molecules of life

Whats the definition of an organic molecule?

• One that contains carbon

Whats the definition of a bio molecule?

• Organic molecule that is commonly associated with life

Whats the 4 biomolecules?

1. Carbohydrates

2. Nucleic acids

3. Lipids

4. Proteins

Whats the general formula of carbohydrates?

• CnH2nOn

Whats the formula for glucose and ribose?

• Glucose = C6H12O6

• Ribose = C5H10O5

What’re some qualities of carbohydrates?

• Most are hydrophilic

• Water soluble

• Very abundant in nature

What’s the role of carbohydrates and provide examples

• Used for structure and energy

• Almost all eukaryotic cells can use glucose for energy and can store some form of glucose (monomer or polymer) for energy

• Many proteins and lipids are modified by the addition of carbohydrates

What are nucleotides and nucleosides involved in?

• Energy metabolism and signaling/ communication

What does a nucleotide consist of?

• Nucleobase/ nitrogenous basE

• Phosphate group

• 5 carbon sugar

What does a nucleoside contain?

• Only nitrogenous base and sugar

• NO PHOSPHATE

What does the structure of the nitrogenous base determine?

• It determines whether the nucleobase is Adenine, Cytosine, Guanine, Thymine or Uracil

What’re some different forms of molecules with adenine?

• AMP, ADP, ATP

What is ATP?

• Basic molecule of energy storage in most organisms, including mammals

Whats is adenosine?

• A nucleoside, works as a neurotransmitter/ signalling molecule

Whats cyclic AMP important for?

• Important signaling molecule within cells

What are some molecules containing guanine?

• GMP, GDP, GTP

What is GTP?

• It’s an energy source in many physiological chemical reactions

Whats cyclic GMP used for?

• Important signaling molecule within cells

What’re some features of lipids?

• Generally hydrophobic

• Contain mostly carbon and hydrogen (a few oxygen atoms, nitrogen, phosphorus)

• Generally non-polar

Whatre some examples of lipids?

1. Fatty acids

2. Glycerides

3. Phospholipids and sphingolipids

4. Steroids

5. Oxylipins

Are lipids water soluble?

• No cuz non polar and water is polar

What’re some roles of lipids?

1. Important for structure of cells/ cell membrane cuz its waterproof and pliable

2. Energy source

3. Communication (within cells and between cells)

What’re fatty acids generally?

• Long unbranched hydrocarbon chain with 8-28 carbons

• Has carboxyl (=acidic) functional group

Whats the difference between saturated and unsaturated FA?

• Saturated = no double bonds, forms straight chain

• Unsaturated = double bonds, has a kink

What happens the more double bonds a FA has?

• The less likely it’ll be solid at room temp

What’re glycerides?

• Derivative of FA

• FA + glycerol = glyceride

• Involves a dehydration reaction where water is lost

What’re the 3 types of glycerides?

What’re phospholipids?

• A derivative of glycerides

• 2 FA tails + glycerol + phosphate + variable R group

• Amphipathic

What can form if you shake up a beaker with water and phospholipids?

What’re sphingolipids?

• They contain FA + phosphate group + R group + sphingospine

• Sphingospine is longer than an FA tail

Whats the difference between phospholipid and sphingolipids?

• No glycerol in Sphingolipids

• 1 less FA in sphingolipid cuz sphingospine subs in for it

What’re glycolipids?

• Decorated with a carbohydrate

What does the basic structure of a steroid contain?

• Basic structure consists of 3 six-carbon rings plus 1 five-carbon ring

• Totalling 17 Carbons

What do different R groups in steroids do?

• Confer different function

What roles do steroids have?

• Communication = Testosterone

• Structure = Cholesterol

What’re oxylipins?

• Oxygenated metabolites of fatty acids

What’re Eicosanoids?

• Subset of oxylipins which are a polyunsaturated fatty acid, having a length of 20 carbon atoms

What’re oxylipins derived from?

• Arachidonic acid, or other unsaturated fatty acids

What’re the roles of oxylipins?

• Not generally stored, but synthesized as needed, main function is communication within cells and between cells

  • Inflammation, pain, platelet aggregation

  • Includes prostaglandins and leukotrienes

What’re some general features of proteins?

