THE STRUCTURE & FUNCTION OF

LARGE BIOLOGICAL MACROMOLECULES

Campbell and Reece CHAPTER 5

Macromolecules are Polymers polymer: long molecule consisting

of many similar, sometimes identical, building blocks linked by covalent bonds

monomer: the smaller units that make up a polymer

Many Monomers Make a Polymer

Making Polymers

2 monomers joined by dehydration reaction

Disassembling Polymers

hydrolysis reaction breaks apart 2 monomers in a polymer

Diversity of Polymers

possible varieties of macromolecules infinite

only use 40 -50 monomers small molecules common to all

organisms are ordered into species unique macromolecules

http://www.google.com/imgres?q=biochemistry+cartoon&hl=en&biw=1366&bih=499&tbm=isch&tbnid=kAUSFPDv1iel2M:&imgrefurl=http://worldofbiochemistry.blogspot.com/2012/01/cartoon-about-free-radicals.html&docid=T0IU7-R6EbSvYM&imgurl=http://3.bp.blogspot.com/-jFLJQHkDP74/TyOS4bC8BSI/AAAAAAAAATk/arPPAggoxFo/s640/Free+radicals.gif&w=330&h=435&ei=CJh8UPTbKMT40gH3-oGwCA&zoom=1&iact=hc&vpx=198&vpy=70&dur=11441&hovh=258&hovw=195&tx=140&ty=159&sig=102733850649124752380&page=5&tbnh=148&tbnw=111&start=76&ndsp=20&ved=1t:429,r:7,s:76,i:352

Carbohydrates

Simple Carbohydrates Sugars Monosaccharides Disaccharides

Complex Carbohydrates Polysaccharides

Monosaccharides

multiples of the unit CH2O glucose most common

monosaccharide

Monosaccharide Diversity depending on position of the carbonyl

group in a sugar it is classified as either:

1. aldose (aldehyde sugar)2. ketose (ketone sugar)

Monosaccharide Diversity 3 to 7 carbons hexose: 6 carbons long pentose: 5 carbons triose: 3 carbons

Monosaccharide Diversity most hexoses and pentoses form

rings in aqueous solutions used in cellular respiration

(especially glucose) serve as raw materials for synthesis

of amino acids and fatty acids

if not immediately used in these ways used to build disaccharides or polysaccharides

Forms of Glucose

Alpha Glucose Beta Glucose

Disaccharides

reaction: 2 monosaccharides joined in a glycosidic linkage covalent bond formed by dehydration

reaction

Disaccharides

2 glucose = maltose (malt sugar) glucose + galactose glucose + fructose = sucrose (table

sugar)

sucrose: form plants use to transport sugars from leaves roots & other nonphotosynthetic parts of plant

Polysaccharides

polymers of hundreds to thousands of monosaccharides joined by glycosidic linkages

function determined by its sugar monomers & positions of glycosidic linkages

2 types:1. storage of monosaccharides to be

used for energy when needed2. building material

Storage Polysaccharides

Plants store glucose (the monomers)as starch (the polymer) represents stored energy

Starch

most is made of α glucose monomers joined in 1-4 linkages simplest form of starch (amylose) is

unbranched complex starch, amylopectin, has 1-

6 linkage

Storage Polysaccharides

Animals: store glucose (the monomers) as glycogen (the polymer) in 1-4 & 1-6 linkages stored mainly in liver & muscle cells humans store about 1 days supply of

glucose this way

Structural Polysaccharides Cellulose: most abundant organic

cpd on Earth is polymer of β glucose (makes

every monomer of glucose “upside down” from its neighbors)

Starch & Cellulose

many are mostly helical

digested by enzymes breaking its α linkages

never branched has –OH groups

available for H-bonds

digested by enzymes breaking its β linkages

Starch Cellulose

Cellulose

digested by very few organisms (don’t have enzymes to do it)

in humans: passes thru GI tract abrading walls & stimulating mucus secretion along the way smoother passage of food thru

not technically a nutrient but is important

“Insoluble Fiber” = Cellulose

Cellulose

Cows: have bacteria and protists in their guts that have enzymes that can digest cellulose nutrients that can be used by cow

Termites unable to digest cellulose in wood it eats have prokaryotes & protists to break it down and so termite can use nutrients

Termite Life Cycle

Termites

Chitin

another structural polysaccharide used by arthropods to build

exoskeletons exoskeletons: made of chitin +

calcium carbonate

Chitin

also in many fungi cell walls monomer has N group attached

Lipids

large group of hydrophobic molecules

do not have true monomers Includes:

