Download Module 8 – Carbohydrates

Module 8 – Carbohydrates


Organic compounds that include a carbonyl & several hydroxyl groups (CH2O)n
Widely distributed throughout natural world
Monosaccharides



Simplest form of carbs  sugar monomers
Provide chemical energy to cells & serve as
building blocks in synthesis of larger
molecules
Glucose – C6H12O6
o Alpha-Glucose – Hydroxyl group
facing down off 1Carbon
o Beta-Glucose – Hydroxyl group facing up off 1Carbon
o
Ring Structure


Reaction that opens & closes ring is reversible, but in aqueous sol. ring is more stable & prevalent
Covalent bond forms between carbonyl & hydroxyl groups
Disaccharides


Consists of two monosaccharides joined by Glycosidic linkage
Breakdown to monomers and used in cellular respiration for energy
Glycosidic Linkage


OH lost from one monomer & H lost from another to form covalent bond
H2O released  Dehydration Reaction
Polysaccharides


Polymers of sugar molecules
Serve for energy storage, structural elements of cells & organisms & cell recognition molecules
Energy Storage




Branched, helical structures allows for compact energy storage
1-4 linkages of alpha-glucose
Starch
o Primary energy storage polysaccharide in plants
o Stored as granules in amyloplasts & chloroplasts
o Hydrolysis of starch produces glucose monomers
Glycogen
o Primary energy storage polysaccharide in animals & fungi
o Primarily stored in liver & muscle cells
o Deplete supply within 1-2 days  thus ingested in food
Cellular Structures


Cellulose
o Important structural polysaccharide in plants
o Linear chain of 1000’s of glucose monomers
o Beta-glucose chains are flat, uncoiled & branch-free thus determining 3-D structure
o Strong HBs occurs between parallel groupings of molecules called microfibrils
Chitin
o Occurs in cell walls of algae & fungi
o Glycosidic linkages join long chain of nitrogen containing monomers
o Strong HBs occur between beta-glucose monomers
Module 9 – Lipids


Diverse range of generally non-polar & hydrophobic molecules
Some lipids contain polar functional groups
Fats
Triglycerol – lipid composed of usually 3 fatty acids
attached to glycerol
Fatty Acids



Amphipathic molecules with long hydrocarbon chains with carboxylic acid at one end
Carboxylic acid group is polar & hydrophilic  undergoes HB
Hydrocarbon chain hydrophobic  repels water
Micelles



Amphipathic molecules aggregate in a way which separates non-polar tails from water whilst
maintaining interactions of polar heads with water
Spherical structures of single bilayer
Formation aids in digestion of fatty acids, fat soluble vitamins (A) & cholesterol
Saturated Fatty Acids




No double bonds in carbon skeleton
Carbons bound to max no. of Hydrogen atoms
Linear structure allows fatty acid chains to pack closely
Often solid at room temperature (butter)
Unsaturated Fatty Acids




One or more double bonds within skeleton
Double bonds usually cis form, produce kink in molecule preventing tight packaging
Usually forms liquid or oil at room temp
Trans Fat – trans double bond thus no kink  solid at room temp due to more dense arrangement
Phospholipids




Commonly derived from glycerol attached to 2 fatty acids & 1 phosphate group
Fatty acids form 2 hydrophobic tails that spontaneously arrange themselves away from water
Glycerol & Phosphate form hydrophilic head
Capable of forming micelles but due to crowded nature of tails, spontaneously form bilayers
Bilayers


Double-layer linear sheet aligned so interior tails are away from water & exterior heads in contact
Controls materials that enter & leave cell
Steroids


Class of lipids including sex hormones & cholesterol necessary for life functions
Composed of carbon skeleton arrange in 4 fused rings
Cholesterol

Cells able to modulate membrane fluidity by adjusting membrane cholesterol levels
Lipoproteins




Transport steroids through bloodstream
Internal hydrophobic region allows for fats & fat soluble compound transport
Low-Density (LDL) – Bad Cholesterol - liver  body cells
o Increase risk of atherosclerosis (thickening of arteries from accumulation of fatty substances)
High-Density (HDL) – Good Cholesterol - body cells  liver
o Decreased cardiovascular disease risk
o Oxidative damage to Apo A-1 causes HDL losing ability to efficiently remove cholesterol
o Oxidative damage to anti-inflammatory components lead to pro-inflammatory agents
Module 10 – Proteins


Single chain polymers made from amino acid monomers
Carry out most cell life functions & contribute to diversity of cell structure
Amino Acids




Monomer composed of central alpha-carbon, NH3+, Carboxyl group & R’ chain
Attached R’ chain differs
Cells use 20 AA to build necessary proteins
Each AA has unique shape & chemistry
4 Levels of Protein Structure
Primary Structure

