CBI 5: Structure and Function of Bio Molecules Flashcards
1
Q
What are the four major categories of biological macromolecules and their small molecule subunits?
A
2
Q
What is the empirical formula of carbohydrates?
A
- typically (CH2O)n
- but there are many exceptions
3
Q
What are the three classes of carbohydrates?
A
- monosaccharides
- disaccharides
- polysaccharides
4
Q
What are the two subclasses of monosaccharides and how are they categorised?
A
- aldoses: if the C=O group is based on an aldehyde
- ketoses: if the C=O group is based on a ketone
5
Q
Name monosaccharides according to the number of carbon atoms
A
6
Q
What is Fischer projection?
A
- a way to draw compounds with multiple tetrahedral centers
- horizontal lines present groups that point towards you (out of the paper plane)
- vertical lines point away from you (into the paper plane)
7
Q
How do you label a monosaccharide as D/L with Fischer projection?
A
- locate carbonyl carbon and draw structure as a Fischer projection
- then identify the stereocenter furthest away from the carbonyl group
- it will be that penultimate carbon in the chain
- if the hydroxyl (-OH) group is on the right-hand side, then this is a D-isomer
- if it is on the L-hand, it is the L-isomer
8
Q
What forms do carbohydrates adopt in aqueous solution?
A
- the open-chain form
- the cyclic form
- occurs when the carbonyl carbon of the open-chain reacts via nucleophilic attack from one of the hydroxyl groups in the chain
- this forms a hemiacetal (starting from aldose) or hemiketal (from ketose) group
- this process can be reversed and most monosaccharides exist as a mixture of these in aqueous solution
9
Q
What is a furanose?
A
- a sugar that has a five-membered ring
10
Q
What is a pyranose?
A
- a six-membered ring
11
Q
What is the anomeric carbon and how are anomers formed?
A
- cyclization of a monosaccharide introduces a new stereocenter into the molecule at the hemiacetal/hemiketal carbon atom (known as the anomeric carbon)
- this is because the nucleophilic attack can occur either above or below the plane
- this forms a pair of anomers
12
Q
How do you differentiate between the two anomers?
A
Alpha-anomer:
- the hydroxyl group of the anomeric carbon is on the opposite side to the substituent at the penultimate carbon in the chain (the one that determines if it is a D- or L- sugar
Beta-anomer:
- the hydroxyl group of the anomeric carbon is on the same side to the substituent at the penultimate carbon in the chain
13
Q
How are disaccharides formed?
A
- when two monosaccharides react with each other and form a covalent bond, called a glycosidic bond, via a condensation reaction
14
Q
How do you name disaccharides?
A
- if only one anomeric carbon is involved, only the configuration of that carbon is included in the bond type
- e.g. in lactose, beta-D-galactopyranose forms the linkage, so the bond is called a beta-1, 4 glycosidic bond
- if the anomeric carbon atoms of both monosaccharides are involved in the glycosidic bond formations, then the configuration of both need to be stated
e. g. for sucrose, alpha-D-glucopyranose and beta-D-fructopyranose are involved, forming an alpha, beta-1,2 glycosidic bond
15
Q
Describe how cellulose is formed
A
- by connecting beta-D-glucose via beta-1, 4 glycosidic bonds
16
Q
Describe how starch and glycogen is formed
A
- formed by alpha-D-glucose connected via alpha-1,4 glycosidic bond that generates a long chain that folds into a helix called amylose
- long-chain polysaccharide branches are formed by connecting other alpha-D-glucose subunits via an alpha-1,6 glycosidic bond, generating amylopectin
- starch contains both amylose and amylopectin
- glycogen is solely formed from amylopectin that is highly branched
17
Q
What are the functions of carbohydrates?
A
- exactly what they do depends on their monosaccharide subunit unit composition that gives rise to their physicochemical properties such as shape and size:
examples are:
- structure: chitin, cellulose
- post-translational modification: e.g. ABO blood groups
- energy storage: glycogen and starch
18
Q
What are the five main lipid classes?
A
- fatty acids
- triacylglycerols
- glycerophospholipids
- sphingolipids
- sterol lipids
19
Q
What are fatty acids?
A
- long hydrocarbon chains with a carboxylic acid group at one end
- can contain C=C double bonds, or not
- use E/Z nomenclature
20
Q
How does the stereochemical configuration of fatty acids contribute to its physicochemical properties?
A
- the Z-configuration leads to a bend/kink in the hydrocarbon chain
- the E-configuration does not
- these isomers will display different properties (e.g. how easily they can pack together in membranes)
21
Q
How do you name fatty acids according to their length?
A
22
Q
How do you write the notation for fatty acids that indicate the number of carbons in a chain and the number of double bonds?
A
23
Q
What are the two ways of stating where the double bond is on a fatty acid?
A
24
Q
Why do fatty acids have an even number of carbons?
A
- they are synthesized in biological systems by the sequential addition of two-carbon units from a metabolic precursor to extend an existing acyl chain
25
Q
How are triacylglycerols formed?
A
- when fatty acids react via their carboxylic acid group with the hydroxyl groups of glycerol to form an ester bond in a condensation reaction
26
Q
What are triacylglycerols used for in the body?
