Lecture 2+3 (BIO-2210)

Chemistry of the cell

• carbon is most important

• they are all made from organic molecules

• 75-85% are water

• they are normally in an aqueous environment

critical attribute of waters polarity

1. cohesiveness

2. temperature-stabilizing capacity

3. solvent properties

Cohesiveness in water

• water molecules are attracted to each other

• they create hydrogen bonds which are 1/10 are strong are covalent bonds

• hydrogen bonds make it cohesive

heat energy in water

• High heat breaks hydrogen bonds in water

• Water has to change temperature slowly to protect living systems from extreme temperature changes

• if not cells would overheat and die

solvent

a fluid in which another substance, the solute can be dissolved (water can dissolve all but non-polar, not charged molecules)

hydrophilic

solutes that dissolve easily in water

hydrophobic

molecules that are not easily soluble in water, this determine chemical structure and interactions in biological molecules

water in nature

barely ever found pure as it dissolves so many molecules

what can break hydrophobic effect

Honey

extracellular

outside of the cell

intracellular

the inside of the cell

membrane

the barrier seperating the inside and outside of the cells (bilayer)

phospholipid head

It is charged which makes it hydrophilic

buliding blocks of cells

polymers and macromolecules

important macromolecules

proteins, nucleic acids, and polysaccharides (lipids share features)

Steps to make polymers

1. activate monomer (requires ATP)

2. condensation of activated monomers (releases C and Water)

3. polymerization (add another polymer)

DNA

shares and transmits biological information.

• deoxyribonucleic acid

RNA

chemically similar to DNA, but used to express genetic information

• ribonucleic acid

Nucleoside

the base pair alone (Ex. Adenosine)

Nucleotide

have a 5C sugar, phosphate group, and a base

deoxynucleotide

only in DNA, where the ribose sugar lack a oxygen

phosphodiester bonds

the bonds that hold together adjacent nucleotides

Nucliec Acid Sythesis

takes a pre-existing template and energy

• DNA triphosphates (dNTP)

• RNA triphosphates ex.ATP (NTP)

DNA Structure

• forms a double-stranded helix

• one with base-pairs, the other complementry

• anti-parallel

RNA base pairing

• RNA is normally single-stranded

• RNA is usually between bases in different areas in the DNA (introns), and less extensive then DNA replication

What orientation of animo acids are used in proteins

L orientation

what makes the amino acid unique

the R-group, it decides certain properties of the amino acid

polypeptide

the product of amino acids polymerization

when in a polypeptide considered a protein?

when it is completely folded and biologically activated

how many hydrophobic amino acids are there

9

how many amino acids are hydrophilic

11,

• 6 are polar and charged

• 5 are charged

acidic R groups

negatively charged R-group

basic R group

postitivily charged R-Group

How are amino acids linked

they are linked by peptide bonds

What part of the amino acid starts the protein

the N-terminus

what part of the amino acid end the protein

the C-terminus

Covalent bonds (disulpher bridges)

• very stable

• formed between sulpher and cytosine residue

• intra- or inter-molecular

Non-Covalent bonds

• individually weak, but strength in numbers

• hydrogen bonds

• ionic bonds

• van der waal interactions

• hydrophobic interactions

Secondary structure

• determined by primary structure

• from an NH and a CO bonding along the backbone

• two major patterns that result from localized folding in a segment

Alpha Helix

• about 10-20 amino acids long

• they have a spiral shape

• R-groups hang outside

• some amino acids help the formation and others disrupt it

The beta sheet

• sheet-like formation from multiple polypeptide strands

• extensive hydrogen bonding in backbone

• R-groups hang out on alternating sides of the sheet

• classifies based on relative directionality

  • parallel or anti-parallel

Tertiary Structure

• depends on R-group interactions

• the sum of

1. hydrophobic residue

2. hydrophilic residue

3. charge repulsion

4. charge attraction

Quaternary Structure

• concerned with subunit and assembly

• only in multimeric proteins

• some have indentical subunits, some do not

Multimeric Protein

made from two or more polypeptide chains