02 - Cell Chemistry and Macromolecules

Unity of Biochemistry

Organisms are quite uniform at the molecular level

Jacques Monod (1954) – Anything found to be true in E.Coli must also be true in Elephants.

Atoms

Basic Unit of Matter

Protons and neutrons in “nucleus”, electrons in outer “shells”.

what determines chemical properties of atom

Number of outer shell electrons determine chemical properties.

__ elements make up ~99% of atoms in a human.

4

C,H,N,O

__ elements make up 0.9%

7,

na, mg, k, ca, p, s, cl

Molecules

2 or more atoms in a definite arrangement held together by chemical bonds

biomolecules

Molecules made by living organism

structure of biomolecules

centred around Carbon

• Carbon binds up to 4 other atoms

• Size and electronic structure is suited to generate large biological molecules

Covalent Bonds

Carbon (C), Hydrogen (H), Nitrogen (N) and Oxygen (O) can be linked together by covalent bonds to form molecules.

Can share electrons to creating stable bond

Atoms are most stable when

their outermost electron shells are full

Polar Covalent Bonds

• Unequal sharing of electrons

• Asymmetric charge distribution

• Electronegative atom

Asymmetric charge distribution

One atom has a partial negative charge and the other atom has a partial positive charge

Electronegative atom

atom with the greater attractive force is called the electronegative atom

Non-polar Covalent Bonds

Equal sharing of electrons

• lack electronegative atoms

Non-Covalent Interactions

Interactions between molecules or different parts of a large biomolecule

Depend on shared attractive forces between atoms of opposite charge

Types of noncovalent interactions important in cells:

• Ionic bonds

• Hydrogen bonds

• Van der waals attractions

• Hydrophobic interactions

Ionic bond

result of electrical attraction because of opposing charges. Involves transfer of electron(s) from one atom to the other.

eg of ionic bond in the cell

e.g. holds macromolecules together (DNA & protein) between positively charged nitrogen (protein) and negatively charged oxygen (DNA)

Hydrogen Bonds

weak bond, result of electrical attraction.

Keeps important biomolecular structures like DNA together

Polar molecules interact with other polar molecules, like water

Van der Waals Forces

weak and nonspecific interaction between two atoms in close proximity.

Temporary charges in nonpolar molecules = ‘dipoles’

Form because electrons are constantly in motion

Hydrophobic Interactions

uncharged non-polar molecules do not interact with polar molecules (e.g. water)

Form clumps or aggregates to minimize exposure

Not an actual bond

What term refers to a noncovalent bond in which an electropositive hydrogen atom is partially shared by two electronegative atoms?

A) Hydrogen bond

B) van der Waals attraction

C) Ionic bond

D) Hydrophobic interaction

a

Biomolecules structure

Biomolecules centred around Carbon - Carbon binds up to 4 other atoms

Simplest group of biological molecules

hydrocarbons (C-H)

Hydrogen is often replaced by

Functional Groups

Functional Groups

particular atom groupings that behave as a unit

what do functional groups affect

Affect the properties of biomolecules (e.g. change chemical reactivity) because:

• Contain electronegative atoms (N,O,P,S)

• Can make molecules more polar or more reactive

• May confer a positive or negative charge due to ionization

methyl

hydroxyl

carboxyl

amino

phosphate

carbonyl

sulfhydryl

Macromolecules

polymers of building blocks known as monomers

Polymers form by joining monomers =

condensation (water is removed)

Polymers are broken down into monomers

hydrolysis (water is added)

Monomers of macromolecules are joined together by

covalent bonds.

examples of macromolecules

polysarcarides, fats, proteins, nucleic acid

Carbohydrates - general formula

(CH2O)n

• Important sugars in cell metabolism have

3-7 carbons

3 sugars = trioses; 4 sugars = tetroses; 5 sugars = pentoses; 6 sugars = hexoses

Carbonyl internal position –

forms ketone = ketose

Carbonyl at one end –

forms aldehyde = aldose

Sugars with 5 or more carbons form

a closed ring structure.

monosaccharide

is the simplest type of carbohydrate—a single sugar molecule.

why are some sugar molecules form a ring structure

Glucose

= 6-membered ring

α-glucose

OH of C1 projects below the plane of the ring

β-glucose

OH of C1 projects up from the plane of the ring

isomers

are small differences in structure that imp

Linking monosaccharides

• Covalent bond formed between C1 of one sugar and hydroxyl (OH) of another sugar

