Ebook Lippincott illustrated reviews flash cards biochemistry: Part 1

(BQ) Part 1 book Lippincott illustrated reviews flash cards biochemistry presents the following contents: Protein structure and function, bioenergetics and carbohydrate metabolism, lipid metabolism.

Denise R Ferrier, PhD

Professor of Biochemistry

Department of Biochemistry and Molecular Biology

Drexel University College of Medicine

Philadelphia, Pennsylvania

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Featuring the same visionary artwork found in

Lippincott Illustrated Reviews: Biochemistry

With Lippincott Illustrated Reviews, Seeing is Understanding.

Lippincott Illustrated Reviews Flash Cards: Biochemistry is a portable study tool designed for self-assessment and review of medical

biochemistry The fl ash cards were developed primarily for use by medical students studying biochemistry and preparing for United States licensing exams, but information is presented with a clarity and level of detail that makes them ideal supplements for any of the allied health sciences The deck contains three card types: Question (Q) cards, Case cards, and Summary cards

CLINICAL CORRELATIONS: Clinical questions highlight the basic science foundations of medicine They help students apply

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Continued, over

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• Illustrations : Richly detailed illustrations from the popular companion text, Lippincott Illustrated Reviews: Biochemistry , appear on both

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• Notes : Answers may be supplemented with information that goes beyond the need-to-know basics to provide context or to enrich and help

anchor a concept

• Emphasis: Key terms, disease names, and pathologic fi ndings are bolded for rapid review and assimilation

CASE CARDS AND SUMMARY CARDS

Case cards use common clinical presentations to highlight biochemical concepts Summary cards (for the vitamins and the fed/fasted states) highlight key features of these information-rich areas of medical biochemistry

The card deck is designed to be comprehensive, covering all signifi cant biochemical concepts

Figure Credits

Card 3.6 Question and Answer: Modifi ed

photo courtesy of Photodyne Incorporated,

Hartland, WI

Card 4.2 Answer: Kronauer and Buhler,

Images in Clinical Medicine, The New

England Journal of Medicine, June 15, 1995,

Vol 332, No 24, p 1611

Card 4.5 Question and Answer: 1 Modifi ed

photo from Web site Derma.de 2 Modifi ed

from Jorde LB, Carey JC, Bamshad MJ,

et al Medical Genetics 2nd ed St Louis,

MO: Mosby; 2000 http://medgen.genetics.

utah.edu/index.htm Card 13.6 Answer: From the Crookston Collection, University of Toronto

Card 21.2 Answer: Modifi ed from Rich MW

Porphyria cutanea tarda Postgrad Med

1999;105:208–214

Card 21.4 Question and Answer: From Custom Medical School Stock Photo, Inc Card 22 Case Card Question: Modifi ed from WebMD Inc http://www.samed.com/sam/ forms/index.htm

Card 23.6 Question and Answer: Modifi ed from Cryer PE, Fisher JN, Shamoon H

Hypoglycemia Diabetes Care 1994;17:

734–753

Contents

1.1 Question

Amino Acid Structure

What effect will raising pH from an acidic value to the physiologic value of 7.4 have on

the structural features shown in red at right?

At physiologic pH, what will be the charge on the side chain (R group) of free Asp? Of Lys?

Which amino acid(s) contains a side-chain hydroxyl group that can be glycosylated?

A secondary amino group?

Is Val ionized when incorporated into a protein?

C

COOH

H C

Carboxylgroup

`

C ` H R

Amino

Side chain

is distinctive for each amino acid.

`-Carbon is linked to the carboxyl, amino, and R groups.

