Biology Chapter 3 - Macromolecules

The Big Six - the most common elements in biological molecules are

Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, and Sulfur

Bonds and Molecules

Molecule - a chemical substance that results from the combination of two or more atoms

Compounds - molecules that are combinations of

two or more different elements

3 Types of Chemical Bonds

Covalent Bonds - strongest; two atoms share one or more pairs of valence electrons to become stable Non - polar is equal sharing Polar is unequal sharing of electrons

Ionic Bonds - electrons are transferred to one atom, forming positively charged atoms cations and negatively charged anions

Hydrogen Bonds - Electrostatic attraction between H, N or O

Hydrogen Bonds

weak bonds between H and other atoms; strength is additive

Solutions

Solution - A mixture of one or more substances called solutes, dispersed in a dissolving medium called a solvent

Aqueous Solutions

Hydrophilic Molecules - dissolve in water

Hydrophobic molecules - repeal water

Amphipathic molecules - have both hydrophilic and hydrophobic properties

Why Water is so special

Liquid at most earth temperatures, resists temperature changes ( it takes a lot of energy to heat water)

superb solvent (carry nutrients to cells and wastes away)

Sticks Together ( high cohesion water molecules sticks to water molecules - adhesion - water sticking to other things, and tension due to hydrogen bonds)

water is a buffer (resists changes in pH)

Ice floats so whole lakes won’t freeze and kill everything in the winter

cells use water as part of their cytoplasm

Acidity, Alkalinity, and the pH Scale

Self - Ionization of H2O releases H ions and hydroxyl ions, pH scale ranges from 0 to 14, expresses the concentration of H ions, is important to the cell because if its too acidic then the cell will be destroyed

Organic Compounds

compounds containing C bonded to H’s, inorganic compounds lack C and H like CO2, carbon in the fundamental element of life

Organic Compounds matter because…..

plants and trees combine water and carbon dioxide into sugars and other carbon based compounds through photosynthesis, which they all depend on. Carbon compounds form structures living organisms, take part in all biological reactions, and serve as energy sources living organisms and industry

Organic Molecule - Four major classes of organic molecules are found in living organisms:

Carbohydrates, Lipids, proteins, and nucleic acids. In organic molecules, carbon atoms bond covalently to each other and to other atoms in molecules that range in size from a few atoms to thousands or millions of atoms.

Hydrocarbons

Molecules consisting of carbon linked only to hydrogen atoms are called hydrocarbons

Carbon has four unpaired outer electrons, Simplest Hydrocarbon is

CH4 methane

Complex Hydrocarbons involve…

two or more carbon atoms arranged in a linear unbranched chain, a linear branched chain, or a structure with one or more rings. Single and double bonds are found in linear and ring hydrocarbons; triple bonds only in two-carbon hydrocarbon

Chemical Evolutions

this resulted in first forms of life on Earth after formations of organic molecules, resulted from reactions involving inorganic molecules on primordial earth and conditions on the planet at that time

Functional Groups

Small reactive groups of atoms which give larger molecules specific chemical properties. Most frequent in biological reactions are hydroxyl, carbonyl, carboxyl, amino, phosphate and sulfhydryl.

Functional groups are linked by…..

covalent bonds to other atoms in biological molecules, usually carbon atoms represented in the collective symbol R

Hydroxyl

(-OH)

Major class - Alcohols

Ex. Ethyl Alcohol

Polar, Hydrogen bonds with water; dissolves organic molecules. Alcohol can form linkages with other organic molecules through dehydration synthesis

Carbonyl

C=O

Major Classes - Aldehydes, Ketones

Ex. Acetone

Major building blocks of carbohydrates and participate in reactions supplying energy for cellular activities

Carboxyl

(-COOH)

Major classes - Carboxylic Acids

Ex. Acetic Acid

Gives organic molecules acidic properties because -OH releases the hydrogen as a proton (H+) in aqueous solutions, turning it from a non-Ionized to an ionized form

Amino

(-NH2)

Major Class - Amines

Ex. Alanine

Acts as an organic base by accepting a proton in aqueous solutions, turning it from a non-Ionized to an ionized form

Phosphate

(-OPO2-3)

Major Classes - Organic Phosphates

Ex. Glyceraldehyde 3-phosphate

React as weak acids because one or both OOH groups release their hydrogens as H+ in aqueous solutions, turning it from a non-Ionized to an ionized form

