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Biochem
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284
Biochemistry
Graduate
09/08/2011

Additional Biochemistry Flashcards

 


 

Cards

Term
What are the topics covered in this lecture?
Definition
Water is solvent of life
Electrolytes are cations and anions
Acids donate H-ions
Bases accept H-ions
Buffers cause solutions to resist changes in pH
Functional groups determine type of reactions
Oxidation is loss of H-atoms, reduction is gain of H-atoms
Carbohydrates: mono, di, polysaccharides
Lipids: fatty acids, trigylcerides, phospholipids, sphingolipid (ceramide)
Nitrogen-containing compounds: amino acids, nucleotides, free radicals
Term
What's water?
Definition

 

 

is the solvent of life.

 

bathes our cells

 

dissolves and transports compounds in the blood

 

dissipates heat, and participates in chemical reactions.
 

50-60% of body weight in adults,

more fat = less water (for obese ppl)

75% o body weight in kids

Term
Total body water contained?
Definition

60% intracellular.

40% extra

-plasma, interstitial water

 

drink more = pee more.

Term
H bonds in water
Definition



-dipolar nature of water

-H bond = weak, noncovalent interaction

-H + more electronegative atom

-Each water mol can have 4 H bonds

 

 

 

Term
How does water act as a solvent?
Definition

 

Polar

 

(A) H interacts with

 

organicmolecules (O/N).

 

inorganic salts

 

(Cl-), (HCO3-), and other anions

 

 

 

(B) O interacts

 

with inorganic cations

 

Na+ and K+.

 

Term
what are electrolytes?
Definition

-bicarbonate and inorganic anions and cations

-Na- and Cl- in ECF

-K+ and phosphates in ICF

Term
What maintains the differentials?
Definition

Principally by energy-requiring transporters that pump Na+ out o fcells in exchange for K+

 

Term
What is osmolality of a fluid?
Definition
{image:|}
Term
Why is osmolality important?
Definition

Different compartments

water mov'ts

osmotic pressure to reach equilibrium

Term
Acids and bases overview
Definition

1.  acids donate a H+ to a solution, pH lower than 7

2.  Bases (OH-) accept Hydrogen ions

 

Term
What about water?  Acid or base?
Definition
neutral, neither acidic nor basic.
Term

What is the [H+] of pure water?

What is the pH of pure water?

Definition

1. 10x-7 mol/L

2.  pH = 7

Term
What do acidic solutions have in terms of H ion concentrations?
Definition
A greater H ion concentration that pure water (pH < 7)
Term
What's the 'p' in pH?
Definition
power
Term
equation for pH?
Definition
pH = -log[H+]
Term
Ion product of water equation?
Definition
Kw = [H+][OH-] = 1 x 10x-14
Term
Strong and weak acids?
Definition

1. undissociated acid

'ic acid'

ie:  acetoacetic acid

ie:  lactic acid

 

2.  dissociated anionic component

'ate'

ie: acetoacetate

ie: lactate

Term

Acids in the blood of a healthy individual

Example of a strong acid?

Definition

Acid:  Sulfuric Acid (H2SO4)

Anion:  Sulfate SO4-2

pKa = completely dissociated

Term

Acids in the blood of a healthy individual

Example weak acid?

Definition

Weak acid:  Carbonic Acid (R-COOH)

Anion:  Bicarbonate (R-COO-)

pKa = 3.8

Term
What is Ka?
Definition
The equilibrium constant for dissociation of a weak acid
Term
What does a higher Ka mean?
Definition

The greater is the tendency to dissociate a proton

pKa = -log Ka

Term
Wich is a stronger acid, pKa 2 vs. pKa 5?
Definition
Acids with pkA of 2 are stronger acids than those with a pKa of 5, because at any pH, a greater proportion is dissociated.
Term
Equation for the Ka of an acid?
Definition
[image]
Term
Henderson-Hasselbalch Equation
Definition

[image]

If the pKa for a weak acid is known, this equation can be used to calculate the ratio of the unprotonated to the protonated form at any pH.

Term

Calculation for pKa:

Salicylic acid, pKa = 3.4

(salicylic acid ↔ salicylate- + H+)

Blood pH = 7.4

Calculate ratio?

Definition
pH = pKa + log [A-]/[HA]
pH = pKa + log [salicylate-]/[salicylic acid]
7.4-3.4 = log [salicylate-]/[salicylic acid]
4 = log [salicylate-]/[salicylic acid]
[salicylate-]/[salicylic acid]
Ratio: 10000/1
Term
Buffers
Definition

= a weak acid and its conjugate base

-can cause a solution to resist changes in pH when H ions or OH ions are added

Term
What pH is optimal for a buffer?
Definition
= compensate for an influx or removal of H-ions within ~1 pH unit of its pKa
Term
How do you increase the capacity of the buffer?
Definition
Add more concentrated buffers.
Term
Bicarbonate buffer system diagram
Definition
[image]
Term
Metabolic Acids and Buffers:  some details
Definition

An avg rate of metabolic activity produces a lot of acid per day.

