Biochemistry: Proteins Flashcards by Yssa Idolor

How many amino acids are found in mammalian proteins?

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Each amino acid has 3 groups (enumerate) except for (identify)

Carboxyl group
Amino group
R group/side chain

Proline
[Amino acids containing a secondary amine group (the only proteinogenic amino acid of this type is proline) are sometimes named imino acids]

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Enumerate the non-polar amino acids

GAP VW LIMP

Glycine 
Alanine
Phenylalanine
Valine
tWyptophan
Leucine
Isoleucine
Methionine
Proline

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Non-polar amino acids
Net charge
Kind of interactions/bonds
Location

Zero net charge
Hydrophobic interactions
Interior of the protein

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Polar uncharged amino acids
Net charge
Kind of interactions/bonds
Location

Zero net charge
Hydrogen bonds
Surface of the protein

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Enumerate the uncharged polar amino acids

Tired Surgeon Aspirated The Gluteal Cyst, Uncharged

Threonine (-OH)
Serine (-OH)
Asparagine (Amide)
Tyrosine (-OH)
Glutamine (Amide)
Cysteine (-SH)

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Charged/Hydrophilic amino acids
Net charge
Kind of interactions/bonds
Location

Positive or negative (Acidic or basic)
Forms ionic interactions
Surface of the protein

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Enumerate the charged/hydrophilic amino acids

The movie Shallow HAL has a POSITIVE message.
Histidine
Arginine
Lysine

Stop being a NEGATIVE ASshole, MATE.
Aspartate
Glutamate

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Which AA is this?

Smallest side chain (H)
Synthesis of: heme, purines, creatine,
Conjugated to bile acids, drugs, other metabolites
Major inhibitory neurotransmitter in the spinal cord
No optical isomer
Like alanine, major fraction of AAs in blood

Glycine/ Gly/ G

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Which AA is this?

Methyl group (CH3)
Carrier of ammonia and carbons of pyruvate from skeletal muscle to liver
Like glycine, major fraction of AAs in blood

Alanine/ Ala/ A

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Branched-chain AAs whose metabolites accumulate in MSUD

Valine/ Val/ V
Leucine/ Leu/ L
Isoleucine/ Ile/ I

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Which AA is this?

Accumulates in phenylketonuria
Precursor of tyrosine

Phenylalanine/ Phe/ F

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Which AA is this?

Largest side chain - indole/bicycle ring
Precursor for niacin, serotonin (5-hydroxytryptamine), melatonin

Tryptophan/ Trp/ W

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Which AA is this?

Transfer of methyl groups as SAM
Precursor of cysteine and homocysteine (homologues)

Methionine/ Met/ M

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Which AA is this?

Imino acid
Fibrous structure of collagen
Interrupts alpha helices in globular proteins

Proline/ Pro/ P

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Which AAs are these?

Have polar hydroxyl group
Site of O-link glycosylation and phosphorylation of proteins
One of them is the precursor of several compounds: Thyroxine, melanin, catecholamines (enumerate pathway)

Serine/ Ser/ S
Threonine/ Thr/ T
Tyrosine/ Tyr/ Y

Catecholamine formation:
Pare, True Love Does Not Exist
Phenylalanine –> Tyrosine –> L-Dopa –> Dopamine –> Norepinephrine –> Epinephrine

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Which AAs are these?

Have carbonyl group and amide group that can form H bonds
One is the site of N-linked glycosylation of proteins
One is deaminated by glutaminase resulting in ammonia formation, and is a major carrier of N to the liver from peripheral tissues

Asparagine/ Asn/ N - N-linked glycosylation

Glutamine/ Gln/ Q - deaminated by glutaminase

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Which AA is this?

Has a sulfhydryl group that is an active part of many enzymes
Biosynthesis of coenzyme A
Two cysteines connected by a covalent disulfide bond to form cysteine
Found in keratin (makes hair curly, rebonding breaks cysteine bonds)

Cysteine/ Cys/ C

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Which AAs are these?

Negatively charged at neutral pH because of the carboxylate group
Participate in ionic interactions
Proton donors
One is the precursor for GABA and glutathione
Magic Sarap granules (umami)

Acidic AAs:

Aspartate/ Asp/ D
Glutamate/ Glu/ E

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Which AAs are these?

Proton acceptors
At neutral pH, 2 are positively charged, the first is the precursor of creatinine, urea and nitric oxide

The third has no charge since it is a weak base
The last is also the precursor of histamine, used in the diagnosis of folic acid deficiency, concentration in thalamus varies according to circadian rhythm

Basic AAs:

Arginine/ Arg/ R
Lysine/ Lys/ K
Histidine/ His/ H

Diagnosis of folic acid deficiency: FIGlu test

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Which AA is this?

