Chapter 5 Campbell biology hunter college, bio 100

Macromolecules/Polymers

Large molecules build up from smaller units (monomers)

-Created through polymerisation

Macromolecules can generate polymers

-carbs proteins nuclei acids

Built by dehydration reaction/synthesis

Break down from hydrolysis

dehydration reaction/synthesizing a polymer

removes a water molecule, forming a new bond

Makes covalent bond in place

Removal of hydroxyl group and hydrogen atom

Can form glycosidic linkage on monosaccharides

hydrolysis reaction

Used to generate monomers or small components of polymers

Adds water to break a bond

Carbohydrates

Sugars, polymers of sugars, contain carbon hydrogen and oxygen, 1:2:1

Simplest: monosaccharides/simple sugars (glucose)

C-H ideal for energy storage -> released during oxidation

Classified by carbonyl group

Glucose has 2 forms

Alpha and beta, based on placement of hydroxyl group

Can digest alpha and not beta

Pass through as insoluble fibers and cannot absorb nutrients through degradation

Lipids aren't polymers or macromolecules

Large biological molecules

Nonpolar, insoluble in water, primarily hydrocarbons

Fats, phospholipids, chlorophyll, steroids

Fats help with connection in nerves, speed up process of sending signal

Monosaccharides can be building blocks for larger structures

Ex. Disaccharide, (oligosaccharides(more than two less than many))

glycosidic linkage

A covalent bond formed between two monosaccharides by a dehydration reaction.

Polysaccharides

Polymers of monosaccharides

Linked through dehydration reactions, and covalent bond from glycosidic linkage

-Monomeric subunit can have multiple sites where glycosidic linkage can take place

Plastids

Storage structures containing starch granules

Starch can react with water -> hydrolysis and release of energy the plant can use

Cellulose

Polymer of glucose

Glycosidic linkage is beta -> generates parallel branching

Suitable structural material

Rods aggregate laterally, which make microfibrils

High level of rigidity, structural integrity

generate Fats (lipids), triacylglycerol

Glycerol (3 carbon alcohol) and a fatty acid(carboxyl group (polar)- long carbon skeleton) non polar

Used in energy storage, used in adipose cells, cushion organs, insulate body

Esterbond/linkage

Dehydration synthesis, forms covalent bond. Connects glycerol and fatty acid

saturated fats

have the maximum number of hydrogen atoms possible and no double bonds

Lack of double bonds, tightly packed, solid at room temp.

unsaturated fats

One or more double bond, kink or bend in fatty acid tail, Cis double bond causes bending

Can't pack closely together, liquid at room temp.

Trans fats

An unsaturated fat, formed artificially during hydrogenation of oils, containing one or more trans double bonds.

Can pack even tighter than saturated fats, can cause problems with health

Phospholipids

a lipid consisting of a glycerol bound to two fatty acids and a phosphate group.

Hydrophilic head (glycerol,phosphate group and ex. Choline ) polar

Hydrophobic tail (2 fatty acid tail, hydrocarbons of similar electronegativity) non polar

Spontaneously assemble into a bilayer

Steroids are lipids

4 ringed hydrocarbon

Polar hydroxyl group (sterol)

Enzymes

Catalysts for chemical reactions in living things

defensive proteins

protection against disease

storage proteins

storage of amino acids

transport proteins

transport of substances

Horomones

Coordinate organismal responses

receptor proteins

receive signals from outside cell

motor proteins

function in cell movement

structural proteins

provide structural support

Amino acid monomers

Amino group, carboxyl group, alpha carbon, hydrogen (backbone at normal pH, both carboxyl and amino group will be ionized)

and side chain (R group) -dictates amino acid properties

Non polar amino acids

hydrophobic

Hydrocarbons

Cluster together in the interior

Hide from surrounding polar environment

Proteins apart of phospholipid bilayer will have a significant amount of non polar, hydrophobic amino acids

Polar side chains

hydrophilic

electrically charged side chains

hydrophilic

Have charge when pH is normal

Acidic, negatively charged, donate a hydrogen ion to environment

Basic, positively charged, accept hydrogen ion from environment

Protein or polypeptide synthesis

Taking present amino acids and joining them together

Unbranched and linear

Condensation reaction ( removal of hydroxyl group, removal of hydrogen, generation of water ) resulting covalent bond is a peptide bond