1.1 Answer Amino Acid Structure

Raising the pH from an acidic value to the physiologic value of 7.4 will result in deprotonation (ionization)

of the ␣-carboxyl group (pK⬃2) to COO⫺ The ␣-amino group (pK⬃9) will remain protonated

At physiologic pH, the charge on the side chain (R group) of free Asp is negative Lys is positive

Ser and Thr each contain a hydroxyl group that can be O-glycosylated [Note: The hydroxyl group

can also be phosphorylated.] Pro contains a secondary amino group Its ␣-amino N and R group form

a rigid ring

Val is not ionized when incorporated into a protein because (1) the ␣-amino and ␣-carboxyl groups are

involved in peptide bonds and, consequently, are unavailable for ionization, and (2) the side chain

is nonpolar

C+H3N

-H C

+H3N

C

CO OH

-These are common to all `-amino acids.

Free amino acid

R

Amino group

Carboxyl group

`

R

Amino group R

Side chain

is distinctive for each amino acid.

`-Carbon is linked to the carboxyl, amino, and R groups.

COOHH

1.2 Question

Amino Acid Structure

Based on the fi gure, where would Leu likely be located in a protein that spans the

membrane? In a soluble protein?

What term refers to the tendency of nonpolar molecules (or regions of molecules

such as amino acid side chains) to cluster together in a polar environment such as

an aqueous solution?

In sickle cell anemia (SCA), why does the replacement of a Glu by a Val on the

surface of the deoxyHb molecule result in the association of these molecules?

Cell membrane

Polar amino acids ( ) cluster on the surface of soluble proteins.

Cell C

C ll

Nonpolar amino acids ( ) cluster

on the surface of membrane proteins.

Nonpolar amino acids ( ) cluster

in the interior of soluble proteins.

Amino Acid Structure

1.2 Answer

Leu, a nonpolar amino acid, would likely be located within the hydrophobic

membrane-spanning domain of the protein It would likely be located in the interior

of a soluble protein

The term hydrophobic effect refers to the tendency of nonpolar molecules

(or regions of molecules such as amino acid side chains) to cluster together in a

polar environment such as an aqueous solution

The replacement of polar Glu by nonpolar Val creates a hydrophobic region on

the surface of the deoxyHb molecule that will interact with a hydrophobic region

on other deoxyHb molecules This interaction creates rigid polymers of deoxyHb

that deform RBCs Thus, it is the hydrophobic effect that drives the association of

membrane Cell Leu

Polar amino acids ( ) cluster on the surface of soluble proteins.

Nonpolar amino acids ( ) cluster

on the surface of membrane proteins.

Nonpolar amino acids ( ) cluster

in the interior of soluble proteins.

1.3 Question

Amino Acid Structure

Which structure shown (A or B) represents L-Ala?

Which amino acid does not possess a chiral (asymmetric) carbon?

Which peptide is less soluble in an aqueous (polar) environment, Ala-Gly-Asn-Ser-Tyr

1.3 Answer Amino Acid Structure

Structure A represents L-Ala The L isomer of an amino acid has the ␣-amino

group on the left The D isomer has the ␣-amino group on the right D and L

isomers are mirror images of each other (enantiomers).

Gly, with its two H substituents, does not possess a chiral (asymmetric) carbon.

Because the Gly-Met-Phe-Leu-Ala peptide contains no charged or polar uncharged

amino acids, it is less soluble than Ala-Gly-Asn-Ser-Tyr in an aqueous (polar)

H C NH

1.4 Question

Acidic and Basic Properties of Amino Acids

What relationship is described by the Henderson–Hasselbalch equation shown?

Is an acid with a large pKa stronger or weaker than one with a small pKa?

The pKa of acetic acid (CH3COOH) is 4.8 What is the pH of a solution containing acetic acid

and its conjugate base (CH3COO⫺) in a ratio of 10 to 1?

Physiologic buffers are important in resisting blood pH changes Maximal buffering occurs

when the pH is equal to the , while effective buffering can occur within

[HA]

+

The Henderson–Hasselbalch equation describes the relationship between the pH of a solution and

the concentration of a weak acid [HA] and its conjugate base [A⫺]

An acid with a large pK a is weaker than one with a small pKa because the large pKa refl ects less

ioniza-tion (fewer H⫹ released) This is because pK a  log Ka

Because pH  pK a  log [A]/[HA], when pKa is 4.8 and the ratio of the acid to its conjugate base is

10 to 1, the pH is equal to 4.8 ⫹ log of 0.1 Therefore, pH ⫽ 4.8 ⫹ (⫺1) ⫽ 3.8

Physiologic buffers are important in resisting blood pH changes Maximal buffering occurs when the

pH is equal to the pK a, while effective buffering can occur within 1 pH unit of the pKa

0 0.5 1.0

Which FORM (I, II, or III) shown represents the isoelectric form of Ala?

