Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > Amino Acids, Peptides and Protiens > Flashcards

Amino Acids, Peptides and Protiens Flashcards

1
Q

Amino Acid Properties

A
  • Amine Group left
  • Carboxylic group on the right
  • Both of these functional groups are joined by an alpha carbon
    • The alpha carbon has a hydrogen and a unique R group, also known as the side-chain
    • The R group is what makes each amino acid distinct
  • Carboxylic acids have a low pKa, and the proton will dissociate at physiological pH creating an negatively charged carboxylate
  • Amines have a high pKa, will accept a proton and act as a base at physiological pH and will be positively charged
    • Hence, amino acids are often called dipolar ions
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Fischer Projection

A
  • All of the 20 proteinogenic amino acids are L-amino acids
    • The reason it is L is because the highest priority group is pointing to the left in a Fischer projection
  • 19/20 proteinogenic amino acids are also chiral, except for glycine.
    • A chiral centre has four different groups attached
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

How Amino Acids join together

A
  • When the nitrogen of the backbone of one amino acid nucleophilically attacks the backbone carbonyl carbon of another amino acid.
  • The resulting bond is commonly called a peptide bond, but it is functionally an amide group.
    • This happens repeatedly in our body using ribosomes to help place and catalyze the creation of the peptide bond.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Amides feature to a peptide bond

A
  • The lone pair on the nitrogen in an amide participates in resonance to create a partial double bond between the carbonyl carbon and nitrogen
    • This creates structural stability within the protein chain
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Glycine

A
  • Three letter code: Gly
  • One letter code: G
  • Property: Achiral
  • Simpliest and smallest amino acid.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Proline

A
  • Three-letter code: Pro
  • One-letter code: P
  • Property: “cis” amino acid
  • In proline the sidechain coming off the alpha carbon is attached on the other end to the nitrogen of the backbone
    • This creates the “cis” amino acid, which creates kinks when proline is included in the middle of a secondary structural element like an alpha helix
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Alanine

A
  • Three-letter code: Ala
  • One-letter code: A
  • Property: Hydrophobic
  • R Group: Methyl group
  • All amino acids EXCEPT glycine have a beta carbon
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Valine

A
  • Three letter code: Val
  • One letter code: V
  • Property: Hydrophobic
  • Adding a “V” of carbons to that beta carbon
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Leucine

A
  • Three-letter code: Leu
  • One-letter code: L
  • Property: Hydrophobic
  • Adding one more methyl group to the chain before it splits into the V
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Isoleucine

A
  • Three-letter code: Ile
  • One-letter code: I
  • Property: Hydrophobic
  • It is an isomer of leusine, so it has the same number of carbons and hydrogens
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Phenylalaine

A
  • Three-letter code: Phe
  • One-letter code: F
  • Property: Hydrophobic, aromatic
  • You start with a methyl group like an alanine and then add a phenyl group.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Tyrosine

A
  • Three-letter code: Tyr
  • One letter code: Y
  • Property: aromatic, mildly hydrophobic
  • Adding an OH group to phenylalanine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Tryptophan

A
  • Three-letter code: Trp
  • One-letter code: W
  • Property: Aromatic, hydrophobic
  • Has one of the largest side chains, with a nitrogen attacked to a phenyl group
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Methionine

A
  • Three letter code: Met
  • One-letter code: M
  • Property: Hydrophobic, start codon
  • Found at the beginning of most proteins
    • Since it also serves as a signal to indicate that protein synthesis is beginning at this part of the mRNA sequence
  • The codon that codes of methionine is AUG, which is also known as the start codon
  • This is one of two amino acids with a sulfur in the side chain
    • The sulfur is flanked by carbons on either side, which cancels out any polarity conferred by the sulfur, making the side chain mostly hydrophobic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Amino Acids with Polar Side Chains

A
  • Serine
  • Threonine
  • Asparagine
  • Glutamine
  • Cysteine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Serine

A
  • Three letter code: Ser
  • One letter code: S
  • Property: Hydrophobic, can be phosphorylated
  • An Alanine with an OH group added
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Threonine

