Introduction lecture

Question 1

Define the term “molecular medicine”

Answer 1

interdisciplinary life science: to understand

• normal/pathological cellular processes
• more precise diagnostics
• targeted therapies

Question 2

define the term “translational medicine”

Answer 2

highly interdisciplinary field of molecular medicine: molecular basic research (bench) to clinical research (bedside)

Question 3

describe the main stages in development of new drugs

Answer 3

1. TARGET (identification, characterization, validation)
2. COMPOUND/POTENTIAL DRUG (high-throughput screening, efficiency & toxicology, in vitro & animal models
   clinical trials
3. APPROVAL by authorities

Question 4

describe the three phases in clinical trials

Answer 4

Phase I: Safety (toxic?), 20-100 individuals
Phase II: Safety/efficacy, 100-300 individuals
Phase III: more individuals, 300-3000

Question 5

what are the major classes of biological molecules, what are the building blocks?

Answer 5

nucleic acids (nucleotides), proteins (amino acids), polysaccharides (monosaccharides), lipids/triacylglycerids (fatty acids)

Question 6

Describe the structure of an eukaryotic cell (what do they have that prokaryotes do not have?)

Answer 6

• nucleus, nucleolus (rRNA)
• mitochondria
• ER & golgi
• peroxisome & lysosome

Question 7

describe the nucleus

Answer 7

chromatin, surrounded by nuclear envelope with pores (diffusion of small molecules, active transport of proteins & RNA)

Question 8

What happens in ER and golgi?

Answer 8

glykosylation, sorting of proteins

Question 9

what happens in peroxisome and lysosome?

Answer 9

degradation of lipids and proteins

Question 10

describe the interphase of the cell cycle and how long the different stages take!

Answer 10

G1: protein synthesis, organelle production, cell growth (10h)
G0: arrested or terminally differentiated cells (muscle cells, neurons)
S: synthesis, replication (2-4h)
G2: preparation for mitosis (1h)

Question 11

what are the 5 stages of mitosis?

Answer 11

Pro-meta-prometa-meta-ana-telo

Question 12

What happens in prophase?

Answer 12

condensation of chromosomes, spindel formation

Question 13

What happens in Prometaphase?

Answer 13

Nuclear envelope breaks apart

Question 14

What happens in Metaphase?

Answer 14

chromosomes line up between spindle poles

Question 15

What happens in Anaphase?

Answer 15

Separation of sister chromatids, movement to opposite sites

Question 16

What happens in Telophase?

Answer 16

formation of nuclear envelope, decondensation of chromosomes, cell division (cytokinesis)

Question 17

how is the cell cycle regulated?

Answer 17

cell-cycle specifc cyclins that activate CDKs (cyclin-dependent kinases), inhibited by CDK inhibitors
CDKs activate nuclear target proteins that drive cell cycle

Question 18

when does the cell cycle normally arrest?

Answer 18

• contact with other cells
• DNA damage
• terminal cell differentiation
• senescence

Question 19

describe the extrinsic apoptosis pathway

Answer 19

external signal - ligand to death receptor (Fas) - initatior caspase8 - executioner: effector caspases cleave substrate proteins - apoptosis

Question 20

describe the intrinsic apoptosis pathway

Answer 20

internal signal - mitochondria release cyt. c - Cyt C and Apaf.1 (apoptic protease activating factor) and ATP form apoptosome - caspase9 - … (same way)

Question 21

what are caspases?

Answer 21

cystein-dependent aspartate-directed proteases (cleave proteins)

Question 22

how is DNA-replication initiated?

Answer 22

DNA-polalpha complex with 7-10 nt RNA-primer, extended by poly alpha

Question 23

what polymerase makes the leading strand?

Answer 23

pol e

Question 24

what polymerase makes the lagging strand?

Answer 24

pol delta

Question 25

what does helicase do?

Answer 25

separates the two strands

Question 26

what does topoisomerase to?

Answer 26

twists up supercoiling (releases topological stress)

Question 27

what is PCNA?

Answer 27

clamploader (coordinates replication), proliferating nuclear cell antigen, binds polymerases etc. (more than 100 proteins for repair, chomatin remodeling, signalling..)

Question 28

why does the chromosome become shorter with every replication?

Answer 28

no obvious way to copy 3’ end (lagging strand) - no RNA-primer beyond end to initiate replication and maintain the telomere

Question 29

what does telomerase do?

Answer 29

reverse transcriptase that provides RNA-template so that DNA-polymerase can complete lagging strand

Question 30

where is telomerase active?

Answer 30

embryonic stem cells, sperm cells, activated lymphocytes, cancer cells (often)

Question 31

job of RNA-polymerase I

Answer 31

rRNA precursors (nucleolus)

Question 32

job of RNA-polymerase II

Answer 32

mRNA precursors, miRNA, lncRNA (nucleoplasm)

Question 33

job of RNA-polymerase III

Answer 33

5S rRNA, tRNA, some miRNAS (nucleoplasm)

Question 34

what is RNA-maturation?

Answer 34

preRNA to mRNA, 7mG-cap, polyA-tail, removal of introns (splicing)

Question 35

how many codons are there?

Answer 35

4^3 = 64 (1-6 per aa, stop)

Question 36

what are the three stages in the ribosome?

Answer 36

aminoacyl, peptidyl, exit

Question 37

what are the two main ways of protein degradation?

Answer 37

1. lysosomal: acidic pH, hydrolytic enzymes, non-selective

2. targeted: marked with ubiquitin by ATP-dependent proteasome

Question 38

difference between southern, northern and western blot?

Answer 38

southern (DNA), northern (RNA), western (proteins)

Question 39

how does CRISPR/Cas9 work?

Answer 39

RNA-guided DNAse (Cas9) that induces a double strand break at the site matching the RNA sequence (CRISPR), repaired by non-homologous end joining or homolog recombination with donor DNA

Question 40

describe the stages of mRNA

Answer 40

transcribed pre-mRNA is modified at 5’ end during transcription (5’ cap) and shortly after transcription (3’ polyadenylation), splicing, export via nuclear pores, transport to ribosomes for translation, excess mRNA is degraded by nucleases