Calculate the pI for Arg, which has three pKs: pK1 ⫽ 2.2, pK2 ⫽ 9.2, and pK3 ⫽ 12.5

What will happen to the charge on His residues in a protein that moves from the cytoplasm (pH ⬃7.4) to a lysosome (pH ⬃5.0)?

1.5 Answer Acidic and Basic Properties of Amino Acids

The isoelectric form has no net charge It is the zwitterionic (“two ion”) form Therefore, FORM II is the isoelectric form of Ala.

The pI corresponds to the pH at which an amino acid is electrically neutral, that is, the average of the pKs on either side of the isoelectric form For Arg,

a dibasic amino acid with pK1 (most acidic group) ⫽ 2.2, pK2 ⫽ 9.2, and pK3 (least acidic group) ⫽ 12.5, the pI is 10.8 (the average of 9.2 and 12.5)

In a protein, the imidazole R group of His can be charged or uncharged depending on the local environment It will be uncharged (deprotonated) at pH 7.4 and

charged (protonated) at pH 5.0 [Note: In free His the pK of the R group is 6.0.]

1.6 Question

Acidic and Basic Properties of Amino Acids

Based on the bicarbonate buffer system shown, what will happen to the availability of HCO 3 ⫺ when H ⫹ is lost, such as with emesis (vomiting)?

Use the Henderson–Hasselbalch equation to determine what will happen to pH when HCO 3 ⫺ is lost (e.g., with diarrhea) and when CO 2 is increased (e.g., with pulmonary obstruction)

Aspirin (pK a ⫽ 3.5) is largely protonated and uncharged in the stomach (pH 1.5) What percentage of the aspirin will be in this lipid-soluble form at pH 1.5?

1.6 Answer Acidic and Basic Properties of Amino Acids

With emesis ( vomiting ), the loss of H ⫹ (rise in pH) results in increased availability of HCO 3 ⫺ as the

result of a compensatory rightward shift in the bicarbonate buffer system

The Henderson–Hasselbalch equation is used to calculate how the pH of a system changes in

response to changes in the concentration of an acid or its conjugate base For the bicarbonate buffer

system, pH ⫽ pK ⫹ log [HCO 3 ⫺ ]/[CO 2 ] Therefore, both the loss of HCO 3 ⫺ (base) with diarrhea and

the increase in CO 2 (acid) because of decreased elimination with pulmonary obstruction result in

decreased pH

pH ⫽ pK ⫹ log [Drug ⫺ ]/[Drug-H] Therefore, for aspirin in the stomach, 1.5 ⫽ 3.5 ⫹ ( ⫺ 2) Because

the antilog of ⫺ 2 is 0.01, the ratio of [Drug ⫺ ]/[Drug-H] is 1/100 This means that 1 out of 100 (1%) of the

aspirin molecules will be the Drug ⫺ form and 99 out of 100 (99%) will be the uncharged, lipid-soluble,

Lipid membrane

LUMEN OF STOMACH

2.1 Question

Protein Structure

Which level of protein structure depicted can be correctly described as the “three-dimensional shape of a folded

polypeptide chain”?

Mutations that insert, delete, or replace amino acids change this level of protein structure

How many different isoforms of the tetrameric enzyme PK can be made from M and/or L subunits?

How many different tetrapeptides could be generated from three different amino acids?