Can bridge two organic building blocks to form a larger structure. Added or removed from biological molecules as part of reactions that conserve or release energy ro to alter protein activity

Sulfhydryl

(-SH)

Major Class - Thiols

Ex. Mercaptoethanol

easily converted into a covalent linkage, in which it loses its hydrogen atoms as it binds

Isomers

Carbons that are linked to four different atoms or functional groups are asymmetric, Can take either of two fixed positions with respect to other carbons in a chain, The two forms (isomers) have the same chemical formula, but have different molecular structures

Stereoisomers

Isomers that are mirror images of each other, Typically only one of the two forms (L-form or D-form) can enter into a reaction

Structural Isomers

two molecules with the same chemical formula but atoms are arranged in different ways

Adding and Removing Water

In many reactions involving functional groups, the components of a water molecule (—H and —OH) are removed from or added to the groups as they interact

Water removed

reaction is called dehydration synthesis, or a condensation reaction

Dehydration - removes the components of a water molecule as new covalent bonds join subunits into a larger molecule

Adding Water

Hydrolysis - add the components of a water molecule as covalent bonds are broken, splitting a molecule into smaller subunits

Macromolecules

large compounds assembled from smaller subunits

monomer: a repeating subunit

polymer: a chain of monomers

Main: Carbohydrates, lipids, proteins, nucleic acids

Polymers

carbohydrates, lipids, proteins and nucleic acids are larger polymers assembled from subunit molecules (monomers) into a chain by covalent bonds

Polymers are assembled from

monomers (polymerization) by dehydration synthesis reactions, the breakdown of polymers into monomers occurs by hydrolysis

Macromolecules - each type of polymeric biological molecule contains….

one type of monomer, individual monomers may be identical or may have chemical variations depending on the molecule

A single polymer with a mass of ——— or more is called a ———

1,000 Daltons, macromolecule

Includes many carbs, proteins, and nucleic acids, lipids are not large enough to be classed as macromolecules

Carbohydrates Functions

Energy Providing: Plants - they are starch Animals - glucose

Structural: cellulose, a primary components in plants cell wall

Cell structure, adhesion, and metabolism

Carbohydrates contain

Only carbon, hydrogen, and oxygen atoms in a ratio of about 1C:2H:1O

Monosaccharides contain three to seven carbons, two monosaccharides polymerize to form a disaccharide. Carbohydrate polymers with more than 5-10 or more lined monosaccharide monomers are polysaccharides

Saccharide, Monosaccharide, Disaccharide, Polysaccharide

simple carbohydrate, 3-7 carbons, two monosaccharide, five or more monosaccharides

Monosaccharides

Carbohydrates occur either as monosaccharides or as polymers of monosaccharide units

Monosaccharides (such as glucose, C6H12O6) are soluble in water and sweet-tasting

The most common monosaccharides contain three carbons (trioses), five carbons (pentoses), or six carbons (hexoses)

All monosaccharides can occur in linear form

Sugar and Polysaccharides general formula

(CH2O)n

Ring Forms

Monosaccharides with five or more carbons (such as glucose) can fold back on themselves through a reaction between two functional groups to assume a ring form

Glucose exists as two different enantiomers

α-glucose, with an —OH group pointing below the plane of the ring

β-glucose, with an —OH group pointing above the plane

Disaccharides

Disaccharides are assembled from two monosaccharides covalently joined by a dehydration synthesis reaction

Common disaccharides: sucrose (glucose + fructose) galactose (glucose + galactose)

Polysaccharides

The most common polysaccharides (plant starches, glycogen, and cellulose) are polymers of hundreds or thousands of glucose units

Chitin is assembled from glucose units modified by the addition of nitrogen-containing groups

Polysaccharides may be linear, unbranched molecules, or they may contain one or more branches in which side chains of sugar units are attached to a main chain

Carbohydrate subunits are linked by

glycosidic bonds

Dehydration synthesis: loss of water in a polymerization reaction

Hydrolysis: Cleavage of the glycosidic bond by the addition of water

Lipids

water-insoluble, primarily nonpolar biological molecules composed mostly of hydrocarbons

Three common types of lipid molecules:

• Neutral lipids are stored and used as an energy source

• Phospholipids form cell membranes

• Steroids serve as hormones that regulate cellular activities

Neutral Lipids

energy storage molecules have no charged groups (nonpolar)

Two types: Oils ( liquid at a biological temperature) Fats (are semisolid)