-If all of this acid were dissolved at one time in unbuffered body fluids, their pH would be <1.

Term

pH of blood?

Intracellular pH?

Definition

pH of blood:  7.36-7.44

Intracellular pH:  ~7.1

Term
What is the widest range of extracellular pH?
Definition
6.8-7.8
Term
How does the body achieve this tight pH regulation?
Definition
= major buffer systems in the body
Term
What are the major buffer systems in the body?
Definition
bicarbonate–carbonic acid buffer system ECF
HCO3- + H+ → H2CO3 → CO2 + H2O
hemoglobin buffer system in RBC
H+ is buffered by (Hb) and phosphate (HPO42-)
phosphatebuffer system in all types of cells
protein buffer system of cells and plasma.
Term
What neutralizes HCl from parietal cells in the stomach?
Definition
Bicarbonate secreted from pancreatic cells and by cells in the intestinal lining.
Term
What are organic molecules?
Definition
consist principally of CHONPS joined by covalent bond
Term
What is the key element or organic molecules?
Definition

-Carbon

CH-: methyl, ethyl, propionyl, butyl, pentanyl

-branched 'iso-'

-double bonds 'ene'

 

aliphatic:  straight chain

aromatic:  ring

Term
What are functional groups?
Definition

Bonds:  C-O, C-N, C-S, C-P

-determines the types of reactions

-alcohol, aldehyde, ketone, ester, amide

Term
Diagram of major types of functional groups
Definition
[image]
Term

Carboxylic + alcohol?

Carbox + amide group?

Definition

1.  ester compound

2.  amine 

Term
Oxidation and Reduced Groups
Definition

Oxidation:  loss of H+ atoms, gain of O atoms

Reduction:  gain of H+ atoms, loss of O atoms

Term

Groups that carry a charge:

- and +

Definition

1.  acidic groups dissociate an anion with a - charge

2.  compounds within nitrogen are usually basic acquire a + charge

Term
What does quaternary amines mean?
Definition
-Secondary, tertiary and quaternary amines:  2,3,4 C-N bonds
Term

1.  anions formed by dissociation of acidic groups

2.  examples of amines

Definition
[image][image]
Term
Polarity of bonds and partial charges
Definition

Polar bonds:  C-O, C-N

Sulfur can carry a slight partial neg charge

Term
What happens in nonpolar C-C, C-H bonds
Definition
-e in the covalent bond shared almost equally
Term
Solubility in water?
Definition
= Polar:  Hydrophilic
Term
Nomenclature of organic compounds
Definition
1) carbons in a compound are numbered, starting with the carbon in the most oxidized group
2) carbons are given Greek letters, starting with the carbon next to the most oxidized group. 
Term

[image]

 

name me.

Definition

Two systems for identifying the carbon atoms in a compound. This compound is called 3-hydroxybutyrate or β-hydroxybutyrate

Term

Carbohydrates:

What are monosaccharides?

Definition

1.  a linear chain of > or equal to 3 C

-one C=O, others C-OH

-general formular Cn H2n On

-suffix = 'ose'

C=O aldehyde = aldose

C=O ketone = ketose

-trioses, tetroses, pentoses, hexoses

 

 

Term

Fructose name?

Glucose name?

Definition

1.  Ketohexose

[image]

 

2.  aldohexose

 

[image]

Term
What is a chiral center?
Definition
A C that contains 4 different chemical groups
Term
What are isomers?
Definition
mirror image, not superimposable
Term
What is the D and L position?
Definition

Position of the hydroxyl group farthest from the carbonyl carbon.

D = right

L = left

Term

D and L example:

glyceraldehyde

Definition

[image]

 

The C in the center of the D and L glyceraldehyde contains 4 different substituent groupd.  A different arrangement creates and isomer that is nonsuperimposabe mirror image.

Term

D or L.  What are most sugars?

D or L.  What are AA's?

Definition

D- sugars

L- AA's

Term
What are stereoisomers?
Definition

They have the same chemical formula but differ in the position of the hydroxyl group on one or more of their asymmetric C's.

 

[image]

Term
What are epimers?
Definition

Stereoisomers that differ in the position of the hydroxyl group at only one of their asymmetric C's.

[image]

D-glucose and D-galactose are epimers at position 4.  D mannose and D-glucose, position 2.

Term
Monosaccharides exist in solution mainly as ring structures.  Details?
Definition

1.  C=O reacted with -OH

2.  a 5 or 6 membered ring

3.  -OH to O part of the ring and C=O to C-OH (anomeric C).

