BIO 1310

Study Material for Dr. Hale's Midterm

Polymers

Polymers

a series of bonded subunits that form one molecule

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

Monomers

the subunit used to build polymers

the repeating units of a polymer

NOTE: not all subunits are monomers

Dehydration Reactions

the process by which the monomers/molecules are covalently bonded together with the loss of a water molecule

• requires at least one hydroxyl group

• produces water (removal of water)

Hydrolysis Reaction

the process by which polymers are broken by the addition of water molecule with hydrogen present in one monomer and the hydroxyl group from the other

• ‘add water’

• H20 separates into hydroxyl and hydrogen

Macromolecules

biological polymers, 4 main types

• carbohydrates

• lipids

• proteins

• nucleic acids

CARBOHYDRATES

saccharides and their polymers “sugars”

almost all contain a hydroxyl group and always contain carbon with a carbonyl group

MONOSACCHARIDES: Carbohydrate Monomers

• Glucose

• Fructose

• Galactose

DISACCHARIDES: Carbohydrate Dimers

• Sucrose

  • glucose + fructose

• Lactose

  • galactose + glucose

• Maltose

  • glucose x2

ALL are bonded by GLYCOSIDIC LINKAGE

OLIGOSACCHARIDES: Carbohydrate Trimer

• Raffinose

  • galactose + glucose + fructose

• Stachyose

  • glucose + 2galactose + fructose

POLYSACCHARIDES: Carbohydrate Polymers

Main Ones:

• Starch (alpha glucose polymer)

  • many glucose monomers bonded by 1-4 glycosidic linkages

• Cellulose (beta glucose polymer)

  • many glucose monomers bonded by 1-4 glycosidic linkages

    • has an alternating orientation

      • produce “sheets” as parallel cellulose strands connect by hydrogen bonds

ALL are bonded by GLYCOSIDIC LINKAGE

Glycosidic Linkage

a covalent bond formed between two monosaccharides by dehydration reaction

• a 1-4 bond is between carbon 1 of one monomer and carbon 4 of the other monomer

Functions of Saccharides

• storage of sugars/energy

  • glycogen and starch

• structural support

  • cellulose and chitin

How to Categorize Monosaccharides

• by number of carbons in backbone

• by location of carbonyl group

Number of Carbon Categories

• triose sugars = 3 carbons on backbone

• tetrose sugars = 4 carbons on backbone

• pentose sugars = 5 carbons on backbone

• hexose sugars = 6 carbons on backbone

Location of Carbonyl Group Categories

• ALDOSE SUGARS (alderhyde sugar)

  • carbonyl is on terminal carbon

    • ‘alderhyde position’

• KETOSE SUGARS (ketone sugar)

  • carbonyl is on interior carbon

    • ‘ketone position’

Glucose

the principle product of photosynthesis

• via CO₂ breakdown and carbon grouping and bonding

• energy from the sun is stored in non-polar covalent bonds between carbon and hydrogen

Glucose Linear and Ring Form

synthesized linearly but modified into ring form

• ring form is more stable in water

  • changes polarity slightly

Glucose Ring Structure

• created by bonding between carbon #1 and the terminating OH-

  • partial positive charge of C bonds to partial negative charge of O

• Process referred to NUCLEOPHILIC ATTACK

• Carbons retain linear assigned carbon numbers

ALPHA & BETA Glucose

• only difference is the location of the hydroxyl group on carbon #1

  • cis-trans isomers

    • generally animals can only produce alpha in large quanitities

Beta Glucose

the enzyme of beta glucose causes alternating pattern of monomers

Isomeric Fructose Ring

• bonding between carbon #1 and #5 or #6 carbon

  • #6 carbon = alpha-D Fructofuranose

    • 5 sided

  • #5 carbon = alpha-D Fructopyranose

    • 6 sided

Amino Sugar (NAG)

N-acetylglucoseamine (NAG) is the primary structure of chitin

LIPIDS

• fats

• phospholipids

• steriods

largely insoluble in water due to lack of Nitrogen or Hydrogen (AKA: hydrophobic)

not a true polymer

Fats

Composed of:

