Biochem ch.2, Biochem ch.3, Biochem Ch. 4, Biochem Ch.5, Physiology Ch.1, Ant ch.3 (split 1) , Ant Ch.8 (split 1), Microbiology Ch.1, Microbiology Ch. 2, Physiology Ch. 7

which of the following amino acids carry a positive charge on the side chain which makes them basic? select all that apply. - lysine - glutamate - arginine - histidine - aspartate - tyrosine

- lysine, arginine, histidine Each of the 20 amino acids found in proteins can be distinguished by the R-group substitution on the a-carbon atom. There are two broad classes of amino acids based upon whether the R group is hydrophobic or hydrophilic. The hydrophobic (non-polar) amino acids tend to repel the aqueous environment and therefore, reside predominantly in the interior of proteins. This class of amino acids does not ionize or participate in the formation of H-bonds. Hydrophilic (polar) amino acids tend to interact with the aqueous environment, are often involved in the formation of H-bonds and are predominantly found on the exterior surfaces proteins or in the reactive centers of enzymes. The functions of amino acids in proteins are determined by the noncovalent interactions and the covalent bonds that their side chains can form: • The small amino acids (glycine and alanine) occupy little space. In proteins they are often found in places where two polypeptide chains have to come close together. • The branched-chain amino acids valine, leucine and isoleucine have hydrophobic side chains. • The hydroxyl amino acids serine and threonine form hydrogen bonds with their hydroxyl group. This group also forms covalent bonds with carbohydrate in glycoproteins and with phos- phate in phosphoproteins. • The sulfur amino acids cysteine and methionine are quite hydrophobic, although cysteine also has weak acidic properties. • The aromatic amino acids phenylalanine, tyrosine and tryptophan are hydrophobic, although the side chains of tyrosine and tryptophan can also form hydrogen bonds. • The acidic amino acids glutamate and aspartate have a carboxyl group in the side chain that is negatively charged at pH 7. The corresponding carboxamide groups in glutamine and aspara- gine are not acidic but can form strong hydrogen bonds. • The basic amino acids lysine, arginine and histidine carry a positive charge on the side chain, although the pK value of the histidine side chain is quite low. • Proline is a freak among amino acids with its nitrogen tied into a ring structure as a secondary amino group. Being stiff and angled, it is often found at bends in the polypeptide.

Both hemoglobin in RBCs and myoglobin in the muscles employ heme as a prosthetic group. Myoglobin consists of a single polypeptide with a noncovalently bound heme group while hemoglobin has four poly peptides, each with its own heme. (a) both statements are true (b) both statements are false (c) the first statement is true, the second is false (d) the first statement is false, the second is true

a

Carbonic acid/bicarbonate is the most important physiological buffer system in the body. Proteins also participate in pH buffering, mainly through their histidine side chains (a) Both statements are true (b)both statements are false (c)the first statement is true, the second is false (d)the first statement is false, the second is true

a

The famous relationship stated in the Henderson-Hasselbach equation can be used to: (a) predict the pH that acid buffers work best at (b) predict the pKa the acid buffers work best at (c) predict the dissociation constant of a weak acid only (d) predict the dissociation constant of a strong acid only (e) predict the dissociation constant of an acid

a

Which of the following properties of a protein is least likely to be affected by changes in pH? (a) Primary structure (b) Secondary structure (c) Net charge (d) Tertiary structure

a

all aminso acids have a carboxyl group and an amino group, both bound to the same carbon. This carbon is called the: (a) alpha carbon (b) beta carbon (c) gamma carbon (d) lambda carbon

a

The isoelectric point (pl): (a) is the pH at which the number of positive and negative charges on a molecule equal each other (b) is the pH at which the number of positive and negative charges in a solution equal each other (c) can be determined using the Henderson-Hasselbash equation (d) is the pKa of a solution at which it is neither basic nor acidic (e) two of the above

a the pl is the pH at which a solute has no net electric charge and thus does not move in an electric field.

