Lecture 1

Question 1

biopolymers

Answer 1

Proteins, Nucleic Acids and Carbohydrates

Question 2

polymerized

Answer 2

linked together

Question 3

condensation

Answer 3

removal od a molecule of water in the joining reaction

Question 4

cellulose

Answer 4

carbohydrate, major constituent of the cells walls in protein

made by removing a water molecule between two adjoining glucose molecules- covalent

Question 5

8 big picture ideas

Answer 5

• 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

Question 6

Three domains in life

Answer 6

eukarya, archae, bacteria, (archae and bacteria are prokaryotes)

Question 7

Bacteria vs eukarya cells

Answer 7

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.

Question 8

Eukarya plant cell

Answer 8

nucleus- contains chromosomal DNA, chloroplast- photosynthesis

Question 9

Eukarya animal cell

Answer 9

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

Question 10

The blood stream form of the malaria parasite

Answer 10

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.

Question 11

Lipids are critical for biomembrane formation

Answer 11

An example of a “Glycerophospholipid”

Three-carbon glycerol backbone + two fatty acid tails + phosphatidylcholine

Question 12

Lipids form Biological Membranes

Answer 12

Membranes are crucial for surrounding “compartments” like:

the cell itself; mitochondria; chloroplasts; nuclei; lysosomes.

Question 13

Compartmentation

Answer 13

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

Question 14

Number of all proteins inside cell

Answer 14

~ 2,600,000

Question 15

Number of external proteins (flagella & pili)

Answer 15

~ 1,000,000

Question 16

Number of all proteins of an E. coli cell

Answer 16

~ 3,600,000

Question 17

major biopolymers and their building blocks

Answer 17

proteins: amino acids
nucleic acids: nucleotides
polysaccharides: sugars

Question 18

Proteins are major macromolecular component of cells
a-helix
rhodpsin

Answer 18

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”

Question 19

3’ terminus

Answer 19

accepts amino acids

Question 20

tRNA

Answer 20

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.

Question 21

Glucose is the monomeric unit for both

Answer 21

• cellulose: used for rigidity in plants

* glycogen: used for energy storage in animals

Question 22

how do cellulose and glycgogen differ

Answer 22

in the degree of mixing 1,4 and 1,6 branching.

Question 23

α-anomeric

Answer 23

α-anomeric carbon atom C1

(When OH is “up”: ß-anomer)c

Question 24

α-amylose:

Answer 24

continuous (α1→4) connections of D-glucose units.

Adding(α1→6) branches every 8 to 14 glucose units gives “glycogen”.

Question 25

catabolism

Answer 25

energy containing nutrients (carbs, fat, protein) —> energy depleted end products (CO2, H2O, NH3)

ADP+, HPO24-, NAD+, NADP+, FAD —> ATP, NADH, NADPH, FADH2

Question 26

Anabolism

Answer 26

cell macromolecules (proteins, polysacc, lipids, nucleic acids) –> precursor molecules ( AA, sugars, fatty acids, nitrogenous bases)

ATP, NADH, NADPH, FADH2 —>
ADP+, HPO24-, NAD+, NADP+, FAD

Question 27

Energy (U)

Answer 27

ΔU =Ufinal −Uinitial = q− w

q = heat absorbed by the system from the surroundings
w = work done by the system on the surroundings

Question 28

Enthalpy (H)

Answer 28

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

Question 29

Entropy (S)

Answer 29

S = kB lnW
kB = Boltzmann constant
W = the number of energetically equivalent ways of arranging components in a system

Question 30

Free Energy (G)

Answer 30

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

Question 31

Chemical equilibria, ΔG0 and the equilibrium constant Ke

Answer 31

aA+bB = cC +dD

Question 32

ΔG is incredibly important

Answer 32

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…

Question 33

ΔG and the rate of a process

Answer 33

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!