LECTURE 2: Introduction to Macromolecules Flashcards
Describe the reactions that add and remove monomers from a growing polymer.
a. List the specialized names we give to the linkages for each type of macromolecule
a) dehydration reaction- add
hydrolysis reaction- remove monomers
fats- ester bonds
carbs- glycosidic linkages
proteins- peptide bonds
nucleic acids- phosphodiester bonds
Explain why proteins have more structural diversity compared to other macromolecule
There are 20 different amino acids
• Average protein is 100 to 500 amino acids
• So there’s 20^500 combinations,
• A protein’s amino acid sequence makes it fold into a specific 3D structure due to chemical interactions
• Their final 3D structure gives them specific roles in the cell
• They have a variety of cellular functions.
Classify the different amino acids into their basic groups (polar, non-polar, etc).
polar uncharged: serine cytosine threonine glutamine asparagine tyrosine
non polar: glycine, leucine, isoleucine, valine, methionine. phenylalanine, tryptophan, proline
polar charged- lysine arginine histidine aspartic acid glutamic acid
List the experimental methods that we use to determine protein structures.
- X-ray crystallography
- Cryo-electron microscopy
- Nuclear magnetic resonance spectroscopy
Describe how the ABO blood system works.
a. List who can and can’t receive certain types of blood.
Sequence differences in the ABO glycosyltransferase gene means the encoded enzyme works differently in different people.
A person with type A RBCs has B antibodies in their blood, so can’t get B or AB blood transfusions. A person with type AB can get blood from anyone. A person with type O blood can donate their blood to anyone.
Describe the functions of different polysaccharides.
- Can serve as a energy source
• starch in plants is made from linear alpha(1,4) linked glucose
• glycogen in muscles and liver is made from branched alpha(1,4)&(1,6) glucose - Can serve structural roles
• cellulose in plant cell walls is made from beta(1,4) linked glucose
• chitin is a more complex polysaccharide; main component of arthropod exoskeletons
Describe the differences between polar, non-polar, and amphipathic molecules.
Polar = different parts of the molecule have net negative or positive charge. From dipoles (e.g. water) or from + or – charges (e.g. acetic acid)
Hydrophobic (“water fearing”) because they contain significant regions with equal electron distribution (i.e. non-polar)
If a molecule has both hydrophilic and hydrophobic parts, it’s called amphiphatic.
. Describe the difference between a fatty acid, a fat and a phospholipid.
a. Describe how the degree of saturation of fatty acids impacts the melting temperature of fats.
List the biological roles of lipids in cells.
- Source of energy in the diet and serve to store energy in the body. Why? Because they’re highly reduced!
e. g. fats and oils - Some hormones (chemical messengers) are lipids.
e. g. steroids and prostaglandins. - Many vitamins are lipids. e.g. vitamins A, D, E
- The basic structural elements of biological membranes.
e. g. phospholipids (later lecture!)
Describe the difference between a nucleobase, a nucleoside, and a nucleotide.
nucleobase- just the base ATCG
Nucleoside- sugar and base
nucleotide- sugar base and phosphate group
List and describe the biological roles of nucleotides in the cell.
- Nucleotides are monomeric units from which DNA and RNA are made
(i. e. the molecules that encode and read out the genetic information of the cell) - Regulatory molecules
a) Second messengers in cell signaling (eg. cAMP)
b) GTP can serve as a switch to activate some proteins (G-proteins) - Agents of energy transfer for metabolism
a) Cleaving of phosphate groups releases
energy (ATP)
b) Co-enzymes in energy transfer
reactions (NAD)
• Co-enzymes are non-protein
compounds needed for enzyme
action
• NAD = nicotinamide adenine
cyclic AMP (cAMP)
dinucleotide
Compare and contrast the structural and chemical differences between RNA and DNA.
• DNA is an antiparallel double stranded helix
• Strands are held together by hydrogen
bonding between bases (‘rungs’ of the ladder)
• A pairs with T, G pairs with C
Note that a purine always pairs with a pyrimidine!
- No OH at 2’
RNA is single stranded (usually)
Can fold back on itself to form complex 3D structures (e.g. ribosomes) by base pairing (A with U, G with C)
Some RNAs have catalytic activity (ribozymes)
- OH at 2”
Macromolecules
are large molecule with over 1000 atoms
play many structural and functional roles in cells.
Often polymers: poly- aggregation of similar units (monomers)
What are the 4 categories of macromolecules?
proteins, nucleic acids, polysaccharides and lipids.