21st AA
Found in some peroxidases and reductases
Inserted in polypeptides during translation, but has no specific codon

Selenocysteine

A selenium atom replaces the sulfur of its structural analog, cysteine

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Plant AAs:

Found in Lathyrus sativus (grass pea) seeds
Neurolathyrism - progressive and irreversible spastic paralysis of the lower extremities

Homoarginine

B-N-Oxalyldiaminopriopionic acid (B-ODAP)

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Plant AAs:

Neurotoxic amino acid in Cycad seeds
Neurodegenerative diseases including amyotrophic lateral sclerosis - Parkinson dementia complex in Guam natives

B-methylaminoalanine

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All amino acids are chiral except for

Glycine/ Gly/ G

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Configuration of AAs in: Proteins Antibiotics

Proteins: L-configuration | Antibiotics and bacterial cell walls: D-configuration

Why can AAs serve as buffers in aqueous solutions?

Can accept or donate protons

AA charge depends on

pH of aqueous environment

Define "zwitterion"

An AA bears no net charge at its isoelectric pH (pI)

What AAs are essential for proper body function since they cannot be synthesized?

Essential Amino Acids PVT TIM HALL Sometimes ARGues, never Completely Tyres ``` Phenylalanine Valine Tryptophan Threonine Isoleucine Methionine Histidine Arginine* Leucine Lysine ``` *Considered nutritionally Semi-essential only Cysteine (from Methionine) and Tyrosine (Phenylalanine) can be synthesized in the body

Primary structure of proteins Attaches alpha amino group of one AA to the alpha carbonyl group of another

Amino acid sequence Peptide bond

Peptide bond Partial ____ in character ____ and planar Generally in ____ configuration Methods of hydrolysis

Peptide bond Partial DOUBLE-BOND in character RIGID and planar Generally in TRANS configuration Methods of hydrolysis: PROLONGED EXPOSURE TO STRONG ACID OR BASE AT ELEVATED TEMPERATURES

First protein to be sequenced

Insulin

Protein sequencing: Attaches to N-terminal AA

Sanger's reagent (1-fluoro-2,4-dinitrobenzene) | Edman's reagent (Phenylisothiocyanate)

Protein sequencing: Attaches to C-terminal AA

Hydrazine | Carboxypeptidase

Protein secondary structure and bonding

Polypeptides form alpha helix and beta sheets | Hydrogen boding stabilizes configurations

Most common protein secondary structure Keratin Hemoglobin

Alpha helix

Parallel or anti-parallel secondary protein structure Amyloid Immunoglobulin

Beta sheet

Supersecondary protein structures such as B-a-B unit, Greek key, B-meander, B-barrel

Motifs

Less regular protein secondary structure forming loops and bends

Non-repetitive secondary structures

3D shape of a protein

Tertiary structure

Examples of tertiary structure: Globular Fibrous

Globular - hemoglobin, myoglobulin | Fibrous - collagen, elastin

Tertiary structure is stabilized by these bonds

Disulfide, Hydrophobic interactions, Hydrogen bonds, Ionic interactions

Functional and 3D structural units of a polypeptide

Domains

Quaternary structure of a protein

Monomeric vs Dimeric | Homodimers vs Heterodimers

Specialized proteins required for proper folding of other proteins Can "rescue" proteins from misfolding, prevents aggregation

Chaperones

Denaturation targets which protein structures?

Secondary and tertiary protein structures, peptide bonds are not hydrolyzed Most denaturation is irreversible Denaturing agents: heat, organic solvents, mechanical mizing, strong acids or bases, detergents, ions of heavy metals such as lead or mercury

Examples or protein misfolding disorders

Prion diseases | Alzheimers Disease

Disease of secondary structure proteins, causes neurologic symptoms

Prion diseases PrPc (alpha-helix, normal) to PrPsc (beta-sheets, pathologic) Protein alone is transmitted

Involves ApoE, most common and important neurodegenerative disease of the brain

Alzheimers Disease

2 configurations of hemoglobin

T (taut form) - low O2 affinity | R (relaxed form) - high O2 affinity (300x)

Property of hemoglobin wherein 4 molecules of O2 may bind, with increasing affinity

Positive cooperativity

Where are hemoglobin and myoglobin found?

