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Fundamentals I
Test I
194
Other
Graduate
08/17/2010

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Cards

Term
Membrane Bound Organelles
Definition

- plasma membrane

- nucleus

- SER

- RER

- golgi

- lysosomes

- endosomes

- peroxisomes

- mitochondria

Term
Non-membrane Bound Organelles
Definition

- ribosomes

- proteasome

- microtubules

- actin filaments

- intermediate filaments

- centrioles / basal bodies

- cilia / flagella

- inclusions

Term
Cell Membrane Functions
Definition

1)Structural integrity
2)Controls in and out transport
3)Signal recognition
4)Intercellular interaction
5)Transduces extracellular signals to intracellular events

Term
Lipid Component of Cell Membranes
Definition

- phospholipids
- glycolipids
- cholesterol

Term
Amphipathic
Definition
- contains both hydrophobic and hydrophilic regions
Term
Protein Component of Cell Membrane
Definition

-Integral (transmembrane, multipass)
-Peripheral (extracellular, cytosolic)

Term
Integral Membrane Proteins: Types
Definition

1) Channel

2) Pumps/Carriers

3) Receptors

4) Linkers/Structural

 

Term
Channel Proteins
Definition

- voltage, ligand, or mechanically gated

- allow passage of particular ion

Term
Pump/Carrier Proteins
Definition

- physically bind to substrate and transport it across membrane

 

- Na+/K+, Ca++, glucose

Term
What are the functions of receptor proteins in the plasma membrane?
Definition

- involved in receptor-mediated endocytosis

- signaling molecules

- kinases or kinase-associated (phosphorylate proteins)

- coupled w/ g-proteins (transduce signals)

- cytokine receptors

- steroid receptors

Term
Secretory Pathway
Definition
rough ER -> (via transport vesicle) cis-golgi -> medial golgi -> trans-golgi -> (via secretory vesicle) plasma membrane -> exocytosis
Term
ER
Definition

- smooth: lipid synthesis

- rough: protein synthesis

- continuous w/ outer nuclear membrane

- contains enzymes that metabolize drugs

- bidirectional traffic b/w golgi and ER

- has pumps and channel proteins that keep Ca++ levels high

Term
Bound Ribosomes
Definition

create proteins for...

- plasma membrane

- secretory vesicles

- lysosomes

Term
Free Ribosomes
Definition

create proteins for...

- nucleus

- mitochondria

- peroxisomes

Term
Golgi
Definition

- terminally glycosylates proteins

- directs proteins to different sites w/ target signals

Term
Lysosome
Definition

- contains degradative enzymes (that arrive at lysosome via phosphorylated mannose signal)

- destroys microorganisms delivered by phagosomes/endosomes

- surrounded by impermeable membrane

Term
Peroxisome
Definition

- contain enzymes that oxidize nutrients like fatty acids (though energy created not used for ATP)

- proteins for peroxisome created in cytoplasm

Term
Mitochondria
Definition

- ATP production

- double membrane

- have own DNA

- make some of own proteins

- reproduce by pinching in two

Term
Ribosomes
Definition

- lg (49 proteins + 3 RNA's) and small (33 proteins + 1 RNA) subunits that associate during transcription

- reusable

- 11-15 on one mRNA strand = polyribosome

- some bind to ER b/c of signal on polypeptide they are making

- no difference functionally b/w bound and free ribosomes

Term
Proteasome
Definition

- contains proteases that degrade old, defective proteins

- proteins arrive via ubiquitin signal

- large cylinder (w/ core and cap) composed of protein subunits and RNA

Term
Cytoskeleton
Definition

- microtubules

- intermediate filaments

- actin filaments

Term
Microtubules: Functions
Definition

1) structural support

2) track for motor proteins (dynein and kinesin)

3) form spindle fibers, pull chromosomes, and push apart cell halves during mitosis

4) components of cilia and flagella

Term
Microtubules: Composition
Definition

- tubulin dimers (w/ alpha and beta subunits)