A fatty acid contains a single hydrocarbon chain with a carboxyl group at one end

Glycerol and Triglyceride Formation

Triglycerides form by dehydration synthesis between three carbon glycerol (an alcohol) and three fatty acid side chains

A covalent bond (ester linkage) forms between the -COOH group of the fatty acid and the -OH group of the glycerol

The polar groups of glycerol are eliminated, forming a nonpolar triglyceride

The most common fatty acids have

chains of 14 to 22 carbons - As chain length increases, fatty acids become less water-soluble and more oily

A saturated fatty acid binds

the maximum number of hydrogen atoms

only a single bond exist between carbon atoms

Fatty acids with one double bond are monounsaturated those with more than one double bond are polyunsaturated

Saturated fatty acids are found in solid animal fats such as

butter

Unsaturated fatty acids

(such as vegetable oil) bend at a double bond and are more fluid at biological temperatures

Unsaturated fats are considered healthier than saturated fats in the human diet

Plant oils are converted commercially to saturated fats by hydrogenation

Functions of Triglycerides ( triglycerides are the most common lipid found in the bloodstream)

Energy reserves in animals

Store more than twice the calories per gram as carbohydrates

A layer of fatty tissue just under the skin acts as insulation in mammals and birds

Triglycerides also help make bird feathers waterproof

Can be saturated or unsaturated

Waxes

Fatty acids combine with long-chain alcohols or hydrocarbon structures to form waxes, which are harder and less greasy than fats

Waxy coatings help animals keep skin, hair, or feathers protected, lubricated, and pliable

Plants secrete waxes that form a protective exterior layer, which reduces water loss and resists infective agents

Phospholipids

Phosphate-containing phospholipids are the primary lipids of cell membranes

The most common phospholipid has a glycerol backbone linked to two fatty acid chains and a polar phosphate group, which is linked to another polar group

The end of the molecule containing the fatty acids is nonpolar and hydrophobic, and the end with the phosphate group is polar and hydrophilic

Phospholipid Bilayer

a film of phospholipids two molecules thick – is the structural basis of membranes

In a bilayer, the polar groups face the surrounding water molecules at the surfaces of the bilayer – the hydrocarbon chains form a nonpolar, hydrophobic region in the interior

Steroid

Steroids are lipids with structures based on a framework of four carbon rings

Sterols, the most common steroids, have a single polar OH group linked to one end of the ring framework and a complex, nonpolar hydrocarbon chain at the other end

Cholesterol is an important component of animal cell membranes

Similar sterols (phytosterols) occur in plant cell membranes

Steroid Hormones

Steroid hormones control development, behavior, and many internal biochemical processes

Examples: The sex hormones that control differentiation of the sexes and sexual behavior

Estradiol (female sex hormone) has an —OH in the position where testosterone (male sex hormone) has an =O, and testosterone has a methyl group (—CH3) that is absent from estradiol

Other Lipids

Several other lipid types have structures unrelated to triglycerides, phospholipids, or steroids

Chlorophylls and carotenoids are pigments that absorb light and help convert it to chemical energy in plants

Lipid groups combine with carbohydrates to form glycolipids, and with proteins to form lipoproteins, which have important structural and functional roles in cell membranes

Proteins

Predominant molecules in cells

Essential to cell structure and function: structural support; enzymes; movement; transport; recognition and receptor molecules; regulation of proteins and DNA; hormones; antibodies; toxins and venoms

Cell type varies based on the type of proteins they can produce

Monomer – amino acids – 20 encoded by codons

Polymer – peptide, polypeptide, protein

Amino Acids

All organisms use 20 different amino acids to build proteins

Most have the same structural plan: a central carbon atom is attached to an amino group, a carboxyl group, a hydrogen atom, and a variable R group

R group can be polar ( hydrophillic), non-polar (hydrophobic; cystine has sulfur and Methionine has sulfur), or electrically charged

The monomers that make up a protein polymer

Proline Amino Acid

differs slightly in that it has a ring structure that includes the central carbon atom – the central carbon bonds to a —COOH group on one side and to an =NH (imino) group at the other side

All amino acids can act as

acids or bases

The amino acid group can produce a basic reaction by accepting H+, or the carboxyl group can produce an acidic reaction by releasing H+

Some chemical groups are

polar and some are nonpolar

Among the polar chemical groups, some carry a positive or negative charge and some act as acids or bases

