3 Structure of Biomolecules

Amino acid parts

an alpha carbon with an amino group, COO- (carboxylic acid), hydrogen atom, and an R group.

proteins only contain (isomer)

L isomers

pH vs pKa amino acids

if the pH is above the pKa, then the protein is most likely to be in its deprotonated form. if the pH is below the regular pKa, then the protein is more in the protonated form. The higher usual pKas are due to R groups.

protein primary structure

amino acids linked by peptide bonds

a residue

a single amino acid unit in a polypeptide

peptide bond formation involved

the loss of a watermolecule through dehydration synthesis and the a-carboxy group of one amino acid links to the a-amino group of another amino acid

C and N terminus

C terminus is carboxyl N terminus is amino end

oligopeptides

polypeptide chains made of small numbers of amino acids

1 dalton =

1amu (for protein molecular mass)

fatty acids

part of lipids, hydrophobic, long hydrocarbon chains that end with carboxylic acid groups

Fatty acid names

derived from the parent hydrocarbon with oic at end. like decanoic acid (10:1). The first number is the number of carbon atoms total, second is the number of double bonds.

Naming fatty acid carbon atoms (2 ways)

1. omega (ω) carbon way

• The methyl carbon end, that carbon is called the omega ω carbon, also carbon 1.

• Number down from there, with the double bond being the ω-first carbon of the double bond double bond. For naming, it is omega-first carbon of double bond.

2. cis/trans way

• the carbon of the carboxylic acid is the carbon 1.

• number down from there, with carbon 2 alpha and 3 beta (organic chem numbering system). Then for naming, denote cis or trans, with a delta Δ symbol and the first carbon from the double bond as a superscript.

number of carbons in fatty acids

fatty acid chains contain an even number of carbon atoms between 14 and 24 - 16 and 18 are the most common.

Three common types of membrane lipids in biological membranes

phospholipids, glycolipids, and cholesterol

phospholipid components

one or more fatty acid tails (hydrophobic), glycerol (platform fatty acids are attatched), phosphate group (charged group), and an alcohol attatched to the phosphate (hydrophilic side, gives up H ion easily).

phosphoglycerides vs sphingophospholipids

both are a type of phospholipid, phosphoglycerides have a glycerol backbone with sphingophospholipids have a sphingosine backbone.

Common phosphoglyceride found in membranes

phosphatidylcholine

Common sphingophospholipid found in membranes

sphingomyelin, found extensively in myelin sheaths around neural axons.

Cholesterol structure

Big, blocky structures. a steroid built from 4 linked hydrocarbon rings. Contains a linked hydrocarbon tail at one end, -OH group at other end.

cholesterol interactions and orientation

-OH group interacts with phospholipid head groups, oriented parallel to fatty acid chains of phospholipids in membranes.

amphipathic

a molecule that has both a hydrophobic and hydrophilic region

moiety

part of portion

phospholipid moietys

head hydrophilic, tail hydrophobic

micelle

a globular structure with the polar head groups on the outside surface and hydrocarbon tails inside. (phospholipid bilayer is NOT a micelle). Usually single tailed salts of fatty acids do.

How are lipid bilyers formed

Spontaneously, stabilized by non covalent interactions.

lipid bilayer - biological consequences of hydrophobic interactons

Bilayers ted to close on themselves so there are no edges with exposed hydrocarbon chains (forms compartments), self-sealing. A hole is very unfavorable.

What passes through lipid bilayer

small molecules that are nonpolar pass well, and water.

Permeability coefficients for lipid bilayer

Denoted by P. Water is around 10^-2. going down to smaller P is Na+ (charged ions that are hard to go across), glucose is around the middle.

Most membrane processes are carried out by

Proteins. they transport molecules and information across.

integral membrane proteins, and how to remove/extract

Stuck inside the lipid bilayer. Interact extensively with the hydrocarbon chains of membrane lipids. They have a hydrophobic section for this (and hydrophilic section!) They are released by agents that compete for nonpolar interactioons. Difficult to extract because deeply embedded, chemicals needed.

