Lecture 1 Flashcards
biopolymers
Proteins, Nucleic Acids and Carbohydrates
polymerized
linked together
condensation
removal od a molecule of water in the joining reaction
cellulose
carbohydrate, major constituent of the cells walls in protein
made by removing a water molecule between two adjoining glucose molecules- covalent
8 big picture ideas
- There are three evolutionary domains of life
- Living organisms consist of one or more cells
- Cells are surrounded by at least one membrane
- Cells contain plenty of water • Cells contain many different biomacromolecules
- Biomacromolecules are made up of building blocks
- The laws of thermodynamics rule
- Understanding the rate of processes is very complex
Three domains in life
eukarya, archae, bacteria, (archae and bacteria are prokaryotes)
Bacteria vs eukarya cells
Bacterial cells are simpler and smaller than eukaryotic cells. They are generally not “compartmentalized”. bacterial cells are not particularly simple… With many protein molecules inside the cell and attached to the cell wall! A eukaryotic cell is highly organized – and “compartmentalized” The different compartments are called organelles.
Eukarya plant cell
nucleus- contains chromosomal DNA, chloroplast- photosynthesis
Eukarya animal cell
Organelles differ in major ways from the cytoplasm, e.g. in: 1. Protein content 2. DNA & RNA content 3. Cofactors 4. pH
Lysosome- protein degradation
The blood stream form of the malaria parasite
A unicellular eukaryote With many highly specialized organelles: micronemes, rhoptries, etc (For the exam, you only need to know that the rhoptry and microneme contain proteins which are essential for host cell invasion by the malaria parasite)
Malaria kills about 1 million people, mainly children, annually. (That is about two children per minute)
microneme and rhoptry: provides proteins for red blood cell entry.
Lipids are critical for biomembrane formation
An example of a “Glycerophospholipid”
Three-carbon glycerol backbone + two fatty acid tails + phosphatidylcholine
Lipids form Biological Membranes
Membranes are crucial for surrounding “compartments” like:
the cell itself; mitochondria; chloroplasts; nuclei; lysosomes.
Compartmentation
Advantages:
• Protect rest of cell from harmful events inside an organelle
Examples:
• Degrading enzymes in lysosomes
• Hemoglobin degradation in food vacuole malaria parasite
• Create specialized membrane-bound machineries inside cells
Examples:
• Photosynthesis in chloroplasts
• Energy generation in mitochondria
Number of all proteins inside cell
~ 2,600,000
Number of external proteins (flagella & pili)
~ 1,000,000
Number of all proteins of an E. coli cell
~ 3,600,000
major biopolymers and their building blocks
proteins: amino acids
nucleic acids: nucleotides
polysaccharides: sugars
Proteins are major macromolecular component of cells
a-helix
rhodpsin
α-helix= “secondary structure element”– A structural element
of many proteins
Rhodopsin= The protein of “vision” A “membrane protein” Note schematic representations of α-helices The molecule in red is “retinal” Brown: “posttranslational modifications”
3’ terminus
accepts amino acids
tRNA
carries a specific amino acid and recognized the corresponding messenger- RNA codon
The ribbon follows the “phospho-ribose backbone” of the tRNA.
• The planar bases of tRNA are often, but not always, engaged in base pairing.
• The lower turn contains the three-nucleotide “anti-codon” which recognizes the
codon of the mRNA.
Glucose is the monomeric unit for both
- cellulose: used for rigidity in plants
* glycogen: used for energy storage in animals
how do cellulose and glycgogen differ
in the degree of mixing 1,4 and 1,6 branching.
α-anomeric
α-anomeric carbon atom C1
(When OH is “up”: ß-anomer)c
α-amylose:
continuous (α1→4) connections of D-glucose units.
Adding(α1→6) branches every 8 to 14 glucose units gives “glycogen”.
catabolism
energy containing nutrients (carbs, fat, protein) —> energy depleted end products (CO2, H2O, NH3)
ADP+, HPO24-, NAD+, NADP+, FAD —> ATP, NADH, NADPH, FADH2
Anabolism
cell macromolecules (proteins, polysacc, lipids, nucleic acids) –> precursor molecules ( AA, sugars, fatty acids, nitrogenous bases)
ATP, NADH, NADPH, FADH2 —>
ADP+, HPO24-, NAD+, NADP+, FAD
Energy (U)
ΔU =Ufinal −Uinitial = q− w
q = heat absorbed by the system from the surroundings w = work done by the system on the surroundings
Enthalpy (H)
Biological processes occur under constant pressure.
A very useful thermodynamic quantity is:
H =U + pV
Under constant pressure and only considering pressure-volume work:
ΔH = qp
Where qp is the heat absorbed by the system at constant pressure
Entropy (S)
S = kB lnW kB = Boltzmann constant W = the number of energetically equivalent ways of arranging components in a system
Free Energy (G)
If a thermodynamic system is at constant temperature and pressure (as is the case with most processes of living beings), the change in Gibbs’ free energy, ΔG = Gfinal − Gstart, is the appropriate measure of processes in such systems:
Where
• G is the Gibbs’ free energy (also called “free energy”)
• H is the enthalpy
• S is the entropy
• T is the absolute temperature.
At constant P and T, ΔG will be negative for a spontaneous process.
And at equilibrium: ΔG = 0
Chemical equilibria, ΔG0 and the equilibrium constant Ke
aA+bB = cC +dD
ΔG is incredibly important
ΔG governs many processes in a living organism:
• the equilibrium of reactions
(you will see ΔG many times later on)
• the structure of proteins
• the stability of RNA and DNA molecules
• the architecture and stability of protein-DNA complexes
• the stability of lipid bilayers
• the affinity of metabolites and medicines for proteins
• etc…
ΔG and the rate of a process
It is important to realize that a large negative value of ΔG means that a process will occur spontaneously going from the state with higher G to the state with lower G, but does
not ensure that this process will proceed at a fast rate.
The rate, or speed, of a process depends on the detailed mechanism of the process and is independent of the
absolute value of ΔG!
