BIOCHEMISTRY- CHAPTER 20: PROTEINS

PROTEIN DENATURATION:

- disruption of secondary, tertiary, quaternary structures of protein that reduces or prevents normal protein function (notice, not the primary!) - can be permanent (irreversible) - can be reversible (renaturation) - examples: 1. heat 2. microwave radiation 3. ultraviolet radiation 4. aggregation 5. detergent 6. organic solvents (ethanol) 7. strong acids/bases 8. salts of heavy metals 9. reducing agents *LOOK IN BOOK AND ADD IN FURTHER DESCRIPTIONS!!*

PROTEINS BASED ON THEIR FUNCTION:

1. *catalytic proteins*: "enzymes" responsible for metabolic reactions 2. *defense proteins*: immunoglobulin or antibodies bind to foreign substances to prevent invasion of a foreign body 3. *transport protein*: binds to small biomolecules because they need to be protected or are insoluble in a biological system 4. *messenger proteins*: relay a signal to other cells/ tissues. ex: hormones 5. *contractile proteins*: proteins that respond to nerve stimuli (they change shape-elongation/or contract) 6. *structural proteins*: provide strength and rigidity to fluid biological systems and also serve as a protective coating 7. *storage proteins*: binds small molecules for future use 8. *transmembrane proteins*: proteins that span the membrane. they are generally associated with movement of small molecules or ions in and out of the cell. 9. *regulatory proteins*: turn on/off cellular functions 10. *nutrient proteins*: proteins that are needed that are not produced by the organism at that time *PUT IN EXAMPLES OF EACH ONE ALEXXXXX!!!!!!*

PROPERTIES OF AMINO ACIDS:

1. *chirality*: occurs when 4 different groups are attached to the carbon center. generally, all amino acids are chiral EXCEPT glycine (quiz question: are all amino acids chiral? the answer is no because of glycine). with chirality, amino acids are naturally L-isomers in nature (can they ever exist as D-isomers? yes, but L-isomers is most commonly found). 2. *acid-base*: amino acids are charged species in both the solid state and in a solution. (look at notes) 3. *zwitterion > isoelectric point > electrophoresis*: key terms: *zwitterion*: is a molecule that contains both a positive charge and a negative charge but is electrically neutral- overall charge is dependent on the pH of the solution. *isoelectric point*: the pH at which an amino acid exists primarily in its zwitterion form and has an overall charge of zero. amino acids all have different pH's though! (*memorize this*: nonpolar + polar neutral = 4.8-6.3 pH, polar acid: < 3.2 pH, polar basic: > 7.5 pH) *electrophoresis*: so, when the net charge is not zero the separate charged particles will migrate toward charged electrodes associated with an electrical field. they will move toward opposite charge *when is the isoelectric point (pI) affected?* when the R-group is protonated or de-protonated

THE MOST CHEMICALLY UNIQUE AMINO ACID- CYSTEINE:

1. *cysteine* is the only amino acid that has a side chain that contains a sulfhydryl group (-SH) 2. it is a polar neutral amino acid (we are probably going to need to know this) 3. in the presence of mild oxidizing agents, cysteine readily dimerizes and forms a cystine molecule (dimer). the two residues are linked through a covalent disulfide bond 4. the disulfide linkage is reduced back to SH- groups in the presence of a reducing agent

PROTEIN CLASSIFICATION:

1. *fibrous proteins*: are made up of polypeptide chains that are elongated that aggregate to form macromolecule structures. these proteins are mechanically strong and are water insoluble. they are often structural proteins that provide strength and protection to cells and tissues. they only have one single type of secondary protein = alpha-helix - examples: a. alpha-keratin: found in protective coatings for organisms, the polypeptides are almost completely alpha-helix that are connected via disulfide linkages. made of hydrophobic amino acids (increase in disulfide linkages, increase in harder substance) b. collagen: has a triple helical structural, but does not fit into alpha-helix. it is long, thin, and rigid. cross-linking causes the strands to increase strength and rigidity. *WHY DOES IT NOT FIT INTO ALPHA-HELIX- LOOK THAT UP ALEXXXX!!!!!* 2. *globular proteins*: is a protein that is folded in a spherical or globular way. they are water soluble because the hydrophobic r-groups are in the interior and the polar r-groups are on the exterior- this causes them to be easy to transport through the bloodstream. they have both alpha-helix and beta-pleated sheets (secondary proteins). also are called: metabolic proteins - examples: a. hemoglobin: an oxygen carrying molecule in blood. transports o2 from lungs to tissue. the structure consists of: tetramer (4 subunits), each subunit contains a heme group, 1 molecule that can transport up to 4 o2 molecules at a time b. myoglobin: an oxygen storing molecule in our muscles. the structure is a monomer and consists of 1 heme unit. it only binds 1 o2 molecules at a time. it has a tertiary structure, but has a higher o2 affinity- this means it binds oxygen more strongly, but it does not make it a better oxygen carrier.