All hydrophobic amino acids (valine, leucine, isoleucine, etc.) share which of the following properties? (a) Acidic R groups (b) Nonpolar uncharged R groups (c) Polar uncharged R groups (d) Basic R groups

b

Identify the amino acids containing nonpolar, aliphatic R groups .a) Phenylalanine, tyrosine, and tryptophan b) Glycine, alanine, leucine c) Lysine, arginine, histidine d) Serine, threonine, cysteine

b

Molecules that can easily penetrate a biologic membrane are usually: (a) Large and non polar (b) Small and polar (c) Large and polar (d) Small and nonpolar

b

The amino acids in hemoglobin (or any protein) uniformly have which of the following configurations? (a) D (b) L (c) R (d) S

b

Which of the following amino acids has a net negative charge at physiologic pH (~7.4)? (a) Histidine (b)Glutamic Acid (c)Lysine (d)Asparagine

b

All G proteins exist in two forms: (a) an inactive GTP-bound from that acts on the effector and an active GDP- bound that does not (b) an active GTP- bound form that acts on the effector and an inactive GDP-bound form that does not (c) an active ATP- bound form that acts on the effector and an inactive ADP-bound form that does not (d) an inactive ATP-bound form that acts on the effector and an active ADP- bound form that does not

b Many neurotransmitters manipulate the membrane potential of their target cell directly by opening a ligand-gated ion channel in the plasma membrane. Water-soluble hormones however, trigger lengthy signaling cascades. Most hormone receptors activate a G protein which triggers the synthe- sis of a second messenger. cAMP, cGMP, IP3 (acting through Ca") and 1-2-diacylglycerol (DAG) are most important. The second messengers activate protein kinases, including kinases A (cAMP-acti- vated), C (Ca'•-diacylglycerol-activated), G (cGMP-activated) and the calmodulin-dependent protein kinases (Ca'•-activated). G proteins (guanine nucleotide-binding proteins) play a pivotal role in the signal transduction pathways for numerous hormones and neurotransmitters. The G protein is loosely bound to the cytoplasmic surface of the plasma membrane and it consists of three subunits designated a, fl andy. The a subunit has a nucleotide binding site that can accommodate either GDP or GTP. fl and y subunits function as a single unit, but the a subunit is only loosely associated with fly. The inactive G protein is associated with the unstimulated receptor, with GDP bound to the a subunit. Hormone binding induces a conformational change both in the receptor and the attached G protein. This conformational change greatly reduces the affinity of the a subunit for GDP. GDP dissociates away and is quickly replaced by GTP. Once GTP is bound, the G protein leaves the receptor and breaks up into the a-GTP subunit and the fly complex. Both the a-GTP subunit and the fly complex diffuse along the inner surface of the plasma membrane, where they bind to target proteins known as effectors. 1. The GTP bound a subunit of the G protein activates adenylate cyclase. 2. Active adenylate cyclase converts ATP to cAMP. cAMP further binds and activates PKA. 3. Active protein kinase A (PKA) phosphorylates specific proteins which up or down-reg- ulates cellular processes depending on the cell type. 4. The components of the activated G protein are membrane-bound messengers that transmit a signal from the receptor to the effector. 5. All G proteins exist in two forms: an active GTP-bound form that acts on the effector and an inactive GOP-bound form that does not.

The primary structure of a protein refers to the spatial arrangement of a portion of a polypeptide chain determined by the amino acids. The secondary structure of a protein refers to the irregular folding of a polypeptide chain (the overall three-dimensional conformation of the polypeptide). (a) both statements are true (b) both statements are false (c) the first statement is true, the second is false (d) the first statement is false, the second is true

b Proteins differ from each other because each has a distinctive number and sequence of amino acid residues. The amino acids are the alphabet of protein structure. No other property so clearly distinguishes one protein from another. The primary structure consists of a sequence of amino acids linked together by covalent peptide bonds. The secondary structure refers to the spatial arrangement of a portion of a polypeptide chain determined by the amino acids present (primary structure). The most common types of secondary structures are the a -helix (coiled conformation of a peptide chain), j}-pleated sheets (an extended, zigzag arrangement of a polypep- tide chain) and 13 -hairpin turns (reverse turns). The tertiary structure refers to the irregular folding of a polypeptide chain (the overall three-dimensional conformation of the polypeptide [e.g., globular, fibrous and pleated sheet]). Note: The best method for determining the three-dimensional structure of a protein is by x-ray diffraction. The quaternary structure refers to the spatial arrangement of subunits in a protein that consists of more than one polypeptide chain. Two examples of proteins with quaternary structures are the hemoglobin and antibody molecules found in the blood of a mammal.

