Macromolecules Flashcards
Learning outcomes lecture 1
- explain what are atoms, molecules, covalent bonds and macromolecules.
- describe the composition, classification, formation and breakdown of carbohydrates.
- explain alpha and beta monosaccharides and the structural implications for the formation of di- and polysaccharides.
- describe examples of cellular roles of carbohydrates.
- remember the composition and characteristics of lipids.
- explain the biological roles of lipids.
Molecules
made up of elements
> elements - “cannot be broken down or converted into other substances by chemical means”
- chemical element consists of one type of atom
Atoms
of electrons = # of protons
“smallest particle of an element that
still retains the elements distinctive chemical properties”
- Protons — positive charge
- Atomic number - number of protons
- Electrons - negative charge
- determine atom’s chemical behavior
- orbit the nucleus of an atom on different energy levels (electron shells)
- Neutrons - neutral
Covalent Bonds between Atoms lecture slide
Electrons in the outer shell determine if an atom can form covalent bonds
Electrons fill electron shells from the innermost to the outer shell
- Most atoms have unfilled outermost electron shells reactive
- able to donate, accept, or share electrons with each other
→ complete outer shell stabilized
atomic number
chemical = covalent
bond formed
Single and Double Covalent Bonds
equal sharing of electrons, e.g. between hydrogen and oxygen or between carbon atoms joins atoms into clusters called molecules
What are Macromolecules?
After water, they are the most abundant compounds inside cells
- They include:
- DNA & RNA, proteins, polysaccharides, lipids
Macromolecules are constructed by linking smaller molecules together via covalent bonds
Carbon plays a central role in Macromolecules
Carbon is part of nearly all cellular molecules
> Forms 4 covalent bonds with other atoms → small organic molecules
Monosaccharides are the simplest
Carbohydrates (Sugars)
= hydrate of carbon (CH2O)n where n
typically is 3, 4, 5, 6
- Basic form: monosaccharide, e.g. glucose, galactose, fructose
Glucose: C6H1206
a monosaccharide with 6 carbons ring structure includes 5 of the carbons and one oxygen
one side of the chain as a hydroxyl and the other has a hydrogen and will either have a ketone or a aldehyde functional group
Monosaccharides are building blocks for
Macromolecules named Oligo- and Polysaccharides
Monosaccharide - one sugar molecule, e.g. glucose
- Disaccharide - composed of two monosaccharides, e.g. sucrose = glucose + fructose
Oligosaccharide - composed of 3-50 monosaccharides
- Polysaccharide - 100’s to 1000’s subunits
- Polysaccharides can be branched & linear
Formation and breakdown of Di- and Polysaccharides
Condensation reaction
- Leads to generation of water molecule as covalent bond forms between subunits
Hydrolysis reaction
- Addition of a water molecule cleaves bond linking two subunits
These reactions are catalyzed by enzymes and commonly found in the formation or cleavage of macromolecules
water consumed
Both reactions are also involved in the formation and breakdown of proteins and nuclei acid macromolecules.
Monosaccharides form a ring structures (ketones)
When a ketose sugar cyclizes, the hydroxyl group on the second to last carbon undergoes an intramolecular reaction with the ketone carbonyl group
Monosaccharides form a ring structures (aldose)
When an aldose sugar cyclizes, the hydroxyl group on the second to last carbon undergoes an intramolecular reaction with the aldehyde carbonyl group.
Glucose cyclisation forms Alpha and Beta Glucose photo
Glucose cyclisation forms Alpha and Beta Glucose
- These are interconvertible
The hydroxyl group on carbon 1 in the glucose ring can be below (alpha) or above (beta) of the ring.
The two glucose molecules are therefore called a-D-glucose and ß -D-glucose.
- Both forms exist at equilibrium
- Many other monosaccharides also form a and ß forms.
- The position of the hydroxyl group (a or B) has implications for macromolecules containing monosaccharides
Linking two Monosaccharides freezes the a or ß form
Disaccharides are sugars composed of two monosaccharide units that are joined by a carbon-oxygen-carbon linkage known as a glycosidic linkage.