- dimers associate to form large cylinder

- dimers bound non-covalently (w/ H-bonds), but very strong

-polymerized in centrioles

Term
Actin Filaments
Definition

- associated w/ cell motility via actin remodeling

- reinforces cell membrane

- composed of actin subunits

- genetic defect involving actin = muscular dystrophy

Term
Intermediate Filaments
Definition

- composed of keratin subunits

- strong "rope" that reinforces cell structure and nuclear membrane

- unlike microtubules, can bend under great pressure

Term
Nuclear Envelope
Definition

- inner and outer membrane

- outer: continuous w/ ER

- inner: associated w/ nuclear lamina

- traffic directed - w/ great energy cost - thru nuclear pores

 

Term
Heterochromatin
Definition

- DNA that is not actively transcribed (e.g., DNA coding for antibodies in a neuron)

- associates near periphery of nucleus

Term
Euchromatin
Definition

- DNA that is actively transcribed

Term
Nuclear Pore Complex
Definition

- 100+ proteins that provide only route of travel in and out of nucleus

- macromolecules require ATP to pass through NPC

- RNA passes through as ribonucleoproteins

Term
Nuclear Proteins
Definition

- histones

- fibrous proteins

- nuclear matrix proteins

- ribosomal proteins

- transcription factors

Term
Nucleolus
Definition

- ribosomes assembled

- RNA synthesized

 

Term
Nucleosome
Definition

- functional unit of euchromatin

- histone proteins: 8 core, 1 peripheral

- 166 DNA base pairs

Term
Cell Cycle
Definition

INTERPHASE

- G1 - normal cell activity

- S - replication of DNA

- G2 - bulking up cell contents for division; DNA proofreading

 

MITOSIS

Term
Apoptosis vs. Necrosis
Definition

apoptosis - programmed disassebling of obsolete cell

necrosis - cell death due to injury, disease

Term
Major Tissue Types
Definition

- epithelial

- connective

- muscle

- nerve

Term
Amphiphilic
Definition

- polar and non-polar regions

Term
Hydrophobic Interactions
Definition

- occur when water re-organizes H-bonds to surround hydrophobic solute

- results in decrease of entropy

Term
Hydrophobic Effect is Most Important Factor in...
Definition

1) protein folding

2) formation of quaternary structure

3) assembly of membranes

4) binding phenomena

Term
Affect of Temperature on Hydrophobic Bonding
Definition

Cooling - removes energy from system, breaks bonds

 

Warming (to physiologically appropriate temp) - adds energy to system, promotes bonding

Term
Dissociation Constant
Definition
Ka = [A-][H+]/[HA]
Term
pH
Definition

pH = -log [H+]

 

10(-pH) = [H+]

Term
pKa
Definition

pKa= - log (Ka)

 

*lower pKa= stronger acid

Term
Henderson-Hasselbalch Equation
Definition

pH = pKa + -log([A-]/[HA])

 

* at isoelectric point, where [A-] = [HA], pH = pKa (because -log(1) = 0)

Term
Buffer System
Definition

-consists of weak acid and its conjugate base: [HA] + [A-]

 

- at point where these to constituents are equivalent, pH varies only slightly w/ increased base or acid

 

- in other words, buffers help maintain a constant pH

Term
Buffering System in Blood
Definition

pH = pKa + log ([HCO3-]/[CO2])

 

- CO2 becomes "conjugate acid" (see slides for derivation of formula)

 

- pH kept at around 7.4

Term
Peptide Bond
Definition

- the a-COOH (carboxyl) and the a-NH3+ (amino) groups of an amino acid covalently bond to form amide linkage, losing water molecule

 

- usually in trans formation

 

- has partial double bond character, so 6 atoms of peptide bond group are planar

Term
Amino Acids: Types
Definition
  1. Non-polar (hydrophobic)
  2. Polar, uncharged
  3. Acidic (negatively charged after deprotonation)
  4. Basic (positively charged)
Term
Amino Acid Groups: Functions
Definition

Non-polar

- establish (globular) folding pattern

- promote hydrophobic interactions

 

Polar

- establish (fibrous) folding pattern

- promote specific interactions (His, Ser, Lys, Asn, Cys)

Term
Only Achiral Amino Acid
Definition
Glycine
Term
Which type of amino acids - R or S - predominate in nature?
Definition

S - used exclusively for robosomal synthesis of proteins in animal kingdom

 

