Exam I (Lectures 6-10: Amino Acids and Proteins)

What is the role of proteases in peptide bond formation?

The hydrolysis of peptide bonds can be catalyzed by enzymes called proteases

Defects in collagen synthesis

1. Osteogenesis Imperfecta - Brittle bones prone to fracture 2. Scurvy: caused by lack of vitamn C (abscorbic acid); general degeneration of connective tissue symptoms: fatigue, irritability hemorrhages, tooth loss, poor wound healing

Amino Acid: Alanine

1. one of the major substrates for gluconeogenesis 2. important in CaHill cycle

Post-translational modification to Amino Acids in Proteins

•Carbohydrate Addition -Cell surface and secreted proteins -Trafficking, cell interactions •Lipid Addition -Anchor proteins to the lipid bilayer •Regulation -Change protein activity in response to a signal •Modified Amino Acids -Influence protein structural roles and interactions

Amino Acids Tryptophan, Phenylalanine, and Tyrosine

1. AROMATIC AMINO ACIDS 2. PHE is a precursor to TYR 3. Tryptophan is needed to synthesize niacin, serotonin, and melatonin

Amino Acids Lysine, Histidine, and Arginine

1. HYDROPHILIC because they're charged 2. Arginine and Lysine are prevalent in histone proteins (Why? Histones need to interact with negatively-charged DNA and their positive charge enables them to do so. This positive/negative relationship is REALLY important in the regulation of transcription) 3. Arginine is ESSENTIAL for cellular growth because it specifically stimulates the release of insulin-like growth factor or IGF-1 4. Histidine's side chain pka is ALOT lower than lysine's and arginine's so its NEUTRAL at body pH; Histidine, however, can accept a proton--which is why it is considered a basic amino acid 5. Histidine is NEEDED for cellular growth, especially in children, during pregnancy, and anyone who is recovering from trauma

Special characteristics of Collagen

1. makes up approximately 25% of protein in mammals 2. major function is structural--found as component of skin, connective tissue, blood vessel walls, bone, sclera and cornea of eye 3. types and organization of collagen dictated by function of the particular organ 4. MOST ABUNDANT PROTEIN IN ANIMAL WORLD

secondary protein structure

1. polypeptide is flexible, which allows proteins to fold in several different ways 2. FOLDS THAT OCCUR BETWEEN NEARBY AMINO ACIDS MAKE UP THE SECONDARY STRUCTURE OF PROTEINS 3. Alpha Helix v. Beta pleated sheet both of these patterns are common because they tend to form when a hydrogen bond connects the carbonyl and amino groups on a polypeptide backbone; THESE HYDROGEN BONDS STABILIZE THE SECONDARY STRUCTURES

amino acid tyrosine

1. precursor to melanin, thyroxine, and the catecholamines dopamine, norepinephrine, and epinephrine

Amino Acid: Glycine

1. smallest amino acid 2. conformationally flexible-found in every 3rd position in collagen 3. frequently present in hydrophobic areas of cell membranes 4. needed to synthesize purine nucleotides and porphyrin, a component of heme

quarternary structure of protein

1. subunits held together sing the same kind of weak binds that are involved in tertiary structure

amino acids cysteine and methionine

1. sulfur-containing amino acids 2. MET is a precursor for SAM, which transfers methyl groups for many reactions 3. MET is needed to make cysteine

Amino Acid: Cysteine

1. sulfur-containing side chain 2. can bind with other cysteine; 2 cysteine molecules form a DISULFIDE BOND- CYSTINE- which stabilizes the tertiary structure of proteins

Amino Acid: Asparagine

1. undergoes post-translational modification, specifically N-oligosaccharides in the ER- helpful for cell trafficking and signaling

Amino Acid: Proline

1. unique side-chian consisting of a 5-membered nitrogen-contraining ring 2. cyclic structure creates conformational rigidity 3. residues are found in collagen because it's important for alpha helix formation

Amino Acid: Glutamine

1. used for nucleotide synthesis- purine and pyrimidine nucleotides

Acid Base properties of amino acids

So if the pH is 2.34, then there will be equal amounts of COO- and COOH. If the pH is greater than 2.34, there will be more glycine molecules with COO- . At a pH of 7, with almost 100,000 -fold fewer H+ than at pH 2, the carboxyl group will be in the ionized carboxylate (or conjugate base form). If the pH is 9.6, then there will be equal amounts of NH3+ and NH2. At a physiologic pH of 7, the carboxyl group will be mostly ionized in its carboxylate form and the amino group will be protonated and positively charged. This rule of thumb usually applies for carboxyl groups and amino groups, so keep it in mind. Now let's practice.