- This linkage is formed via a condensation reaction .
- In the example
the reacting parts are the C1-OH (alpha) group of one a- D-glucose and the C4
-OH group (can also be another of the C-OH groups) of another a- D-glucose.
The alpha hydroxyl group is now ‘frozen’ in the glycosidic linkage.
- The glycosidic linkage formed is an alpha glycosidic linkage.
suffix -ose means carbohydrate
Linking two Monosaccharides freezes the a or ß form photo
Linking two monosaccharides to another freezes the a or ß form photo
Carbohydrates can have Structural Roles lecture photo
lipids photo
Fatty acids are amphipathic
Amphipathic have both:
- hydrophilic (water-loving) |
- carboxylic head.
- chemically reactive - nearly all covalently linked to other molecules
- hydrophobic (lacking affinity to water)
- hydrocarbon tails
- differ in length & position of double & single bonds
- insoluble in water
- soluble in fat & organic solvents
Types and functions of lipids - Overview
- Fatty acids
- monoglycerides
- Diglycerides
- Fats - In(acyl)glycerides
- Phospholipids
- Glycolipids
- G
- Waxes
- Sterols
- fat-soluble vitamins (vitamins A, D, E and K)
- Prostaglandins
- and others
Usually hydrophobic or amphiphilic.
lipid function
The functions of lipids include storing energy, signaling, and acting as structural components of cell membranes
glucose as energy photo
Fatty acids are amphipathic photo
Saturated and unsaturated fatty acids
Unsaturated
double bond(s) linking carbon atoms in hydrophobic tail kinks formed - do not allow close packing liquid at room temperature plant oils, e.g. corn oil, canola oil
Saturated and unsaturated fatty acids photo
Saturated and unsaturated fatty acids
Saturated
- no double bonds tight packing
- solid at room temperature
- animal fats, e.g. butter, lard
Saturated and unsaturated fatty acids photo
Tri(acyl)glycerides
Tri(acyl)glycerides - type of fats, glycerol group covalently linked (ester linkage) to carboxylic acid heads of tree fatty acids
- Derivatives: phospholipids,
- energy reserve in cells
- 6x as much usable energy as glucose per weight
- General: fat - solid at 25 °C, oil - liquid at 25°C (TAC, cholesterol)
Tri(acyl)glycerides photo
Phospholipids
two fatty acids linked to
glycerol = two hydrocarbon
tails
- 3rd site on glycerol linked to a phosphate group that is attached to glycerol
- small hydrophilic group attached covalently to phosphate group
- Example phosphatidylcholine with choline covalently attached to the phosphate group
hydrophobic
- fatty acid tails
phosphatidyicholine
strongly amphipathic
Phospholipids photo
Phospholipids as components of cellular membranes
hydrophilic heads associate with aqueous environment outside and inside cells
- hydrophobic fatty acid tails orientate with one another
Result: formation of
bilayer = energetically
favourable - unsaturated tails increase membrane fluidity
- saturated tails
decrease membrane fluidity
Other Membrane Lipids - Steroids photo
Phospholipids as components of cellular membranes photo
Other Membrane Lipids - Steroids
Fused four-ring core structure made up of carbons and hydrogens. May contain oxygen.
The Central Dogma
Nucleic Acids & Proteins
DNA transcribed into RNA which is translated into protein
Can you….
- … relate the number of electrons in an atom to its ability to form molecular bonds?
- … recognise and explain the composition and structures of carbohydrates and explain their formation?
- … give examples of the roles carbohydrates play in biological systems?
- … explain the composition and structures of lipids using correct terminology?
- … describe the roles of lipids in biological systems and how these relate to their composition and structure?
