Biochemistry Exam I

Front 1

Name and describe 6 dietary components

Back 1

1.Carbohydrates - NOT required in diet, liver can synthesize from other sources
2.Fats - 2 essential fatty acids are required in the diet - LINOLEIC and LINOLENIC acids
3.Protein- required to sustain life, there are 10 essential amino acids in children (9 in adults)
4.Vitamins - cofactor for enzymatic reaction,some act as hormones (A, D)
5.Minerals- maintain electrolyte balance (Na and K), provide structure (Ca and P)
6.Water- universal solvent

Front 2

Whats the name of the process that generates energy

Back 2

Oxidative

Front 3

Whats the name of the process that uses energy for biosynthetic reactions

Back 3

Reductive

Front 4

Glycogen is the storage form of what?

Back 4

Carbohydrates, glycogen and starch are very similar in structure, glycogen is stored in animals, starch in plants
-consists of monomeric units of glucose in chains

Front 5

Where is glycogen stored?

Back 5

LIVER and MUSCLE

Front 6

Triacylglycerol is a storage form of what?

Back 6

Fat

Front 7

Where is triacylglycerol stored?

Back 7

In healthy individual stored in adipose tissue

Front 8

Protein is a storage of what?

Back 8

Amino acids, consists of amino acids linked together by PEPTIDE bond - very strong bond

Front 9

How many essential amino acids? Name them

Back 9

10 (9 in adults)
PVT TIM HALL -
Phenylalanine
Valine
Threonine
Tryptophan
Isoleucine
Methionine
Histidine
Arginine
Lysine
Leucine

Front 10

Amount of energy produced by oxidizing carbohydrates

Back 10

4 kcal/g

Front 11

Amount of energy produced by oxidizing proteins

Back 11

4 kcal/g

Front 12

Amount of energy produced by fats

Back 12

9 kcal/g

Front 13

Amount of energy produced by alcohol

Back 13

7 kcal/g

Front 14

Describe general structure of amino acid

Back 14

-Contain a CARBOXYL group, AMINO group and SIDE CHAIN, all attached to alpha carbon
-xcept GLYCINE (no side chain) and PROLINE (N part of the ring)

Front 15

What is the usual configuration of amino acids (L or D)

Back 15

L (except GLYCINE which is neither L nor D, because its not optically active and does not rotate polarized light)

Front 16

What is the ionization of carboxyl and amino group of amino acids

Back 16

At physiologic pH, amino acids carry a positive charge on their amino groups and a negative charge on carboxyl groups

Front 17

Name 20 amino acids and their abbreviations

Back 17

Alanine (Ala)
Arginine (Arg)
Asparagine (Asn)
Aspartate (Asp)
Cysteine (Cys)
Glutamate (GLu)
Glutamine (Gln)
Glycine (GLy)
Histidine (His)
Isoleucine (Ile)
Leucine(LEu)
Lysine(Lys)
Methionine(Met)
Phenylalanine (Phe)
Proline (Pro)
Serine (Ser)
Threonine(Thr)
Tryptophan(Trp)
Tyrosine (Tyr)
Valine (Val)

Front 18

Name non polar aliphatic amino acids

Back 18

1. GLYCINE - simplest amino acid, doesnt have an R group, only H
2.ALANINE
3.LEUCINE
4.ISOLEUCINE
5.VALINE
6.PROLINE-N is part of the ring
Isoleucine, leucine, valine and alanine all have non polar bulky hydrophobic side chains. Electrons are shared equally between C and H, so there is no H bonding with water.

Front 19

Name aromatic amino acids

Back 19

Aromatic amino acids have 6 membered rings and 3 double bonds
PHENYLALANINE
TRYPTOPHAN
TYROSINE
Phenylalanine has no substituents on the ring so its hydrophobic (nonpolar)
Tryptophan has N as a substituent on the ring so it can H bond with water and therefore is polar hydrophilic
Tyrosine has OH group on the ring and is also polar hydrophilic

Front 20

Name aliphatic, polar, uncharged amino acids

Back 20

Those are amino acids whose side chain is an amide - ADPARAGINE and GLUTAMINE or hydroxyl group - SERINE and THREONINE