C

H

H C

H

CH 3

O H

N O O C C N C O

C OO N

C C N N R

C

C R

C R

3 2

1

H

4

2.1 Answer Protein Structure

The “three-dimensional shape of a folded polypeptide chain” describes a protein’s tertiary structure (No 3 shown)

At a minimum, the primary structure (amino acid sequence) will change with mutations that insert, delete, or replace

amino acids [ Note: Changes in the primary structure can also affect the higher levels of protein structure (No 2

to 4 shown) Such changes frequently result in protein misfolding and can lead to loss of function, aggregation, or

degradation.]

Five different forms of tetrameric PK can be made from M and/or L subunits: M 4 , M 3 L, M 2 L 2 , ML 3 , and L 4 Because PK

is composed of more than one subunit, it has a quaternary structure

There are 3 4 or 81 (where 3 ⫽ the number of amino acids and 4 ⫽ the chain length) different tetrapeptides that could

be generated from three different amino acids

C

H

H C

H

CH 3

O H

N O O C C N C O

C O O N

C C

N N R

C

C R

C R

Quaternary structure

4

Tertiary structure

3

2Secondary structure

Primary structure

1

H

2.2 Question

Primary Structure of Proteins

What is the name given to the bond outlined by the black box shown?

What are the characteristics of this bond?

With fever , why might proteins begin to unfold but not be hydrolyzed to peptides

and free amino acids?

Free carboxyl end of peptide

2.2 Answer Primary Structure of Proteins

A peptide bond , a type of amide bond, is outlined by the black box Peptide bonds

link the amino acid residues in a peptide or protein by joining the  -amino group of

one amino acid to the  -carboxyl group of the next as water is released

The peptide bond has partial double-bond character, is rigid and planar, uncharged

but polar, and almost always in the trans confi guration that reduces steric

interference by the R groups

Peptide bonds are resistant to conditions (such as the heat from a fever ) that can

denature proteins and cause them to unfold However, they are susceptible to

cleavage by enzymes known as proteases or peptidases [ Note: Strong acids or

bases at high temperatures can nonenzymatically cleave peptide bonds.]

Free carboxyl end of peptide

C N H

C N H O

Cis peptide bond

R

2.3 Question

Primary Structure of Proteins

Sequencing large polypeptides involves cleavage reactions, as shown Which sites in a peptide are

susceptible to cleavage by the endopeptidase trypsin ? By cyanogen bromide?

What is the Edman degradation method?

What is the amino acid sequence of a nonapeptide if trypsin digestion yields three products (Asn,

Met-Gln-Lys, and Ala-Gly-Met-Leu-Arg) and cyanogen bromide cleavage yields three products

(Leu-Arg-Met, Gln-Lys-Asn, and Ala-Gly-Met)?

1 Cleave with trypsin

Peptide of unknown sequence

2 Determine sequence of peptides using the Edman method

What is the correct order?

Peptide B Peptide A

2.3 Answer Primary Structure of Proteins

Trypsin , an endopeptidase , cleaves at the carboxyl side of Lys and Arg residues within a peptide

[ Note: Exopeptidases remove the terminal amino acid.] Cyanogen bromide cleaves at the carboxyl

side of Met residues

The Edman degradation method chemically determines the sequence of amino acids through the

sequential removal and identifi cation of the N-terminal amino acids in the small peptides generated

from a polypeptide by cleavage reactions

Based on the overlapping amino acids in the products of the trypsin (Asn, Met-Gln-Lys, and

Ala-Gly-Met-Leu-Arg) and the cyanogen bromide (Leu-Arg-Met, Gln-Lys-Asn, and Ala-Gly-Met)

cleav-age reactions, the amino acid sequence of the nonapeptide is Ala-Gly-Met-Leu-Arg-Met-Gln-Lys-Asn

[ Note: The sequence of amino acids in a protein is always written from the N-terminal to the C-terminal

What is the correct order?

Peptide B Peptide A

Peptide X Peptide Y

Peptide C

1 Cleave with cyanogen

2 Determine sequence of peptides using the Edman method

2.4 Question

Secondary Structure of Proteins

Which type of secondary structure is illustrated at right?