Other Membrane Lipids - Glycolipids
Nucleotides contain Nitrogenous Bases
- Contain nitrogen (N)
Pyrimidines (single ring structure): cytosine (C), thymine (T) and uracil (U) - Purines (double ring structure): adenine(A) and guanine (G)
Note numbering to distinguish carbons and nitrogens in bases
Nucleotides contain Nitrogenous Bases photo
Nucleic Acids
Deoxyribonucleic acid (DNA)
and
- Ribonucleic acid (RNA)
- information storage and retrieval
- RNA - transient carrier of information
- DNA - long-term storage of hereditary materiali
- composed of nucleotides
- nitrogenous base
- five carbon sugar (pentose)
Nucleic Acids photo
Nucleotides contain Pentose sugars
Note numbering to distinguish carbons in sugars has a prime (*) behind the number to distinguish the numbering from the numbering of carbons in a nitrogenous base
- RNA contains ribose
> DNA contains 2’-deoxyribose: hydroxyl group (-OH) on 2’ carbon is replaced by a hydrogen → this makes
DNA a lot more stable than RNA against chemicals
Nucleotides contain Pentose sugars photo
Nucleotides contain Phosphate Groups, Phosphoanhydride bonds
Phosphoanhydride bonds
- connect phosphate groups
→ minus water = anhydrid
Nucleotides contain Phosphate Groups, Phosphoanhydride bonds photo
phosphate groups
In DNA (RNA), the phosphates are normally joined to the C5 hydroxyl group of the deoxyribose (ribose) sugar.
- Mono-, di- and triphosphates are common
phosphate groups photo
Nucleotides differ in DNA and RNA
- DNA had 2-desoxyribose
- RNA has ribose
- DNA has thymine as a base in addition to guanine, adenine and cytosine
- RNA has uracil as a base in addition to guanine, adenine and cytosine
- DNA has 2-desoxyribonucleotides: dATP, dCTP, dGTP and dTTP
- RNA has ribonucleotide: ATP,CTP, GTP and UTP
Nucleic Acids -
Linear Polymers of Nucleotides
- Nucleotides are joined together through condensation reactions (water released)
- Breaking the bond requires water:
hydrolysis - Phosphodiester bonds link adjacent nucleotides in nucleic acids
- hydroxyl group on 3’ carbon of pentose covalently linked to phosphate group attached to 5’ carbon of adjacent pentose
sugar -> sugar phosphate backbone
Nucleic Acids -
Linear Polymers of Nucleotides photo
Nucleic Acids -
Sequence and Directionality
- polymers (or strands) have directionality a 5’ end and a 3’ end
- by convention the sequence of bases (the genetic information) in a nucleic acid strand is read 5’ to 3’, using the single letter code
*5’-G-A-T-C-3’
- in cells
- RNA is usually single stranded
- DNA is nearly always double stranded
Nucleic Acids -
Sequence and Directionality photo
Nucleic Acids - DNA Double Helix
two DNA strands are anti-parallel sugar-phosphate backbone on the outside, bases projecting inward
- strands are held together by hydrogen bonds between bases
- G pairs with C (3 H-bonds)
- A pairs with T (2 H-bonds)
> strands are complementary
- The ratio of purines to pyrimidines is 1:1
Nucleotides - Other Functions
Carriers of chemical energy
- Phosphoanhydride bond can_ be hydrolysed → e.g ATP
- high energy conserved in this bond
- cleavage releases energy →
used by prokaryotic and eukaryotic cells
Nucleotides - Other Functions photo
Nucleotides - Other Functions as Signalling molecules photo
Nucleic Acids - DNA Double Helix photo
Nucleotides - Other Functions Combined with other groups as Coenzymes photo
Amino acids are building blocks of proteins
amino acids
- building blocks of proteins
- Amino acids have:
- An alpha carbon
- carboxylic acid group
- amino group
- side chain (R group)
gives distinctive property of individual amino acids - when free in solution, carboxylic acid, amino and some side chain groups are ionised at pH 7 (inside cell)
Same 20 amino acids found in proteins of bacteria, animals and plants
The carboxylic acid, amino and side chain groups are all covalently attached to same carbon atom, the a-carbon
ionised and non-ionised amino acids photo
Proteins are Linear Polymers of Amino Acids
Peptide bonds
- link amino acids
carboxylic acid group of one amino acid reacts with amino group of a second amino acid - condensation reaction = water removed
- Breaking the bond requires water: hydrolysis
water