A
  • Three-letter code: Thr
  • One-letter code: T
  • Property: Hydrophobic, can be phosphorylated
  • Adding a methyl group to the beta carbon of serine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Cysteine

A
  • Three-letter code: Cys
  • One-letter code: C
  • Property: Mildly hydrophilic, covalent disulfide bonds
  • The oxygen in the side chain is replaced with the sulfur
  • While it is not normally phosphorylated, if you put two cysteine side chains close together in an oxidizing environment, it forms a disulfide bond, which is a covalent link between two sulfur atoms
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Cysteine

A
  • Three-letter code: Cys
  • One-letter code: C
  • Property: Mildly hydrophilic, covalent disulfide bonds
  • The oxygen in the side chain is replaced with the sulfur
  • While it is not normally phosphorylated, if you put two cysteine side chains close together in an oxidizing environment, it forms a disulfide bond, which is a covalent link between two sulfur atoms
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Asparagine

A
  • Three letter code: Asn
  • One letter code: N
  • Property: Hydrophilic
  • Has amide as its side chain attached to a beta carbon
    • Unlike the amino groups common to all amino acids, the amide nitrogens do not gain or lose protons with chains in pH; they do not become charged.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Glutamine

A
  • Three-letter code: Gln
  • One letter code: Q
  • Property: Hydrophilic
  • Almost the same as asparagine, but with one more carbon in the side chain before ending with the amide.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Negatively Charged (Acid Amino Acids ) Side chains

A
  • Aspartic Acid (Aspartate)
  • Glutamic Acid (Glutamate)
  • At physiological pH, the carboxylic acid in both side chains is deprotonated and negatively charged
  • The “ate” ending indicated the deprotonated from of an acid.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Aspartic Acid (Aspartate)

A
  • Three letter code: Asp
  • One-letter code: D
  • Property: Negative charge
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Glutamic Acid (Glutamate)

A
  • Three-letter code: Glu
  • One letter code: E
  • Property: Negative Charge
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Positively Charged (Basic) Side Chains

A
  • Lysine
  • Histidine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Lysine

A
  • Three-letter code: Lys
  • One letter code: K
  • Property: Positive charge
  • Long alkyl chain that is capped with an amine
  • At physiological pH, the amine is protonated and positively charged
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Arginine

A
  • Three letter code: Arg
  • One letter code: R
  • Property: Positive Charge
  • Also has a long alkyl chain, but it is capped by an unusual functional group called a guanidino
  • One of the nitrogens at physiological pH is protonated and positively charged
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Histidine

A
  • Three letter code: His
  • One letter code: H
  • Property: Can be positive charged
  • The side chain is an imidazole ring, which is aromatic
  • One of the nitrogen’s in the imidazole ring has the capability of accepting a proton and becoming positively charged, which is why it is classified along with arginine and lysine as a base.
    • However, the pKa of the nitrogen is around 6.5, and so remains neutral and uncharged in physiological conditions since that is below physiological pH
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Isoelectric Point (pl)

A
  • pH at which the greatest concentration of the compound may carry a charge, but with the net charge of zero
  • For a molecule to have a pI must mean that the compound has at least two ionizable groups
  • Since all amino acids have at least the backbone amine and carboxylic acids, they will also have an isoelectric point
29
Q

Isoelectric point Alanine (example)

A
  • Has two ionizable groups - the backbone amine and carboxylic acid.
  • At physiological pH, the amine is protonated and the carboxylic acid is deprotonated
  • When the pH dips below 2.3, the carboxylic acid regains its proton and loses its charge
  • The fully protonated form of alanine has a +1 charge
  • On the other side when the pH is greater than 9.7, the amine donates its proton and loses the positive charge.
  • The fully deprotonated from of alanine has a -1 charge
30
Q

