Week 1: Concepts of biomolecules Flashcards
Give 7 examples of small biomolecules. Give a general explanation of what each example does.
Sugars - monosaccharides, such as glucose. Involved in biological processes.
Fatty acids - involved in biological processes.
Amino acids - building blocks of proteins.
Cholesterol - steroid and key component of cell membranes.
Vitamins - involved in biological processes.
Hormones - involved in biological processes.
Neurotransmitters - involved in biological processes.
Name the 4 main classes of large biomolecules.
Carbohydrates - made up of monosaccharides, which are monomers containing carbon, hydrogen and oxygen.
Lipids
Proteins - can be made up if thousands of atoms and are major structural components of cells.
Nucleic acids - DNA and RNA are examples of nucleic acids, which store an organism’s genetic code.
What elements make up biological compounds?
Carbon, hydrogen, oxygen, nitrogen and phosphorus.
What does it mean if a molecule is organic?
It contains Carbon.
What are carbohydrates used for?
Commonly known as sugars and starches, carbohydrates are the primary source of energy used for cellular processes and brain function.
How are lipids formed and what is a lipid’s job?
Like carbohydrates, lipids are composed of carbon, hydrogen and oxygen.
In addition to storing energy, lipids help build certain hormones, provide insulation and form cell membranes.
How are proteins formed and what is a protein’s job?
Proteins contain atoms from the main three elements plus nitrogen. They are formed from 21 types of monomers called amino acids.
Proteins comprise the majority of the biological molecules in your cells. They build tissues like muscles, and help direct many other bodily functions, including the immune response.
How are nucleic acids formed and what is their job?
Nucleic acids - like DNA and RNA - are constructed from monomers called nucleotides, which add phosphorus to the other four composite elements.
Nucleic acids carry your genetic code and translate it into the actual proteins that perform your bodily functions.
What happens in the transcription step of the central dogma?
DNA is read by RNA polymerase, which creates a complementary strand of RNA.
What happens in the translation step of the central dogma?
The RNA is read by ribosomes to make proteins.
What happens in the DNA replication step of the central dogma?
DNA makes a copy of itself during cell division.
What are the steps of the central dogma?
- DNA replication
- Transcription
- Splicing
- Translation
What is the exception of the central dogma?
Reverse transcription - Information can flow from RNA to DNA, which then forms RNA again and is translated to form proteins.
List the properties of liquid water.
Polarity and H bond.
Liquid state 0 - 100°C.
Lowest density at 4°C.
High surface tension.
Heat capacity.
Fluid properties.
Soluble to ions such as Na+, K+, Ca2+, Cl-.
What ideas does the dissociation of water molecules reflect?
Competition between the energetics of binding and the entropy of charge liberation.
What is the formula for ionic strength?
What do each of the symbols mean?
I = 1/2 * Sum(CiZi^2)
Sum = Capital sigma.
C = ion concentration
Z = charge
What is the nature of most binding interactions?
Most binding interactions are electrostatic in origin and are often dependent on the concentration of ions in the solution.
What is the electrostatic force between two charged particles?
F = (q1*q2) / (4pi * relative permittivity * r^2)
What is the electric field created by a single charged particle?
E(r) = Q /(4pi * relative permittivity * r^2)
What is the principle of superposition for a charge distribution?
Etot = Sum(Ei)
= Sum( E(r -ri))
What is the result of the polarisation of molecules on the dielectric constant?
Increase it.
What is the dielectric constant of water at room temperature?
80
What are the 4 DNA basis?
A (Adenine)
T (Thymine)
G (Guanine)
C (Cytosine)
What are the 2 (or 4) pairings of the DNA basis?
A - T
G - C
(Could argue the reverse are pairings)
Draw the DNA base pairs.
(1)
What is the general structure of DNA?
Phos - Sugar - Base
(2)
In eukaryotic life, how many amino acids are there?
20
Draw the general structure of an amino acid. Label each part.
(3)
List the 9 nonpolar side chains.
Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
Phenylalanine
Tryptophan
Proline
Draw the Glycine structure.
(4)
Draw the Alanine structure.
(4)
Draw the Valine structure.
(4)
Draw the Leucine structure.
(4)
Draw the Isoleucine structure.
(4)
Draw the Methionine structure.
(4)
Draw the Phenylalanine structure.
(4)
Draw the Tryptophan structure.
(4)
Draw the Proline structure.
(4)
List the 6 polar side chains
Serine
Threonine
Cysteine
Tyrosine
Asparagine
Glutamine
List the 2 acidic charged side chains.
Aspartate
Glutamate
Draw the Aspartate structure.
(6)
Draw the Glutamate structure.
(6)
List the 3 basic charged side chains.
Lysine
Arginine
Histidine
Draw the Lysine structure.
(7)
Draw the Arginine structure.
(7)
Draw the Histidine structure.
(7)
Draw the Serine structure.
(5)
Draw the Threonine structure.
(5)
Draw the Cysteine structure.
(5)
Draw the Tyrosine structure.
(5)
Draw the Asparagine structure.
(5)
Draw the Glutamine structure.
(5)
Draw the structure of a typical beta sheet. Label which parts are parallel and anti-parallel, and where the n and c terminus are.
(8)
Draw the structure of a typical alpha helix, taking into account the H bonds and the side chains.
(9)
Draw the structure of a lipid and label it.
(10)
What are 4 key features of a lipid?
Hydrophobic
Hydrophilic
Polar
Charged
What are the key structural features of parallel and anti-parallel beta sheets?
The sheets are held together via hydrogen bonds.
Parallel beta sheets have polypeptide strands that run in the same direction.
In contrast, anti-parallel beta sheets have polypeptide strands that run in opposite directions.
The difference in strand directionality results in variations in the stability of the hydrogen bonds.
Why do anti-parallel beta sheets have stronger hydrogen bonds than parallel beta sheets?
As the bonds in parallel sheets have a non-linear arrangement, they are further away and thus weaker than the anti-parallel counterpart.
Explain why pH is important to the function of a protein.
Some proteins carry charge groups whose extents of charges are pH dependent. This means that as pH changes, the net charges vary, affecting their structural stability and function.
This is particularly the case when the active centres involve charge groups.
List 5 structural features of DNA.
Double strand, helical, unique base pariing, projecting charges outside the helix, each base pairing contributing about 3.4A to the length and 10 base pairs to a helical pitch of 34A. The double strand is about 20A wide.