• 1 glycerol backbone

• 3 fatty acid chains (highly water insoluble)

synthesized by dehydration reactions

Glycerol

• not considered a saccharide due to its lack of carbonyl group

• considered an alcohol

Fatty Acids

• long carbon chains

• absolutely PACKED with energy

• made 2 carbons at a time

  • food is broken down 2 carbons at a time and sequestered to form fatty acids (Acetyl CoA) to preserve excess energy

• have two ends that help name them

  • alpha

  • omega

ALPHA End: fatty acids

the carboxyl group end, in the form of carboxylic acid (COOH)

OMEGA End: fatty acids

the methyl group end (CH₃)

Ester Bonds

the linkage between fatty acid’s CARBOXYL group and glycerol’s HYDROXYL group needed for form fats

What are Fats Used For?

• energy storage

• organ cushioning

• insulation

Saturated Fatty Acids

~NO DOUBLE BONDS~

• can become solid at room temperature

• can pack tightly together

• typically made by animals

Unsaturated Fatty Acids

~CONTAINS DOUBLE BONDS~

• produces a bend in fatty acid chain

• typically fluid at room temperature

• cannot pack tightly together

• contain less hydrogen

• typically made by plants

polyunsaturated = 2+ double bonds

Cis-Double Bonds

• breakdown more easily

• cause less health risk

  • vegetable oils

Trans-Double Bonds

• stack well in arteries

  • cause heart disease

• a byproduct of hydrogenation

HYDROGENATION

an attempt to turn fragile cis-unsaturated fat into a saturated fat, to increase shelf-life

• chemically forcing hydrogen into fat

• removing the double bonds

also produces trans-unsaturated fats by accident

ESSENTIAL Fatty Acids

• Linoleic Acid → omega-6

• Alpha Linolenic Acid → omega-3

  • free fatty acid

Phospholipids

• key component of cellular membranes

  • phospholipid bilayer

  • contributes to semipermiability

• also form little spheres

  • micelle

  • liposome (delivery)

Micelle

a sphere

Liposome

hollow sphere

Phospholipid: STRUCTURE

• hydrophilic head:

  • phosphate group (reason for hydrophilic nature)

  • glycerol

• hydrophobic tails:

  • 2 fatty acids

    • saturated or unsaturated

Sphingolipids

a type of phospholipid/membrane molecule

• important in certain classes of cellular signalling and the structure of lipid rafts in mammalian systems

composed of → 2 fatty acid chains, glycerol and hydrophilic head

Steriods

• a 4 ringed structure with specialized attached side chains

• virtually completely hydrophobic/nonpolar

• make up most humane hormones

Steroids: CHOLESTEROL

• a steroid that helps produce other steroids

7-Dehydrocholesterol is the pre curser to serum cholesterol, converted to vitamin D by ultraviolet light

Steroids: NUMBERING

carbon numbering always starts on the top of ring A

PROTEINS

arguably the most important constituent of cells

they do a great variety of jobs within cells

• enzymatic

• storage

• defensive

• transport

• hormonal

• receptor

• contractile and motor

• structural

ENZYMATIC Proteins

biological catalysts

function → selective acceleration of chemical reactions

bind to specific substrate using Induced Fit

“ase”

example-sucrase

STORAGE Proteins

function → storage of amino acits

example-caesin (milk) is a source of amino acids for baby mammals

DEFENSIVE Proteins

function → protection against disease

example-antibodies deactivate and destroy foreign pathogens

TRANSPORT Proteins

function → transport substances

example-hemoglobin

HORMONAL Proteins

functions → coordination of an organism’s activities

example-insulin, hormone secreted by the pancreas

RECEPTOR Proteins

function → response of cell to chemical stimuli

example-membrane receptor proteins

CONTRACTILE & MOTOR Proteins

function → movement

they change shape in response to a trigger (ATP hydrolysis)

example-motor proteins undulate cilia and flagella

STRUCTURAL Proteins

function → support

example-keratin in hair and horns

Protein vs Polypeptide

Protein - modified polypeptide

Polypeptide - a combination of monomers (amino acids) not yet functional/finished

Protein Polymer

polypeptide

bonded by peptide bonds

Protein Monomers

amino acids

AMINO ACID: Structure

• BACKBONE

  • amino group

  • central/alpha carbon

  • carboxyl group

• SIDE CHAIN

  • R group

humans use 20 different amino acids - 11 are synthesized metabolically - 9 are obtained through diet (essential amino acids)