Primary Structures of Proteins

A
  • Linear chain of amino acids that are linked together by peptide bonds
    • Reminder, peptide bonds are a special type of an amide bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid
  • These individual amino acids that are linked together by these peptide bonds are referred to as residues.
  • One end of the chain as an exposed amino group which is called the N-terminus and at the other end of the chain there is an exposed carboxyl group called that C-terminus.
  • These individual residues will dictate how all our proteins will fold at all the higher structural levels.
31
Q

Secondary Structures of Proteins

A
  • Consist of two thing:
    • Alpha-helices
      • Thing of long coiling structures that snake up clockwise
      • A carboxyl oxygen atom and an amide hydrogen atom further down the chain form intramolecular hydrogen bonds at the core of the helix, allowing for side chains of the amino acids to point outwards.
    • Beta-pleated sheets
      • They can be either parallel or antiparallel, where our linear peptide chains basically lie on top of and alongside one another.
      • These create rows that are again held together by those intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in the adjacent chains
      • The pleats come from the fact that the structure wants to create as many hydrogen bonds as possible; it will contort the sheets slightly to get those oxygen and hydrogens close enough to interact and stabilize the structure.
  • These structures are formed by H-bonds between nearby amino acid residues.
  • Intramolecular hydrogen bonding between the residues dictate a protein’s secondary structure
32
Q

Proline in Beta-Pleated sheet

A
  • Plays a role in the formation of beta-pleated sheets
  • Due to the tight hydrocarbon loop on its side chain, proline is the perfect size for creating turns between chains of beta-pleated sheets
  • Its tight loop makes it unideal to be found in the middle of either alpha-helices or beta-pleated sheets because there proline will introduce a kink
    • It would be found at the end of rows not in the middle of the structure
33
Q

Tertiary Structure of Proteins

A
  • Instead of one interaction causing the shape there are multiple which include:
    • Hydrophilic interaction
    • Hydrophobic
    • Covalent linkages
  • Hydrophobic structures are often hidden in the centre and as they are tucked away toward the centre of the protein structure, the hydrophilic linkers from the amino and carboxyl groups get dragged inward too, stabilizing themselves through electrostatic interactions and hydrogen bonding.
  • When this happens the hydrophilic side chains have no where else to go but to stick out on the surface of the protein
34
Q

Quaternary Structures

A
  • High-end feature that is not available unless you are a “luxury” model of a protein.
  • All proteins have primary, secondary and tertiary structures, but not all have quaternary structure characteristics
  • QS involves subunits of smaller globular peptides that all come together and dictate the overall function and stability of these “luxury-class” proteins
  • Lower surface area provides more stability
  • Needs less DNA to encode them
  • Structurally flexible to bring together catalytic sites
  • Allows for allosteric effects through conformational changes
35
Q

Enzyme

A
  • A protein that functions as a catalyst in biological process
  • Each enzyme only works with specific chemical reactions and substrates
  • Molecules that are affected by an enzyme are called substrates.
  • The active site is where the substrate is being held and is where all the action happens
  • For Example: in a ribosome subunit enzyme, the mRNA substrate fits into the active site to undergo translation.
    • This is where the enzyme can assist in the reaction and in this case to initiate, elongate and terminate the growing peptide chain
36
Q

Catalysts

A
  • accelerate chemical reactions by lowering the activation energy of the reaction
  • They remain unchanged and are not consumed during the course of a reaction, and must be regenerated
  • Thus an enzyme catalyst should appear in both the initial and final stages of a reaction in the exact same state
37
Q

Active Site

A
  • Where we expect to change the molecule or to affect a chemical reaction
38
Q

Active Site

A
  • Where we expect to change the molecule or to affect a chemical reaction
39
Q

Enzyme-Substrate Specificity

A
  • The active site needs to match a substrate based on a variety of factors that include the shape, the size, charge, polarity and hydrophilicity and hydrophobicity.
40
Q

Induced Fit Model

A
  • A conformational change occurs in the enzyme, the substrate or both
  • Conformational changes can happen before during and after the actual reaction
  • Physical changes can happen to both the active site on the the enzyme and the substate
    • The end result is that they fit together properly and the reaction can move forward.
41
Q