EXAMPLES OF CONJUGATED PROTEINS:

1. *glycoproteins*: a protein that contains a carbohydrate component - conjugated protein: glycoprotein - prosthetic group: carbohydrate - glycoproteins are a part of the cell membrane (think of the phospholipid bilayer components!) - a part of the blood group markers - 2 common glycoproteins: collagen and immunoglobulins 2. *lipoproteins*: a protein that contains a lipid component - conjugated protein: lipoprotein - prosthetic group: lipid - lipids are insoluble in blood because of their nonpolar structure- so they use a *plasma lipoprotein*, which is a transport system for lipids in the bloodstream. - *4 major classes of plasma lipoproteins*: a. chylomicrons: transports dietary triacyglycerols from the intestine to the liver and to adipose tissue. b. VLDL (very-low density lipoproteins): transports triacylglycerols synthesized in liver to adipose tissue c. LDL (low density lipoproteins): transports cholesterol in liver to cells d. HDL (high density lipoproteins): collects excess cholesterol and transports it back to liver 3. *hemoproteins*: a protein that contains a heme unit - conjugated protein: hemoprotein - prosthetic group: heme unit - consists of a porphyrin ring and metal center - found in many metabolic enzymes which allows for catalyzing a chemical reaction - found in hemoglobin and myoglobin: at the oxygen binding site

BIOCHEMICALLY IMPORTANT PEPTIDES:

1. *hormones*: - oxytocin: regulates uterine contractions and lactation - vasopressin: regulates the excretion of water by the kidneys, affects BP (oxytocin and vasopressin are both nonapeptides with 6 of the residues held in the form of a loop by a disulfide bond. they differ in identities of amino acids that are present) 2. *neurotransmitters*: - enkephalins: produced by the brain to reduce pain (pentapeptide) 3. *antioxidants*: - glutathione: regulates oxidation-reduction reactions (tripeptide)

PROTEIN STRUCURE:

1. *primary*: amino acid S E Q U E N C I N G - critical for overall protein structure and function - everything protein has its own unique amino acid structures - ultimately determines the secondary, tertiary, and quaternary structures - linked via peptide bonds 2. *secondary*: repeating pattern in the backbone resulting from oxygen of the carbonyl interacting with H of amino group further down the peptide chain or on a different peptide - secondary proteins are usually a mixture between alpha-helix and beta-pleated sheets. it is never just one. - found when r-groups are small - two types: a. *alpha-helix*: a single polypeptide coiled around itself i. h-bonding occurs between every 4th amino acid to maintain its shape ii. r-groups point to the outside b. *beta-pleated sheets*: two fully extended protein chain segments that are held together by h-bonds. i. h-bonding occurs between two side-by-side chains or a single chain that is folded back on itself (forms a u-turn structure) ii. all r-groups points above or below the plane of the sheet 3. *tertiary*: the overall 3D shape of a protein that results from the interactions between amino acid side chains (r-groups) that are widely separated from each other within a peptide chain - interaction types: a. *disulfide linkages*: the strongest interaction, results from the -SH groups of two cysteine residues reacting with each other to form a covalent disulfide bond. this is the only reaction with covalent bonds! b. *electrostatic interactions (salt bridges): i. pH dependent, the pH can change protonation state from acidic and basic amino acids ii. COO- and NH3+; interaction between charged side chains (+/-)- this is why the bridge is formed c. *hydrogen bonds*: i. any of the polar r-groups have the ability to h-bond (any group that contains O,N, or H bonded to N or O) ii. changes in the temperature and pH can disrupt h-bonding interactions since they are so weak d. *hydrophobic/hydrophilic interactions*: *hydrophobic*: attraction of nonpolar r-groups drawn toward the interior of the protein away from the water. i. LDF'S ii. weak alone, stronger together *hydrophilic*: i. attraction of polar r-groups toward the exterior of the protein ii. exposed to the aqueous environment 4. *quaternary*: - highest level of organization - found with two identical alpha-helix and two identical beta-pleated sheets -requires two or more peptide chains to interact - units are held together by all the 4 interactions, but dominantly by the hydrophobic interaction force making it more easily disrupted than a tertiary structure - changes in pH or temp will disrupt interactions - heme group is folded into each subunit (it is where the oxygen binds to the protein!) - usually contains an even number of units (dimer, tetramer, etc.)

