CHAPTER 5: MACROMOLECULES

by: hanna and jasmine :D

Synthesis and Breakdown of polymers

• Facilitated by enzymes

• Assembled by dehydration synthesis

• Disassembled by hydrolysis

Condensation reaction

• Reaction that connects a monomer to another monomer or a polymer

• Two molecules are covalently bonded to each other with the loss of a small molecule

Dehydration Reaction/Synthesis (condensation)

• Water is lost

• Anabolic - building into larger (more complex) molecules

• Increases complexity

• Requires energy (endergonic) & enzymes

• Produces water molecules

  • Ex. Carbs and protein polymers are synthesized by dehydration reactions

    • Each reactant contributes part of the water molecule that is released during the reaction

    • One provides a hydroxyl group (—OH), while the other provides a hydrogen (—H)

Hydrolysis

• Polymers are disassembled

• “lysis” - breaking

• Catabolic

• Reduces complexity

• Water is needed as an input

• Releases energy when bond is broken (exergonic)

• Bond between monomers is broken by the addition of a water molecule

  • Ex. Process of digestion: bulk of the organic material in our food is in the form of polymers that are much too large to enter cells, in digestive tract, various enzymes attack the polymers, speeding up hydrolysis.

Carbohydrates

• C H O

• A source of energy and provide structural support.

• Serve as fuel and building material

  • Simplest forms are the monosaccharides, or simple sugars (monomers)

• Disaccharides are double sugars consisting of two monosaccharides joined by covalent bonds (glycosidic linkage)

• Polymers are polysaccharides composed of many sugar building blocks.

Monosaccharides (structure)

• Generally have molecular fomulas that are some multiple of the unity CH2O.

  • Most common monosaccharide is glucose (C6H12O6)

• Trademarks of a monosaccharide: carbonyl group, and multiple hydroxyl groups

• Depending on location of carbonyl group, a monosaccharide is either an aldose (aldehyde sugar) or a ketose (ketone sugar)

• Most name for sugars end in -ose. Ex. Glucose, galactose, fructose, ketose, aldose, etc.

• Another criterion for classifying monosaccharides is its carbon skeleton which ranges from three to seven carbons long.

Monosaccharides (function)

• Major nutrients for cells

  • Major fuel for cell work and their carbon skeletons serve as raw material for teh synthesis of other types of small organic molecules, such as amino acids and fatty acids

Disaccharide (structure)

• Two molecules joined by glycosidic linkage (covalent bond formed between two monosaccharides by dehydration synthesis)

  • Ex. Maltose, disaccharide formed by linking of two molecules of glucose

• Most prevalent dissacharide is sucrose w/two the two monomers glucose and fructose

Disaccharide (function)

• Must be broken down into monosaccharides to be used for energy by organisms

Polysaccharides

• macromolecules, polymers w/ a few hundred to a few thousand monosaccharides joined by glycosidic linkages.

• some polysaccharides serve as storage material, hydrolyzed as needed to provide monosaccharides for cells.

• others serve as building materials for structures that protect the cell or the whole organism

  • architecture and function of a polysaccharide are determined by its monosaccharides and by the positions of its glycosidic linkages

• they are NOT soluble in water & too large to pass through cell membrane

• glycogen in animals in live and muscle cells

• amylose or amylopectin (starch) in plants

Storage Polysaccharides

• plants and animals store sugars for later use in the form of storage polysaccharidse

  • Plants store starch (polymer of glucose monomers), as granules within cellular strctures know as plastids

  • synthesizing starch enables the plant to stockpile surplus glucose

  • can later by withdrawn by hydrolysis

  • most animals, including humans have enzymes that can hydrolyze plant starch

Structural Polysaccharides

Organisms build strong materials from structual polysaccharides

• Ex. Cellulose is a major component of the tough walls the enclose plant cells

Difference between Starch and Cellulose

• Linkages in two polymers differ w/ slightly different ring structures for glucose

  • When glucose forms a ring, hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring

  • The two rings for the glucose are called alpha and beta, respectively.