Coenzymes

A
  • Extrinsic organic molecules that are necessary for protein and enzyme function
  • Examples are vitamin C and A
42
Q

Prosthetic Group

A

non-peptide compounds that mostly attach to proteins and assist them in different ways

42
Q

Prosthetic Group

A

non-peptide compounds that mostly attach to proteins and assist them in different ways

43
Q

Cofactors

A
  • Inorganic molecules that are necessary for protein function
  • Usually free metal ions, but can be polyatomic
  • Dietary mineral requirements:
    • Fe, Zn, Cu, Mg, Mn, Co
  • When an enzyme has a metal ion bound to it, it’s referred to as a metalloprotien
44
Q

Holoenzyme

A

The whole enzyme is called a holoenzyme (with all the necessary components)

45
Q

Apoenzyme

A

The enzyme does not have all the necessary components and can not get it’s job done

46
Q

Types of Enzymes

A
  • Mnemonic: LIL HOT
  • Ligase
  • Isomerase
  • Lysases
  • Hydrolases
  • Oxidoreductases
  • Transferases
47
Q

Ligases

A
  • Use ATP to link biological molecules together
  • Generally functioning during DNA synthesis or DNA repair
  • Come in to fill in the gaps between Okazaki fragments
48
Q

Isomerases

A
  • Rearrange the atomic connection within a molecule
  • Can catalyze one molecule to reconfigure itself into another molecule entirely, like phosphoglycerate mutase, which moves a phosphate group between two carbons turning phosphoglycerate to 2-phosphoglycerate in glycolysis
49
Q

Lyases

A
  • Cleaving enzyme
  • Split molecules without water
  • when these portions are broken off, they tend to form rings or multiple bonds in order to reestablish the octet of electrons around each atom
50
Q

Hydrolyses

A
  • Add water into a reaction, causing a molecule to break into its components and bond to the hydrogen and hydroxide molecules
  • For example: Pepsin is a hydrolase that breaks down proteins into peptides and amino acids
    • Since it breaks down proteins it can also be characterized more specifically as a protease
51
Q

Oxidoreductases

A
  • Catalyze the transfer of electrons between biological molecules
  • Example: glyceraldehyde-3-phosphate dehydrogenase, which transfers an electron from glyceraldehyde-3-phosphate to NAD+, generating 1,3-bisphosphoglycerate and NADH
52
Q

Transferases

A
  • Transfer functional groups between independent molecules, often using coenzyme donors
  • Typically named after the functional group being moved
    • One exception to this rule though is kinase.
    • Kinase transfer phosphate groups to another molecule, but these are often names based on the molecule they’re phosphorylating
53
Q

Enzyme Kinetics

A
  • The study of the rates of enzyme catalyzed reactions
  • Involves measuring the rate of a reaction under varying conditions
54
Q

Michaelis-Menten Equation

A
  • Describes how the rate of an enzyme catalyzed reaction depends on the concentration of both the enzyme and the substrate
55
Q

Michaelis-Menten Equation pt2

A
  • Km → Michaelis Constant: measure of enzyme affinity
  • Higher Km → Lower affinity for substrate since more substrate is requires to meet half of the enzyme velocity
  • Lowe Km → Higher affinity for substrate since less substate is required to reach the half-max speed.
  • Rate increases much more slowly as it approaches Vmax and at Vmax the reaction rate is independent of substrate concentration
56
Q

Catalytic Efficiency

A
  • Large Kcat → Increased catalytic efficiency
  • Small Km → High affinity for the substrate and increased catalytic efficiency
57
Q

Cooperativity

A
  • When the binding of a ligand to one site influences the binding at a second site
  • Cooperative enzymes are always made of multiple subunits with multiple active sites
  • The enzyme subunits can exist in one of two state”
    • Low affinity tense (T) state → Inactive form
    • High-affinity relaxed (R) state → Stabilized active form
  • The binding of substrate to one subunit encourages the transition of another subunit from the tense to the relaxed state
  • These newly relaxed subunits have an increased likelihood of binding structures to substrates, and more substrate binding means an increase in reaction rate.
  • Thus the substrate concentration increases, the slope of the curve gets steeper, indicating an acceleration in reaction rate
  • Loss of substrate by one subunit can encourage the transition of other subunits from the R state to the T state, promoting dissociation of substrate from those subunits
58
Q