Note: Each amino acids, even in the peptide chain, still has an amino group and a carboxylic acid group
Proteins
- Linear Polymers with directionality photo
Proteins are Linear Polymers of Amino Acids photo
Proteins
- Linear Polymers with directionality
- polymers have directionality:
- amino (N-) terminus &
- carboxyl (C-) terminus
- by convention an amino acid sequence is read from the N-terminus to the C-terminus
- three-letter abbreviations -
Phe-Ser-Glu-Lys - single-letter abbreviations -
FSEK
Macromolecules - Some Common Themes
Condensation reactions form:
- polysaccharides from simple sugars
- proteins from amino acids
- nucleic acids from nucleotides
Macromolecules - Some Common Themes photo
non covalent interactions: (Macro)molecules interact via Noncovalent Interactions
- lonic interactions
- Hydrogen bonds
- Hydrophobic forces
- Van der Waals attractions
Individually: - Most are weak interactions
Many together: - tight binding
- Mediates molecular interactions
- Stabilise macromolecule
structures
(Macro)molecules interact via Noncovalent Interactions
Noncovalent Interactions - lonic Interactions
- electrons lost or gained by atoms → electrically charged (ions):
positive charge (lost electron) → cation (e.g. Na+)
- negative charge (gained electron) → anion (e.g. CI)
- opposite charges attract each other and hold together by an ionic bond
- In absence of water - very strong (e.g. NaCI)
- In presence of water - weak (charges shielded by water)
Noncovalent Interactions - lonic Interactions photo
Polar Covalent Bonds
> Unequal sharing of electrons belonging to a bond between two atoms
Caused if one atom in a bond has a higher affinity = electronegativity to electrons than the other atom(s)
Example:
Oxygen in water attracts electrons more strongly than hydrogen
Oxygen in methanol attracts electrons more strongly than hydrogen and more strongly than carbon
Noncovalent Interactions - Hydrogen ‘Bonds’
> Polar covalent bonds create a polarized molecule (Dipole) which can attract other polarized molecules
- Hydrogen bonds form if the polarized molecule contains a hydrogen atom AND this hydrogen atom is between two electron attracting atoms (in water for example these are oxygen but it can also be nitrogen in other molecules)
- Hydrogen bonds are based on electrostatic interactions and not as covalent bonds on the sharing of electrons
> 1/20 as strong as a covalent bond
- Strongest when the three atoms are in a straight line
salts dissolved in water photo
Noncovalent Interactions - van der Waals Attractions
Van der Waals forces include attraction and repulsions between atoms, molecules, and surfaces, as well as other intermolecular forces
- Result from a transient shift in electron density around a nucleus that creates a transient charge to which a nearby atom can be attracted or repelled.
- Weak interactions
- Effective when atoms have a specific distance from each other
Cells - The Basic Unit of Life
> comprise all living things
- small membrane-bound units
Cytosol: aqueous, gel like solution of water and chemicals - divide
> grow
- respond to stimuli
- energy conversion.
- highly specialised
- Huge diversity
- single-celled organisms
- multi-celled organisms
- cells make up tissues, which make up organs, which make up organisms
Hydrophobic definition
Hydrophobic (water-hating)
molecules cluster together to
exclude water molecules
Example: oil droplets in water
Noncovalent Interactions - Hydrophobic Forces
Adding oil (hydrophobic) to water makes the drops combine to form a larger drop because water molecules are attracted to each other squeezing the oil drops together to form a larger drop
Why Are Cells So Similar?
Same common ancestor - 3.5 billion years ago
HOWEVER
Mutation & selection of descendant cells (evolution), resulted in divergence, modification, adaptation,
specialisation AND this is on-going
Cells have a similar basic chemistry
- All composed of the same sorts of molecules
- All carry out the same basic chemistry
- All store their genetic material as DNA
- All have same basic genetic mechanisms
- genetic material is replicated & passed on to next generation by cell division
- information flow uses the same chemical machinery