Directionality of polypeptide synthesis

Is from N' terminus to C' terminus

A new amino acid will connect to the carboxyl group of the other with its amino group

Proteins are monomeric

Talks about the parts of protein, some have one polypeptide bond and others have more

primary protein structure

sequence of amino acids

Focusing on specific order of which they appear from N terminus to C terminus

secondary structure

consists of coils and folds in the polypeptide chain coming from hydrogen bonding

Depends on the amino acids there, dictates whether or not there's beta pleaded sheets or alpha helix

Coils alpha helix

intramolecular bonding, bonding within the same polypeptide

-spiral shape

-organization assist with the formation of hydrogen bonds between amino groups of an adjacent peptide with carboxyl group of another

beta pleated sheet

polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.

Intra and intermolecular bonding, beta pleated sheets between more than one polypeptide

tertiary structure

The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.

Hydrogen bonds in tertiary structure of a protein

Far apart from each other to interact through polypeptide folding

Ionic bonds in tertiary structure of a protein

R groups with charges

Repel groups with same charge and attract with different charge

Must both be in a charged state, hydrophilic and charged category

One acidic and the other basic

Must remain in a charged state in order to uphold the opposites attract theory

PH can mess with this

Hydrophobic interactions

Will fold in order to minimize contact with the hydrophilic environment and maximize with hydrophobic ones

If most a=amino acids are hydrophobic then the protein is most likely insoluble

Exist in non polar environments

Van der waals interactions

Based in temporary changes in attraction

Depends on close proximity

Dipole

Asymmetric distribution of electrons that lead to separation if charge within a molecule

disulfide bridges

Depends on sulfhydryl functional groups

Seen on cystine

Contribute to stability of structure through a covalent bond

Intramolecular disulfide bond

Can be intermolecular if done on another peptide

quaternary structure

Results from two or more polypeptide chains form one macromolecule

Denaturation

loss of normal shape of a protein due to heat or other factor

In denatured state, linear structure is intact

But don't have any of the higher level structures that give function

renaturation

Regaining the correct tertiary structure after denaturation of a protein

Sickle cell alters primary structure of protein

In tern affects the beta subunit in tetramer, which affects secondary tertiary and quaternary structure hemoglobin making red blood cell which in tern gives it its sickle shape

Nuclei acids

Have a role in storing genetic information, transmitting and expressing

Genes are specifically DNA, linear subunits, linear polymer of genetic information that influences cell behavior

Gene is DNA

Nucleic acid can be DNA or RNA

Nucleic acid to polypeptide

Harness the information in DNA to create a special rna called mRNA

MRNA leaves nucleus into the cytoplasm

Synthesis of protein

Nucleic acids will contain non identical monomeric subunits

Specific sequence

Monomeric subunit is called a nucleotide

Nucleotide

3 components, nitrogenous base, Pentose(5 carbon sugar), phosphate group

4 different varieties of nucleotide monomer

Building, linked by a phosphodiester linkage, allows polynucleotide to exist

phosphodiester linkage

covalent bonds that join adjacent nucleotides between the -OH group of the 3' carbon of one nucleotide and the phosphate on the 5' carbon of the next

Link 2 sugars of nucleotide

Sugar and phosphate make up backbone

Nucleoside

nitrogenous base + sugar

Nitrogenous base

purines and pyrimidines

Pyrimidines

6 member ring structure

C T (DNA) U (RNA)

Purines

2 fused ring structure, 6 membered and 5 membered

A and G

Pure as gold

Sugars in DNA and RNA

DNA: deoxyribose H at 2'

RNA: ribose hydroxyl group at 2'

ATP is a nucleotide

Composed of nitrogenous base A

Ribose sugar

3 phosphate groups

phosphoanhydride bond

linkages between phosphate groups

Much more energy in this bond compared to a phosphoester bond

phosphoester bond

linkage between the 5' sugar hydroxyl and a phosphate group

Sugar and a phosphate group on ATP and other nucleotides

Directionality of nucleotides, phosphoester bridges in backbone

Phosphoester bridge made from phosphoester bonds is connected in the 5' end to the 3' end

Phosphate group interacting with the 5' carbon nucleotide at the 3' carbon nucleotide

Dniester bride, 2 ester bridge

Has polarity

Complimentary base pairing