3a.  -OH down = alpha position

3b.  -OH up, beta position

3c.  interchange up and down = mutarotation

Term
Examples of carbs changing into ring form
Definition

[image]

 

**Highlighted = anomeric C's

Term
Example of mutarotation of glucose in solution
Definition
[image]
Term
N- and O- glycosidic bonds.  What are they?
Definition

1.  Anomeric C-OH can react with -OH or -NH group of another compound to form glycosidic bond.

2.  the linkage may be either alpha or beta

3.  N-glycosidic bonds = nucleosides/tides

4.  O-glycosidic bonds = lactose

Term
Lactose diagram
Definition
[image]
Term
N glycosudic bond diagram?
Definition
[image]
Term
What are disaccharides?
Definition
=2 monosaccharides joined by an O-glycosidic bond.
Term
Examples of disaccharides:
Definition
Lactose (milk) = galactose and glucose, β(1→4) bond 
Sucrose = glucose + fructose
Maltose = glucose + glucose        
Term
what are oligosaccharides?
Definition

3-12 monosaccharides (glycoprotein)

 

[image]

Term
what are polysaccharides?
Definition
tens to thousands of monosaccharides in linear or branched structures.
Amylopectin (a form of starch) and glycogen (human cells) are branched. [image]
Term
What are fatty acids?
Definition

1.  Lipids

2.  Aliphatic: CH-3@ one end (ω-carbon) & -COOH @ the other end.

 

3.  Most have an even # of C's 
Term
Saturated fatty acids?
Definition
= single bonds
Term
unsaturated?
Definition
> or equal to 1 C=C
Term
How does melting point change?  Increases with?
Definition

1.  Chain length

2.  Unsaturation

Term
Unsaturated and saturated examples
Definition

1.  vegetable oil = unsaturated.  liquid at Rt

2.  Butter = saturated.  solids at RT

Term
Chart of Fatty Acids
Definition
[image]
Term
What is an acylglycerol?
Definition

= a glycerol with one of more fatty acids attached through ester linkages.

-monoacylglycerols, diacylglycerols, triacylglycerols

 

[image]

 

 

Term
What are phosphoacylglycerols?
Definition
= FA's esterfied to positions 1 and 2 of glycerol and a phosphate group attached to carbon 3
Term
Example of a phosphoacylglycerol
Definition
[image]
Term
What is phoshatidylcholine?
Definition

= lecithin

-major phosphoacylglycerols found in the membranes

-Amine (+), phosphate (-):  amphipathic (both + and - charges in functional groups).

Term
What are sphingolipids?
Definition
Formed by attaching different groups to the hydroxyl group on ceramide.
Term
What is ceramide?
Definition
Amides formed from sphingosine (attach a fatty acid to the amino group).
Term
What is sphingosine?
Definition
serine + palmitate
Term
What are cerebrosides and gangliosides?
Definition
-contain sugars via glycosidic bond on the -OH of ceramide.
Term
What is sphingomyelin?
Definition

Phosphorylcholine group attached to ceramide

-cell membranes and myelin sheath

Term
Diagram of sphingtolipids
Definition
[image]
Term

What are steroids?

-number of rings?

Definition

steroid nucleus:  four ring structure

**cholesterol is the steroid precursor in humans

-al of the steroid hormones are synthesized by modifications to the ring or C-20 side chain

Term
What are Nitrogen-containing compounds?
Definition

= Amino Acids

1.  An amino + a carboxylic acid group

2.  In proteins, L-alpha AA's

Term
What does the structure of AA's look like?
Definition
[image]
Term
What are N containing ring structures?
Definition
1.  Purines, pyrimidines and pyridines.
Term
What are purines?
Definition
A and G
Term
Pyrimidines?
Definition
C and T
Term
Pyridines?
Definition
Niacin, vitamin B6
Term
What does 'ine' indicate?
Definition

= presence of nitrogen (amine) in the ring.

**except uracil (pyr)

 

Term
Diagram of the nitrogenous bases
Definition
[image]
Term
Diagram of uracil
Definition
[image]
Term
What are free radicals?
Definition

Compounds that have a single electron, usually in an outer orbital.

-free radicals from eating BBQ!  Oxidizing H+ from overcooking meat etc.

Term
In what substances are free radicals present?
Definition

1.  Nitrogen dioxide

2.  Smog

3.  Cigarette smoke

Term
A free radical produced in the cell?
Definition
= superoxide anion O2
Term
Formation of free radicals picture
Definition
[image]
Term

Lecture 2:

Topic 1:  Compartmentation in Cells

 

What are membranes?

