Chemical Properties and Classes Flashcards
TELL ME THE FOLLOWING ABOUT LIPIDS:
* Their class
* Polarity
* Major constituent of
* Made of
* Differernt types
- A class of** hydrocarbons**
* Nonpolar compounds or possess a nonpolar portion - Major constituent of **storage fat and cell membranes **
- The hydrocarbon (H bound to C) may be** saturated (no C=C)** or unsaturated (contains C=C)
- Longer saturated hydrocarbons are rigid, or solidify at warmer temperatures
Tell me the following about Phospholipids:
* Their class
* Composed of and bonds present
* polarity
* What happens when added to water
* Major component of what
- Class of lipids whose molecule has a** hydrophilic “head”** containing a phosphate group and two hydrophobic “tails” derived from fatty acids
- The head and tail are joined via an alcohol residue (joined via ester bond)
- In a phospholipid, 2 fatty acids and 1 phosphate group are attached to a glycerol (C3H8O3)
- The Fatty acid tails = hydrophobic
- Phosphate group head = hydrophilic
- When phospholipids are added to water they self-assemble into a bilayer, in this structure the hydrophobic tails point toward the interior and hydrophilic head pointing towards the water extracelluarly
- This bilayer arrangement is found in cell membranes
- Phospholipids are a major component of all cell membranes
Tell me the following about carbohydrates:
* What do they consist of
* Their empirical formula
* Different types
- They consist of C, H and O atoms
- Have the empirical formula Cm(H2O)n (where m may be different from n)
- They can be monosaccharides, polysaccharides and oligosaccharides
Tell me some general facts about monosaccharides
o These are the simplest carbohydrates meaning they cannot be hydrolysed to small carbohydrates
o They are **aldehydes or ketones with two or more hydroxyl groups **
o The general chemical formula of an unmodified monosaccharide is (C*H2O)n, literally a “carbon hydrate”
o Monosaccharides are important fuel molecules as well as **building blocks for nucleic acids **
What is the smallest monosaccharide?
o The smallest monosaccharide, for which n=3, are dihydroxyacetone and D- and L-glyceraldehyde’s
Tell me about the monosaccharide D-glucose
An aldohexose(a monosaccharide whose molecular structure contains both an aldehyde (an aldose) and six carbons (hexose)
Glucose can exist in both linear and cyclic form
When glucose is in cyclic form it the alcohol group interacts with the aldehyde group to form the cyclic shape
Tell me about polysaccharides
o Most abundant carbohydrate found in food
o Long chain polymeric carbohydrates composed of monosaccharide units, bound together by glycosidic linkages **
o This carbohydrate can react with water (hydrolysis**) using amylase enzymes as catalyst, which produces constituent sugars (monosaccharides, or oligosaccharides)
o Polysaccharide + Water –> Monosaccharides/ oligosaccharides (hydrolysis)
How do the properties of polysaccharides differ from monosaccharides?
These macromolecules can have distinct properties from their monosaccharide building blocks.
They may be amorphous or even insoluble in water
Tell me the importance of nucleic acids, what they are composed of and the different forms
- Nucleic acids are the biopolymers
essential to all known forms of life - The term nucleic acid is the name for
both DNA and RNA - They are composed of nucleotides, which
are the monomers of nucleic acids
made of three components: ** a 5-carbon
chain, a phosphate group and a nitrogenous base** - If the sugar is a compound ribose,
The polymer is RNA (ribonucleic
Acid); if the sugar is **deoxyribose, the polymer is DNA **(deoxyribose nucleic acid)
What are the different nucleic acid bases
Cytosine
Guanine
Adenine
Thymine (DNA)
Uracil (RNA)
How many phosphate groups can nucleotides have?
1, 2 or 3
e.g.,UMP Vs ATP
How do phosphates bind together and tell me some properties of this bond
Phosphates bind together by phosphoanhydride bonds;
o very high energy
o ATP is the common storage molecule for chemical energy in the cellular environment
With the bases, which ones are purines and which ones are pyrimidines?