A
- as chemical energy storage molecules
- represents a major component of adipocytes (fat cells)
27
Q
What is a glycerolphospholipid composed of?
A
- when glycerol is connected to two fatty acids and the remaining hydroxyl group bonds to a phosphate that can then connect to different groups
- glycerophospholipids can have one of many head groups: e.g. choline, serine, inositol
- these head groups give the lipid different chemical characteristics
28
Q
Describe the structure of phospholipids and hence their properties
A
- they are amphiphilic molecules
- they have a hydrophobic tail formed by the fatty acids and a hydrophilic head group
- their amphiphilic character allows them to form bilayers with a non-polar core and the polar head groups arranged as such that they more favourably interact with aqueous media
29
Q
What are sphingolipids?
A
- a type of phospholipid
- they share a common structure feature: the sphingoid base backbone
- the sphingoid base (sphingosine) is synthesized from the amino acid serine and the long-chain fatty acyl CoA
- a fatty acid and a head group are then added to generate the three major classes of sphingolipids (next flashcard)
30
Q
What are the three major classes of sphingolipids?
A
Sphingomyelins:
- contain a phosphate group that is most commonly bound to a choline or ethanolamine group
- mainly found in myelin sheaths
Cerebrosides:
- the simplest sphingolipids
- contain a monosaccharide as a head group and are found in the membrane of neurons
Gangliosides:
- complex sphingolipids that contain an oligosaccharide as head groups with a minimum of one sialic acid unit
- they make up around 6% of lipids in the brain
31
Q
What function do sphingolipids have?
A
- they perform several biological functions
- most importantly is their protective effect by stabilising lipid membranes of which they are part
32
Q
What are sterol lipids derivatives of?
A
- steroids are derivatives of cyclopentanoperhydrophenanthrene
33
Q
What type of cell generates steroids most of the time?
A
- eukaryotes
34
Q
Describe the structure and function of cholesterol
A
- a sterol lipid
- the most common steroid in the plasma membrane of animal cells
- ring system is hydrophobic and quite rigid, while the polar hydroxyl group is hydrophilic
Function:
- ensures biological membranes remain both stable and fluid,s so they maintain viable cellular functions
- it is also a biosynthetic precursor for steroid hormones, such as progesterone and testosterone, and bile acids
35
Q
How do lipids aggregate in an aqueous solution?
A
- due to their hydrophobic tails and hydrophilic head groups, they spontaneous aggregate in a way that the tails interact with each other and the hydrophilic head groups face out towards the surrounding water molecules
- this is driven by the hydrophobic effect:
- the energetically unfavourable disruption of the hydrogen bond network of water molecules by the lipid side chains is minimised by lipid chains orientating inwards/toward each other
- London forces are thus maximised between fatty acid tails
- and the hydrophilic head groups point outwards and so can form electrostatic and hydrogen bonds with the surrounding water molecules
- overall, the surface area over which hydrophobic and hydrophilic species are in contact are minimised
36
Q
What are leaflets?
A
- the two opposite sides of a lipid membrane
37
Q
What are the main properties of lipid bilayers?
A
- they are cooperative structures
- they can extend and fuse with themselves
- they are self-repairing
- they are impermeable for ions and polar molecules
38
Q
What affects a lipid membrane’s fluidity
A
- the viscosity is dependent on the kind of lipids found in the membrane and the order of their lipid chains
- when the lipid chains are highly ordered, the membrane is in solid phase
- they are in liquid phase when chains can move more freely
- different kinds of lipids (saturated and unsaturated) can change the melting temperature (Tm)
- cholesterol is the main regulator for membrane fluidity in mammals:
- due to its rigid steroid structure and the small polar hydroxyl group, it intercalates (is inserted) into the membrane and stabilises the membrane at high temperatures while preventing stiffening and clustering at low temperatures
39
Q
What are the major components of DNA and RNA?
A
- the nucleotides
- these are small subunits assembled from a phosphate and a nucleoside (a sugar attached to one of the nitrogenous bases)
40
Q
What are the differences between DNA and RNA?
A
41
Q
Which bases are purine and which are pyrimidine?
A
42
Q
How do you build a strand of DNA/RNA?
A
- the nucleotides react with the phosphate group and their 3’ carbon of the their sugar
43
Q
What are some other functions of nucleotides (other than to make DNA and RNA)?
A
- monomeric nucleotides often function as components of energy-rich chemical units (ATP, GTP), second messenger molecules (cAMP), or substrates for enzymes (ATP, GTP)
44
Q
How many hydrogen bonds are formed between guanine and cytosine?
A
- 3 hydrogen bonds
45
Q
How many hydrogen bonds are formed between adenine and thymine/uracil?
A
46
Q
How are nucleic acids formed?
A
- joined together by a bond between the phosphate and the third carbon atom of the sugar
- a condensation reaction, forming the sugar-phosphate backbone
- the connections are formed via the 3rd and the 5th carbon of the sugar ring
- these determine the expression of the 3’ to 5’ direction along the strand which is often used in relation to specific enzymes like RNA and DNA polymerases
47
Q
Describe the structure of the DNA double helix
A
48
Q
What are amino acids?