Respiratory acidosis results from hyperventilation. Metabolic acidosis results from excessive vomiting. (a) both statements are true (b) both statements are false (c) the first statement is true, the second is false (d) the first statement is false, the second is true

b. Even small deviations from the normal blood pH lead to severe clinical disturbances. An arterial pH lower than 7.35 is called acidemia and an arterial pH exceeding 7.45 is called alkalemia. The pathological states leading to these outcomes are called acidosis and alkalosis, respectively. Respiratory acidosis is caused by any impairment in t he disposal of C02. Conversely, respiratory alkalosis results from hyperventilation. For example, a doubling in the rate of alveolar ventilation raises the blood pH from 7.40 to 7.62. A 50% reduction in alveolar ventilation lowers t he blood pH from 7.40 to 7.12. Note: If you administer a high nitrous-oxygen mixture (for example, 90:10) to a patient, this will cause respiratory depression and result in respiratory acidosis. Metabolic acidosis is caused either by an overproduction of organic acids or by an in- ability of t he kidneys to excrete excess acid. The normal urinary pH varies over a range of 4.0 to 7.0, depending on the need to excrete excess protons. Conversely, metabolic alkalosis is caused by the abnormal loss of acids from t he body: for example, as a re- sult of excessive vomiting. The most important laboratory test for t he distinction between metabolic and respira- tory acidosis is t he determination of the total plasma carbon dioxide (C02 + H2C03 + HC03lln respiratory acidosis, the total carbon dioxide is elevated because C02 reten- tion is by definition, the cause of the acidosis; in metabolic acidosis, it is reduced be- cause the patient hyperventilates in an attempt to eliminate excess carbonic acid. The converse applies to alkalosis.

Most plasma proteins are derived from the: (a) Kidney (b) Liver (c) Plasma cells (d) T cells

b. Most plasma proteins are derived from the liver.ln all, the liver synthesizes about 25 g of plasma proteins every day, which accounts for nearly 50% of the total protein synthesis in the liver. Only the immunoglobulins are not produced by the liver. They are synthesized by plasma cells. Most plasma proteins (exception: albumin) are glycoproteins. They circulate for several days and are eventually removed from the circulation when their oligosaccharide chains are worn down. Although albumin accounts for only 60% of the total plasma protein, it provides 80% of the col- loid osmotic pressure of the plasma. This is because the colloid osmotic pressure depends on the amount of water and electrolytes that a protein attracts to its surface and albumin is one of the most hydrophilic plasma proteins. Remember: The colloid osmotic pressure is necessary to prevent edema. Usually, edema develops when the albumin concentration drops below 2.0 g/dl. Edema can also be caused by an increase in capillary permeability, venous obstruction, im- paired lymph flow and CHF with an increased venous pressure. Globulins (are soluble in salt solutions but not pure water) make up 35% of plasma protein and are used in the transport of ions, hormones and lipids. They also assist in immune function. Fib- rinogen accounts for 4% of plasma protein and is essential in the clotting of blood and can be converted into insoluble fibrin. Regulatory proteins, which make up less than 1% of plasma protein, are proteins such as enzymes, proenzymes and hormones. Remember: Plasma proteins act as buffers that help stabilize the pH of the internal environment. Intracellular proteins absorb hydrogen ions generated by the body's metabolic processes. Note: Other plasma proteins include the following: 1. Lipoproteins (chylomicrons, VLDL, LDL, HDL) that are responsible for the transport in the blood of triglycerides, phospholipids, cholesterol and cholesterol esters from the liver to tissues or organs. 2. Transferrin (for iron transport) 3. Prothrombin (a blood-clotting protein)

A peptide bond forms between the _____ group of one amino acid and the ______ group of the adjacent amino acid (a) amino; amino (b) carboxyl; carboxyl (c) carboxyl; amino

c

A polypeptide with a net positive charge at physiologic pH (~7.4) most likely contains amino acids with R groups of what type? (a)Aliphatic R groups (b)Aromatic R groups (c)Basic R groups (d)Acidic R groups

c

The alpha helix is an example of which of the following structural properties of proteins? (a)primary structure (b)tertiary structure (c)secondary structure (d)quaternary structure

c

The cell (plasma) membrane is a fluid mosaic of: (a) lipids and carbohydrates (b) proteins and carbohydrates (c) lipids and proteins (d) carbohydrates

c

Which of the following is an imino acid? a) Alanine b) Glycine c) Proline d) Serine

c

Which part of the amino acid gives it uniqueness? a) Amino group b) Carboxyl group c) Side chain d) None of the mentioned

c Different amino acids contain different side chains which make them unique. (R-group side chains)