Linear sequence of AA linked in polypeptide chain
Secondary Structure



Coiled & folded patterns formed by segments of polypeptide chain
HB between repeating atoms of peptide backbone
Different patterns formed by different HB formations
o A-Helices & B-Pleated Sheets
Tertiary Structure



Globular unit unto which amino acid chain folds
Interactions between R-groups & peptide backbone contribute to unique 3-D shape
Each unit held by ionic bonds & disulphide bridges
Quaternary Structure


Aggregation of separate identical or different polypeptide subunits
Each subunit is separate amino acid chain
o Haemoglobin – quaternary structure of 4 separate polypeptides
Collagen


Key component of cartilage, bone & skin tissues
Made up of 3 separate polypeptides each with LH helical secondary structure
Module 11 – Enzymes
Biological catalysts that speed up chemical reactions inside cells without taking part
Catalysts – provide alternative reaction pathway with lower activation energy
Role of Enzymes in Metabolism




Most enzymes are proteins but can be composed of RNA  Ribozymes
Interact with specific molecules allowing them to proceed down specific biochemical pathway
Necessary to produce consistent & abundant supply of ATP
Detoxify toxic substances
How do Enzymes Work
Substrate binds to Active Site of enzyme forming Enzyme-Substrate Complex

Interact via transient HB, ionic & hydrophobic interactions between substrate & R’ group
Facilitate transformation of substrates into products, going through transition state; unstable intermediate
condition of substrate before products formed. Return to original state once products leave.
Enzymes Lower Activation Energy in 4 Ways
1.
2.
3.
4.
Active site positions substrates in orientation favourable for breaking & reforming binds
Applies torque on substrates providing mechanical stress on bonds
Chemical microenvironment (pH, charge) more energetically favourable to transition state
Transfer of protons, electrons or functional groups
Enzyme Activity

Cells must maintain homeostasis to survive
Temperature



Optimal State – Temperature at which enzyme functions most efficiently
Temperature is proportional to Brownian motion of substrate molecules
Too high a temp denatures enzyme by breaking bonds that hold 3-D structure


If pH too low  enzyme becomes deprotonated  changing shape of active site
If pH too high  enzyme becomes deprotonated  disrupts bonds in 3-D structure  denature
pH
Substrate Concentration




Above certain conc. all active sites become saturated with substrate
Addition of more enzyme molecule increases reaction rate
Vmax – maximum RR for enzyme
Km (constant) – measure of how well enzyme can bind to substrate
o Low Km – enzyme has low affinity for substrate
o Defined as substrate conc. at which RR = 0.5Vmax
Enzyme Regulation



Only some enzymes are active at any given time
Cell regulates enzymes by turning on/off (activated/inhibited), are reversible
Poisons (nerve gas & drugs) can cause irreversible inhibition of enzymes
Feed Inhibition

Products of enzymatic pathway bind to & inhibit enzyme usually at beginning of pathway so fewer
intermediates produced are committed to pathway
Competitive Inhibition

Inhibitor molecules similar to substrate bind to enzymes active site but do not react  reduce RR
Allosteric Inhibition (non-competitive)

Binding of molecule to allosteric site in way that promotes binding of substrate to active site
Covalent Modification



Addition or removal of chemical groups (methyl & acetyl)
Phosphate groups regulate enzyme function by binding to protein causing conformational damage,
turning enzymes on or off
Kinases – enzymes that add phosphate groups
o Enzymes involved in sending signals within cells often activated when kinases add PO4o Cascade of kinases involve kinases activating each other
Proteolytic Cleavage

Removal of part of enzyme activates enzyme
o Pancreas produce inactive digestive enzymes
o Small intestines produce other enzymes that cleave away parts of pancreatic enzymes
o Ensures pancreatic enzymes do not digest proteins while still in pancreas, but digest food
once secreted into small intestine
Cooperativity – Substrate binds to 1 active site  conformational changes occur in subunit active sites in
quaternary structure  favour further substrate bindings
Module 12 – Nucleic Acids

Repeating monomers are nucleotide arranged in wide variety of sequences  polynucleotides
Structure





Phosphate group, 5-Carbon sugar (pentose) & nitrogenous base
Nucleoside – Phosphate group absent
Carbons in nitrogenous base numbered 1, 2, 3 etc.
Carbons in pentose numbers 1’, 2’, 3’ etc.
Nitrogenous base attaches to 1’ Carbon
Nitrogenous Bases
Pyrimidine


Cytosine, Thymine & Uracil  CUT the Py
6-member ring containing 4 Carbon’s & NItrogens
Purine