Purines: adenine and guanine
Pyrimidines: Thymine and cytosine
Tell me about DNA structure
- H bonds between bases
* AT have 2 H bonds and GC have 3 H bonds - In GC the =O is a H bond acceptor and the NH2 on the C is the H bond donor
The NH on G is the H bond donor and the =N is the H bond acceptor
NH2 again on G is the donor and the lone pair on =C on C is H bond acceptor
Tell me the following about amino acids:
* type of compound
* What they contain
* Key elements
* number occuring naturally
* draw basic structure
* Organic compounds
* Contain amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R groups) specific to each amino acid
* The key elements of an amino acid are **C, H, O and N, other elements are found in the side chains of certain amino acids
* There are about 500 naturally occurring amino acids which are known (20 of then appear in the genetic code**, 0.04%)
How many proteinogenic alpha-amino acids are there in eukaryotes?
Tell me the different groups and the amino acids in each group and draw their structures
- The 21 Proteinogenic alpha- amino acids found in eukaryotes, grouped according to their side chains’ PKa values and charges carried at physiological pH (7.4)
What are the AA with hydrophobic side chains and tell me some properties
*** Alanine, Valine, Isoleucine, leucine, and methionine **
- The AA in this group lack polar functional groups in their side chains
- Due to the hydrophobicity of their R groups, they often cluster together within the interior of proteins, stabilising the protein structure via hydrophobic interactions
Tell me about the aromatic AA with hydrophobic side chains and tell me some properties of them
- The side chains of the aromatic amino acids; phenylalanine, tyrosine and tryptophan are very hydrophobic
- The R group of tyrosine also contains a polar hydroxyl group that can participate in H bonding interactions
- The R groups of tyrosine, and particularly tryptophan, **absorb UV light at a maximum of 280nm wavelength **
What are the AA with polar uncharged side chains and tell me some properties
- The R groups of the polar, uncharged amino acids all contain polar functional groups that can H bond to water
* Serine and threonine contain hydroxyl groups, asparagine and glutamine contain amide groups - They all contain CONH2 which gives them a different polarity
What another AA with the polar uncharged side chain
what bond is present between the thiol groups
Cysteine
* The cysteine contains a sulfhydryl group
* The sulfhydryl group of the cysteine side chain is a weak acid (pKa= 8.2)
* The cysteine side chain therefore is mostly uncharged at neural PH
Adisulphide bind is present between thiol groups
What are the AA with positiviely charged side chains and what are the properties
- The most hydrophilic R group are those that are either +ve or -ve charged
- The side chains of lysine and arginine are fully +ve at neutral pH
- In** lysine**, a primary amino group is attached to the e carbon of the side chain
- In** arginine**, the guanidinium group of the side chain is +ve charged
- In histidine, the R group contains an aromatic imidazole group that is partially positively charged at neutral PH
What are the amino acids with negaitively charged side chains and their properties
- The R groups of aspartate and glutamate contain carboxyl groups that are fully negatively charged at neutral PH (PKa 3.65 and 4.25)- they are deprotonated
- Negative charge is due to presence of carboxyl group
- In aspartate, the carboxyl group is attached to the Beta carbon of the amino acid backbone)
- In glutamate, the carboxyl group is attached to the gamma carbon
To recap, what are the five groups of (-R) amino acids
What are the post-translational modifications that each AA can undergo
When the AA undergo post translational modifications, what cellular functions does this help with
AA can come in zwitterionic form. What does this mean?
- A zwitterion, also called an inner salt, is a molecule that contains an equal number of +ve and -ve charged functional groups
What can zwitter ions act as
Each AA has an isoelectric point. What is this and what does it depend on
- Each AA has a characteristic isoelectric point which is the PH at which the +ve = -ve charge
- This will vary depending on side chain
How is the isoelectric point (pI) of an amino acid calculated?