The unique cyclic structure of which of the following amino acids plays a central role in the formation of alpha helices and beta sheets? (a)Arginine (b)Valine (c)Lysine (d)Proline

d

Which one of the following statements about protein structure is correct? (a) Proteins consisting of one polypeptide can have quartenary structure (b) the formation of a disulfide bond in a protein requires that the two participating cysteine residues be adjacent to each other in the primary sequence of the proteins (c) The stability of the quaternary structure in proteins is mainly due to covalent bonds among the subunits (d) The information required for the correct folding of the proteins is contained in the specific sequence of amino acids along the polypeptide chain

d *** The correct folding of a protein is guided by specific interactions among the side chains of the amino acid residues of a polypeptide chain. Proteins are polymers built from amino acids j oined by peptide bonds. The resulting chain of amino acids (called a polypeptide) is then folded in different ways and to different extents. Generally, amino acids have a central or alpha carbon to which is attached a hydrogen atom (H), a carboxyl group (COOH), an amino group (NH2) and a fourth group that differs from one amino acid to another and is often indicated by the letter R. Approximately 20 different amino acids (they possess different R groups) are commonly found in proteins of the body. Proteins are formed from amino acids by reactions that bond the alpha amino group of one amino acid to the alpha carboxyl group of another. This bond is called a peptide bond. Two amino acids joined together by a peptide bond form a dipeptide. Ten or more amino acids linked in a chain by peptide bonds form a polypeptide chain. A protein is a polypeptide chain of approximately 100 or more amino acids linked by peptide bonds. The order of amino acids in a protein from the amino terminal to the carboxy terminal of the protein chain is referred to as the primary structure of the protein. Higher-order structures are dependent on the primary structure. 1. The two cysteine residues that react to form the disulfide bond (a covalent bond) may be a great distance apart in the primary structure but are brought into close proximity by the three-dimensional folding of the polypeptide chain. 2. Many proteins are composed of two or more polypeptide chains, generally referred to as subunits, which associate through non covalent interactions and occasionally, disulfide bonds to form protein quaternary structures. It has been known for long that the functions of proteins are closely related to their quaternary structure.

Proteins account for about one quarter of the total mass in most membranes. Membrane proteins are globular proteins. (a) both statements are true (b) both statements are false (c) the first statement is true, the second is false (d) the first statement is false, the second is true

d Proteins account for about one half of the total mass in most membranes. Membrane pro- teins are globular proteins. According to the fluid-mosaic model of membrane structure, they associate with the lipid bilayer in different ways: • Integral membrane proteins: are embedded in the lipid bilayer. In most cases, the polypeptide traverses the lipid bilayer by means of a transmembrane helix. The nonpo- lar side chains of these amino acids interact with the membrane lipids. Note: Integral membrane proteins can be solubilized only with treatments that destroy the lipid bilayer (action of detergents). • Peripheral membrane proteins: interact with integral membrane proteins or the hy- drophilic head groups of the membrane lipids, but they do not traverse the lipid bilayer. Note: They can be detached from the membrane by manipulating pH or salt concentra- tions. Six Common Features of Biological Membranes: 1. Sheetlike structures, only a few molecules thick (60 to 100 A thick). 2. Consist mainly of lipids and proteins (carbohydrates are attached to exterior). 3. The membrane lipids are small molecules with hydrophobic and hydrophilic groups that form lipid bilayers in aqueous media. The hydrophobic center of the bilayer forms a barrier to the flow of polar molecules across the membrane. 4. The proteins function as transporters, enzymes, receptors, and mediators. S.They are non covalent assemblies. The protein and lipid molecules are held together by many noncovalent interactions. 6. Their lipid distribution in the membrane is asymmetrical, meaning they contain most of their phospholipids (phosphatidylethanolamine, phosphatidylserine and phosphatidylinositol) in the cytoplasmic (inner) leaflet and most of their glycolipids (phosphatidylcholine and sphingomyelin) in the exoplasmic (outer) leaflet. Saad Alqahtani, Twitter

The factor which does not affect pKa value of an amino acid is _________ a) The loss of charge in the α-carboxyl and α-amino groups b) The interactions with other peptide R groups c) Other environmental factors d) Molecular weight

d Explanation: The loss of charge in the α-carboxyl and α-amino groups, the interactions with other peptide R groups and other environmental factors can affect the pKa.

All of the following are mechanisms the body uses to control the blood's acid-base balance EXCEPT one. Which one is the EXCEPTION? (a) Excess acid is excreted by the kidneys (b) pH buffers are found in the blood (c) excretion of carbon dioxide (d) filtering blood by the spleen

d The body employs regulatory systems that are designed to restore the normal blood pH. There are three lines of defense against acidosis and alkalosis: 1. The buffer systems act immediately to prevent excessive fluctuations of the blood pH. 2. Alveolar ventilation increases in acidosis and decreases in alkalosis. The respira- tory center in the medulla oblongata of the brain responds directly to pH and C02. This mechanism works on a time scale of minutes. 3. The kidneys excrete excess W in acidosis and excess HC03· in alkalosis. This is a long term mechanism that acts on a time scale of hours to days.