Adenine & Guanine
5-member ring attached to 6-member ring
Each ring has 2 Nitrogen’s
Phosphodiester Linkages



Forms when phosphate group of one nucleotide covalently bounds to OH - group at 3’ carbon of
another nucleotide
Entire polymer has 5’ & 3’ end
Hydrophilic PO42- faces outward, Hydrophobic Nitrogenous base faces inwards
DNA






Encodes all info. needed to create life’s diversity
Consists of deoxyribose sugar molecule i.e. minus oxygen
Chargaff’s Rule – in cellular DNA: amount of C = amount of G & amount of T = amount of A
Double Helix structure consisting of 2 intertwined strands of DNA  Watson & Crick
5’3’ opposite to 3’5’ complementary strand
o Antiparallel – Complementary strands runs opposite directions
Helix can be twisted in three biologically active conformations
o B-DNA – Most common, close to Watson & crick model
o A-DNA – Similar but shorter & more complex in nature
o Z-DNA – Resembles B-DNA but helix is LH directionally
RNA




Delivers info. from DNA to sites of protein synthesis
Consists of Ribose sugar molecule
Uracil instead of Thymine
Folds over & bases on one part to form base pairs with complementary bases on other part
o Results in wide variety of secondary structures e.g stem loop/hairpin
Roles & Types of RNA




Structural diversity of RNA molecules is basis for RNA’s functional roles in cells
mRNA – messenger RNA which encodes info. from genes & carries to machinery to decose
rRNA – Ribosomal RNA
tRNA – Transfer RNA

Process of RNA synthesis known as transcription
Nucleotide Bases & Hereditary Info.


Order of bases preserved from DNA template strand/parent molecule to new
daughter cells
Sequence of nitrogenous bases makes up gene which contain instructions to make
proteins
Module 45 – DNA Replication
Semi-Conservative Model




Meselson & Stahl used 15N isotopes as biomarkers to distinguish parental & daughter
DNA strands
If replication were Conservative, one round of replication would yield a DNA
molecule that contained 2 strands of parental DNA & another DNA molecule with 2
new strands
If replication were Dispersive, one round of replication would yield 2 DNA molecules
with each strand containing mixtures of fragments of both original & newly
synthesized DNA
Replication is Semi-Conservative, as each daughter molecule contains 1 intact strand
of parental DNA molecule & 1 intact newly synthesized DNA molecule
Prokaryotic DNA Replication (E.coli)












Replication process begins at certain sequence of nucleotides known as Origin of
Replication
Double helix unwinds creating 2 Replication Forks forming Replication Bubble
Replication proceeds in both directions away from origin
DNA Helicase binds to each replication fork & breaks HB between strands, unwind
DNA at forks
Single-Strand DNA-Binding Proteins (SSB) prevents separate strands from re-joining by
binding to separated strands & stabilizing them
Topoisomerase protein binds to double helix ahead of fork & relives torsional strand
placed on helix
Single RNA Primer added near origin of Leading Strand
DNA polymerase III adds nucleotides in continuous fashion as 3’ end of growing
strand faces fork
DNA polymerase III cannot add nucleotides in 3’ to 5’ direction, thus DNA Primase
synthesize short, temporary RNA primers on Lagging Strand before falling off
Discontinuous Okazaki Fragments synthesized in 5’ to 3’ direction
RNA polymerase I uses 3’-OH end to extend fragment, replacing RNA primers with
nucleotides
DNA Ligase joins gaps within backbone
Proofreading & Repair


DNA polymerase remove & replace incorrectly paired bases
If error slips past polymerases, daughter strands may be repaired via other means

Some errors in DNA sequence may go unrepaired and passed onto daughter strand
causing permanent mutation
Mismatch Repair

Enzymes cut out incorrect nucleotide from daughter strand & replace with
appropriate nucleotide
Nucleotide Excision Repair




Replaces portions of DNA chemically damaged by environmental effects e.g. UV
from Sun
Nucleases make incisions on either side of lesions
DNA polymerase replaces damaged DNA with new nucleotides
DNA Ligases reconnects newly replaced fragments
Eukaryotic DNA Replication





Multiple replication bubbles at different stages of replication process along linear
chromosomes
Linear nature of eukaryotic DNA leads to DNA polymerase III being unable to add
final sequence of DNA to 5’ end of lagging daughter strand
Chromosomal DNA have special sequences at end called Telomeres
Telomerase enzyme containing own RNA template used to lengthen telomerase of
lagging strand
Telomeres contain repeating sequence of bases that don’t code for proteins but
protect genetic info. at ends of eukaryotic chromosomes  DNA primary & p3 can
then synthesize lagging strand