Term
Generally , what is the pKa of the alpha carboxyl group of an amino acid?
Definition
2 (at pH of 2, half of the carboxyl groups will be deprotonated, half will be protonated)
Term
Generally, what is the pKa of the alpha amino group of an amino acid?
Definition
9 (at a pH of 9, the amino group has a 50% chance of being deprotonated)
Term
Isoelectric Point
Definition
pH at which amino acid has net charge of 0 (the carboxyl group has been deprotonated and negatively charged, but the amino group remains protonated and positively charged)
Term
What is the pH of a glutamic acid solution if the alpha carboxyl is 1/2 dissociated? (pKa of alpha carboxyl = 2)
Definition
2
Term
What do carboxyl groups of amino acids typically form in reactions?
Definition
amides and esters
Term
What do amino groups in amino acids typically form in reactions?
Definition
amides and Schiff bases
Term
Protein
Definition
- unbranched polymer of amino acids
Term
Peptide Backbone
Definition

- repeated sequence of N-Ca-Co

- N = amide nitrogen

  Ca = alpha carbon 

  Co = carbonyl carbon

Term
Peptide
Definition

- short polymers of amino acids

- >12 = oligopeptide

- several dozen = polypeptide

Term
Primary Structure
Definition
- amino acid sequence
Term
Secondary Structure
Definition

- patterns of polypeptide chain along 1 dimension

- caused by hydrogen bonds b/w amino acids

- helices or pleated sheets

Term
Tertiary Structure
Definition
- bending, folding of polypeptide chains to form 3-dimensional shape
Term
Quaternary Structure
Definition
- subunit organization
Term
Nonpolar Aminos
Definition

- leucine

- proline

- alanine

- valine

- methionine

- tryptophan

- phenylalanine

- isoleucine

Term
Acidic Aminos
Definition

- aspartic acid

- glutamic acid

- histidine

 

Term
Basic Aminos
Definition

- lysine

- arginine

Term
Ion Exchange Chromatography
Definition
- molecule of interest is exchanged for another ion onto and off of a charged solid support; concentration of salt in solution then increased so that molecules are displaced from support sequentially; affinity of molecule in question for positively or negatively charged support is dependent on pH of solution
Term
HPLC
Definition

- High Performance Liquid Chromatography

- reproducible, cheap

- long runtimes, needs protein precipitation

Term
Gas Chromatography
Definition

- robust, reproducible

- doesn't work well with thermolabile AA's

Term
When are proteins least soluble?
Definition
- at their isoelectric point
Term
RPHPLC
Definition

- HPLC for non-polar amino acids (those that are polar must first be derivatized)

- used in synthesis of drugs, which must have large non-polar component in order to get thru cell membrane

Term
Which bond in a peptide group has partial double bond character?
Definition

Co - N

 

(a-C is the one with the R-group attached)

Term
Which bonds in a peptide group have rotational freedom?
Definition
Ca- Cand  Ca - N
Term
Dialysis
Definition
- proteins separated based on size, solubility: small molecules dissolve and diffuse thru pores in bag, while large molecules remain in bag
Term
Gel Filtration Chromatography
Definition

- separates proteins based on size

- larger molecules aren't trapped by gel beads, so they emerge from column faster than smaller ones

Term
Gel Electrophoresis
Definition

- proteins separated by size

- larger molecules move more slowly through gel than smaller ones

Term
Affinity Chromatography
Definition

- proteins separated based on their affinities for binding to certain ligands (e.g., antibodies)

- ligands immobilized in column, and protein solution pushed thru

- specific proteins that bind with antibodies will not pass through column; everything else in solution will

Term

What do each of the numbers mean in the following helix designation?

 

3.613 p = 5.4

Definition

3.6 = number of residues in each complete turn

13 = number of atoms in each residue

5.4 = measure of axial length of each complete turn (in angstroms)

Term
What factor contributes most to stability of a-helices?
Definition
- H-bonds
Term
Beta Turn
Definition

- allows peptide chain in B-pleated sheets to reverse direction

- made possible by h-bond b/w carbonyl O of 1 residue to H on amino group of residue facing it

Term
Hairpin Turn
Definition
- link b/w 2 anti-parallel strands
Term
Crossover Connection
Definition
- link b/w 2 parallel strands
Term
a-Keratin
Definition