AMINO ACIDS: 20 Human Ones

• nonpolar

  • Glycine (gly)

  • Alanine (ala)

  • Valine (val)

  • Leucine (leu)

  • Isoleucine (ile)

  • Methionine (met)

  • Phenylalanine (phe)

  • Tryptophan (trp)

  • Proline (pro)

• polar

  • Serine (ser)

  • Threonine (thr)

  • Cysteine (cys)

  • Tyrosine (tyr)

  • Asparagine (asn)

  • Glutamine (gln)

• electrically charged

  • Aspartic Acid (asp)

  • Glutamic Acid (glu)

  • Lysine (lys)

  • Arginine (arg)

  • Histidine (his)

Types of R Groups/Side Chains

• polar (hydrophilic) [6]

  • generally have a hydroxyl group (OH)

• non-polar (hydrophobic) [9]

  • generally contain only carbon and hydrogen

• electrically charged (hydrophilic) [5]

  • acidic/carboxyl end

    • negatively charged side chain

  • basic/amino end

    • positively charged side chain

determine the type of amino acid and has a great deal of affect on protein shape and structure

Enzymes

biological catalysts (usually proteins)

act on SUBSTRATE specific to the ACTIVE SITE of the enzyme

Zwitterion

amino acids ionized via the donation of OH’s hydrogen to the amino group

done inside cytosol

LEVELS of PROTEIN STRUCTURE

• primary

• secondary

• tertiary

• quaternary

PRIMARY Protein Structure

• linear chain of amino acids in SPECIFIC SEQUENCE

SECONDARY Protein Structure

• hydrogen bonding between backbones of amino acids determining primary function

  • alpha helix

  • beta pleats

TERTIARY Protein Structure

• side chain interactions via:

  • hydrogen bonds (weak)

  • disulfide bridges (strong)

  • hydrophobic interactions

  • van der Waals interactions

  • ionic bonds (weak)

• forming a 3D structure

QUANTERNARY Protein Structure

• the combination of multiple tertiary structure proteins via:

  • hydrogen bonds

  • ionic bonds

  • disulfide bridges

  • hydrophobic interactions

• 2 or more tertiary structure polypeptides

Chaperonin

• a structure that functions as a space for polypeptides to fold properly into proteins

  • 3 part protein and nucleic acid based structure

• when cap attaches a hydrophobic environment is formed inside the “pocket space”

  • this stimulates proper form

Native Form

the naturally occurring protein prior to denaturation

Denaturation

the breaking-down of protein via unfolding and bond breaking

deactivates protein

can be caused by pH, temperature, and ion concentration changes

Renaturation

the reformation of protein via refolding and bond reattaching

only possible to reform weak interactions

reactivates protein

NUCLEIC ACIDS

store and transmit hereditary information

primarily encode information for proteins

DNA and RNA

Nucleic Acid Monomer

NUCLEOTIDES

many nucleotides bonded by phosphodiester bonds produces polynucleotides (polymer)

examples - DNA and RNA nucleotides

Phosphodiester Bonds

covalent bond between nucleotide 1’s #3 carbon and nucleotide 2’s #5 carbon of each’s pentose sugar

Types of Pentose Sugar

Ribose (OH)

Deoxyribose (H)

Types of Nitrogenous Bases

• Pyrimidines (one ring)

  • Cytosine (C)

  • Thymine (T)

  • Uracil (U)

• Purines (two rings)

  • Adenine (A)

  • Guanine (G)

Sugar-Phosphate Backbone

a series of nucleotides bonded by phosphodiester bonds

5’ prime to 3’ prime

DNA Macromolecules: Structure

• double stranded

• uses deoxyribonucleotides

• genetic material

• does not use Uracil

• DOUBLE HELIX

  • Sugar-Phosphate Backbone

  • Nitrogenous Bases

polynucleotides strands prefer double-strand configuration

DOUBLE HELIX

• two strands of bonded nucleotides hydrogen bonded by nitrogenous bases

  • bases must be properly paired and orientated

• strands are complementary antiparallel

two lane highway

Base Pairs

Adenine - Thymine (2 hydrogen bonds)

Guanine - Cytosine (3 hydrogen bonds)