Many chemical groups contain reactive functional groups such as

—NH2, —OH, —COOH, or —SH, which interact with other atoms in the same protein or outside the protein

Sulfhydryl groups (in cysteines) can produce disulfide linkages (—S—S—) that help hold proteins in their 3-D shape

Peptide Bonds

Covalent peptide bonds link amino acids into polypeptide chains - the subunits of proteins

A peptide bond is formed by a dehydration synthesis reaction between the -NH2 group of one amino acid and the -COOH group of another amino acid

The growing polypeptide chain has an N-terminal end and a C-terminal end

New amino acids are linked only to the C-terminal end

Amino Acids are attached through

peptide bonds to form proteins

Four Levels of Protein Structure

Primary structure is the unique sequence of amino acids forming a polypeptide

Secondary structure is produced by the twists and turns of the amino acid chain

Tertiary structure is the folding of the amino acid chain, with its secondary structures, into the overall 3-D shape of a protein, where a lot of proteins stop

Quaternary structure, when present, is formed from more than one polypeptide chain, multiple proteins to make something

Structure =

Function

Primary Structure of a protein is the

precise sequence in which amino acids are linked

Changing even a single amino acid alters secondary, tertiary, and quaternary structures, which can alter or destroy the biological function of a protein

Secondary Structure

The amino acid chain (primary structure) is folded into arrangements that form the protein’s secondary structure

The alpha (α) helix is twisted into a regular right-hand spiral

The beta (β) strand zigzags in a flat plane, forming a sheet

Most proteins have segments of both arrangements

An α Helix

Amino acid chemical groups extend outward from the twisted backbone

Stabilized by regularly spaced hydrogen bonds

Forms rigid, rod-like structures

A β Sheet

The amino acid chain zigzags in a flat plane

β strands are aligned side by side in the same or opposite directions

Hydrogen bonds stabilize the sheet

The Random Coil

A random coil has an irregularly folded arrangement

Segments of random coil provide flexible sites that allow α helical or β-strand segments to bend or fold back on themselves

Segments of random coil act as “hinges” that allow major parts of proteins to move with respect to one another

Tertiary Structure

Tertiary structure gives a protein its overall three-dimensional shape, or conformation

The positions of secondary structures, disulfide linkages, and hydrogen bonds play major roles in folding each protein into its tertiary structure

Attractions between positively and negatively charged chemical groups and polar or nonpolar associations also contribute to tertiary structure

Tertiary Structure determines

a proteins function

The distribution and 3-D arrangement of chemical groups, in combination with their chemical properties, determine the overall chemical activity of the protein

Tertiary structure also determines the solubility of a protein, depending on the arrangement of polar (hydrophilic) and nonpolar (hydrophobic) segments

Tertiary structure of most proteins is flexible, allowing them to

undergo limited conformational charges

Conformational charges are important to the function of enzymes, and to proteins involved in cellular movements or transport of substances across cell membranes

Denaturation

Unfolding a protein from its active conformation so that it loses its structure and function (caused by chemicals, changes in pH, or high temperatures) is called denaturation

For some proteins, denaturation is permanent – for others, denaturation is reversible (renaturation)

Anfinsen’s Experiment

showed that breaking the disulfide linkages holding the protein ribonuclease in its functional state caused it to unfolded and lose enzyme activity

Chaperonins

present in the Golgi apparatus

Proteins fold gradually as they are assembled – as successive amino acids are linked into the primary structure, the chain folds into increasingly complex structures

For many proteins, “guide” proteins called chaperone proteins or chaperonins bind temporarily with newly synthesized proteins, directing their conformation toward the correct tertiary structure and inhibiting incorrect arrangements

Quaternary Structure

Some complex proteins, such as hemoglobin and antibody

molecules, have quaternary structure – the presence and

arrangement of two or more polypeptide chains

• Hydrogen bonds, polar and nonpolar attractions, and disulfide linkages hold the multiple polypeptide chains together

• Chaperonins promote correct association of the individual amino acid chains and inhibit incorrect formations

Functional Domains

In many proteins, folding of the amino acid chain (or chains) produces large subdivisions called domains

In proteins with multiple functions, individual functions are often located in different domains

Domains with similar functions are found in different proteins

3-D arrangement of amino acid chains within and between domains produces highly specialized regions called motifs

Protein Combinations

Proteins link with lipids to form lipoproteins, which form parts of cell membranes