Front 21

Name sulfur containing amino acids

Back 21

CYSTEINE
METHIONINE
-Cysteine has SH as a substituent and can react with another cysteine and form CYSTINE through disulfide bonds
Methionine has only S as a substituent and cant form disulfide bonds

Front 22

Which amino acids are acidic

Back 22

Negatively charged amino acids - ASPARTATE and GLUTAMATE

Front 23

Which amino acids are basic

Back 23

Positively charged amino acids - ARGININE, LYSINE, HISTIDINE

Front 24

What is the main function of an amino acid in the protein

Back 24

it forms PEPTIDE BOND, covalent bond between alpha carboxyl group of one amino acid and alpha amino group of next one

Front 25

What does linear sequence determine in protein

Back 25

LINEAR SEQUENCE determines 3D structure of the protein and its biological properties

Front 26

What determines function of the protein

Back 26

3D structure

Front 27

Whats a primary structure of the protein

Back 27

Sequence of amino acids along polypeptide chains

-Ser-Ala-Glu-Val-

Front 28

Whats a secondary structure of a protein

Back 28

various types of local conformations in which atoms of side chains are not involved

Front 29

Define tertiary structure of protein

Back 29

Overall 3D conformation

Front 30

Quaternary structure of a protein

Back 30

Spatial arrangement of subunits in a protein that consists of more then one polypeptide chains, subunits are joined together by NONCOVALENT INTERACTIONS (same as 3D)

Front 31

Name 3 types of proteis

Back 31

FIBROUS
GLOBULAR
MEMBRANE SPANNING

Front 32

Describe fibrous proteins

Back 32

-structural or mechanical roles
-polypeptide chains interwined to form fibers
-example - hair, fur, skin

Front 33

Describe globular proteins

Back 33

-functional, non-structural
-chains folded on itself to give compact, rounded structure
-most are water soluble
-example - enzymes, antibodies, transport proteins

Front 34

Name two types of H bonding in secondary structure of protein

Back 34

Intramolecular - between different parts of same chain - ALPHA HELIX
Intermolecular - between different chains- BETA PLEATED SHEET

Front 35

What stabilizes secondary structure of protein

Back 35

H bonding between carbonyl oxygen of one peptide bond and amino hydrogen of another

Front 36

Alpha helix

Back 36

common in globular proteins, membrane spanning proteins and DNA binding proteins
-has stable rigid conformation
-carbonyl of peptide bond interacts with NH of peptide bond four amino acid residues along the chain

Front 37

Beta Sheet

Back 37

-H bonding occurs between neighboring strands running parallel to each other

Front 38

Describe structure of keratin

Back 38

-strong rope like structure of interwined ALPHA HELIXES
-major component of external protective layer
-skin, hair, nails

Front 39

What is the difference between hard and soft keratins

Back 39

-HARD KERATINS have high sulfur content and form many S-S bonds between chains
-SOFT KERATINS have low sulfur content and very few S-S bonds between chains

Front 40

Describe structure of collagen

Back 40

-consists of THREE CHAINS that wind around each other to form a TRIPLE HELIX
-Collagen contains about 1000 amino acids, 1/3 of them is GLYCINE, others are PROLINE, HYDROXYPROLINE, or HYDROXYLYSINE

Front 41

What offers rigidity to collagen

Back 41

PROLINE
HYDROXYPROLINE

Front 42

What is a fundamental unit of collagen

Back 42

TROPOCOLLAGEN - triple hellical rod, rigid (not elastic like alpha helix), wider then alpha helix to accomodate bulky residues of PROLINE and HYDROXYPROLINE

Front 43

Describe post translational modification of collagen

Back 43

-PROLINE and LYSINE are HYDROXYLATED by reaction that requires vitamin C and O2
HYDROXYPROLINE forms H bonds between chains
HYDROXYLYSINE forms covalent bonds between chains
CROSS LINKS are produced and stabilize structure

Front 44

Name collagen disorders

Back 44

-SCURVY - defficient collagen
-Osteogenesis imperfecta (brittle bone disease)
-Alports syndrome
-Ehlers-Damons syndrome
-Epidermolysis Bullosa Dystrophica

Front 45

Describe protein folding

Back 45

Proteins fold during and following synthesis along same principles as micelle formation - POLAR amino acids on surface, NON POLAR inside

