.
Negative feedback inhibition is typical in many _____ _____ synthesis pathways. It is wasteful and unnecessary to synthesize amino acids that are readily available in the environment. Therefore, upstream enzymes involved in a particular synthetic metabolic pathway typically have ______ ______ sites that bind the ____ _____ ____ product. If the final product is present in the environment, it acts as an _____ _____ in a ______ feedback loop, preventing synthesis of additional product.
- amino acid
- allosteric inhibitory
- final amino acid
- allosteric inhibitor
Products that exert negative feedback inhibition do not resemble the substrates of the enzymes that they inhibit and do not bind to the active site. In stead, they bind to the enzyme and cause a ______ change. This process is called _____ _____ (Greek: alios --+ different or other, stereos --+ solid), which can be exerted by both _____ _____ and _____ _____.
- allosteric regulation
- allosteric inhibitors and allosteric activators
Not all allosteric inhibitors and activators are necessarily _____ inhibitors (discussed in the next section), because many alter ____ without affecting _____. Allosteric enzymes, meaning enzymes that have sites for allosteric regulation, do not exhibit typical kinetics, why?
- Because they normally have several binding sites for different inhibitors, activators, and even substrates.
At low concentrations of substrate, small increases in concentration ______ enzyme efficiency as well as reaction rate. The first substrate changes the shape of the enzyme, allowing other substrates to bind more easily. This phenomenon is called _____ ____. The opposite phenomenon, ____ cooperativity, occurs as well. Cooperativity in the presence of the allosteric inhibitor i what gives the oxygen dissociation curve of hemoglobin its _____ shape.
- positive cooperativity
Enzyme inhibitors provide an important mechanism for regulation of enzymatic activity in the body. Some inhibitors bind to the active site, thus blocking the _____ from binding. Others bind elsewhere on the enzyme and cause a change in its _____, thus disrupting its specific _____ for the substrate. These general mechanisms for altering enzymatic activity make regulation by _____ and ______ ______ possible.
- positive and negative feedback
Enzyme inhibitors ca n be broadly classified as either _____ or ______. Agents that bind irreversibly to enzymes and disrupt their function are _____ _____. Most inhibitors of this type bind to enzymes via _____ bonds, but a few bind ______. Irreversible inhibitors tend to be highly toxic. Any of the following types of inhibitors can be irreversible if _____ modification occurs.
- irreversible or reversible
- irreversible inhibitors
- covalent bonds
Competitive inhibitors compete with the substrate by binding ______ with ______ bonds to the _____ site. They are the only type of reversible inhibitor that binds directly to the _____ site rather than binding to a different site on the enzyme. Compare both possiblities
- They typically bind directly to the active site for only a fraction of a second, blocking the substrate from binding during that time.
- Of course, the reverse is also true; if the substrate binds first, it blocks the inhibitor from binding.
- Thus, competitive inhibitors raise the apparent Km but do not change Vmax.
In the presence of a competitive inhibitor, the rate of the reaction can be increased to the original, uninhibited vmax by ______ the concentration of the substrate. However, since an _____ concentration of substrate is required to reach Vmax, an increased concentration is also required to reach 1/2Vmax; thus the Km is raised, reflecting the _____ affinity of the enzyme for the substrate.
What is the classic indication of a competitive inhibitor
The ability to overcome inhibition by increasing substrate concentration is the classic indication of competitive inhibitor.
Explain how you would identify each of the four inhibitors
In order to identify each of the four inhibitors, think first about where on the enzyme the inhibitor binds:
- If the inhibitor binds to the enzyme's active site when the substrate is not bound, it is a competitive inhibitor. If it binds to an allosteric site or to the E-S complex, it is one of the other three types.
- Next, ask whether it binds to the enzyme or to the enzyme-substrate complex.
- An inhibitor that binds only to the E-S complex is uncompetitive.
- If it can bind to either the enzyme alone or the E-S complex, it is a mixed inhibitor.
- A noncompetitive inhibitor is a special type of mixed inhibitor that binds with the same affinity whether to the enzyme alone or to the E-S complex.
_______ inhibitors often resemble the substrate. ______ is an antibiotic which competitively inhibits a bacterial enzyme that manufactures folic acid, leading to the death of bacterial cells. Although humans require folic acid, sulfanilamide does not harm humans because we use a different enzymatic pathway to manufacture folic acid.