- consists of a-helical rods

- hair, fingernails, claws, horns, beaks

Term
B-keratin
Definition

- stacked B-sheets

- silk fibers

Term
Which type of proteins fold in order to maximize internal bonds and minimize sovent contact?
Definition
- globular
Term
Which type of proteins fold to maximize intermolecular bonds and intermolecular contact?
Definition
- fibrous
Term
The triple helix is characteristic of what class of protein?
Definition
- collagen
Term
4 Structural Classes of Globular Proteins
Definition

- all a-helices

- all B-pleated sheets

- a-helices and B-sheets intermingled

- both a-helices and B-sheets present, but occupy different domains

Term
At what temp does protein denaturation occur?
Definition
50-55 degrees C
Term
Examples of Diseases Related to Protein Folding
Definition

- cancer

- emphysema

- cystic fibrosis

- alzheimer's

- creutzfeldt-jacob disease

- familial amyloidotic neuropathy

Term
What kind of bonding is involved in the quaternary structure of globular proteins?
Definition
- noncovalent, hydrophobic interactions
Term
What kind of bonding is involved in the quaternary structure of fibrous proteins?
Definition
- likely covalent
Term
What are the advantages of quaternary association?
Definition

- stability (decreased surface to volume ratio)

- exclusion of mutated proteins

- small subunits more accurately made than huge proteins

- facilitation of catalytic site assembly

- cooperativity possible

Term
In which protein type are you more likely to find B-pleated sheets?
Definition
- globular
Term
In which type of protein are you more likely to find disulfide bonds?
Definition
- globular (these bonds are relatively weak, so they are not typically found in fibrous proteins, which utilize covalent bonds)
Term
For a spontaneous reaction, what are the ideal signs for delta G, delta H and delta S?
Definition
(- H) - (+S) = (-G) = spontaneous reaction, as in the folding of globular proteins
Term
Is the folding of globular proteins driven primarily by (a decrease in) enthalpy or (an increase in) entropy?
Definition

- an increase in entropy

- Internal hydrophobic bonds are formed, which creates a decrease in enthalpy (-H), but bonds are also broken b/w protein and solvent, which creates an increase in enthalpy (+H)

- so, the folding must be entropy driven

Term
Is the folding of fibrous proteins enthalpy driven or entropy driven?
Definition
- enthalpy driven (driven by formation of bonds, which results in (-H))
Term
Why are protein folding chaperones needed?
Definition

- to keep them from binding to nearby proteins during synthesis

- to ensure correct folding

- to accelerate slow steps

Term
How does the prion protein contribute to Creutzfeldt-Jacob disease?
Definition
- if the prion is liberated from the membrane of a nerve cell, its a-helical structure will denature and renature as a B-pleated sheet. This influences other molecules and form large aggregates of B-pleated sheets that precipitate in nerve cells
Term
What structure acts as the functional prosthetic in hemoglobin or myoglobin?
Definition
- the porphyrin ring
Term
Why is hemoglobin initially reluctant to bind to oxygen?
Definition

- the iron atom to which the oxygen bonds is somewhat obscured below the plane of the porphyrin ring (it's pulled below by the 5 constituents it's bonded to)

- when oxygen initially binds to the Fe, it initiates conformational changes in other subunits that push the Fe out of its hole, facilitating subsequent bonding

Term
In hemoglobin, what structural components are disrupted upon oxygenation, resulting in a twisting of the molecule?
Definition
- the salt bridges (ionic bonds) b/w the alpha and beta chains
Term
Bohr Effect
Definition

- describes competition b/w H+ and O2 for binding w/ Fe in hemoglobin

- in acidic environments, O2 will be delivered more readily b/c it is displaced by protons

Term
In hemoglobin, does BPG promote the oxy or deoxy state?
Definition
- deoxy; the presence of BPG decreases the binding of oxygen
Term
What causes sickle cell anemia?
Definition

- in hemoglobin, the replacing of a glutamic acid with a valine creates a hydrophobic pocket which appears in the deoxy form

- certain hemoglobin molecules (hemoglobin S) will bind to this hydrophobic pocket, creating fibrous aggregates which elongate the shape of the RBC

Term
What is the most prevalent amino acid in elastin?
Definition

- valine

- its side chain is totally hydrophobic, which facilitates the sliding of molecules back and forth on top of one another

Term
What structures compose the cross-links present in elastin?
Definition

- desmosine and isodesmosine

- composed of a pyridinium ring w/ 4 lysyl residues attached

Term
Which two proteins associate with actin in muscle fibers and regulate muscle contraction by regulating the binding of myosin?
Definition