Amino Acid Metabolism

The carbon skeleton of amino acids are an important source of energy in metabolism. Some of the first steps in amino acid metabolism involve removal of the alpha amino group (oxidative deamination) and the alpha carboxyl group (decarboxylation) Ex: decarboxylation of histidine produces the neurotransmitter, histamine Ex: oxidative deamination of amino acids produces alpha-keto acid, like pyruvate, which can be used as fuel

isoelectric point

LOW pH will cause amino acids to GAIN a POSITIVE charge; HIGH pH will cause amino acids to GAIN a NEGATIVE charge. This pH, where the amino acid is electrically neutral, is called the ISOELECTRIC POINT

What is a peptide bond?

VERY tight covalent bonds formed between the carboynl group of one amino acid and the amino group of the next amino acid in the chain

protein regulation

Phosphorylation: the most common regulatory modification of amino acids in proteins Phosphate groups are incorporated into amino acids with -OH groups (Ser, Thr, Tyr) to form phosphoester bonds. These modifications increase or decrease the activity of a protein. PROTEIN KINASES: add phosphates from ATP to -OH of amino acid R groups PROTEIN PHOSPHATASES remove them

Carbohydrate Addition to Proteins

Proteins with carbohydrates attached are usually trafficked for either the plasma membrane or secretion outside of the cell.

define the planar peptide group

Rotation about the C-N peptide bond is limited to 180o rotation in either cis or trans configuration. Trans:R1 and R2 on opposite sides of C-N bond Cis: R1 and R2 on the same side of the C-N bond Trans favored 1000 to 1 over Cis for all amino acids except glycine and proline. Which two amino acids do NOT favor the Trans:Cis configuration 1000:1? In most amino acids the ratio of trans to cis is >1000 to 1. The cis-trans transition is also a relatively slow process. So for most amino acids the C-N bond is in the trans configuration. However, for proline and glycine the C-N cis configuration is more prominent. Practically, this means proline and glycine tend to disrupt certain common secondary structures and favor others.

Complete this sentence: in a basic solution or high pH- high pH (low [H+])--amino acids behave like ____________________, ______________________ protons from their carboxyl sites

acids, donating

Clinical Tests for Amino Acids

1. Blood consists of cells and proteins, electrolytes and fuels such as glucose and amino acids 2. measuring amounts of amino acids in the blood can be used in the diagnosis of disease For example, an inherited condition called Maple Syrup Urine Disease (MSUD) results from block in metabolism of branched chain amino acids, BCAAs 3. Untreated infants born with MUSD will suffer neural degeneration within the first weeks of life and death within month

TRUE OR FALSE: A protein's structure DOES NOT determine its function

FALSE!! A protein's structure DOES determine its function

amino acids leucine, isoleucine, and valine

BRANCHED-CHAIN AMINO ACIDS

Ionizable groups of Amino Acids

FIGURE 3-2 General structure of an amino acid. This structure is common to all but one of the α-amino acids. (Proline, a cyclic amino acid, is the exception.) The R group, or side chain (red), attached to the α carbon (blue) is different in each amino acid.

Formation of disulfide bonds requires oxidizing conditions. Why do you think this is the case?

Proteins that contain disculfide bonds are usually destined for secretion outside of the cell, like peptide hormones and extracellular matrix proteins like collagen

modification of amino acid side chains

Some amino acids are hydroxylated after translation. Hydroxylation of proline and lysine is an important postranslational modification to collagen. What types of interactions are possible when -OH groups are added to proline?

Hydroxyproline: important to collagen structure

Some amino acids are hydroxylated after translation. Hydroxylation of proline is an important postranslational modification to collagen. What types of interactions are possible when -OH groups are added to proline? Tensile strength of collagen greater than a steel wire of equal cross section. Hydroxyproline contributes to this strength. Its unique stereochemistry allows close packing of the 3 chains and it participates in H-bonding between the strands. Ascorbic acid is required for modification of hydroxylation of the proline.

Lipid Addition to Proteins

Some proteins are covalently attached to lipid moieties. This post-translational modification helps to anchor proteins to the membrane.

TRUE or FALSE: Amino Acids are Amphoteric

TRUE!! This means that depending on the environmental conditions, Amino acids will behave as either a Bronsted-Lowry Acid or a Bronsted-Lowry Base

Why is the structure of an amino acid so important?