Proteins link with carbohydrates to form glycoproteins, which function as enzymes, antibodies, recognition and receptor molecules, and parts of extracellular supports

Proteins link with nucleic acids to form nucleoproteins, which form structures such as chromosomes

Nucleic Acids

monomer - Nucleotide

All living cells have both DNA and RNA

DNA

deoxyribonucleic acid

A,T,G,C – nitrogen bases

Double helix

Function – hereditary material in all eukaryotes and prokaryotes and in a large group of viruses

Double stranded

RNA

ribonucleic acid

A,U,G,C – nitrogen bases

Usually single stranded

Function –is the hereditary molecule of another large group of viruses – three major types of RNA are involved in protein synthesis

Single stranded

Nucleotides

A nucleotide, the monomer of nucleic acids, consists of three parts linked together by covalent bonds:

A nitrogenous base formed from rings of carbon and nitrogen atoms

A five-carbon, ring-shaped sugar

One to three phosphate groups

Pyrimidines

Nitrogenous bases with one carbon-nitrogen ring

Uracil (U), thymine (T), and cytosine (C)

Purines

Nitrogenous bases with two carbon–nitrogen rings

Adenine (A) and guanine (G)

DNA Nucleotides

Deoxyribose (sugar)

A, T, G, C

nitrogenous base

phosphate

RNA Nucleotides

Ribose (sugar)

A, U, G, C

nitrogenous base

phosphate

Ring Shaped Sugars

Nitrogenous bases link covalently to a five-carbon sugar:

Deoxyribose in DNA deoxyribonucleotides

Ribose in RNA ribonucleotides

The two sugars differ only in the chemical group bound to the 2′ carbon (—H in deoxyribose, —OH in ribose)

In unlinked nucleotides: 1, 2, or 3 phosphate groups bond to the ribose or deoxyribose sugar at the 5′ carbon

Nucleosides and Nucleotide Phosphates

A structure containing only a nitrogenous base and a five-

carbon sugar is a nucleoside

A nucleotide is a nucleoside phosphate

Examples: Adenosine monophosphate (AMP) Adenosine diphosphate (ADP) Adenosine triphosphate (ATP)

DNA Base Pairs

The two polynucleotide chains of a DNA double helix are held together by hydrogen bonds between the base pairs

A base pair consists of one purine and one pyrimidine

Adenine pairs only with thymine (A–T), forming two stabilizing hydrogen bonds

Guanine pairs only with cytosine (G–C), forming three hydrogen bonds

DNA and RNA consist of

Polynucleotide chains, with one nucleotide linked to the next by a phosphodiester bond

One nucleotide is linked to the next by a bridging phosphate group between the 5′ carbon of one sugar and the 3′ carbon of the next sugar

Alternating sugar and phosphate groups form the backbone of a nucleic acid chain

DNA Molecule

The DNA molecule is a double helix (double-stranded) consisting of two polynucleotide chains wrapped around each other in a spiral that resembles a twisted ladder

The sides of the ladder are the sugar-phosphate backbones of the two chains

The rungs of the ladder are nitrogenous bases which extend inward from the sugars toward the center of the helix

DNA is formed by two very long polynucleotide strands linked along their length by hydrogen bonds

Complementary Base Pairing

Formation of A–T and G–C pairs allows the sequence of one polynucleotide chain to determine the sequence of its partner in the double helix

The nucleotide sequence of one chain is said to be complementary to the nucleotide sequence of the other chain

In DNA replication, one polynucleotide chain is used as a template for the assembly of a complementary chain according to the A–T and G–C base-pairing rules

Chargraff’s Rule

number of purines = number of pyrimidines

DNA Passing on the Genetic Message

Each strand is copied

Semi-conservative replication

Replication is guided by base pairing

A=T and G=C

RNA Molecules

RNA molecules exist mainly as single polynucleotide chains (single-stranded) – however, RNA molecules can fold back on themselves to form double-helical regions

In RNA, the uracil (U) base takes the place of thymine (T), forming A–U base pairs

“Hybrid” double helices (an RNA chain paired with a DNA chain) are formed temporarily when RNA copies DNA

ATP

The energy molecule of cells

Adenosine Triphosphate

Nucleotide - adenine, ribose, and three phosphates

Function - transfer and storage of energy

ATP is made by

dehydration synthesis

Is broken by hydrolysis to liberate useful energy for the cell