Definition
lipid structure, compartmental wall
Term
What are organelles?
Definition
nucleus, mitochondria, lysosomes and peroxisomes
Term
What are organelles surrounded by?
Definition
Surrounded by a membrane system
Term
What are in the compartment/organelles?
Definition
= Enzymes and other molecules that serve a common fxn.
Term
What controls the localized environment?
Definition
= Transporters and receptors in the membrane system.
Term

Topic:  Plasma Membrane

 

What is the structure of the PM?

Definition

= a lipid bilayer with embedded proteins

-selectively restricts polar compounds

Term
What is the fluid mosaic model? (in relation to the PM)
Definition
biological membranes can be considered as a two-dimensional liquid where all lipid and protein molecules diffuse more or less easily
Term
Topic:  What's the difference between integral and peripheral proteins?
Definition

Integral:  span the cell membrane

Peripheral:  attached to the membrane surface, does not span the membrane.

Term
WHat do external leaflet's consist of?
Definition
= glycoprpoteins and glycolipids
Term
What is a glycocalyx?
Definition
On PM, cell recognition markers, restricts uptake of hydrophobics
Term
How many carbs are part of the PM?
Definition
2-10% of weight of PM
Term
What lipids are in the lipid bilayer in the PM?
Definition
Primarily phospholipids:  hydrophilic heads and fatty  acyl tails
Term
What are the principal phospholipids?
Definition
glycerol lipids (including sphingomyelin)
Term
What is the major PM lipid?
Definition
Phospatidylcholine
Term
What is the fxn of cholesterol in the PM?
Definition
makes bilayer less deformable and decreases its permeability to small water-soluble molecules
Term
What are flipases in the PM?
Definition
a family of transmembrane lipid transporter enzymes located in the membrane responsible for aiding the movement of phospholipid molecules between the two leaflets that compose a cell's membrane (transverse diffusion)
Term

Topic:  Proteins in the PM

 

What is the fxn of integral proteins?

Definition

-They are channels/transporters and receptors

-They are also structural proteins

Term
Can peripheral membrane proteins be released?
Definition

-yes, by ionic solvents.  integral proteins are permanent.

-spectrin-actin skeleton (filaments) create this mesh.

Term
What are lipid-anchored proteins (inner/outer) called?
Definition
glycophosphatidylinositolglycan (GPI) 
Term
What is the major function of the PM?
Definition
= hydrophobic barrier.
Term
What ions can pass through the PM?
Definition

1.  small polar compounds can pass by ion channels

-glu, K+ in

-Ca and NA out

Term
What are the transport systems?
Definition
[image]
Term
What molecules use simple diffusion?
Definition

Gases:  02 and CO2

Lipid soluble substances (steroid H)

Water diffuses randomly

Term

Concentration gradient in:

1.  simple diffusion and facilitative diffusion

Definition
High to Low
Term
What type of diffusion is saturable and Inhibitable?
Definition
Facilitative
Term
How do gated channels work?
Definition

1.  Transmembrane proteins form a pore for ions

2.  Either open or closed in response to stimulus

3.  voltage-dependent calcium channel

and 

4.  Ligand-gated CFTR (cystic fibrosis transmembrane conductance regulator) via phosphorylation

 

Term
What is involved in active transport?
Definition

1.  Protein transporters (carriers)

2.  energy used

3.  Na+, K+, ATPase and Na+/Ca2+ exchanger (antiporter), Na-Glu symporter

 

 

 

 

 

 

 

 

 

 

 

 

 

Term

Topic:  Vesicular Transport across the PM

What is phagocytosis?

Definition
Endocytosis of particulate matter 
Term
What is pinocytosis?
Definition
= Vesicle forms around fluid containing dispersed molecules
Term
What are lysosomes?
Definition
Intracellular organelles of digestion
Term
What can lysosomes do?
Definition

1.  Eliminate unwanted materials and recycling (aa)

2.  destroy infectious bacteria and yeast

3.  provide normal turnover of cells and organelles

Term

Endosomes and lysosomes?

Phagosomes and lysosomes?

Definition

Endosomes give rise to lysosome

Phagosomes fuse with lysosome

Term
What are lysosomal digestive hydrolases?
Definition
nucleases, phosphatases, glycosidases, esterases, proteases
Term
What are the fxn of lysosomal digestive hydrolases?
Definition
cleave amide, ester and other bonds (H200
Term
What is the optimal pH of lysosomal hydrolases?
Definition
pH ~ 5.5
Term
How is pH achieved in lysosomes?
Definition
Vesicular ATPases pump H+ in
Term
How do lysosomal enzymes, hydrolases, work?
Definition
-cleave peptide, ester and glycosidic bonds by adding components of water across the bond.
Term
What is the fxn of mitochondria?
Definition
ATP
Term
How many membranes do the mitochondria have?
Definition
2, outer and inner separating the mitochondrial matrix from the cytosol.
Term
What is the shape of the inner membrane of the mitochondria?
Definition
-Forms invaginations cristae
Term
What does the inner membrane contain?
Definition
electron transport chain and ATP synthase
Term
Is the inner membrane permeable or imperm?
Definition
Highly impermeable
Term
What does the inner membrane use to transport materials?
Definition
Facilitative transporters
Term
What does the outer mitochondrial membrane contain?
Definition
contains numerous integral proteins called porins, which contain a relatively large internal channel (about 2-3 nm) that is permeable to all molecules of 1,000 kDa or less
Term
What are lysosomes similar in size to?
Definition
Peroxisomes
Term

Topic:  Peroxisomes

What type of rxns happen in peroxisomes?