• Starch’s glucose are in the alpha configuration, and cellulose’s glucose are in the beta configuration, making ever glucose monomer “upside down”

Other Carbs

• Chitin: a derivative of glucose used in cell walls of fungi, arthropod skeletons, and dissolving stitches

  • Similar to cellulose with beta linkages

• Peptidoglycan: a derivative of glucose used in bacterial cell walls

Lipids

• Only macromolecule to not include true polymers

  • Grouped with each other b/c they are hydrophobic

• Consists mostly of hydrocarbon regions with relatively polar C—H bonds.

• Major function is energy storage

  • A gram of fat stores more than twice as much energy as a gram of a polysaccharide.

• Plants function with bulky energy in the form of starch

• Humans and other mammals stock their long-term food reserves in adipose cells which swell and shrink as fat is deposited and withdrawn from storage

  • Adipose cells also cushion such vital organs as the kidneys, and a layer of fat beneath the skin insulates the body

Fats (triglyceride)

• Large molecules assembled from smaller molecules by dehydration synthesis

• Consists of a glycerol molecule joined to three fatty acids

  • Glycerol is an alcohool; each of its three carbons bears a hydroxyl group

  • Fatty acid has a long carbon skeleton, ususally 16 or 18 carbon atoms in length

    • Carbon at one end of the skeleton is part of a carboxly group, gives the name fatty acid.

  • Rest of skeleton consists of hydrocarbon chain

    • Non polar C—H in hydrocarbon makes fats hydrophobic

• Connected by ester linkage, via dehydration synthesis (bond between a hydroxyl group and carboxyl group)

Saturated fats (triglycerides)

• No double bonds between carbon atoms composing a chain.

• As many hydrogen atoms as possible are bonded to the carbon skeleton

• Solid at room temp

• Typically found in animals

• Called fats

• Too much contributes to plaque buildup in arteries

  • Ex. butter, lard, fat drained off from meat

• Flexibility allows the fat molecules to pack together tightly

Unsaturated fats (triglycerides)

• One or more double bonds

• One fewer hydrogen atom on each double-bonded carbon

• Liquids at room temp

• Called oils

• Can be mono or polyunsaturated

• One double bond is most common

• 2 or more double bonds are more rare

• Typically found in seeds & provides energy to growing plants

  • Ex. olive oil, sunflower oil

• The kind where the cis double bonds are located prevent the molecules from packing together closely enough to solidify at room temp.

Cis-isomers

• very common in nature

• the hydrogen atoms are on the same side of the two carbon atoms

• the double bond causes a bend in the fatty acid chain

• the refore cis-isomers are only loosely packed

• Triglycerides formed from cis-isomers have melting points - they are usually liquids at room temp.

Trans-isomers

• Rare i nature - usually artificially produced to produce solid fats, e.g. margarine from vegetable oil

• the hydrogen atoms are on different sides of the two carbon atoms

• the double bond does not cause a bend in the fatty acid chain

• trans-isomers can be closely packed

• triglycerides formed from trans-isomers have melting ponts - usually solid at room temp.

Atherosclerosis

• Diet rich in saturated fats contribute to the cardiovascular disease know at atherosclerosis

  • Deposits called plaques develop within the walls of blood vessels, causing inward bulges that impede blood flow and reduce the resilience of the vessels

Phospholipids

• Essential for cells because they are major constituents of cell membranes

• Their structure provides a classical example of how form fits function at the molecular level

• Has a hydrophilic (polar) head and two hydrophobic (nonpolar) tails

  • Only has two fatty acids attached to glycerol rather than three

  • The third hydroxyl group of glycerol is joined to a phosphate group

  • Typically, an additional small charged or polar molecule is also linked to the phosphate group

  • Ex. Choline

Phospholipid bilayer

• Shields the hydrophobic fatty acid tail from water

• Hydropholic heads of the molecules are on the outside of the bilayer, in contact with the aqueous solutions inside and outside of the cell.