How does the orientation of the hydrogen bonds differ between the ␣ -helix and the

␤ -sheet structures?

In proteins (e.g., the GPCRs for glucagon and the catecholamines) that contain

several ␣ -helical membrane-spanning domains, why would Pro not be one of the

amino acids found in these domains?

Side chains of amino acids extend outward

NHC

OCNCNH

HCOCC

N

CCOO

CC

NH

NHR

2.4 Answer Secondary Structure of Proteins

The fi gure illustrates an  -helix , a right-handed, helical, secondary structural element commonly

encountered in both fi brous and globular proteins

The hydrogen bonds in a coiled ␣-helix are intrachain bonds that are parallel to the polypeptide

back-bone, whereas those in a  -sheet (an extended structure) can be intra- or interchain bonds (depending

on whether they form between sections of one polypeptide or between two polypeptides) that are

perpendicular to the backbone [ Note: ␣ -Helices and ␤ -sheets may be components of supersecondary

structures (motifs), such as a ␤ -barrel.]

Pro contains a secondary amino group that is not compatible with the right-handed spiral of the ␣ -helix

because (1) it cannot participate in the hydrogen bonding and (2) it causes a kink in the protein

Consequently, Pro is not found in the membrane-spanning domains of proteins such as GPCRs

[ Note : Amino acids with bulky or charged R groups can also disrupt formation of an ␣ -helix.]

Side chains of amino acids extend outward Intrachain

hydrogen bond

N C

OCO C C N C O C

C N

H O C C O

O H

C C

N H

N H R

COOH H

2.5 Question

Tertiary Structure of Proteins

What type of molecular interaction involved in stabilizing the tertiary structure of a

protein is shown?

What type of interaction would likely occur between Asp and Lys?

The tertiary structures of proteins (such as albumin) that function in the extracellular

environment are stabilized by the formation of covalent links between the oxidized

side chains of which sulfur-containing amino acid(s)?

H3C CH3

H

C C

H N O H

H C N H C O

Polypeptide backbone

Isoleucine

Leucine

2.5 Answer Tertiary Structure of Proteins

Shown are hydrophobic interactions between Ile and Leu, two amino acids with nonpolar R groups

Ionic interactions ( salt bridges ) would likely occur between Asp (acidic R group) and Lys (basic R group)

Two sulfur-containing Cys residues, brought into close proximity by the folding of the peptide(s),

are covalently linked through oxidation of their thiol side chains The disulfi de bonds formed

stabilize the tertiary structure of the folded peptide, preventing it from becoming denatured in the

oxidizing extracellular environment [ Note: Cys-containing albumin transports hydrophobic molecules

(e.g., fatty acids and bilirubin) in the blood Its levels are used as an indicator of nutritional status.]

H 3 C CH 3

H

C C H N O H

H C

N C O

Polypeptide backbone

Isoleucine

Leucine

C H 3 CH C

O

peptide kbone

Leucine

Hydrophobic interactions

Cystine residue

H C

CH 2

H

S

C C H

C O

CH 2

N O H

Two cysteine residues

H C

CH 2

H

SH SH

C C H

C O

CH 2

N O H

S

Polypeptide backbone

Cystine residue

H C H

CH

C 2 H

S

C O

Disulfide bond

Oxidant (for example, O 2 )

2.6 Question

Protein Misfolding

As illustrated, what secondary structural feature is enriched in the infectious form of a prion

protein (PrP) as compared to the noninfectious form?

Why do most large denatured proteins not revert to their native conformations even under

favor-able environmental conditions?

What misfolded peptide formed by abnormal proteolytic cleavage is the dominant component of

the plaque that accumulates in the brains of individuals with Alzheimer disease ?

to fold into the infectious form.