- troponin

- tropomyosin

Term
A mysoin molecule consists of how many light and heavy chains?
Definition

- 4 light chains

- 2 heavy chains

Term
What property promotes the coiling of myosin's heavy chains?
Definition

- repetitive primary structure

- hydrophobic residues on each chain interact, causing them to wrap around each other

Term
Describe the mechanism of skeletal muscle contraction
Definition

- ATP hydrolysis detaches myosin head from actin, promotes resting state

- nerve impulse causes Ca to leave lumen of sarcoplasmic reticulum and go to muscle fibers

- Ca stimulates release of ADP and phosphates, and dissociates troponin and tropomyosin from actin

- latent energy from ATP hydrolysis released, and myosin head attaches to actin and undergoes power stroke

- ATP causes myosin head to release its clutch on actin and return to resting state

- calcium returns to SR lumen via ATP pump

Term
How does Ca function in the contraction of smooth muscles?
Definition
- it serves as an enzyme activator: it activates kinase, which phosphorylates the myosin head and triggers attachment to actin
Term
List 3 smooth muscle effectors
Definition

epinephrine - affects lungs and heart; used for asthma

 

albuterol - affects mostly lungs; used to prevent premature labor

 

oxytocin - stimulates uterine contraction, inducing labor

Term
What is the largest class of proteins in vertebrates?
Definition

- collagen

 

Term
Describe the structure of a collagen chain
Definition

- two globular domains: 1 large @ C terminus, 1 small @ N terminus

- uninterrupted fibrous (Gly-X-Y) domain between

- small ahelical domain near  N terminus

Term
Where is collagen located in the human body?
Definition

-skin

- basement membranes (b/w dermis and epidermis)

- blood vessels (elastin)

- cartilage

- bones and teeth

- eye (sclera, cornea, vitreous humor, lens capsule)

Term
What type of molecules monitor collagen fiber size?
Definition
- pN molecules (created in the pro-collagen to collagen conversion)
Term
What structure controls the association of collagen chains?
Definition
- the globular domain at the C terminus
Term
Where is collagen synthesized?
Definition
- in the lumen of the rough ER
Term
By what process is a collagen chain converted form hydrophobic to hydrophilic?
Definition
- prolyl hydroxylation (Gly-Pro-Pro becomes Gly-Pro-Hydroxyproline)
Term
Why is glycine important in the formoation of a collagen triple helix?
Definition
- it is small (side chain = H), so does not sterically hinder formation of helix
Term
What modification is made to the collagen triple helices before they associate to form fibers?
Definition
- the N (sometimes) and C (always) termini are cleaved (about 1/3 of molecule)
Term
Which amino acid residue is instrumental in the formation of collagen cross-links?
Definition
- lysine
Term
How is bone formed?
Definition
- hydroxyapatite crystals are deposited over a collagen matrix
Term
What are 3 industrial applications of denatured collagen?
Definition

- foods

- coatings

- capsules

Term
What are 3 clinical uses for native collagen?
Definition

- surgical dressing

- tissue engineering

- implants

Term
What is the most abundant class of biological molecule?
Definition
- carbohydrates
Term
Epimers
Definition
- sugars that differ only by the configuration about 1 carbon atom
Term
The reduction of sugars yields what compound?
Definition
- alditols
Term
Maillard Reaction
Definition

- non-enzymatic browning

- rxn b/w amino acid and reducing sugar

Term
Alcohols and Aldehydes react to form...
Definition

- hemiacetals

- since sugars are both alcohols and aldehydes, they react with themselves to form rings

Term
Alcohols and ketones react to form...
Definition
- hemiketals
Term
Anomers
Definition
- cyclic sugars that differ only in the configuration of hemiacetal or hemiketal carbon
Term
Honey is composed of what 2 sugars?
Definition
- fructose and glucose
Term
Phytate
Definition

- honorary sugar found in chicken and pig (non-ruminant) manure

- binds to nutrients (Ca, Mg, etc.) and makes them unavailable ("anti-nutrient")