Definition

-oxidation rxns using molecular oxygen.

-specifically, oxidation of fatty acids, cholesterol to bile acids.

Term
What do peroxisomes produce?
Definition
-The toxic chemical (H202) which is subsequently used or degraded within the peroxisome by catalase and other enzymes 
Term

Topic:  Nucleus

 

What is the largest subcellular organelle?

Definition
Nucleus
Term
What does the nucleus contain?
Definition

Most of the genetic material,

-chromosomes, chromatin, DNA and histones (histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes.)

 

Term
What is the nucleolus?
Definition
A substate of the nucleus
Term
What happens in the nucleolus?
Definition

-rRNA transcription and processing

-ribosome assemly

Term
What is the outer nuclear membrane continuous with?
Definition
The Rough ER
Term

Topic:  ER

-What is the ER composed of?

Definition
-A network of membranous tubules within the cell
Term
What is the function of the rough ER?
Definition
Synthesizing protein
Term
What is the function of the smooth ER?
Definition

1.  synthesize lipids and steroids (via enzymes)

-triaclglycerols and phospholipids

2.  metabolize carbohydrates and steroids (but not lipids), and regulate calcium concentration

3.  drug metabolism

-cyt 450 oxidative enzymes metabolize drugs and toxic chemicals

4.  Glycogen is stored in sER in liver

Term
Where do the proteins go once they are synthesized in the rER?
Definition
1.  travel to the golgi complex in vesicles
Term
What can happen to proteins once they are in the golgi?
Definition

1.  secreted from cell

2.  sequestered within lysosomes

3.  embedded in PM

Term
What are posttranslational modification of the proteins produced in the rER?
Definition

1.  N-linked glyosylation (enzymatic process that attaches glycans to proteins, lipids, or other organic molecules)

2.  Addition of GPI anchors

Term
What is the fxn of the Golgi complex?
Definition

1.  modifies the proteins made in the rER?

2.  Sort and distribute these proteins

Term
Where does the golgi sort and distribute the proteins to?
Definition
Lysosome, secretory vesicles or the PM
Term

Topic:  Cytoskeleton

What is the purpose of the cytoskeleton?

Definition

1.  structure

2.  shape of the cell surgace

3.  arrangement of subcellular organelles

Term
What are the cytoskeletons 3 major protein components?
Definition

1.  microtubules (tubulin)

2.  thin filaments (actin)

3.  intermediate filaments (keratin)

Term
Function of microtubules?
Definition
Move and position organelles, vesicles
Term
Form of thin filaments, actin?
Definition
Form the cytoskeleton
Term
What is the structure of microtubules?
Definition

1.  all nucleated

2.  platelets in blood

Term
In what ways do microtubules move vesicles?
Definition
either by phagocytosis or exocytosis
Term
Where do the microtubules transport vesicles?
Definition
Between ER, golgi and endosomes
Term
How are microtubules involved in cell division?
Definition
Form the spindle apparatus
Term
Can microtubules move stuff within the tube?
Definition

Yes, via proteins kinesins (carrier move to PM) and dyneins (carrrier to move to the membrane).

-use atp to move

Term
What is the function of actin filaments?
Definition
= Form a network that controls the shape of the cell and mov't of cell surface.  This allows cell to move, divide, engulf particles and contract.
Term
Function of short actin filaments?  Bind to what?
Definition
Bind to cross-linking protein spectrin to form the cortical skeleton network
Term
What is the purpose of long actin filaments in muscle cells?
Definition
-combine with filaments, myosin, to produce muscle contraction.
Term
What are the purpose of intermediate filaments?
Definition
Provide structural support to membranes of cells and scaffolding for attachment of other cellular components.
Term

Topic:  Signaling molecules

Receptor types?  How many are there?

Definition

=4

1.  Ligand-gated ion channels, not much signaling pathway.  ligand binds to ion channels

2.  G-protein coupling receptors

3.  Tyrosine kinase coupling receptors (receptor with an intracellular segment with an enzyme fxn (ie:  kinase-  puts a phosphate on another protein)

4.  steroid receptors-  ligand goes into cytoplasm, binds to receptor inside and cell.  gets into nucleus and regulates transcription.