- For an AA with one amine and one carboxyl group, the pI can be calculated from the mean of the PKas of his molecule
- pI= isoelectric point
- pKa1=PKa of amino group
- pKa2= Pka of carboxylic group
- At the isoelectric point, net charge is zero
- The AA is least soluble in water and the AA does not migrate in electric field (important in electrophoretic separation of peptides)
How can peptide bonds be broken? What is the downside to this
- A peptide bond can be broken by hydrolysis
- In the presence of water, they will break down and release 8-16 kilojoule/mol (2-4 kcal/mol) of Gibbs energy
- This process is** extremely slow**, with the half-life at 25˚c of between 350-600 years per bond
Tell me about the proteins secondary structure
-
The alpha helix is a common motif in the secondary of proteins and is a right hand-helix conformation in which every backbone N-H group H bonds to the backbone C=O group of the AA located three or four residues earlier along the protein sequence
*** The beta-sheet **(also beta-pleated sheet) is a common motif of regular secondary structure in proteins. beta sheets consist of beta strands (also beta-strand) connected laterally by at least two or three backbone H bonds, forming a generally twisted, pleated sheet
Tell me about the proteins tertiary structure
**o Hydrophobic interactions **
These amino acids orient themselves towards the centre of the polypeptide to avoid the water
**o Disulphide bridge **
The AA cysteine forms a bond with another cysteine through its R group
o Hydrogen bond
Polar ‘R’ groups on the AA form bonds with other polar R groups
**o Hydrophilic interactions **
These AA orient themselves outward to be close to the water
o Ionic bonds
Positively charged R groups bond together
Tell me about the proteins quaternary structure
- The quaternary structure of a protein is the associated of several protein chains or subunits into a closely packed arrangement
- Each of the subunits has its own primary, secondary and tertiary structure
- The subunits are held together by H bonds and Van der waal forces between nonpolar side chains
What are functional groups, what do they help predict and draw some
- Functional groups are groups of one or more atoms of distinctive chemical properties no matter what they are attached to
What are hydrocarbons and draw the types
Tell me about alcohol, the types of alcohols and ethers
Tell me about phenol
Tell me about aldehydes and ketones
Tell me about carboxylic acids
Tell me about carboxylic acid derivatives (amides and esters)
Tell me about amines
Functional groups in drug
Functional groups in these compounds
Why do atoms bond and what is a bond, why does a bond form?
- Atoms bond to gain** stability**, molecules more stable than single atoms
- A chemical bond, is a lasting attraction between atoms, ions or molecules that enables the formation of chemical compounds
- It forms because of valence electrons (furthest from the nucleus) (indicated by group number of periodic table)
Bonding- hybridisation of carbon
Bonding-methane
Bonding- ethene
Bonding- acetylene (ethyne)
Tell me abount ionic bonding
- A type of chemical bonding that involves the electrostatic attraction between oppositely charged ions or between atoms with sharply different electronegativities, and is the primary interaction occurring in ionic compounds
- Ionic bonds (strong electrostatic attraction): atoms with extra electrons are negatively charged (called anion)
- Atoms with fewer electrons are positively charged (called cations)
- These ions of opposite charge attract to form salts
- Salts dissolve in water because individual cations and anions become dissociated by water molecules
Tell me about covalent bonding
- A chemical bond that involves the sharing of electron pairs between atoms
- These electron pairs are known as shared pairs or bonding pairs, and the stable balance of attraction and repulsion forces between atoms, when they share electrons, is known as covalent bonding
- Covalent bonding includes many kinds of interactions, including sigma-bonding, Pi-bonding where one shared pair is a single bond; two shared pairs is a double bond, and three shared pairs is a triple bond
Tell me about electronegativity
- Symbol, , measures the tendency of an atom to attract a shared pair of electrons (or electron density)
- An atoms electronegativity is affected by both its atomic number and the distance at which its valence electrons reside from the charged nucleus
- The higher the associated electronegativity, the more an atom or a substituent group attracts electrons
What are dipoles
- Not equal sharing of electrons in a molecule result in a **dipole **
- HCl is not charged but it contains a permanent dipole
- More electrons on the Cl atom (more electronegative) result in a partial negative charge on Cl
- Less electrons on the H atom (less electronegative) result in a partial positive charge on H
Tell me about dipole-dipole interactions
Tell me about dipole-induced dipole interactions
- The permanent dipole of a molecule can induce a dipole in a non-polar molecule
- A dipole can also be induced by the effect of an instantaneous dipole
Tell me about H bonding
- Is a primarily electrostatic force of attraction between a H atom which is covalently bound to a more electronegative atom or group, particularly the second-row elements N, O or F- the H bond donor (Dn)- and another electronegative atom bearing a long pair of electrons- the H bond acceptor (Ac)
Tell me about the conjugate acids/base formulas for acids and bases
How do you work out the pH from the Ka
Whats the releationship between pH,PKa and ionisation?
pH > pKa = deprotonated
pH < pKa= protonated
pKa of functional groups
pKa- drugs
pKa- Aspirine
pKa- amphetamine
pKa of functional groups