Peripheral membrane proteins, and how to remove/extract

Bound to membranes mainly, sit on the surfaces and don’t penetrate deep into core. Primarily bound through electrostatic and hydrogen bond interactions with the head groups of lipids. Hydrophilic. Disrupted by using salts of pH, or shaking loose. Easier to remove than integral.

lateral diffusion

a process by which lipids and membrane proteins are constantly in lateral motion (moving side to side throughout a membrane).

transverse diffusion

movement of lipids and membrane proteins across to other end of membrane (flip-flop). Much more difficult to do. Slow process compared to lateral diffusion.

FRAP

way to visuzalize lateral diffusion. Fluorescence recovery after photobleaching. you bleach an area, and see how long it takes for the bleached spot to recover, showing the amount of lateral diffusion occuring. The recovery is the increase in fluoresence after photobleaching.

Tm (melting temperature) of a fluid membrane.

The transition from rigid to fluid state takes place above the Tm. Depends on the degree of unsaturation, saturated fatty acids favor rigid state. unsaturated (with a double bond) interfered with highly ordered packing. Think about it, because of the kink in the bond, they have more room to wiggle around and move, increasing fluidity, however it causes weak intermolecular attraction and inability to pack tightly. Unsaturated bonds lower the Tm necessary to be fluidlike.

Cholesterol and fatty acid tight packing

Disrupts this because it is a 4-ring bulky steroid. Disrupts the regular interactions between the chains, helps maintain proper fluidity in animal membranes.

current plasma membrane model

fluid mosiac model

lipid rafts

membrane domains having reduced fluidity. cholesterol forming complexes with lipids that contain the sphingosine backbone.

monosaccharide and structure.

the basic building block for carbs. empirical formula (CH2O)n. contain an aldehyde or ketone with 2+ hydroxyl group.

Epimers

sugars that are diasteromers differing in configuration only at a single asymmetric center.

most monosaccharides exist as

interchanging cyclic forms

identify pyran and furan

anomer

a diasteriomeric form of sugars that forms when a cyclic hemiacetal is formed (ring created) and an additional symmetric center is created.

d fructose

rapidly interchanges between four distinct ring structures. pyranose form predominates due to reduced steric hinderance.

ISOMER TYPES (6)

See chart. know this.

pyranose and furanose ring conformations

chair or boat.

Beta - D - glucose conformation

the chair form predominates because all axial positions are occupied by H, the boat form is disfavored because it is sterically hindered.

glycosidic linkage

monosaccharides are joined to alcohols and amines. O and N type.

O-linkage: covalent linkage between the oxygen atom of alcohol

N-linkage: covalent linkage formed between the nitrogen atom of an amine.

oligosaccharides

sugars that contain two or more monosaccharides linked by o-glycosidic bonds.

sucrose

common disaccharide. glucose + fructose. table sugar.

lactose

milk sugar, galactose +glucose.

maltose

disaccharide resulting from the hydrolysis of large oligosaccharides that consists of two linked glucose.

glycogen

most common polymer in animal cells, storage form of glucose. hydrolyzed by alpha amylase.

starch

polymer for nutrition in plants. amylose and amylopectin. amylose is unbranched with no 1-6 linkage, amylopectin is branched.

cellulose

main structural polysaccharide of plants. B configuration of linkage that allows cellulose to form long straight chains for structure. Interact together with hydrogen bonds.

insoluble fiber in diet

while we cant digest it, they increase the rate digestion products pass through the large intestine. softens stools.

Soluble fiber in diet

slows the movements of food through the digestive tract (harder to break down).

RNA vs DNA

ribose is the sugar in RNA, deoxyribose is the sugar in DNA. Ribose has an extra 2’ OH group that increases ability to be hydrolyzed.

backbone of DNA and RNA

sugars linked by phosphodiester bridges with a negative charge.

Purines and Pyrimidines (and attatchment)

The nitrogenous bases of DNA and RNA. Attatched to the 1’ carbon atom of sugar. Purines are adenineand guanine with two rings. pyrimidies are thymine and cytosine with one ring. RNA has uracil instead of thymine.

identify

adenine on left, guanine on right. Guanine has an extra carbonyl.

identify

Cytosine, uracil, and thymine left to right. Pyrimidines have one ring. cytosine only has one carbonyl, uracil doesn’t have an extra methyl.

nucleoside

the unit consisting of a base bonded to a sugar (no phosphate group).

nucleoside triphosphates

has three phosphate groups. high energy bonds are between the phosphate groups that can provide energy.