Term
Glycosides
Definition

- sugar acetals

- C1 bonded to -O-R

- stable, do not mutarotate

Term
What enzyme is involved in the synthesis of lactose?
Definition

- lactose synthase

- dimer of B-D-galactosyl transferase and a-lactalbumin

Term
What two sugars are combined in the formation of lactose?
Definition
- glucose and galactose
Term
What enzyme is involved in the degradation of lactose?
Definition
- B-galactosidase
Term
What is the most abundant biological molecule in the biosphere?
Definition
- cellulose
Term
Of what is cellulose composed?
Definition
- B(1-4) linked glucoses
Term
Of what is chitin composed?
Definition
- B(1-4) linked N-acetylglucosamines
Term
Of what is a-amylose (soluble starch) composed?
Definition
- a(1-4) linked glucoses
Term
Of what is amylopectin composed?
Definition
- a(1-4) linked glucose w/ a(1-6) glucose branches (every 24-30 residues)
Term
Which gycosaminoglycan is a powerful anticoagulant?
Definition
- heparin
Term
Which glycosaminoglycan ALLEGEDLY combats arthritis?
Definition
- chondroitin-4-sulfate
Term
Glycosaminoglycan
Definition

- long, unbranched polysaccharide consisting of repeating disaccharide units:

 

1. hexose or hexuronic acid

2. hexosamine

Term
Proteoglycan
Definition

- consist of a protein core w/ one or more attached glycosaminoglycans

- usually heavily glycosylated

- occur in connective tissue

Term
Versican
Definition
- large chondroitin sulfate proteoglycan associated w/ fibroblasts (cells that synthesize extracellular matrix and collagen)
Term
Aggrecan
Definition

- very large proteoglycan in cartilage

- contains chondrotin sulfate, keratan sulfate, and oligosaccharide chains

Term
Perlecan
Definition

- large heparan sulfate-containing proteoglycan found in basement membranes

- promotes attachment of cells and participates in assembly of basement membranes

Term
Glypican
Definition

- proteoglycan containing heparan sulfate chains

- modulates cell attachment and shape

- helps assemble extracellular matrix

Term
Syndecan
Definition

- integral membrane proteoglycan (contains heparan sulfate and chondroitin sulfate)

- regulates shape and organization of epithelial cells

Term
Decorin
Definition

- SLRP that helps assemble collagen fibrils

- mice w/o decorin had easily damaged skin

Term
Mucopolysaccharidoses
Definition
- diseases that arise from lack of lysosomal enzymes that break down glycosaminoglycans
Term
Glycoprotein
Definition

- proteins w/ oligosaccharide side chains

- side chains typically smaller than those of proteoglycans

- usually integral membrane proteins, but found in blood serum and secretions

Term
O-linked oligosaccharides
Definition

- linked to protein thru O of serine or threonine

- sugar attached to protein is GalNAc (N-acetylgalactosamine)

- a-linked

Term
N-linked oligosaccharides
Definition

- linked to protein thru N of asparagine

- sugar linked to protein is GlcNAc (N-acetylglucosamine)

- B-linked

Term
Mucins
Definition

- membrane-associated and secretory glycoproteins

- cover mucosal epithelia

- provide barriers, modulate bacteria, lubricate, protect tissue surfaces

Term
Why does helicobacter not cause gastric ulcers in all people?
Definition
- many people have gastric mucins w/ oligosaccharides that have antibacterial properties
Term
Which blood type is a universal donor?
Definition
- type O
Term
Which blood type is a universal acceptor?
Definition
- type AB
Term
How are O-linked glycoproteins synthesized?
Definition
- post-translationally, one sugar at a time
Term
How are N-linked glycoproteins synthesized?
Definition

- sugars added in blocks, cotranslationally:

 

1) 2 GlcNAcs and 5 mannoses added (one at a time) to Dolichol on cytoplasmic side of ER

2) structure flipped to luminal side of ER

3) subsequent mannoses (4) and glucoses (3) attach to Dolichol on cytoplasmic side, then are flipped to lumen and added to growing chain

4) oligosaccharide chain transferred from dolichol to Asn on nacent polypeptide

5) 3 glucose and 1 mannose removed, which signals transport to golgi (if glycoprotein defective, 1 glucose added back, and structure returns to ER)

Term
Does the diversity of N-linked glycoproteins result from synthesis in the ER or processing in the golgi?
Definition

- processing in the golgi

- ER synthesis is highly conserved; same basic glycoprotein made in all animals and plants