• Some amino acids are acidic, basic, polar, non-polar

• Proteins are macromolecules

• Linear chains of amino acids

How many amino acids are essential and non-essential?

• 9 are essential: need to consume them

• 11 are non-essential: we can synthesize them

Whats a short chain of AA called?

• A peptide

Whats a long chain of AA called?

• Proteins

What’re the different categories of proteins?

• Primary structure

• Secondary structure

• Tertiary structure

• Quaternary structure

What determines the complex structures of proteins?

• The amino acids that make them up

What do all amino acids have?

• They all have a carboxyl group (COOH), an amino group (NH2), and a hydrogen attached to the same carbon. The fourth bond of the carbon attaches to a variable R group

Whats primary structure of protein?

• Sequence of amino acids

Whats secondary protein structure?

• alpha helix and beta pleated sheets

• Determined by pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone

Whats tertiary structure?

• Overall 3D arrangement of the polypeptide chain in space: determined by side chain interactions and secondary structures

Whats quaternary structure?

• How multiple proteins interact with each other

• Fibrous proteins: Collagen

• Globular proteins: Hemoglobin

How many proteins does the genome encode for?

• 33,000 proteins

In a mammalian cell, how many proteins are expressed?

• 10,000 to 15,000

Whats the difference between fibrous vs globular proteins?

• Fibrous proteins are generally insoluble

• Globular are usually soluble

  • 7 categories of soluble protein

What’re the 7 categories of soluble protein?

1. Enzymes

2. Membrane transporters

3. Signal molecules (ligand)

4. Membrane receptors

5. Binding proteins

6. Regulatory proteins

7. Immunoglobulins

What must a protein do to do something?

• It must interact with or bind to other proteins, molecules or ions

  • At a binding site

How vague or specific is protein binding?

• Very specific: binds to a specific molecule in a specific way

Whats a ligand?

• A molecule that binds to a protein binding site is called a ligand

Whats an endogenous ligand?

• Something natural in your body: for example a hormone or neurotransmitter (Ex: insulin)

Whats a non-endogenous ligand?

• May be a drug or toxin for example (Ex: snake venom)

Whats the difference between weak and strong affinity?

• High affinity means it binds strongly

• Weak affinity means weak binding

What’s an agonist?

• A ligand that binds to a protein binding site and alters the state of the protein, resulting in a biological response (Ex: insulin)

• A hormone or neurotransmitter or a drug activating a receptor for example

• Causes a response/ activator

Whats an antagonist?

• A ligand that reduces the action of an agonist (ie: binds but causes no biological response)

• Also called inhibitors, blockers

Whats the 2 ways agonists and antagonists may be?

• Competitive

• Allosteric

What happens when agonists and antagonists are competitive?

• Act to block an agonist at its normal binding site

• Competes to bind at same binding site

What happens when agonists and antagonists are allosteric?

• Act to block a competitive agonist by binding to the the protein away from the binding site and inactivate the binding site

What can the rate of proteins/ activity be modulated by?

1. Cofactors

2. Physical factors

   • ph, temperature

3. Modulation

What occurs in covalent modification in modulation?

What are phosphorylation and dephosphorylation?

• Processes that modulate rates of protein binding and activity

• Turns “up” or “down” rate of activity

Whats the protein responsible that catalyzes the phosphorylation of casein and became known as protein kinase?

• Liver enzyme

How many proteins in a typical mammalian cell are covalently bound to phosphate?

• 1/3 of the proteins

Where is the phosphate added in phosphorylation?

• On one of the amino acid side chains chains of a protein.

Is phosphorylation reversible?

• Yes, by dephosphorylation

What’re the most common targets of phosphate?

• Hydroxyl groups of serine, threonine, tyrosine or histidine amino acid side chains

What’re some advantages of the use of phosphorylation/ dephosphorylation as a control mechanism?

• It is rapid, taking as little as a few seconds

• It doesnt require new proteins to be made or degraded

• It is easily reversible

Can external signals activate protein kinases and phosphotases?

• Yes

In animal cells what’re phosphorylation cascades mediated by?

• 2 types of kinases

  • Serine/ threonine kinases

Whats the second outcome in response to phosphorylation of a signal?