It's the structure of an amino acid that will determine how strongly their carboxyl groups will hold protons or how readily their amino groups will accept protons Amino acids with more electronegative groups on their side chains--like aspartic acid--will readily give up their protons; meanwhile, amino acids, such as Lysine, will freely accept protons to help delocalize charge on their amino group

If the Km is greater than the amount of substrate, is the reaction dependent on substrate or not?

Km > [S] --> Velocity of the reaction is dependent on substrate concentration, [S] Km < [S] --> velocity of the reaction is INDEPENDENT of substrate concentration, [S]

Ex: Ionizable Groups of HIstidine

a) pka1= carboxylate group b) pka2= amine group c) PkR= R group/chain

How are Isoelectric points and Zwitterions related?

at the isoelectric point, when the amino group has a positive charge and the carboxyl group has a negative charge, making the whole molecule neutral, an amino acid is called a ZWITTERION

Complete this sentence: in a solution of low pH (acidic solution)- low pH (high [H+])--amino acids behave like _______________________, ______________________ protons on their amino ends

bases, accepting

Amino Acids Glutamate and Aspartate

both are hydrophilic

List the types of proteins

•Simple-comprised only of amino acids •Conjugated-contain non-polypeptide chemical groups e.g. heme in hemoglobin •Membrane-interact with biological membranes e.g. glucose transporter •Globular-spherical, usually water soluble •Fibrous-elongated shape, usually structural proteins for example collagen

How are peptide bonds broken?

hydrolysis: H20 molecules attacks the peptide bond w/ its lone pair of electrons, breaks the bond, then leaves the two halves of the old peptide chain In living organisms, this process is catalyzed by hydrolase enzymes to make cleaving easy!

pka values of amino acids

pKa1: the carboxyl group and is usually around 2 pKa2: the amino group and is usually around 9-10

define pka (of amino acids)

pka= a measure of a series' tendency to donate or accept protons! pka represents the pH at which an acidic species is in equilibrium between its protonated and deprotonated states lower pka values = more acidic carboxyl groups higher pka values = more basic amino groups pH* > pka (for that carboxylic acid site) --> DEPROTONATION AND NEGATIVE CHARGE pH* < pka (for that particular amino group) --> PROTONATION AND POSITIVE CHARGE

How to calculate Vmax and Km from a lineweaver-burk plot?

see photo from example that Jo drew

What is a peptide?

short chain of amino acids, between 2 and 50 amino acids long; peptides begin with an N-terminus and end at the C-terminus

What is the difference between tertiary and quaternary protein structure?

tertiary structure refers to the 3D structure of the SINGLE polypeptide chain; quaternary structure refers to the 3D structure of multiple, interacting polypeptide chain complexes

how to calculate pI values for amino acids

AMINO ACIDS w/ pI VALUES < 6 = ACIDIC; AMINO ACIDS w/ pI VALUES >6 = BASIC

general structure of an amino acid

FIGURE 3-2 General structure of an amino acid. This structure is common to all but one of the α-amino acids. (Proline, a cyclic amino acid, is the exception.) The R group, or side chain (red), attached to the α carbon (blue) is different in each amino acid. Alpha amino acids are the building blocks of proteins. They are amino acids because they contain an amino group and a carboxylic acid group. Both of these groups are ionizable in water. That is they readily pick up and release protons in water. They are alpha amino acids because the amino group and carboxylic acid group are on the same carbon atom which is called the alpha carbon (a name reserved for the carbon with the main substituents attached). The R group attached to the alpha carbon is sometimes called the side chain. The 20 different amino acids found in proteins differ in the chemical group at this R or side-chain position. The chemical group at the R positions is sometimes called the "residue" For instance the amino acid Alanine contains a methyl group at the R- position. But if you look closely at this amino acid----what do you notice?If the R group is a methyl group then, there are 4 different substituents around the alpha carbon.This means that alanine is a chiral molecule, that is it has two stereoisomers which are non superimposable mirror images of one another.But which stereoisomer of alanine is found in proteins and how do we name it?

Which amino acid is not an alpha amino acid?

PROLINE IS AN IMINO ACID

List the characteristics of the peptide bond

Partial double bond character due to unpaired e- on amide nitrogen & resonance Rigid and planar (6 atoms lie in a plane) Trans Configuration (carbonyl O and the amide H) Uncharged but polar oThe amide proton does not ionize in water

What are the 9 essential amino acids that cannot be synthesized by the body?