Noninfectious PrP C

2.6 Answer Protein Misfolding

The ␤ -sheet secondary structure is enriched in the infectious PrP Sc

form of a PrP , which causes the transmissible spongiform encephalopathies , as compared to the noninfectious PrP C form that is ␣ -helical rich

The folding of most large proteins is a facilitated process that requires the assistance of proteins known as chaperones

and ATP hydrolysis

A  is the misfolded peptide produced by abnormal proteolytic cleavage of amyloid precursor protein by

secretases A ␤ forms an extended ␤ -sheet and spontaneously aggregates to form fi brils that are the dominant

component of the amyloid plaque that accumulates in the brains of individuals with Alzheimer disease

[ Note: The ␤ -sheets in A ␤ have exposed hydrophobic amino acid residues The hydrophobic effect drives the

aggregation and precipitation of A ␤ ]

Interaction of the infectious PrP causes the normal form

to fold into the infectious form.

Infectious PrP Sc (contains a-sheets)

Infectious PrP Sc (contains a-sheets)

Noninfectious PrP C (contains `-helix)

Aa Cell membrane Amyloid

Spontaneous aggregation to fibrils of a-pleated sheets

3.1 Question

Myoglobin Structure and Function

Which His residue (A or B), as shown, is the proximal His? What is its function?

What is special about the location of this amino acid?

What type of secondary structure is most abundant in Mb? Does Mb have a

quaternary structure?

Rhabdomyolysis (muscle destruction) caused by trauma, for example, is

characterized by muscle pain, muscle weakness, and dark-colored urine The

dark color of the urine is the result of excretion of , a condition known as

Oxygen molecule (O2)

Heme

A

B Fe

Choice A is the proximal His It forms a coordination bond with the Fe 2

Rhabdomyolysis (muscle destruction) caused by trauma, for example, is

characterized by muscle pain, muscle weakness, and dark-colored urine (shown)

The dark color of the urine is the result of excretion of Mb , a condition known as

myoglobinuria

Oxygen molecule (O2)

Heme

Fe

Proximal histidine (F8)

Distal histidine (E7)

3.2 Question

Hemoglobin Structure and Function

Which form of Hb (deoxygenated or oxygenated) is referred to as the R form? What determines the equilibrium concentrations of deoxyHb and oxyHb?

How does the structure of Hb change as O 2 binds to the heme Fe 2 ⫹ ?

What condition, characterized by a “ chocolate cyanosis ,” results from the oxidation of Fe 2

Weak ionic and

hydrogen bonds occur

between αβ dimer pairs

in the deoxygenated state.

Some ionic and hydrogen bonds between αβ dimers are broken in the oxygenated state.

Strong interactions, primarily hydrophobic, between α and β chains form stable

αβ dimers.

3.2 Answer Hemoglobin Structure and Function

The oxygenated, high-O 2 -affi nity form of Hb is referred to as the R form The availability of O 2 determines the equilibrium concentrations

The binding of O 2 to the heme Fe 2 ⫹ pulls the Fe 2 ⫹ into the plane of the heme This causes salt bridges between the two ␣␤ dimers to rupture, thereby

allowing movement that converts the T to the R form

Methemoglobinemia , characterized by a “ chocolate cyanosis ” (dark-colored blood, bluish colored skin), results from the oxidation of Fe 2 ⫹ to Fe 3 ⫹ in

Hb Because the distal His stabilizes the binding of O 2 to the heme Fe 2

"R," or relaxed, structure of oxyhemoglobin

"T," or taut, structure of deoxyhemoglobin

Weak ionic and

hydrogen bonds occur

between αβ dimer pairs

in the deoxygenated state.

Some ionic and hydrogen bonds between αβ dimers are broken in the oxygenated state.

Strong interactions, primarily hydrophobic, between α and β chains form stable

αβ dimers.

3.3 Question

O 2 Binding to Myoglobin and Hemoglobin

Use the fi gure to determine the approximate amount of O 2 that would be delivered by

Mb and Hb when the pO 2 in the capillary bed is ⬃26 mm Hg

Why is the O 2 -dissociation curve for Hb sigmoidal and that for Mb hyperbolic?

How might RBC production be altered to compensate for changes to Hb that result

in an abnormally high affi nity for O 2 ?