Hill’s Coefficient

A
  • Used to indicate the nature of the cooperativity
  • When the coefficient is greater than 1, positive cooperative binding is occurring, meaning binding is encouraged
  • When it is less than 1, negative cooperative binding negative cooperativity is occurring, which meaning that the binding of 1 ligand decreases the enzyme’s affinity for further ligands
  • When it is =1 the enzyme does not exhibit cooperative binding
58
Q

Hill’s Coefficient

A
  • Used to indicate the nature of the cooperativity
  • When the coefficient is greater than 1, positive cooperative binding is occurring, meaning binding is encouraged
  • When it is less than 1, negative cooperative binding negative cooperativity is occurring, which meaning that the binding of 1 ligand decreases the enzyme’s affinity for further ligands
  • When it is =1 the enzyme does not exhibit cooperative binding
59
Q

Feedback Regulation

A
  • A common method of enzyme control
  • In this process, products further down a metabolic pathway regulate an enzyme’s activity
  • Negative Feedback (Feedback inhibition)
  • Positive Feedback (Feedback Activation)
60
Q

Negative Feedback (Feedback Inhibition)

A
  • When enough of a product has been produced, we turn off or inhibit the pathway
  • Maintains homeostasis
  • This occurs by having the product bind to the active site of the enzyme that acted earlier in the pathway, making that enzyme unavailable
61
Q

Feedback Activation

A
  • The end product of a pathway activates an enzyme involved in that pathway
62
Q

Feedforward Regulation

A

An intermediate earlier in the process goes forward and acts on one of the enzymes later in the process

63
Q

Types of Feedback Inhibition

A
  • Competitive Inhibition
  • Non competitive Inhibition
64
Q

Competitive Inhibition

A
  • An inhibitor competes with the substrate for occupying the active site
  • If more substrate is added, the enzymes are more likely to bind substate than inhibitor, and the inhibition may be overcome
  • This means that in competitive inhibition Vmax remains unchanged
  • If enough substrate is added, the substrate will outcompete the inhibitor so that the reaction can proceed at maximum velocity
  • But, a higher substrate concentration will be required than if no inhibitor was present, so the Km value increases
  • A higher substate concentration is now required to reach half of vmax
64
Q

Competitive Inhibition

A
  • An inhibitor competes with the substrate for occupying the active site
  • If more substrate is added, the enzymes are more likely to bind substate than inhibitor, and the inhibition may be overcome
  • This means that in competitive inhibition Vmax remains unchanged
  • If enough substrate is added, the substrate will outcompete the inhibitor so that the reaction can proceed at maximum velocity
  • But, a higher substrate concentration will be required than if no inhibitor was present, so the Km value increases
  • A higher substate concentration is now required to reach half of vmax
65
Q

Non competitive Inhibition

A
  • The inhibitor does NOT compete with the substrate, rather it binds to an allosteric site somewhere else on the enzyme, and this binding changes the enzymes conformation, making it unable to bind the substrate
  • The enzyme is therefore effectively removed from the pool of enzymes and with fewer active enzymes, Vmax is reduced.
  • Those enzyme molecules are still uninhibited, however they have the same affinity for the substrate, meaning Km is unchanged
  • It will seem as the graph has been crushed.
  • Vmax is reduced so the asymptotic maximum is lower, but Km remains the same, so the curve is neither right or left shifted.
66
Q

Holoprotien

A

Many tertiary structures require a cofactor to function properly, and a protein bound to a cofactor is known as a holoprotien.

67
Q

Heme

A

Is a common cofactor found in many proteins, and it is required for oxygen binding in hemoglobin and myoglobin. The characteristic structure of heme is a poryphyrin ring with a central iron (Fe) atom.

Biochemistry (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions