C-C (alkane)

C=C (alkene)

H-C=O (aldehyde)

Ketones

Carboxylate Esters

Phosphate Esters

Amines

Amides

Lipids:

-Are very hydrophobic

-The only monomers we talk about (very small)

-Don't have "activity" or normally store information (like DNA or RNA)

-Are the long-term energy storage molecules ( CHO [starch and glyco.] are the mid-term energy storage molecules, and ATP is the short-term energy storage molecule)

-Sometimes form lipid bilayers (membranes)

-Sometimes are steroids (cholesterol as precursor)

-Sometimes are enzyme cofactors (vit. A)

-Sometimes are messengers (hormones)

The overarching theme to all of these characteristics/roles is that lipids have very diverse roles in the human body. 

What are Fatty Acids?

How can fatty acids have "split personalities?"

Biomolecules containing a carboxyl functional group (-COOH) connected to an unbranced aliphatic chain. 

Since they have one polar and somtimes ionic end (where the carboxyl group is present, and another nonpolar end (hydrocarbon chain), the molecules are described as being amphiphilic. 

What are the most important interactions in Fatty Acids?

What do Fatty Acids spontaneously form?

Hydrophobic interactions

Micelles

Fatty Acids are rarely found in a free form in a cells and tissues, but are most often bound in what?

How many carbon atoms are typically found in a Fatty Acid?

What are the two types of Fatty Acids that exist?

Triglycerides

12-14 carbon atoms

Saturated and unsaturated

What does it mean for something to be saturated?

How do saturated Fatty Acids differ from unsaturated Fatty Acids?

If something is saturated, that mean that every Carbon is surrounded by the maximal amount of Hydrogens, indicating that only C-C single bonds are present. 

Saturated Fatty Acids only have single bonds present in their hydrocarbon chain and therefore have an unbranched, straight chain. Unsaturated Fatty Acids may have one or more C=C double bonds. This means that the chain has a bend in it. 

What is the name of a Fatty Acid with two or more double bonds?

One?

Two?

Double bonds in naturally occurring fatty acids are almost always of what configuration?

Polyunsaturated 

Monounsaturated

Diunsaturated

Cis configuration

Saturated Fatty Acids lead to maximum...

submaximal energy minimization (remember= energy minimization is what all structures want to achieve)

rotate

What are some general rules for naturally occurring Fatty Acids?

Why are some Fatty Acids oil at room temperature, and other solid at room temperature?

- Have an even # of Carbon atoms

-The hydrocarbon chain is always unbranched

-Most C-C bonds are single

-Double bonds that occur are in the Cis conformation

Fatty Acids 10 C or under that are saturated will form a solid at room temperature because of the maximal amount of hydrophobic interactions and energy minimization. Fatty Acids 10 C or under that are unsaturated will be oily at room temperature because they unable to effectively line up and therefore unable to be solid. 

What are the constituents of triacylglycerols?

How is each hydrozyl group linked to a Fatty Acid?

-The trihydroxyl compound, glycerol

-three of the same (simple TAGs= rare), or two or three different Fatty Acids (more common)

Through the process of esterification

What happens during esterification?

What is the purpose of esterification?

The polar hydroxyl groups of glycerol and the polar (sometimes ionic) carboxyl group of each fatty acid are tied up in neutral ester linkages.

To render the molecule as nonpolar and hydrophobic (neutralizing the carboxyl group of the fatty acid and the polar hydroxyl groups of the glycerol with the neutral ester linkage). 

Why don't we want free Fatty Acids to float around in our body?

TAGs isolated from aminal issues are called what, what form are they commonly in at room temperature, and why?

TAGs isolated from plant sees are called what, what form are they commonly in at room temperature, and why?

Fatty Acids floating around in the the body would lower the pH of our body (physiological pH is 7.4), and micelles could spontaneously form and dissolve our cellular membranes.

Fats are typically solid at room temperature due to the property that they contain mostly saturated Fatty Acids.

Oils are typically liquid at room temperature due to the property that they contain many unsaturated acids. 

What are the enzles called that aid in the hydrolysis of triacylglycerols?

What are the two primary giological roles of TAGs?

Lipases

Energy metabolism and temperature insulation

What are the two types of polar lipids named?

What the special functions of these polar lipids due to?

Glycerophosopholipids and sphignolipids

The fact they are amphiphilic in nature.

protein

biological membranes

What is the purpose of the biological membrane?

The polar lipids are found almost exclusively in __________ and are not stored in ____________ as energy molecules like triacylglycerides.

To provide a protective shield around cells and cellular organelles, but to make the membrane permeable so that some selected molecules are available for passage, but not others.

membranes

adipocytes

What are glycerophospholipids made of?

What are some characteristics of these polar lipids?

A glycerol backbone + 2 FA + a phosphate.

-They form a bilayer spontaneously

-They are not commonly used as energy stores

-There is a great diversity of phospholipids

-Packing has a profound effect on the membrane's fluidity/viscosity (i.e. increased packing means increased viscosity)

-Increased hydrophobic interactions (longer hydrocarbon chains) leads to decreased energy and therefore increased stabilization. 

What are two things organisms can control in regards to phospholipids?

What happens if the polar head is too large, or the tails are too long?

1. The length of the acyl chain, which influences viscosity

2. Saturation level (increased saturation leads to tighter packing)

There is a loss of hydrophobic interactions

How are phospholipids able to segregate proteins?

How do organisms control the fluidity of membranes?

By size sequestering.

Too fluid- lyse

Too viscous- enzymatic reactions cease (cells die too)

What are steroids comprised of?

What is the most chemically reactive portion of the cholesterol structure?