• Generates C-O-C linkage between sugars

• Alpha(1,4) linkage

Disaccharides

2 monosaccharides covalently bonded together

• energy storage, ex. Sucrose, maltose, lactose

Oligosaccharides:

a small chain of sugars

• if attached to lipids or proteins = glycolipids or glycoproteins

Polysaccharides:

a long chain of sugars

• very large molecules with a structural or storage function, ex: Chitin, cellulose, starch, glycogen

All carbohydrates have the following:

A. Ketone group.

B. Aldehyde group.

C. Hydroxyl group.

D. All of the above.

c

Lipids

A large group of nonpolar biological molecules

• Composed mainly of C,H and O

• Dissolve in organic solvents but not in water (lack polar groups)

Lipids with important cell functions:

• Fats

• Steroids

• Phospholipids

Fats

triacylglycerol

glycerol + 3 fatty acids

Fatty acids

long hydrocarbon chains with a single carboxyl at one end

they vary in length

saturated fatty acids

No double bonds

unsaturated Fatty acids

Double bonds

Linking Fatty Acids

Ester bonding links fatty acids to glycerol

Steroids

Complex ring structures = 4 hydrocarbon rings

example of Steroids

Cholesterol = important animal plasma membrane component

estrogen

testosterone

Cholesterol are the Building blocks of

many steroid hormones

is cholesterol in plant cells

• Not present in plant cells, “cholesterol-free”

Phospholipids

Composed of glycerol + 2 fatty acids + phosphate group

Major component of plasma and organelle membranes

Hydrophilic end on Phospholipid

phosphate head

hydrophobic end on Phospholipid

fatty acid tail

amphipathic

Hydrophilic on one end and hydrophobic on the other

phosphatidyl choline

Positively charged choline group attached to the phosphate

what do phospholipids form

Lipid bilayers are formed by phospholipids.

Lipid Bilayers Form Cell Membranes

Polymers of nucleotides

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

Nucleotides

5-carbon sugar + nitrogenous base + phosphate

dna vs rna sugar

DNA has deoxyribose sugar, RNA has ribose sugar

Linking Nucleotides

Nucleotides are joined by sugar-phosphate linkages

• 3’ hydroxyl attached to 5’phosphate of the adjoining nucleotide

• Phosphodiester bond

bases are paired with which type of bond

hydrogen

purine

2 rings

a, g

pyramidines

1 ring

t, c

Which statement is true?

A. Thymine is only found in RNA.

B. In RNA, the pentose is ribose.

C. Uracil is only found in DNA

D. Adenine and Guanine form a complementary base pair

b

functions of a nucleotide

As nucleoside di- and triphosphates, they carry chemical energy in their easily hydrolyzed phosphoanhydride bonds

They combine with other groups to form coenzymes.

They are used as small intracellular signaling molecules in the cell.

function of protein

Carry out almost all cellular functions. Examples:

• Enzymes - accelerate chemical reactions in the cell

• Signaling - kinases, phosphatases are involved

• Hormones - long range messenger molecules

• Growth factors

• Membrane receptors - communication between cells

• Cell movement - cytoskeleton

what are amino acids composed of

Composed of H, C, O, N and also S or P

how many types of amino acids are there

20

structure of a amino acid

• Amino (NH2) and Carboxyl (COOH) groups

• -These groups are separated by a single carbon (α-carbon)

• R groups (side chains) give amino acids their variability

4 categories of R groups:

• Polar charged

• Polar uncharged

• Nonpolar

• Other

Polar charged

form ionic bonds

Polar uncharged

form H bonds

Nonpolar

hydrophobic interactions

Other

e.g. sulfhydrl or cysteine

Cysteine amino acids

can form disulfide bonds in oxidizing conditions.

Peptide bonds

Carboxyl group of one amino acid becomes attached to the amino group of another

polypeptide chains

proteins

How many water molecules would be produced in making a

polypeptide that is 14 amino acids long?

A. 13

B. 14

C. 27

D. 28

a

how can macromolecules assemble in complexes

is reversing disorder spontaneous or not

not spontaneous

Second law of thermodynamics

cannot reverse the state of a system without increasing entropy of surroundings

Need release of heat (energy conversion)

Catabolic

lose heat

breakdown

Anabolic

build up