Waxes Steroids Some Pigments Oils, Fats Phospholipids

Fats

large molecules assembled from smaller molecules by a dehydration reaction

2 parts:1. Glycerol2. Fatty Acid

Glycerol

Fatty Acids

long (16-18) chain of carbons (hydrophobic)

@ one end carboxyl group (hence fatty acid)

Triglyceride

3 fatty acids + glycerol

Saturated & Unsaturated

Saturated Fats

include most animal fats most are solids @ room

temperatures

Unsaturated Fats

fats of plants, fish usually liquid @ room temperature

Hydrogenated Vegetable Oil seen on some food labels means that unsaturated fats have

been synthetically converted to saturated fats to keep from separating

Plaques

deposits of saturated & trans fats (hydrogenated vegetable oils with trans double bonds) in muscularis of arteries

Plaques

lead to atherosclerosis (leading cause of heart attacks) by decreasing resilience of vessel & impeding blood flow

Trans Fats

USDA now requires nutritional labels to include amount of trans fats

some cities & Denmark ban restaurants from using trans fats

Essential Fatty Acids

cannot be synthesized in body so must be included in diet

include: omega-3 fatty acids:required for normal growth in children

probably protect against cardiovascular disease in adults

Omega-3 Fatty Acids

Energy Storage

1 g fat has 2x chemical potential energy as 1 g of polysaccharide

plants (generally immobile) can store majority of their energy in polysaccharides except vegetable oils extracted from their seeds

Functions of Fat

Plants: storage of energy Animals: 1. storage of energy2. protect organs3. insulation

Phospholipids

essential component of cell membranes

Phospholipids

when added to water self-assemble into lipid bilayers

Steroids

lipids characterized by a carbon skeleton made of 4 fused rings

cholesterol & sex hormones have functional groups attached to these fused rings

Cholesterol in Animals

part of cell membranes precursor for other steroids vertebrates make it in liver +

dietary intake saturated fats & trans fats increase

cholesterol levels which is ass’c with atherosclerotic disease

In plant seeds, the inside of the seed is rich in lipids (oils). Describe & explain the form the membrane around a droplet of oil would need to take:

Proteins

word in Greek from “primary” account for >50% of dry mass of

most cells instrumental in almost everything

organisms do

Proteins are Worker Molecules

Proteins

humans have tens of thousands of proteins, each with specific structure & function

all made from 20 amino acids (a.a.)

Proteins are biologically functional molecules made of 1 or more polypeptides, each folded & coiled into a specific 3-D structure

Amino Acid Monomers

all a.a. share common structure:

Amino Acid Structure

alpha carbon: center asymmetric carbon

its 4 covalent bonds are with:1. amino group2. carboxyl group3. H atom4. R = variable group= side chain

Amino Acids

http://www.johnkyrk.com/aminoacid.html

20 Amino Acids

R Groups

its physical & chemical properties determine the unique characteristics of a.a. so affect the physical & chemical properties of the polypeptide chain

Peptide Bonds

Polypeptide Backbone

polypeptide chain will have 1 amino end (N-terminus) and 1 carboxyl end (C-terminus)

R side chains far outnumber N & C terminus so produce the chemical nature of the molecule

Protein Structure & Function

polypeptide ≠ protein

Functional Protein

is not just a polypeptide chain but 1 or more polypeptides precisely twisted, folded, & coiled into a uniquely shaped molecule

Protein Shape

determined by a.a. sequence

Protein Shape

1. Globular Protein

roughly spherical

2. Fibrous Protein

long fibers

when polypeptide released from ribosome it will automatically assume the functional shape for that protein’s (due to its primary structure)

Name that Shape

Protein Structure

determines how it functions almost all proteins work by

recognizing & binding to some other molecule

1st Level of Protein Structure

Secondary Structure

segments of each polypeptide chain that coil or fold in patterns

result of: H-bonds in polypeptide backbone α helix: every 4th a.a. held together by

H-bonds β pleated: 2 parallel β strands held

together by H-bonds (is what makes spider silk so strong)

Secondary Structure

Tertiary Structure

3-D shape stabilized by interactions between side-chains

1. hydrophobic interactions a.a. with nonpolar side chains usually

end up together at core of protein: result of exclusion of nonpolar parts by water

once nonpolar side chains away from water, van der Waals forces hold them together

Tertiary Structure: Hydrophobic Interactions

Tertiary Structure

2. Disulfide Bridges covalent bonds that form between 2

S in side chains of different a.a.