Term
Tyrosine Kinase receptors.  When are they used?
Definition

Growth, development, differentiation.

-Tend to be used a lot with cancer drugs-  regulate cell growth.  inhibit kinase receptors if they are too active.

Term
Signal transduction and G-proteins coupling receptors signaling pathway.  What are 2 important pathways?
Definition

1.  Phospholipase C pathway- involves GQ protein (a G protein):  So, if drug binds to a receptor, the receptor activates GQ protein-  thsi will activate a phospolipase C:  converts a phospolipid to diacyglycerol.

 

 

Term
What is the function of diacyglycerol?
Definition

Activate protein kinase C. 

Other:

IP3 will mobilize calcium from ca storage inside the cells.  Calcium will activate protein kinase C.

Term
How is G protein activated?
Definition
Ligand bonds to G protein couple receptor-  changes conformation-  allows G protein to become activated.
Term
What are the g-protein subunits?
Definition
1.  Alpha, Beta, Gamma
Term
Inactive G-protein?
Definition
Alpha, Beta and Gamma subunits don't split apart.
Term
Active G protein?
Definition
The alpha subunit will separate from Beta and Gamma----phospholipase C---DAG---IP3.
Term
3 G-protein subunits to focus on.  What are they?
Definition

1.  Alpha s (stimulates adenyl cyclase) , Alpha i (inhibits adenyl cyclase), Q (activates phospholipase C).

 

-accounts for the majority of G protein coupling receptor signaling.

Term
How do you terminate the protein coupling signal?
Definition

If it deals with a receptor-  desensitization, desensitization of signal

 

Phosphotase- removes phosphate to terminate signal.

 

Phosphodiasterase-  enzyme that helps to reduce cAMP (2nd messenger made by adenyl cyclase).

Term

Session 3-

Amino Acids and Proteins

Amino acids are composed of?

Definition

1.  Carboxyl group, -COOH

2.  Amino Group, -NH3

3.  1 of 20 side chains

Term
AA's with nonpolar side chains?
Definition

1.  Alanine

2. Glycine

3.  Isoleucine

4. Methionine

5.  Phenylalanine

6.  Proline

7.  Tryptophan

8.  Valine

Term
AA with uncharged polar side chains?
Definition

1.  Asparagine

2.  Cysteine

3.  Glutamine

4.  Serine

5.  Threonine

6.  Tyrosine

Term
AA's with acidic side chains?
Definition

1.  Aspartic Acid

2.  Glutamic acid

Term
AA's with basic side chains?
Definition

1.  Arginine

2.  Histidine

3.  Lysine

Term
What are the functions of AA?
Definition

1.  Metabolism:  Enzymes and polypeptide Hormones

2.  Movement:  Contractile proteins in muscle

3.  Bloodstream:  hemoglobin and albumin

4.  Immunoglobulins-  fight microbes

Term
What forms do AA exist in?
Definition
[image]
Term
How are AA's classified?
Definition
By their R group
Term
Nonpolar side chain AA's- chart
Definition
[image]
Term
What are some properties of AA with nonpolar side chains?
Definition

1.  Does not bind or give off protons or participate in H or ionic bonds.

2.  Promotes hydrophobic interactions

Term

How are nonpolar AA's located in proteins?

1.  Protein in an aq solution (polar environment)

2.  In a hydrophobic environment (a membrane)

Definition

1. R of nonpolar AA tend to cluster together in interior of protein

2.  non-polar R groups are found on the outside surface of a protein, interacting with the lipid environment.

Term
Proline, what's special about this AA?
Definition

-differs from other AA in that proline's side chain and a-amino N form a rigid, 5 membered ring.

= has a secondary, rather than primary, amino group = Imino acid.

Term
Where do you find proline?
Definition

1.  fibrous structure (collagen)

2.  Interrupts a-helices in globular proteins.

Term
Chart of uncharged polar side chain AA's.  They have the tendency to ionize.
Definition
[image]
Term
What is unique about cysteine?
Definition
It tends to form disulfide bonds (ie:  albumin)
Term
What charge do AA with uncharged side chains have at neutral pH?
Definition
0
Term
What is unique about uncharged side chain AA's: serine, threonine, tyrosine?
Definition

1.  Can participate in H bonds

2.  Have an attachment site for phosphate group

3.  Have an attachment side for oligosaccharide

Term
AA with uncharged polar side chains:  What is unique about asparagine and glutamine?
Definition

1.  Can participate in H-bonds

2.  Have an attachment site for oligosaccharides (amides)

Term
Chart of Acidic Side chains, basic side chains
Definition
[image]
Term
What is a buffer?  Can AA's be buffers?
Definition

A buffer is a molecule that resists changes in pH (by donating or accepting protons).  