Small molecules
are those less than 1000 atoms (including monomers)
Macromolecule and monomer examples
Starch, glycogen, cellulose(ALL POLYSACCHARIDES); monomer- Monosaccharides
DNA; monomer- nucleotides
RNA; monomer- nucleotides
Protein; monomer- amino acids
Monomer
is a molecule that can react together with other monomer molecules to form a larger polymer chain o
Describe lipids
are diverse organic molecules that are insoluble in H2O but soluble in nonpolar organic liquids (e.g. chloroform).
are all hydrophobic
Describe how micelles form.
FA hydrophilic heads are towards the outside and interact with water and hydrophobic tales point inwards and interact with each other. A monolayer of lipid.
Why is H20 a dipole?
Water is a dipole because shared electrons spend more time by the electrophilic oxygen
Fats
are made of glycerol and linked by three ester bonds to three fatty acids (FAs).
fatty acids (FAs).
are unbranched hydrocarbons with one carboxyl group; they are amphipathic
can be saturated or unsaturated
Saturated FAs
FAs lack C=C double bonds and are solid at room temperature (closer packing of carbons, more van der Walls force)- high melting temp
Stearic acid is an 18 C saturated fatty acid
Unsaturated FAs
have one or more C=C double bonds and are liquid at room temperature.- low melting temp
Oleic acid is an 18 C unsaturated fatty acid The double bond puts a kink in the chain
Carbohydrates
include simple sugars and sugar polymers
are made of carbon, oxygen & hydrogen
monosaccharides
Carbohydrate monomers
generally some combination of
CXH2XOX (eg glucose = C6H12O6)
Describe the reaction that adds carbohydrate monomers
dehydration reactions by the loss of a hydroxyl from the a carbon of one monomer and a hydrogen from another carbon of the co-joining monomer (one oxygen & two hydrogens are lost to water). Forms a glycosidic bond.
alpha
OH IS DOWN
Beta
OH is up
How can a Monosaccharide exist in solution?
can be linear (middle), or spontaneously close to form alpha- or beta-rings. The difference is whether the terminal hydroxyl (OH) is up or down (in red). A monosaccharide will ‘flip’ between these states rapidly.
Oligosaccharide
oligo = ‘a few’)
Small chains of monosaccharides. Often many different types of monosaccharides in the chain with different branching combinations.
• Can be added onto lipids to make glycolipids and proteins to make glycoproteins. These often play a role in cell recognition (e.g. ABO blood type, displayed on red blood cells (RBCs))
Polysaccharides
are long polymers of sugars
What is the central dogma’ of molecular biology?
DNA-> RNA>PROTEINS
A gene is transcribed by RNA polymerase to make RNA (either mRNA to make a protein, tRNA, or rRNA)
RNAs are then exported from the nucleus.
If it’s an mRNA, it gets translated by the ribosome to make a protein of a specific amino acid sequence that’s based upon the original DNA sequence
Gene
stretch of DNA which encodes a protein or RNA
DNA is stored in nucleus
Nucleic acids
are polymers of nucleotides that store and transmit genetic information.
What is a nucleotide composed of?
consists of three parts:
• A five-carbon sugar (ribose in RNA, 2’ dexoxyribose in DNA)
• A phosphate group linked to the 5’ carbon of the sugar
• A nitrogenous base linked to the 1’ carbon of the sugar
Describe nitrogenous bases
– Bases are either purines or pyrimidines.
– The purines are adenine and guanine in both DNA and RNA.
– The pyrimidines are cytosine and uracil in RNA; uracil is replaced by thymine in DNA.
Deoxyribonucleic acid (DNA
olds the genetic information in all cellular organisms and some viruses.
Four bases: A, C, T, G
Ribonucleic acid (RNA)
encodes the message of DNA and is the genetic material in some viruses. Four bases: A, C, U, G
How are nucleotides connected?
Nucleotides are connected by 5’-3’ phosphodiester bonds between the phosphate of one nucleotide and the 5’ carbon of the next. Thus nucleic acids have a direction (5’ phosphate end to 3’ hydroxyl end)
Proteins
are the most chemically diverse macromolecules in the cell
are polymers of amino acids
What are the 2 major classes of proteins?
- Globular proteins are usually inside the cell
- Fibrous proteins are usually exported
outside the cell (extracellular matrix)
Describe what roles proteins play
Enzymes –catalysts that perform chemical reactions
Structural elements – e.g. tubulin
Contractile elements – e.g. myosin in
muscle cells
Control of gene transcription
– Transcription factors bind to DNA and control if a gene is transcribed
– Ribosomes (rRNA protein hybrids)
Transport proteins – move material across membranes (e.g. glucose transporters)
Carriers – hemoglobin
Hormones – e.g. insulin
Antibodies – defense against invaders
How are proteins made
made by linking together amino acids
Amino acids have an α carbon, an amine group, a carboxyl group, and a variable R group.
Amino acids are linked together (dehydration rxns) by peptide bonds into a polypeptide chain to make a protein.