RNA Macromolecule: Structure

• single strand

• uses ribonucleotides

• not genetic material but transport for it

• uses Uracil not Thymine

RNA Classifications

• mRNA

  • messenger

• rRNA

  • ribosomal

• tRNA

  • transfer

    • bring amino acids to ribosome

• small RNA

  • small nuclear

    • splicsosomes

CELLS

• the functional unit of life

organisms can be multicellular or unicellular

Cell Theory States

all living things are comprised of cells

Robert Hooke

developed one of the first microscope that used reflective light

Anton Van Leeuwnehoek

developed light transmitted microscope

Electron Microscopes

uses electron beams, with very small wavelengths increasing resolution, rather than light

• Two types:

  • Scanning Electron Microscope

    • surface view of specimen '“SEM”

  • Transmission Electron Microscope

    • internal view of sample “TEM”

      • cut slices then view

Prokaryotes

simple cells

• no membrane bound organelles

• no proper chromosomes

  • found in nucleoid region

• Plasma Membrane (external)

  • coated in Cell Wall infused with Peptidoglycan

• protein/carbohydrate based Capsule may coat the cell

  • this is a sticky shell that helps bond colonies and slow down WBC

• Fimbriae (hair like) help with bonding and adherence

• Flagella helps with motility

  • one or more

  • structure is different in eukaryotes

• No Histones

Eukaryotes

more complex

• many membrane bound internal structures

• significantly higher surface area

  • ENDOMEMBRANE SYSTEM to combat this

two types

Animal vs Plant Cells

• Animal

  • no cell wall

  • no central vacuole

  • no chloroplasts

  • centrosome

  • lysosome

• Plant

  • cell wall

  • central vacuole

  • chloroplasts

  • not regular centrosome

  • no lysosomes

ENDOMEMBRANE SYSTEM

membrane surfaces are run through the cell to bring SA:V ratio to better range

• functions to transport proteins through and out of the cell, also modifies peptides

  • extra membrane gives space for biological processes (most of which occur along membrane)

basically any membrane based organelles except mitochondrion, chloroplasts, peroxisomes

Nuclear Envelope: endomembrane system

• double membrane

  • inner and outer

• flows seamlessly into Rough ER

• encloses around Chromatin and Nucleus

• has pours for extra-envelope transfer

Nucleolus

not a membrane bound section but an organized portion of nucleus

this is where ribosomes are born (put together)

Nucleosomes

“beads” made of several histone proteins wrapped tightly with DNA strands. many nucleosomes result in chromatin

~10nm diameter

Nuclear Lamina: endomembrane system

fibrous matrix

• located against inner nuclear envelope membrane

• provides envelope extra support and defense

Ribosomes: endomembrane system

function: synthesis of proteins, by translating mRNA and assembly of coded amino acid chains

• made of ribosomal RNA and ribosomal proteins

• Two subunits

  • Large Subunit

  • Small Subunit

    • subunits remain separate until active transcription/translation

• can be free floating or bound to ER

Rough Endoplasmic Reticulum (ER): endomembrane system

• has ribosomes bound to it

• function:

  • primarily to produce secretory proteins (modified)

    • outside the cell or to organelles

  • site of phospholipid formation

    • this synthesizes more endomembrane

  • post-translational modifications of peptides

• attached to nuclear envelope

protein assembly line

Smooth Endoplasmic Reticulum (ER): endomembrane system

• no ribosomes

• function:

  • synthesis of lipids

    • steroids and phospholipids

  • detoxifies poisons and drugs

  • site of glycogen metabolism

  • storage of calcium

    • sarcoplasmic reticulum

  • also some post-transcriptional protein modifications

• vesicles bud off here

export

Cisternae: endomembrane system

the folds of the ER

has its own Lumen → the inner area/pockets formed by folds

begins modifications

Golgi Apparatus: endomembrane system

• a series of “flattened sacks”

• function:

  • further modification of proteins for exocytosis

    • proteins are received via vesicles on the CIS FACE

    • protein is taken up via golgi cisternae and modified

    • packaged into vesicle and shipped out via TRANS FACE

motor proteins help vesicles move between “sacks”

Common Protein Modifications

• chain cleaving/shortening

• attachment of

  • carbs

  • lipids

  • other proteins

• folding and shape changes