-AA's can do this if they are free standing.

Term
AA with acidic side chains
Definition

= proton donors.

-at physiologic pH, fully ionized (- charge)

Term
AA's with basic side chains
Definition

= accept protons

-at pH 7.4, fully ionized (+ charge)

Term
What is unique about histidine?
Definition

-It is weakly basic, but its side chain can be either positively charged or neutral depending on the ionic environment.

-Role in hemoglobin.

Term

What are a few optical properties of AA's?

 

Definition

1.  alpha C of each amino is chiral (except for GLYCINE).

2.  AA's have an optically active C atom.

3.  AA's can exist in 2 forms, D and L.

[image]

Term
What form are all AA's in proteins found?
Definition
L-form
Term
Where is a D AA found?
Definition
Some antibiotics, in plant and bacteria.
Term
What do AA's look like in an aq. solution?
Definition

1.  contain weakly acidic alpha carobxyl groups

2.  contain weakly basic alpha amino groups.

Term
How can AA's act as a buffer?
Definition
[image]
Term

Topic:  Titration of an AA

 

What is the isoelectric point (pI)?

Definition
the pH at which an AA is electrically neutral (+ = -)
Term
Alanine and the isoelectric point
Definition
[image]
Term
Isoelectric point calculation?
Definition

pI = average pK1 and pK2 for AA's with 2 pKa's-  2 H's to give away

For charged AA's with 3 H's to give away, average the 2 closest in nature.

Term
What are other applications of the henderson-hasselbalch equation?
Definition

1.  Bicarbonate as a buffer

2.  Drug absorbtion

Term
What are primary and secondary structures of AA?
Definition

Primary:  The sequence of AA

Secondary:  Regular arrangements of AA's located near to each other in primary structure

Term
What are the tertiary and quaternary structures of AA's?
Definition

Tertiary:  The 3 dimensional shape of the folded chain

Quaternary:  The arrangement of multiple polypeptide subunits in the protein.

 

[image]

Term
What is the definition of a protein?
Definition
= AA's joined together by peptide bonds
Term
What is the primary structure of AA's?
Definition

1.  Linear sequence of AA

2.  Joined covalently by peptide bonds

3.  amide linkages between the alpha-carboxyl group of 1 AA and the alpa amino group of another.

 

[image]

Term
How are AA sequences read?
Definition
From the N- to the C- terminal end of the peptide.
Term
What are the components of secondary structure?
Definition
alpha helix, beta sheet and beta bend (turn)
Term
Some details about the alpha helix?
Definition

1.  The most common helix

2.  A spiral structure, 3.6 AA's/turn

3.  side chains point toward the outsides

 

[image]

Term
What is the purpose of alpha helices?  Where are they used?
Definition

1.  keratins

2.  fibrous proteins

3.  myoglobin

Term
What amino acid tends to disrupt an alpha helix?
Definition

-Proline

-Charged AA's-  glu, asp, his, lys, arg

-AA's with bulky side chains- trp

Term
How does a beta sheet work?
Definition

-all of the peptide bond components are involved in H bonding.

 

Term
How does B sheet differ from a helix?
Definition
Beta sheets are composed of greater than or equal to 2 peptide chains.
Term
What is a beta pleated sheet?
Definition
The surfaces of beta sheets appear 'pleated'
Term
What is the orientation of sheets in the beta sheet?
Definition

=antiparallel to each other, N and C terminals alternate.

=parallel to each other 

 

[image]

Term
What is a Beta bend?
Definition
it reverses the direction of a polypeptide helping it form a compact, globular shape.
Term
Where are Beta bends found?
Definition
On the surfaces of protein molecules, and often include charged residues.
Term
Which AA can be involved in beta turns?
Definition
proline, glycine
Term

What is 'random coil'?

 

Definition
The disordered structure obtained when proteins are denatured.
Term

Topic:  Supersecondary Structures (motifs)

 

How are globular proteins constructed

Definition

1.  Composed of alpha helix, beta sheet, nonrepetetive sequences, beta bends

2.  motifs are usually produced by packing side chains from adjacent secondary structural elements close to each other.

Term
What determines the tertiary structure of a protein?
Definition
The primary structure of a polypeptide chain 
Term
How are AA's arranged in a globular protein?
Definition
Hydrophobic side chains are interior, whereas hydrophilic groups are on the surface.
Term
What are domains?
Definition

= functional and 3D structural units of polypeptides.

(>200 AA in length generally consist of 2 or more domains)

Term

AA interactions stabalizing tertiary structure.