Like DNA, they have a direction. From “N-terminus” to “C-terminus”
Describe Primary structure
is the sequence of amino acids in the polymer. This is the order that the polypeptide will be made by the ribosome, from N-terminus to C-terminus
Describe secondary structure
refers to the conformation of adjacent amino acids into α- helix, β-sheet, hinges, turns, turns, loops, and ‘disordered’ sections.
Alpha-helix
a) 360 degree turn of the helix = 3.6 amino acid residues
b) H bonds between the carbonyl group and the imine group (H-N) of the backbone hold the helix together
Beta-sheet
a) Residues go in a pleated pattern called a β- strand, with the R groups sticking up and down
b) H bonds between the backbone carbonyl groups and the imine group (H-N) hold the adjacent strands together
Describe the Tertiary structure
is the overall 3D
conformation of a single protein polymer.
• Driven largely by R-group chemistry:
Hydrophobic R-groups in the centre of the protein, hydrophilic R-groups on the exterior
• It is stabilized by noncovalent bonds.
• e.g. van der Walls’ bonds, salt bridges
• NOT static… protein parts move around!!
• Conformational changes are non-random
movements triggered (for example) by the binding of a specific molecule.
What was the First Globular Proteins Whose Tertiary Structure Was Determined?
Myoglobin
• Stores oxygen in muscle cells.
• Has a heme prosthetic group that binds O2.
• Structure derived using X-ray crystallography
3-D structure of myoglobin. Heme group is located in red in the center of the protein.
Describe Quaternary structure
structure refers to protein complexes composed of more than one protein
refers to the manner in which subunits interact.
Homodimer = 2 proteins encoded by the same gene Heterodimer = 2 or more different
proteins encoded by different genes
There are proteins that have many different subunits encoded by different genes!
when the individual polypeptides are bound to each other for the protein complex to work. Like hemoglobin, which has strong protein-protein interactions between the polypeptides.
Describe the Quaternary structure of hemoglobin.
α is encoded by one gene, and there are two units in the final complex (α1 and α2). Globin β is encoded by a different gene, and there are also two units in the final complex (β1 and β2).
What do proteins often do?
very often interact with each other
- proteins will be separate
- and then transiently come together to form an active complex
Separate proteins (which may or may not have activity on their own) transiently come together to form an active complex. This is still ‘quaternary structure’, but the protein-protein interactions are weaker
i
proteins can become physically associated to form a multiprotein complex.
– Which proteins interact can be determined using the yeast two-hybrid (Y2H) assay
– The Y2H is an indirect assay and includes lots of uncertainties.
– Results from large-scale studies can be presented in the form of a network.
– A list of potential interactions can be elucidate unknown processes.
Why is protein structure important?
A protein’s structure determines its function!
– Subtle changes in a protein’s structure can have a huge impact on its ability to perform its function within the cell
– Cells routinely modify protein structures (phosphorylation, etc) to regulate activities
– The structure is based upon the chemistry of the amino acids, the order of the amino acids are determined by the gene that encodes the protein
– Mutations in DNA can be (but are not always) damaging to the protein’s function
Briefly describe how X-ray crystallography works.
Tertiary and quaternary structures can be determined using a variety of methods: 1. X-ray crystallography
1. Get your proteins to form into a crystal.
(all proteins in crystal are arranged as a lattice)
- Put your protein crystal into a strong Xray beam
- The Xrays will interact with atoms as they pass
through the crystal, and will be diffracted
depending on how the protein atoms are lined up - Capture the diffracted xrays with a detector
- Rotate the crystal a bit (new atoms are now in row)
and repeat 3&4 - Do crazy math (Fourier transformations)
- This gives an electron density map
- With help of a computer, ‘fit’ amino acid shapes
and the backbone in the electron densities
*Myoglobin and hemoglobin were discovered this way
Describe how Cryo-electron microscopy works?
Proteins ‘fixed’ in a crystal may not have the same conformation as they do in a cell.
Also, crystallography doesn’t work with really huge complexes and integral membrane proteins. Cryo-EM solves these problems!
2017, the Nobel Prize in Chemistry was awarded for this
protein is flash frozen, done in a liquid ethane and in a way that the protein freezes but its done so quick that water droplets dont form so it gives you a clear image of the protein and then with transmission electron microscopy and help of computer you can get 3D structure of protein
Describe how Nuclear magnetic resonance spectroscopy works and what are the limitations associated with it?
Stick your protein(native protein) (in solution) in a really strong magnet.
Magic chemistry happens
Limitation: only works for really small proteins (and small molecules)
advantage- get to see how protein functions in native state
What is a problem associated with x- ray crystallography?
you have to crystallize the protein and some don’t crystalize well or structures change during