Unlike competitive inhibitors, ______ inhibitors bind at a site other than the active site. ______ molecules can also bind to a site other than the active site and exert a positive feedback effect, rather than an inhibitory effect.
- uncompetitive inhibitors
Uncompetitive inhibitors do not bind to the enzyme until it has associated with the substrate to form the enzyme-substrate complex. Once the uncompetitive inhibitor has bound, the _____ remains associated with the ______. Thus the apparent affinity of the enzyme for the substrate increases, meaning that Km ______ .
Because the uncompetitive inhibitor only affects enzymes that have already bound substrate, adding more _____ does not overcome the affect of the inhibitor, and Vmax is _____.
Like uncompetitive inhibitors, _____ inhibitors bind at a site on the enzyme other than the active site and thus do not prevent the substrate from binding. Explain the choice of naming
- Their name comes from the fact that they can bind to either the enzyme alone or the enzyme-substrate complex.
Most types of mixed inhibitors have a preference for one or the other, which dictates the effect on Km and Vmax. Mixed inhibitors that act like competitive inhibitors by binding primarily to the enzyme before the substrate is associated ______ Km, just as competitive inhibitors do. In contrast, mixed inhibitors that act more like uncompetitive inhibitors by preferring to bind to the enzyme-substrate complex ____ Kill. All mixed inhibitors ____ Vmax to some extent.
Define Noncompetitive inhibtor
- A special type of mixed inhibitors, they bind
- just as readily to enzymes with a substrate as to those without.
Like other mixed inhibitors, noncompetitive inhibitors bind _______ to an enzyme at a spot other than the _____ site and change the ______ of the enzyme. Because noncompetitive inhibitors do not resemble the _____, they commonly act on more than one type of ______. Unlike competitive inhibitors, they cannot be overcome by _____ _____, so they lower ____. They do not, however, lower the enzyme's _____for the substrate, so ____ remains the same.
- active site
- excess substrate
State the binding site, if it inhibits binding of substrate, its effect on Km and its effect on Vmax
Enzymes are named according to the reactions that they catalyze. Very often, the suffix "-ase" is simply added to the end of the ______ upon which the enzyme acts. For instance, _________ acts upon the ester group in acetylcholine.
According to systematic naming conventions, enzymes are classified into six categories, name them:
- 1. Oxidoreductases catalyze the transfer of electrons or hydrogen ions, i.e. oxidation reduction reactions; .
- 2. Transferases catalyze reactions in which groups are transferred from one location to another;
- 3. Hydrolases regulate hydrolysis reactions;
- 4. Lyases catalyze reactions in which functional groups are added to double bonds or, conversely, double bonds are formed via the removal of functional groups;
- 5. Isomerases catalyze the transfer of groups within a molecule, with the effect of producing isomers (discussed in the Chemistry Manual);
- 6. Ligases catalyze condensation reactions coupled with the hydrolysis of high energy molecules.
- 7. Kinase and Phosphotase
One major distinction between classifications is between ____ and ____. The particular type of lyase that catalyzes the addition of one substrate to the double bond of a second substrate is sometimes called a _____ . ATP synthase is an example of a ____. Ligase enzymes require energy input from _____ or some other _____. Ligases are sometimes called ______.
- lyases and ligases
Kinases and phosphatases may also come up on the MCAT®. Define both
A kinase is an enzyme that phosphorylates a molecule, while a phosphatase is an enzyme that dephosphorylates a molecule.
Often a kinase phosphorylates another enzyme in order to ______ or _______ it. ________ is the enzyme that phosphorylates glucose as soon as it enters a cell (See the Metabolism Lecture to learn how this phosphorylation assists metabolic processes).
- activate or deactivate
The best way to remember the structures of different types of biological molecules is to think back from their ________. Carbohydrates need to be ______, uniform molecules so that they can be used for ______ storage and _______ by all cells. Similarly, nucleotides have to be _______ and highly _______ molecules (including they carbohydrate component) in order to create a stable structure for _______ material
Carbohydrates and lipids are both used for ______ ______, so they both must have a high density of ____ bonds. However, lipids are also used to construct ________, so it makes sense for them to have a _______ end and a _______ end.
- energy storage
- C-H bonds
- polar end
- nonpolar end
Finally, proteins are needed for many different functions in the cell, so they need to be able to have a wide array of possible structures. Thus the building blocks of proteins, in contrast to nucleic acids and polysaccharides, need to have a large ______ of structures amino acids meet the needs of proteins through their ___ groups that vary in ______ and other structural features