Term
Lectins
Definition

- proteins that bind to specific sugar residues

- used in separation and analysis of glycoproteins

Term
Selectins
Definition
- proteins on walls of blood vessels that bind to glycoproteins on membranes of certain blood cells (e.g., lymphocytes will adhere to selectin in capillaries at site of infection)
Term
Lysozyme
Definition
- small protein in tears, saliva, etc. that lyses cell walls of non-pathogenic bacteria by cleaving bonds in peptidoglycan
Term
What does the transpeptidase reaction consist of (in staph aureus)?
Definition
- attack of amino group of pentaglycine cross-bridge on peptide bond b/w D-Ala residues to form a cross-link
Term
How does penicillin work?
Definition
- it mimics the D-ala-D-ala moiety of peptide stems in peptidoglycan, so transpeptidase complexes with penicillin instead of helping to form cross-links
Term
How does penicillin resistance work?
Definition

- some bacteria produce B-lactamase, which cleaves the B-lactam ring in penicillin, making it ineffective

(it no longer mimics D-ala-D-ala, so it does not complex w/ transpeptidase)

Term
Teichoic Acids
Definition
- polysaccharides on surface of cells involved in adherence of bacteria to cells
Term
Lipopolysaccharide
Definition

- large molecule containing lipid covalently bound to polysaccharide

- present on outer membrane of gram (-) bacteria

- endotoxin

Term
How are lipopolysaccharides detected?
Definition
- limulus amebocyte lysate from horseshoe crab hemolymph is mixed into solution; if LPS present, solution will become gelatinous
Term
What is the component of endotoxin (lipopolysaccharide) that is responsible for its toxicity?
Definition
- lipid A
Term
E. coli O157
Definition
- deadly food-borne pathogen identified by immunological detection of its O-polysaccharide
Term
Catalytic Power
Definition
- ratio of enzyme-catalyzed rate of reaction to uncatalyzed rate
Term
Enzyme Specificity
Definition

- defines selectivity of enzymes for their substrates

- controlled by structure (unique fit of enzyme with substrate)

- dictates product yield

Term
Enzyme Regulation
Definition

- ensures that the rate of metabolic reactions is appropriate for cellular requirements

- depends on availability of substrates and co-factors

- amount of enzyme present depends on genetic regulation of synthesis and decay

Term
Cofactors
Definition
- metal ions that are essential to enzyme activity
Term
Coenzymes
Definition
- vitamins or other non-protein components that are essential to enzyme activity
Term
Haloenzyme
Definition
- enzyme that has a coenzyme and/or cofactor tightly bound to it (prosthetic group)
Term
Apoenzyme
Definition
- enzyme without a prosthetic group (tightly bound cofactor or coenzyme)
Term
Km
Definition

- kinetic activator constant

- derived from rate constants

- estimate of dissociation of E from S

- high Km = weak binding (much dissociation)

- low Km = tight binding (little dissociation)

Term
Vmax
Definition

- constant

- theoretical maximum rate of reaction

- never achieved

Term
Kcat
Definition

- measure of catalytic activity

- number of substrate molecules converted to product per enzyme molecule per unit of time

 

Term
Kcat/Km
Definition

- measure of catalytic efficiency

- 2nd order rate constant

- measures how enzyme performs when [S] is low

Term
Competitive Inhibition
Definition

- inhibitors compete with substrate for same site on enzyme

- alters Km but not vmax

- can be overcome with increased [S]

Term
Non-competitive Inhibition
Definition

- inhibitor binds to allosteric site (site other than active site) on enzyme

- alters enzyme, lowering affinity for susbstrate

- does not alter Km , but lowers vmax

- cannot be overcome w/ increased [S]

Term
Uncompetitive Inhibition
Definition

- I binds only to ES complex, rendering it ineffective

- alters both Km and vmax

Term
Mixed Inhibition
Definition

- resembles the non-competitive, except that the EIS-complex has residual enzymatic activity

- alters both Km and vmax

Term
Single Displacement Reaction
Definition

- leading substrate A binds to E

  - substrate B binds to AE

- A and B converted to P and Q

- Q released

- P released

 

 

 

Term
Double Displacement Reaction
Definition

- leading substrate A binds to E

- E converted to E' and A converted to P

- P released

- E' binds with substrate B

- B converted to Q and released

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