Quarternary Structure

for proteins that are made of >1 polypeptide chain

the overall protein structure that results from aggregation of all polypeptide subunits in protein

http://www.learner.org/courses/biology/archive/animations/hires/a_proteo1_h.html

Protein Structure

http://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swf

Collagen

fibrous protein: 40% of all protein in human body

3 identical polypeptides “braided” into triple helix

gives collagen its great strength

Hemoglobin

globular protein made of 2 alpha & 2 beta subunits (polypeptides)

each has nonpolypeptide part = heme which has Fe to bind O2

Sickle Cell Disease

due to substitution of one a.a. (valine) for the normal one, glutamine

causes normal disc-shape of RBC to become sickle shaped because the abnormal hemoglobin crystallizes

Sickle Cell Disease

go thru periodic “sickle-cell crises” angular sickled cells clog small

blood vessels impedes blood flow causes pain

Protein Structure

also depends on physical & chemical environment protein is in:

1. pH2. salt concentration3. temperature

all of the above can change weak bonds & forces holding protein together

Denaturation

process in which a protein loses its native shape due to the disruption of weak chemical bonds & interactions

denatured protein becomes biologically inactive

Denaturation Agents

taking protein out of water nonpolar solvent: hydrophilic a.a that were on outer edge to core vise versa with hydrophobic a.a.

Protein Structure

most proteins probably go thru some intermediate shape stages b/4 achieving their stable shape

chaperonins: protein molecules that assist in the proper folding of other proteins

Chaperonins

Misfolded Proteins

ass‘c with: Alzheimer’s Mad Cow disease Parkinson’s Senile Dementia

X-ray Crystallography

used to determine the 3-D shape of proteins

Nuclear Magnetic Resonance (NMR) Spectroscopy

does not require crystallization of protein

Bioinformatics

uses computers to store, organize, & analyze data to predict 3-D structure of polypeptides from a.a. sequences

NUCLEIC ACIDS

are polymers made of monomers called nucleotides

genes code for a.a. sequences in proteins

1. DNA deoxyribonucleic acid1. RNA ribonucleic acid

Nucleic Acid Roles

DNA:1. self-replication2. reproduction of organism3. flow of genetic information: DNA

RNA synthesis protein synthesis

Nucleic Acid Roles

RNA:1. mRNA

conveys genetic instructions for building proteins from DNA ribosomes

in eukaryotic cells means from nucleus cytoplasm

prokaryotic cells also use mRNA

Nucleic Acids

polymers of nucleotides (the monomers)

Nucleoside

portion of a nucleotide w/out any phosphate group(s)

Nitrogenous Bases

each has 1 or 2 rings that include N are bases because the N atoms can

take up H+ 2 families:1. Pyrimidines

(1) 6-sided ring made of C & N

2. Purines (1) 6-sided ring fused to a 5-sided

ring

Pyrimidines 1. Cytosine

2. Thymine

3. Uracil

Purines

1. Adenine

2. Guanine

Sugars in Nucleic Acidsadded to

1. Deoxyribose

2. Ribose

Phosphate Group

added to 5’ C of the sugar (base was added to 1’ C)

Nucleotide Polymers

1 nucleotide added to next in phosphodiester linkages

Nucleic Acid Backbone

Phosphodiester linkages repeating pattern of phosphate – sugar – phosphate – sugar..

notice: phosphate end

is 5’ sugar end is 3’

Polynucleotides have built-in direction along their sugar-phosphate backbones

DNA bases held together by H-bonds with backbones going in opposite directions

Linear Order of Bases

specifies start, stop of transcription/translation and codons determine primary structure of proteins (which determines the 3-D structure of a protein which in turn determines the function of the protein)

DNA Molecules

dbl stranded (in opposite directions = antiparallel)

bases held together by H-Bonds most have thousands – millions base

pairs bases pair using complementary

base rules

Complimentary Bases

DNA Molecules

RNA

complementary base pairing occurs between:

1. 2 strands of RNA2. 2 stretches of same RNA strand

Uracil pairs with Adenine instead of Thymine (none in RNA)

DNA & Proteins

genes & their proteins document the hereditary background of an organism

able to expect 2 species that appear to be closely related based on fossil & anatomical evidence to also share a greater proportion of their DNA & protein sequences than do more distantly related species

Hemoglobin

human & gorilla hgb differ only by 1 a.a out of 46 in β chain

human & frog differ by 67 a.a.