What is the precursor to steroids?

a fused-ring system of three six-membered rings labeled A, B and C, and one five-memebered ring called the D ring. 

The hydroxyl group.

Cholesterol

What helps digest cholesterol?

What is the name of the structures similar to cholestrol that have been isolated from plants?

Bile salts

Phytosterols (phytoestrogen)= high in soybeans and other vegetables

What are pheromones?

What are some characteristics of pheromones?

Chemical signals released by some organisms into the environment that alter the behavior of members of the same species or of organisms they interact with. 

-Highly volatile

-Sexual attractants (insects)

-No proof of existance in higher organisms

-Plant defense mechanisms (i.e. corn secretes in insect intestations, ethylene and jasmonic acid=ripen fruits)

What are membranes made up of?

Describe passage through a membrane?

Phospholipids, glycolipids, steroids, cholesterol (embeds itself), and protein.

A membrane is a semi-permeable barrier that allows nonpolar lineral molecules to go through. The only molecules that can pass through the membrane must be hydrophilic enough to go into solution. 

What are the two main divisions of membrane proteins based on the ease of their extraction from the membranes?

What is the name of the third type?

Peripheral proteins and integral proteins.

Lipid-linked

Describe integral/intrinsic membrane proteins?

How can a second extraction be made?

Integral proteins have an a.a. segment that spans the lipid bilayer. They are able to span that membrane by arranging hydrophobic regions in the protein into distince secondary structures, usually an alpha-helix or beta-barrel (hydrophobics go on the surface within that internal spanning region). They can use up to 20 a.a. residues.

A second extraction can be removed by detergebts (micelles), which will destroy the membrane.

amino acid residues

amino acid residues

-interact with integral proteins or phopholipid head groups

-ionic interaction

-removed by salt wash (NaCl)

-Have acyl chain covalently attached (prosthetic group)

-chain is hydrophobic- embeds and anchors protein

-acyl chain can be removed by protein modification

-localization/recruitment of free protein in cytosol to membrane

-can interact with other proteins at the membrane (ON/OFF)

This model views membranes as a sea of lipids and proteins. 

-not static, changes based on viscosity

-free to diffuse in 2D (x & y), most stuck at fixed (z)

-membrane viscosity can be measured using lazer bleached color spon on a cell= measure time if diffusions

-lipids in bilayers

Nonpolar molecules can diffuse through the membrane because of the hydrophobic nature of the central region. Polar, hydrophilic molecules must be assisted in transport

What types of molecules require help getting across the membrane? Which molecules do not?

What helps regulate the flow of molecular traffic?

What are the two forms of membrane transport?

Large, polar molecules require help. Small, nonpolar molecules do not. 

Membrane proteins, especially integral proteins. 

Passive transportand active transport, the difference is the dependence on energy

-Energy is required to transport against the concentration gradiant (usually low to high membrane)

-hydrolysis of ATP to ADP +Pi, loses phosphate, energy out

What are the two types of passive transport?

Describe both types of passive transport:

Simple diffusion and facilitated diffusion

Simple diffusion is just the downhill running across the concentration gradient. Facilitated diffusion is a protein-mediated process that requires no energy, but helps molecules through the layer by means of a transmembrane facilitator protein and a concentration gradient. 

What are the three types of facilitator proteins?

Which of these are examples of cotransport?

1. Uniport- one thing, one way

2. Symport- 2 things, one way, input/output linked

3. Antiport- 2 things, both/opposite ways, input/output linked.

Symport and Antiport

What is the Central Dogma to Biochemistry?

What are the three parts of nucleic acids?

DNA-->RNA-->proteins-->Cell structure/function

1. A Base, purine or pyrimidine

2. Ribose attached to the base covalently, always b-ribose & linked vial glycosidic bond/ 5 carbon carbohydrate

3. Phosphate attached to ribose C-5

What is the difference between deoxyribose and ribose?

How does the half-life of mRNA compare to the half-life of DNA.

What are the major purines in DNA?

What are the major pyrimidines in DNA?

Deoxyribose has 2 H attached to C-2 whereas Ribose has 1 H and 1 OH attached to C-2.

mRNA has a half-life of minutes whereas DNA has a half-life of centuries.

Adenine and Guanine

Thymine and Cytosine

-Exists as a double helix consisting of 2 DNA strands interacting with one another

-The bases align on the inside since they are slightly hydrophobic, whereas the Ribose and Phosphate are very hydrophilic.

-As a whole, DNA is hydrophilic

-Strands are anti-parallel (one reads 3'-5', the other 5'-3')

1. Hydrogen bonds between complementary bases on opposite strands

2. Van der Waals and hydrophobic interactions between "stacked bases"

How many H-bond interactions exist between Adenine and Thymine?

How many H-bond interactions exist between Guanine and Cytosine?

What implications does this have?

2 H-bond interactions

3 H-bond interactions

Guanine-Cytosine bonds are stronger and more stable (higher melting points) than Adenine-Thymine bonds. 

How do we separate two complimentary H-bonding pairs?

What type of process is this?

Enegry released from a phosphoanhydride bond 

Endothermic (requiring energy)

What are the two fundamental differences in the primary, covalent structures of RNA and DNA?

What is a third difference between RNA and DNA

1. RNA contains the carbohydrate ribose rather than 2-deoxyribose (-OH group at C-2)

2. One of the major bases in RNA is Uracil (U) instead of Thymine (T) in DNA

RNA is single stranded and therefore does not exist in a double helix. While it does not exist in a double helix, it does have some secondary structure. The complimentary H-bonding that may occur is anti-parallel

1) mRNA- messenger

2) rRNA- ribosomal

3) tRNA- transfer