1.  Disulfide bonds

Definition

A covalent linkage (-SH) of each of 2 cysteine residues to produce a cysteine residue.

ie:  immunoglobulins, albumins

Term
2.  Hydrophobic interactions
Definition

nonpolar side chains tend to be located in the interior of the polypeptide molecule

 

[image]

Term
3.  Hydrogen Bonds
Definition
Serine and threonine (-OH)
Term
4.  Ionic interactions
Definition

(-COO-) aspartate or glutamate interact with (-NH3+) lysine

 

[image]

Term
Are these interactions reversible?
Definition
Yes
Term
How and when do proteins fold?
Definition

-controlled by interactions between side chains of AA's

-occurs within seconds to minutres

-employs a shortcut via all folding possibilities

-Use all 4 types of interactions

Term
What is the result of protein folding?
Definition
Results in a low energy state.
Term
What are chaperones?
Definition
Proteins that interact with the polypeptide at various stages during the folding process.
Term
What happens to misfolded proteins?
Definition
They are usually tagged and degraded within the cell.
Term
What if degradation of misfolded proteins fails?
Definition
They can accumulate with age.  Deposits of these misfolded proteins are associated with a number of diseases, including amyloidoses and alzheimers.
Term
What is amyloidoses?
Definition
the misfolding of the amyloid protein.  accumulation of amyloid B---toxic to brain cells.
Term

Topic:  Quaternary Proteins

What are monomeric proteins?

Definition

Consist of a single polypeptide chain.

 

-The arrangement of these polypeptide subunits is called the quaternary structure of the protein.

Term
How are quaternary subunits held together?
Definition

noncovalent interaction, H bonds, ionic bonds and hydrophobic interactions

 

[image]

Term
What are globular proteins?  = hemoglobin, myoglobin
Definition

= a group of specialized proteins

-heme (iron as a prosthetic group-  prosthetic group = something is needed for protein to function) acts as a tightly bound prosthetic group

-4 N keep the iron in place.

Term
Sickle cell anemia
Definition

Mutation on beta chain on heme changing from charged Glu to nonpolar Val.

-why sickle cells?  they get caught in the microvasculature.  can't fit through the capillaries.  clogging of the pipes.

Term
Where do we see heme groups?
Definition

1.  cytochrome P450-  drug metabolism

2.  cytochrome C

3.  catalase:  gets rid of hydrogen peroxide

4.  myoglobin-  single unit of O2

5.  Hemoglobin

Term
Where is myoglobin present?
Definition
Heart and skeletal muscle
Term
What is the fxn of myoglobin?
Definition
a reservoir for O2 and an O2 carrier
Term
What is the structure of myoglobin?
Definition
A single polypeptide chain
Term
Where is hemoglobin located?
Definition
In RBC's only.
Term
What is the main function of hemoglobin?
Definition
O2 transport
Term
What is Hb structure in adults?
Definition
= 4 polypeptide chains, each subunit has a heme-binding pocket.
Term
Is Hb cooperative?
Definition
Yes-  bind 1 O2, increase the capacity to bind more O2.
Term
Quaternary structure of hemoglobin-  what are the 2 forms that it can assume?
Definition

1.  T form-  deoxy form (TAUT) = tense

-low oxygen affinity

2.  R form- O2 bound, relaxed form

-high 02 affinity


[image]

Term
What are the allosteric affects of Hb?
Definition

allosteric because 4 different subunits cooperatively working together.

-Hb reversibly binds oxygen

-allosteric, other site, effectors

-pO2, pH, pC02, and 2,3 bisphosphoglycerate.

Term
The Bohr Effect
Definition

The release of 02 from Hb is enhanced when the pH is lowered (change affinity of Hb to 02).

-OR, when the Hb is in the presence of an increased partial pressure of CO2.

 

[image]

Term
What is the effect of 2,3-bisphosphoglycerate on O2 affinity?
Definition

-2,3-BPG:  the most abundant organic phosphate in RBC.

-2,3 BPG:  synthesized from an intermediate of the glycolytic pathway.

-Decreases O2 affinity of Hb by binding to deoxyHb.

-Reduces affinity, enables Hb to release O2 (stabalizes T form).

Term
How does CO bind to the Hb iron?
Definition
tightly, but reversibly.
Term
What happens with CO binds?
Definition
Shifts to the relaxed conformation
Term
What causes CO poisoning?
Definition
Tissue hypoxia and direct CO-mediated damage at the cellular level.
Term
How is CO poisoning treated?
Definition
100% O2 therapy
Term
What is the effect of CO2 binding?
Definition
Stabilizes the T (taut) or deoxy form, resulting in a decrease in its affinity for oxygen.
Term
Sickle cell anemia. 2 types:
Definition
S form, more prevalent and more severe than C form.
Term
Sickle cell and malaria
Definition
Normally RBC's life span is ~ 120 days.  Sickle cell life span is ~ 20 days.  The malaria cycle needs a full 120 days.  So, ppl with malaria don't tend to get sickle cell.
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