Front 46

What assists in vivo proten folding

Back 46

Molecular chaperones (heat-shock proteins) - use ATP energy to change conformation of a protein

Front 47

Describe domains in proteins

Back 47

Domains are physically independent regions within overall tertiary structure of large, complex protein.Usually visually obvious, like different regions within molecule
Example - extracellular domain, catalytic doman, transmembrane domain

Front 48

Describe solubility of globular proteins

Back 48

Soluble in water, core of globular protein has high content of non polar amino acids, its not in contact with water and its densely packed to maximize van der waals forces.
On the surface of the protein are polar amino acids which are charged which are in contact with water

Front 49

Describe prion diseases

Back 49

-Protein conformational disease caused by misfolded proteins

Front 50

Name forms of prion disease

Back 50

-genetic (point mutation)
-Creutzfeld-Jacobs
-Bovine spongiform encephalopathy
-Scrapie (sheep)

Front 51

How are prion diseases acquired

Back 51

-spontaneous mutation in gene encoding PrPc
-ingesting nervous tissue of infected animals
-injection of human growth hormone
-cannibalism

Front 52

Describe normal and misfolded proteins in prion disease

Back 52

PrPc is a normal protein foind on surface of neurons
PrPsc is disease form of protein that has same sequence of amino acids but different tertiary structure (3D), it aggregates and is abnormally resistant to breakdown
INTRODUCTION OF ABNORMAL PROTEIN CAUSES CONVERSION OF NORMAL TO ABNORMAL PROTEINS

Front 53

Describe polymorphism

Back 53

Variation of primary structure of protein, generally arise from mutations in DNA
Can be without or with consequences (sickle cell disease
-called polymorphism only when there is a significant frequency of population (20-30%)

Front 54

Describe sickle cell polymorphism

Back 54

-Different structure of sickle cell Hb tends to polymerize in deoxy form
-Distorts RBC into rigid sickle shape
-Sickle cells are more easily degraded which results in anemia
-Sickle cells tend to block peripheral blood vessels causing ischemia and pain

Front 55

Define homolog proteins

Back 55

-Proteins with highly similar sequence
-evolved from same ancestor

Front 56

Define Orthologs

Back 56

-From DIFFERENT species
-originated from same gene in ancestor
-normally retain function- insulin is same in humans and pork

Front 57

Define Paralogs

Back 57

-from SAME species
-originate from common ancestral gene
-may have differnet functions - myoglobin, different hemoglobin chains

Front 58

Protein isoforms

Back 58

-Perform essentially same function
-are highly homologous
-evolved from same ancestral gene
-possess DIFFERENT amino acid sequences and chemical and physical properties

Front 59

Define isozyme

Back 59

Proteins isoforms which are enzymes

Front 60

Structure of hemoglobin

Back 60

HbA (adult) consists of FOUR POLYPEPTIDE CHAINS each containing molecule of HEME
Chains are SIMILAR in 3D configuration and to single chain of myoglobin, but have DIFFERENT sequences.

Front 61

Describe function of hemoglobin

Back 61

OXYGEN SATURATION curve for Hba is SIGMOIDAL. Each HEME binds ONE O2. When O2 binds, HbA changes from T form (taut) to R (relaxed). Binding to one heme increases affinity for others.

Front 62

What effect does binding of 2,3-BPG have on affinity

Back 62

DECREASES affinity og HbA for O2, so its more readily released in tissues when its bound

Front 63

Fetal Hb

Back 63

-Has LOWER affinity for BPG then HbA, so HIGHER affinity for O2

Front 64

Define denaturation of proteins

Back 64

3D structure and biological activity of protiens is lost without breaking peptide bonds

Front 65

Conditions that can denature proteins

Back 65

-Extremes of pH
-High temperature
-Organic sollvents (alcohol)
-Salts of heavy metals (mercury)
-Radiation

Front 66

Describe cystinuria

Back 66

Normally amino acids are filtered by glomerular capillaries. Cystinuria is a genetic disease where protein is missing that normally responsible for rabsorption of cystine, arginine and lysine from kisneys. So, urine has elevates cystine, which precipitates and forms renal stones