GENERAL STRUCTURAL CHARACTERISTICS OF PROTEINS:

1. *there has to be a minimum of 40 amino acids present for it to be a protein* 2. proteins are classified as monomeric or multimeric key terms: *monomeric*: a protein in which only one peptide chain is present *multimeric*: a protein in which more than one peptide chain is present 3. on the basis of chemical compositions, proteins can be classified as either simple or conjugated key terms: *simple*: a protein in which only amino acid residues are present *conjugated*: a protein that has one more non-amino acid components present in the structure. the non-amino acid group that is present in a conjugated protein is called the *prosthetic group* (you'll see examples in the next slide)

GENERAL CHARACTERISTICS OF AMINO ACIDS- THE BUILDING BLOCKS FOR PROTEINS:

1. *what are amino acids?* organic compounds that contain both an amino group (-NH2) and a carboxyl group (-COOH) 2. amino acids are found in proteins and are always alpha-based 3. *why are amino acids generally alpha based?* because the amino group is always attached to the central carbon (second carbon), which is the alpha group in terms of the greek system!

question: what are the 9 essential amino acids?

1. methionine (M) 2. threonine (T) 3. histidine (H) 4. valine (V) 5. phenylalanine (F) 6. isoleucine (I) 7. tryptophan (W) 8. lysine (K) 9. leucine (L) MY-TALL-HANDSOME-VEGAN-FRIEND-IS-WATERING-KALE-LEAVES

question: what are the amino acid classifications?

1. nonpolar 2. polar (neutral, acidic, basic) depends on the r-group!

GENERAL CHARACTERISTICS OF PROTEINS:

1. proteins are the most abundant substances in nearly all cells 2. all proteins contain the elements: carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur 3. *what are proteins?* they are naturally occurring unbranched polymers, in which the monomer units are amino acids

PEPTIDES:

1. under proper conditions, amino acids can bond together to produce an unbranched chain of amino acids 2. *what is a peptide?* an unbranched chain of amino acid polymers, but the number of amino acids can vary - dipeptide: 2 amino acids - tripeptide: 3 amino acids - oligopeptide: 10-20 amino acids - polypeptide: many amino acids (long chain) 3. quick notes regarding peptides: - the backbone: everything BUT r-groups - how to read the amino acid chain: N -> C - the variables are the R-groups - *what is a peptide bond?* a covalent bond between the carboxyl groups of one amino acid and the amino group of another amino acid. aka: amine linkages! - isomers: same amino acids, just in a different order

question: what percent of a cell's overall mass is accounted for by proteins?

15%

question: why are the notations Ser-Cys and Cys-Ser represent two different molecules rather than the same?

2 different N-terminals

question: in order for a peptide to be considered a protein, how many amino acid residues must be present?

40

question: what is the general name for the building blocks (monomers) from which a protein is made?

amino acids

question: why don't all proteins have quaternary structures?

because quaternary structures only arise when a protein is made up of 2 or more polypeptide chains

PROTEIN HYDROLYSIS:

breaking of a peptide linkage by addition of a water molecule

question: what is the interaction between the sulfur atoms in two cysteine molecules?

disulfide bond

question: what is the interaction between charged side chains?

electrostatic = salt bridges

T/F: in a beta-pleated sheet structure, the h-bonding is always between different protein chains?

false

T/F: a simple protein contains only one type of amino acid?

false *LOOK UP WHY*

CLASSIFICATIONS OF AMINO ACIDS:

good way to remember: nonpolar (hydroPHOBIC): r-group consists of mainly hydrocarbons polar (hydroPHILIC): r-group depends on whether it is acidic, basic, or neutral. acidic: contains extra -COOH group basic: contains an amino group neutral: contains OH, SH, and amide *remember these! these were on the quiz and literally my brain got so confused and I remember telling myself during the quiz that it would've been easier if i just remembered all of them*

question: what is the interaction between polar side chains?

h-bonding (containing -OH groups)

question: which two of the standard amino acids are constitutional isomers?

leucine and isoleucine

question: most amino acids have an isoelectric point between 5.0 and 6.0, but which odd ball has 9.7?

lysine

question: what elements is always present in proteins that is seldom present in carbohydrates and lipids?

nitrogen and sulfur

question: are all of the 20 amino acids found in proteins have the L-stereochemical form?

no, glycine is not chiral

question: which of the protein structures refers to the sequencing of amino acids that make up a protein?

primary

question: what is meant by the term: isoelectric point?

the pH at which the zwitterion concentration is a solution is maximized

question: oxytocin and vasopressin are produced by?

the pituitary gland

R-GROUP IMPORTANCE:

the r-group that is a part of the formula is *IMPORTANT* because it is the distinguishing part that allows for the many classifications of amino acids

question: why are room temperature are amino acids solid with high decomposition points?

they exists as zwitterions

question: when 2 cysteine molecules dimerize what happens to the r-groups?

they react with each other to produce a covalent disulfide bond

T/F: a simple protein can also be a multimeric protein?

true