• The hydrophobic tails point toward the interior of the bilayer, away from the water

• The bilayer foarms a boundary between the cell and its external enviorment and established seperate compartments within eukaryotic cells.

Steroids

• Lipids characterized by a carbon skeleton consisting of four fused rings

  • Distinguished by the particular chemicals groups attached to the ensemble of rings

  • Some may have a hydrocarbon tail

    • Ex. Cholesterol: Cruicial to animls

      • Common component of animal cell memberans and also the percursor from whihch other steroids, such as the vertebrae sex hormones, are synthesized

      • High level may contribute to atherosclerosis

Write the formular for a monosaccharide that has three carbons

C3H6O3

A dehydration reaction joins two glucose molecules to form maltose. The formula for glucose is C6H12O6. What is the formula for maltose?

C12H22O11

WHAT IF? After a cow is given antibiotics to treat an infection, a vet gives the animal a drink of “gut culture” containing various prokaryotes. Why is this necessary?

The antibiotic treatment is likely to have killed the cellulose-digesting prokaryotes in the cow’s gut. The absence of these prokaryotes would hamper the cow’s ability to obtain energy from food and could lead to weight loss and possibly death. Thus, prokaryotic species are reintroduced, in appropriate combinations, in the gut culture given to treated cows.

Compare the structure of a fat (triglyceride) with that of a phospholipid/

Both have a glycerol molecule attached to fatty acids. The glycerol of a fat has three fatty acids attached, whereas the glycerol of a phospholipid is attached to two fatty acids and one phosphate group.

Why are human sex hormones considered lipids?

Human sex hormones are steroids, a type of compound that is hydrophobic and thus classified as a lipid.

WHAT IF? Suppose a membrane surrounded an oil droplet, as it does in the cells of plant seeds and in some animal cells. Describe and explain the form it might take.

The oil droplet membrane could consist of a single layer of phospholipids rather than a bilayer, because an arrangement in which the hydrophobic tails of the membrane phospholipids were in contact with the hydrocarbon regions of the oil molecules would be more stable.

polymerization

chemical merchanims by which cells make polymers; facilitated by enzymes

polymer

long molecule consisting of many similar identical building blocks linked by covalent bonds

macromolecules

basis of complex cellular life

• single molecules that consists of many covalently linked single units

• small units of monomers linked together to form polymers

monomer

building block unit of a polymer

enzymes

specialized macromolecules (proteins) that speed up chemical reactions

condensation reaction

a reaction in which two molecules are covalently bonded to each other without loss of small molecules

dehydration synthesis

a process in which two monomers/molecules are covalently bonded with the loss of a water molecule

• anabolic

• increases complexity

• requires energy (endergonic) and enzymes

• produces water molecules

• type of condensation reaction

hydrolysis

a process where polymers are disassembled into monomers by adding a water molecule

• enzymes speed up hydrolysis

• catabolic (breaking)

• reduces complexity

• water is needed as an input

• releases energy when bond is broken (exergonic)

• ex: process of digestion (breaking down starch and other carbs)

carbohydrates

• monomer: monosaccharide [ratio is 1:2:1]

• polymer: polysaccharide (ex: glycogen/starch)

• type of bond/linkage: glycosidic linkage via dehydration synthesis

• biological function:

  • short term energy

  • structural support

  • cell-to-cell communication

• arrangement: around asymmetric carbon; ring-shape skeletons are most stable in aqueous solution (5-6 carbons)

aldose

aldehyde sugar (ex: glucose)

ketose

ketone sugar (ex: fructose)

oligosaccharide

3-10 carbon sugar molecules

hexoses

6 carbon sugars (ex: glucose, fructose)

tricoses

3 carbon sugars (ex: glycealdehyde)

pentoses

5 carbon sugars (ex: ribose and ribulose)

disaccharide

two monosaccharides joined by a covalent bond (glycosidic linkage)

• ex: table sugar/sucrose (glucose + fructose), maltose (glucose + glucose), lactose (glucose + galactose)

cellulose

strengthens plant cell walls

starch

stores glucose for energy in plants (ex: amylose/amylopectin)