Hemoglobin - Heme protein only in RBCs | Myoglobin - Heme protein in heart and skeletal muscle

Factors that cause a shift to the right in the oxygen dissociation curve

``` Increase in CO2 Increase in acidity (Decrease in pH) Increase in 2,3 bisphosphoglycerate Increase in exercise Increase in temperature ``` When you get LEFT behind, you HOLD ON, but LETTING GO is the RIGHT thing to do.

What has more affinity for O2 in infants? HbF or HbA?

HbF, since 2,3 BPG binds more weakly to it

Why does prolonged exposure high altitude lower affinity of HbA for O2?

Increased RBC production --> Increased Hgb --> Inc 2,3 BPG

What binds to Hgb following: Bohr effect Haldane effect

``` Booohr = Proooton Haaaldane = Caaarbon (polite, will only bind to Hgb if O2 is not bound) ```

HbA1C | When blood glucose enters RBCs, it glycosylates what?

epsilon-amino group of lysine residues | amino terminals of hemoglobin

Hgb that consits of 2 alpha and 2 gamma chains, 60% of hemoglobin in fetus, higher affinity for O2 than HbA

Fetal hemoglobin (HbF)

Hgb that consists of 2 alpha and 2 delta chains, 2% of hemoglobin of adults

Hemoglobin A2 (HbA2)

Treatment for carbon monoxide poisoning

100% oxygen therapy Carboxyhemoglobin: Hgb bound to CO, since CO has 200x more affinity for Hgb than O2

Inherited/intrinsic RBC membrane defect (spheroidal in shape), ankyrin mutation, splenic sequestration, manifest as anemia, jaundice and splenomegaly, Dx: osmotic fragility test, Tx: splenectomy

Hereditary spherocytosis

Point mutation in both genes coding for beta chain (Glu --> Val), homozygous recessive Effect on RBC: Distorted RBC membrane Misshape, rigid RBCs occluding capilaries Polymerization and decreased solubility of the deoxy form of Hgb Manifestation: Anemia, tissue anoxia, painful crises, protective against malaria Treatment: Hydration, analgesics, antibiotics if with infection, transfusions, hydroxyurea

Sickle Cell Disease

(Lys --> Glu) in beta-globin chain, homozygosity: mild hemolytic anemia, no therapy needed

Hemoglobin C Disease

Inadequate synthesis of alpha globin chains, anemia, accumulated Hgb Bart (gamma 4) and H (B4) and beta chain precipitation Symptoms appear at birth since alpha chains needed for HbF and HbA synthesis

Alpha thalassemia Silent carrier (1 gene missing)--> Alpha thalassemia trait (2 genes missing)--> Hgb H disease (3 genes missing)--> Hydrops fetalis

Inadequate synthesis of beta chain | Anemia, accumulation of Hgb Barts (4 gamma globulins) and alpha chain precipitation

Beta thalassemia B thalassemia minor (one gene affected)--> B thalassemia major (2 genes affected)

Most common form of collagen

Type I

Roles of proline and lysine in collagen formation

Proline/X: Kinking | Y: Hydroxyproline or hydroxylysine strengthens

Type of collagen found in bone, skin, tendon, dentin, fascia, cornea, late wound repair

Type I | tendbONE

Type of collagen found in cartilage (including hyaline), vitreous body, nucleus pulposus

Type II | carTWOlage

Type of collagen found in skin (reticulin), blood vessels, uterus, fetal tissue, granulation tissue

Type III | THREEticulin

Type of collagen found in basement membrane or basal lamina

Type IV | under the FOUR is the basement

Type of collagen found beneath stratified squamous epithelium

Type VII

Manifestation of Classical subtype of Ehlers-Danlos Syndrome

Type I and V defect Joint hypermobility Skin > Joint

Manifestation of Hypermobility subtype of Ehlers-Danlos Syndrome

``` Type III defect Joint hypermobility Skin abnormalities Osteoarthritis Severe pain ```

Manifestation of Vascular subtype of Ehlers-Danlos Syndrome

``` Type III defect Fragile blood vessels, organs, small stature Thin and translucent skin, easy bruising Intracranial aneurysms Most serious ```

Brittle bone disease, autosomal dominant, multiple fractures, blue sclerae, hearing loss (ossicles, conductive hearing loss), dental imperfection, type I collagen defect

Osteogenesis Imperfecta

``` Type IV collagen defect, basement membrane of renal glomeruli affected Hematuria Ocular lesion Hearing loss (sensorineural) ESRD ```

Alport Syndrome | alFOUR

Epidermolysis bulosa is a defect in what type of collagen?

Basal lamina, blistering | Type VII

Vitamin C deficiency hampers post-translational modification of collagen (hydroxylation = strengthening), sore gums, loose teeth, poor wound healing, petechiae on skin and mucous membranes

Scurvy

Kinky hair, growth retardation, copper deficiency (required by lysyl oxidase)

Menkes Disease

Rich in proline and lysine, but little hydroxyproline and no hydroxylysine

Elastin

Mutation in fibrillin gene, autosomal dominant Taller and thinner than family members, aortic dilatation and dissection, ectopia lentis, arachnodactyly, dolichostenomelia

Marfan syndrome

Prevents proteolytic enzymes in lungs such as elastase from destroying alveolar walls (pan-acinar) which lead to emphysema

Alpha-1-antitrypsin deficiency