A
49
Q
What are the four different classes of amino acids and how do you assign them?
A
- you assign them based on the chemical functionality of their side-chains
50
Q
Describe protein structure
A
51
Q
What is the driving force for folding a protein? How are some proteins assisted?
A
- Gibbs energy
- some proteins need help to fold into their final structure (as many possibilities may exist and they may become folded into a conformation that represents a local energy minimum)
- the proteins that facilitate correct folding are called chaperones (i.e. heat shock proteins, HSPs)
52
Q
How do you begin the process of protein purification?
A
- the protein needs to be released from the cell by disrupting/destroying the plasma membrane, a process called lysis
- this can be done by pressing cells through a small gap with high pressure (French press) or by repeatedly freezing (liquid nitrogen) and thawing cells, or by using detergents that dissolve the membrane
- then the soluble part can be separated from the cell debris by centrifugation
- to isolate the target protein from all other soluble parts of a cell, we can make use of the different properties of different proteins
- one way of isolating a specific protein is chromatography, which can be implemented in these ways:
- size-exclusion chromatography (SEC)
- ion exchange chromatography (IEX)
- affinity chromatography (AC)
53
Q
Describe size-exclusion chromatography
A
54
Q
Describe ion-exchange chromatography
A
- separates molecules depending on their charge
- e.g. a protein that contains many amino acids with acidic side chains will have a negative charge at pH 7
- due to their charge, the proteins can interact via ionic forces with beads (column matrix) that have been modified with a charged group
- molecules with the same charge as the matrix will flow through the column
- the protein of interest can be eluted by changing the pH or using high ion concentrations that replace the proteins from the beads
55
Q
What is the isoelectric point or pl?
A
- the pH when a protein has an overall net charge of zero
- the charges of all amino acid side chains cancel each other out
56
Q
Describe affinity chromatography
A
- similar technique to IEX, but far more specific
- a specific amino acid sequence or even a whole protein can be attached to the protein of interest
- these add-ons are called tags and they can specifically interact with certain groups, molecules or even ions
- if a protein with a tag enters a column in will interact with the column matrix and stay attached to the column, while most other proteins will flow through
- afterwards, the protein is eluted with a high concentration of small molecules that interact either with the column matrix or the tag itself
- the picture shows some tags commonly used in protein purification
57
Q
Describe how SDS-PAGE works
A
another method to separate molecules by size is sodium dodecylsulfate-poly acrylamide gel electrophoresis (SDS-PAGE)
- the biomolecules are first given a negative charge using a strong detergent called sodium dodecylsulfate (SDS)
- this denatures the proteins and due to its sulfate head group, gives each protein an overall negative charge
- if a current is applied, the protein will migraate towards the positively charged anode and away from th cathod
- by placing a gel that is formed by a polymer in between the electodes, the larger molecules take longer to migrate through the mesh while the smaller ones can pass quickly through
- this way, separation by size is achieved
- afterwards, the proteins in the gel are typically coloured with a blue dye (Coomassie blue) that makes the proteins appear as visible bands
- in order to determine the size of the band, a marker is applied to one of the pockets of gel that contains proteins of known sizes
- often SDS-PAGE is used to verify the purification of a protein (single band on the gel) or for further analysis via a Western blot
58
Q
How is the gel for SDS-PAGE made?
A
- the gel is formed by a polymerisation reaction where a bond between two monomers is formed by breaking a C=C double bond
- the monomer used is acrylamide
- the polymerisation takes place via a radical reaction that is initiated by two other ingredients called ammonium persulfate (APS) and tetramethylethylenediamine (TEMED)
- acylamide by itself will only form long chains, thus the mixture also contain a small amount of bisacrylamide that can form connections between the long chains and leads to the formation of a gel/mesh
59
Q
Definition of carbohydrates
A
- Carbohydrates have the chemical formula (CH2O)n
- they are sugar molecules that are involved in structure and energy storage in the cell
60
Q
Definition of fatty acids
A
- Fatty acids are long carbohydrate chains with a carboxylic acid group at the end.
- Those that do not contain C=C double bonds are called saturated fatty acids; those that do contain C=C double bonds are called unsaturated fatty acids.
61
Q
Definition of lipids
A
- Lipids are amphiphilic molecules with a hydrophilic head group and a hydrophobic tail.
- We distinguish between phospholipids, triacylglycerides and sphingolipids.
62
Q
Definition of membranes
A
- Membranes are lipid bilayers with a hydrophobic core and a hydrophilic border.
- They form the diffusion barrier of cell membranes and cell compartments.
63
Q
Definition of nucleotides
A
- Nucleotides are the basic elements that form DNA and RNA.
- They consist of a ribose sugar, a phosphate group and a nitrogenous base.
64
Q
Definition of proteins
A
- Proteins are comprised of amino acid subunits that are connected by peptide bonds.
- Their structure is determined by secondary elements (i.e. alpha-helix and beta-sheets) that are arranged in 3D.
- This structure is stabilised by several different covalent and non-covalent bonds.