• a polymer of glucose monomers, as granules within cellular structures known as plastids

• plants withdraw starch using hydrolysis

• amylose: most simplest form of starch; unbranched

glycogen

stores glucose for energy in animals (in liver and muscle cells)

• polymers off glucose that is extensively branched

• in humans, glycogen stores are depleted in about a day, which raises concern for low carb diets

• extensive branch allows for its free ends to break down for energy

chitin

strengthens animal exoskeletons and fungal cell walls

problem of herbivory

herbivores need to digest cellulose from the plants that they eat, but animals lack the enzymes necessary to break down the beta linkages in cellulose

• ex: termites cannot break down cellulose, so they have developed a symbiotic relationship with a protist (in exchange of the protist living in the termite’s gut, the protist does the cellulose digestion)

ruminants

animals, such as cows, that have a vastly expanded upper GI tract; cellulose is digested from bacteria and continual regurgitation/chewing of the “cud”

caecophores

animals, such as bunnies, with an expanded lower GI tract

• food cannot be regurgitated (cellulose is only partially digested), but it can be digested further by re eating their partially digested cellulose (they eat their poop)

peptidoglycan

a derivative of glucose used in bacterial cell walls (carbs)

lactose intolerance

common condition in humans who lack lactase, the enzymes that breaks down lactose

• instead, lactose is broken down by the intestinal bacteria in your gut, which causes cramping and gas

polysaccharide

polymers with 100+ monosaccharides joined by glycosidic linkages

• structure and function is determined by its monosaccharides and positions of its glycosidic linkages

lipids

• elements: CHO

• monomers:

  • triglyceride - glycerol + 3 fatty acid chains

  • phospholipids - glycerol + 2 fatty acid chains + phosphate group

  • steroids - 4 ringed structures; lipids characterized by a carbon skeletons consisting of four rings

• polymer: none

• type of bond: ester bond via dehydration synthesis

• biological functions: long term energy source, makes up cell membrane (phospholipids), insulation, hormones

• ex: fats, oils, waxes

triglyceride

glycerol and 3 fatty acids

phospholipid

glycerol, 2 fatty acid chains, and a phosphate group

• ampipathic

• third hydroxyl group of glycerol is joined to a phosphate group (ex: choline)

• when in contact with water, they self-assemble into a double layer sheet called “bilayer” that shields the hydrophobic fatty acid tails from water

steroids

lipids characterized by a carbon skeletons with cortisol, and consists of four fused rings

• ex: cholesterol, estrogen, testosterone and some lipid hormones

• some may have a hydrocarbon tail

• functional groups give different characteristics

characteristics of lipids

• hydrophobic (hates water)

• mixes poorly due to molecule structure

• hydrocarbon regions w/ non-polar C-H bonds

characteristics of saturated fatty acids

• solid at room temperature

• typically found in animals

• called fats

• too much contributes to plaque buildup

• ex: butter, fat drained from meat, lard

characteristics of unsaturated fatty acids

• liquid at room temperature

• called oils

• can be mono or polyunsaturated

• one double carbon bond is most common

• 2 or more double bonds are rare

• **usually are cis-isomer bonds

• typically found in seeds and provide energy to growing plants

• ex: olive oil, sunflower oil

what are the three parts of the phospholipid layer

hydrophilic head (polar), hydrophobic tail (non polar), and the phospholipid bilayer (essentially everything)

wax

long chain of fatty acid bonds to a long chain alcohol

• plants use: serves as protective covering + slows water loss

• maintains skin/fur, traps dust/dirt, and form honeycombs

ampipathic

has both polar and non polar regions

cholesterol

type of steroid that helps maintain fluidity in cell membrane; too much can cause plaque buildup in arteries

nucleic acid

• elements: CHONP

• monomers: nucleotide (one pentose, nitrogenous base, 1-3 phosphate groups)

• polymers: polynucleotide

• type of bond: phosphidester bond via dehydration synthesis

• biological function:

  • carry genetic blueprint

  • gene expression

  • carrying instructions from DNA to ribosomes (RNA)