Threonine, Leucine, Isoleucine, Methionine, Tryptophan, Phenylalanine, Lysine, Histidine, Valine

tertiary protein structure

1. TERTIARY STRUCTURE IS WHAT MAKES UP THE FOLDED PROTEIN STRUCTURE 2. proteins fold even more because of interactions that occur between the R groups that hang off of the polypeptide backbone COMMON R GROUP INTERACTIONS: hydrogen bonds, ionic bonds, van der waals attractions, salt bridges (or electrostatic bonds), hydrophobic tertiary structure interactions LOWER molecular disorder or ENTROPY 3. Hydrophobic side chain folding LOWERS ENTROPY a) tend to group together on the inside of the protein structure because this arrangement is more stable and LOWERS ENTROPY b) leaves polar and charged hydrophilic side chains exposed, which are free to bond to other polar molecules or make hydrogen bonds with H20; when these external groups interact with H20 molecules, they form the SOLVATION LAYER (hydrophilic interactions) 4. DISULFIDE BOND IS THE ONLY COVALENT BIND INVOLED IN TERTIARY STRUCTURE; strongest bind in tertiary structure. 2 cysteine amino acids binding together

Amino Acids serine and threonine

1. both undergo post-translational modification- helpful for cell trafficking

How can proteins be denatured?

1. breaking down the bonds that hold the folds of the secondary, tertiary, and quaternary structures 2. proteins typically only function well in a narrow range of temperatures; ONE WAY TO BREAK DOWN THE BONDS WITHIN PROTEINS IS TO ADD HEAT- Heat irreversibly denatures proteins by disrupting hydrophobic interactions and hydrogen bonds 3. PROTEINS CAN BE TEMPORARILY DENATURED--> denaturation by solvents; denaturation is REVERSED once the solvent is removed ex: Alcohol, Acids and Bases, and heavy metal salts

List the functions of proteins

1. catalysis 2. Transport 3. contractile mechanisms 4. protection 5. Hormones 6. Regulation 7. Structural

supersecondary structure

1. composed by combining secondary structures usually by the packing of side chains of adjacent secondary structures 2. They are connected by loop regions (turns)

primary structure of protein

1. linear chain of amino acids that is stabilized by covalent peptide bonds 2. primary structure influences how a protein folds

Notice that the first amino acid in a peptide or polypeptide, has a free amino group. And the last amino acid has a free carboxy group. Can you explain why this is the case?

Amino acid sequences are always written left to right from the 1st amino acid (often called the amino terminus) to the last amino acid (the carboxy terminus). The main chain atoms in a polypeptide include all atoms not in the side chain: CaH, C=O, NH Convince yourself that the order of the main chain atoms is different from the Amino to Carboxy Terminus than from the Carboxy to Amino Terminus

Which two amino acids FAVOR cis over trans conformation?

Glycine and Proline

Absolute configuration of amino acids

To decide on the configuration you first have to orient the amino acid with the carboxylic acid at the top (this substituent has the highest priority). If the amino group is on the left it is an L amino acid, if it is on the right it is D amino acid. All the amino acids incorporated in proteins are in the L-configuration. There is one amino acid which is not an enantiomer. (Remember enantiomers are stereoisomers that are non-superimposable mirror images of one another.) Can you guess the chemical group at its R position? The Absolute configuration of amino acids and sugar are based on the absolute configuration of glyceraldehyde (a 3 carbon sugar). The sugars that we eat and metabolize are D-sugars. when the main substituent on the chiral center is on the left it is in the L configuration when it is on the right it is in the D- configuration. (the D- and L- configuration do not tell you the direction of the optical rotation.) ---this representation is a fisher projection---in a three dimensional representation, the horizontal bonds would be pointing towards you (out of the board), the vertical bonds would be pointing away from you (behind the plane of the board). Try drawing the three dimensional representations and convince yourself that they are mirror images of one another. Compounds with chiral center, rotate plane polarized light; they have optical activity. A dextrorotary (+ or d) compound rotates plane polarized light to the right; A levorotary (- or l) compound rotates to the plane polarized light to the left. A racemic mixture (with dl optical forms) will not have optical activity. These distinctions of optical activity do NOT correlate with the absolute configuration of a chiral compound. ALL AMINO ACIDS OF METABOLISM ARE OF THE D GROUP

How are peptide bonds formed?

dehydration synthesis: a nucleophilic substitution reaction between the amino group of one amino acid and the carboxyl group of the other w/ H20 as a leaving group. This reaction can also be called a CONDENSATION REACTION