  • protein synthesis

  • energy

nucleotide

has one pentose, a nitrogenous base, and 1-3 phosphate group

pyrimidine

nitrogenous base w/ one six-membered ring of carbon and nitrogen atoms (CTU)

• has one carbon ring (ex: cytosine, uracil, thymine)

purine

six membered ring fused to a five-membered ring

• has two carbon rings (ex: adenine and guanine | AGGIES ARE PURE)

what bonds hold the two DNA chains together?

hydrogen bonds

mRNA

messenger RNA that interacts with the cell’s proteins, synthesizing machinery to direct production of polypeptides

what is the flow of genetic info?

DNA → RNA → protein

ribosome

site of protein synthesis

antiparallel (in DNA)

two sugar phosphate backbones are outside the helix while nitrogenous bases are in the interior of the double helix

tRNA

transfer RNA that brings amino acids to the ribosome during the synthesis of a polypeptide

DNA sequencing

determining the sequence of nucleotides along a DNA strand

nucleoside

molecule that only has the pentose and nitrogenous base of a nucleotide (NO PHOSPHATE GROUP)

genome

the entire sequence of the full component of DNA

human genome project goal

goal was to sequence the entire human genome

• benefits: rapid development of faster and cheaper methods of sequencing

bioinformatics

the use of computer software and other computational tools that can handle and analyze large data sets

genomics

analyzing and comparing genomes of different species

proteomics

analysis of large sets of proteins

• protein sequences → found by using biochemical techniques of translation of DNA sequence

• linear sequences in DNA (nucleotides) can determine amino acid sequence of proteins

proteins

• elements: CHON

• monomers: amino acid

• polymer: polypeptide

• type of bond: peptide bond via dehydration synthesis

• biological function:

  • catalyze chemical reactions

  • protect against disease

  • store amino acids

  • transport substances

  • provides structural support

  • receives signals from outside cell

  • functions in cell movement

• ex: hemoglobin, lactase, growth hormones, other enzymes

catalysts

chemical agents that selectively speed up chemical reactions w/o being consumed in the reaction

protein (definition)

a biologically functional molecule made up of one or more polypeptides coiled in a specific 3D structure

primary structure

sequence of amino acids in one polypeptide chain

• formed via peptide bonds

secondary structure

repeating 3D structures found in all polypeptide chains

• hydrogen bonding of the peptide backbone (H of amino group & oxygen of the carboxyl group) causes the amino acids to have a repeating pattern

• R groups do NOT play a role (yet)

tertiary structure

three dimensional folding pattern of a polypeptide chain/protein due to side chain (R group) interactions

• protein is now functional bc it is folded in 3D structure

• structure bends in a certain way due to the interaction between R groups and the local environment of the cell

quaternary structure

specific 3D shape of a protein that contains more than one polypeptide chain, also known as subunits

• NOT all proteins will be functional →due to the interactions between the subunits help to stabilize the overall structure

• ex: sickle cell anemia; part of hydrophobic region of the RBC exposed will cause it to cave in

storage proteins

storage of amino acids

• ex: casein (protein of milk); major amino acid source for baby mammals (also found in plant seeds)

• ex 2: evalburmin (protein of egg white source for embryos)

hormonal proteins

coordination of an organism’s activities

• ex: insulin, regulates blood sugar concentration

structural proteins

provides support

• ex: keratin (hair), horns, feathers, skin appendages

  • collagen, elastin

defensive proteins

proteins that defend against infection

• ex: antibodies

transport proteins

transports substances

• ex: hemoglobin transport oxygen

receptor proteins

response of cell to chemical stimuli

• ex: receptors built in membrane of a nerve cell detect signaling molecules of other nerve cells

contractile and motor proteins

provides movement

• ex: motor proteins are responsible for cilia and flagella

  • acting and myosin are responsible for muscle contractions

enzymatic proteins

selective acceleration of chemical reactions

• ex: digestive enzymes catalyze the hydrolysis of bonds in food molecules