Week 1

Question 1

origins of mitochondria (endosymbiosis) - entangle - engulf - endogenies (E^3) model

Answer 1

• archaean cell was anaerobic
• bacterial ecosymbiont was aerobic
• surface protrusions on archaea expanded over time
• this led to enclosure of ectosymbiont by archaeal membrane fusion
• escape of endosymbiont into cytosol and formation of new intracellular compartments
• over time, this evolved into modern-day mitochondria

Question 2

did prokaryotes or eukaryotes form first?

Answer 2

prokaryotes formed much earlier, and then eukaryotes

Question 3

what is an alternative model for endosymbiosis?

Answer 3

some models involve a more predatory mea hanse where the aerobic bacterium is engulfed via a process similar to phagocytosis

Question 4

common features of both types of endosymbiosis models

Answer 4

• ancient anaerobic archaeal cell
• ancient aerobic bacterium
• over evolutionary time, a symbiotic relationship

Question 5

Asgard cell

Answer 5

• type of archaea belonging to the group Asgard
• has a cell body and protrusions with ectosymbionts on their surface

Question 6

describe and draw the sequence of the tree of life

Answer 6

ancestral prokaryote (3.5-3.8b years ago)
bacteria and archaea separated
1b years later, the first single-celled eukaryote was formed

Question 7

lines of evidence to support endosymbiont hypothesis

Answer 7

1. mitochondria and chloroplasts still have remnants of their own genomes, which are circular. their genetic systems resemble that of modern-day prokaryotes
2. mitochondria and chloroplasts have kept some of their own protein and DNA synthesis components and these resemble prokaryotes too. they have their own ribosomes and multiply by pinching in half — the same process used by bacteria. are also sensitive to similar antibiotics.
3. membranes in mitochondria and chloroplasts often similar to those in prokaryotes and appear to have been detached from engulfed bacterial ancestor.

Question 8

general attributes of model organisms

Answer 8

• rapid development with short life cycles
• small adult (reproductive) size
• readily available (collections or wide-spread)
• tractability - ease of manipulation or modification
• understandable genetics

Question 9

central dogma of molecular biology

Answer 9

DNA -(transcription)-> RNA -(translation)-> protein

Question 10

tRNA

Answer 10

• transports amino acids
• protein synthesis

Question 11

rRNA - ribosomal RNA

Answer 11

• part of the ribosome
• does catalytic work of making protein by creating peptide bonds
• has a structural role as part of RNA

Question 12

refined central dogma

Answer 12

not all RNA is translated into protein - it has many other uses

Question 13

draw a diagram for the elaborated central dogma information flow

Question 14

genome

Answer 14

cell’s complete set of DNA, including mitochondria and chloroplasts

Question 15

transcriptome

Answer 15

all the RNA in a particular cell at a particular point in time

Question 16

genome vs transcriptome/proteome

Answer 16

transcriptome/proteome are much more dynamic

Question 17

proteome

Answer 17

entire set of proteins in a cell at a particular point in time

Question 18

how are the proteome and transcriptome related?

Answer 18

the proteome feeds information into the transcriptome

Question 19

interactome

Answer 19

set of all protein-protein interactions taking place in a cell at a single point in time

Question 20

metabolome

Answer 20

full set of small molecules that can be found in a cell at a certain point in time (anything that is generally smaller than a protein, like ATP, sugars, vitamins, some hormones)

Question 21

example of metabolome affecting transcription

Answer 21

lac operon

Question 22

phenome

Answer 22

comprised of everything (all the -omes), and together with the observable characteristics of what you’re looking at (cell, organ, etc)

Question 23

describe the directionality of transcription and translation

Answer 23

• DNA, RNA, and proteins are synthesised as linear chains of information with a definite polarity
• info in RNA sequence is translated into an amino acid sequence via a genetic code which is essentially universal among all species

Question 24

what are nucleic acids?

Answer 24

an organism’s blueprints - the genetic material in a cell
- DNA: deoxyribonucleic acid
- RNA: ribonucleic acid

Question 25

three parts of a nucleotide

Answer 25

1. pentose sugar - scaffold for base 2. nitrogenous base 3. phosphate group - backbone. There may be 1 (mono), 2 (di), or 3 (tri) phosphate groups

Question 26

pyrimidines

Answer 26

UC The pyramids? - single ring - uracil - cytosine - thymine

Question 27

purines

Answer 27

pure Animals Gobble - double ring - adenine - guanine

Question 28

where is the base attached?

Answer 28

1'

Question 29

distinguish between ribose and deoxyribose in terms of functional groups

Answer 29

2' carbon in ribose has a hydroxyl group - in deoxyribose it just has a hydrogen

Question 30

nucleoside monophosphate

Question 31

nucleoside vs nucleotide

Answer 31

nucleoside = base + sugar nucleotide = base + sugar + phosphate

Question 32

adenosine

Answer 32

sugar + adenine

Question 33

guanosine

Answer 33

sugar + guanine

Question 34

cytidine

Answer 34

sugar + cytosine

Question 35

uridine

Answer 35

sugar + uracil

Question 36

thymidine

Answer 36

sugar + thymine

Question 37

nucleoside monophosphate

Answer 37

sugar + base + 1P

Question 38

nucleoside diphosphate

Answer 38

sugar + base + 2P

Question 39

nucleoside triphosphate

Answer 39

sugar + base + 3P

Question 40

dNTPs

Answer 40

deoxyribonucleoside triphosphates - DNA is synthesised from them - N stands for A, C, T, G

Question 41

NTPs

Answer 41

- N stands for A, C, U, G - ribonucleoside triphosphates - RNA is synthesised from them

Question 42

nucleotides are linked by

Answer 42

phosphodiester bonds

Question 43

overall charge on nucleic acids

Answer 43

negative all the way along

Question 44

interactions between individual molecules are usually mediated by

Answer 44

noncovalent attractions: 1. electrostatic attractions (happen within and between large molecules) - weakened by water 2. hydrogen bonds - strongest in a straight line 3. van der Waals attractions - two atoms very close together, causing temporary dipole due to uneven distribution of electrons. not weakened by water 4. hydrophobic force - water pushing non-polar things away from itself. individually weak, but add up. individually, very weak forces - BUT can sum to generate strong binding between molecules

Question 45

Cell theory

Answer 45

- the cell is the basic organisational unit of life - all organisms are comprised of 1 or more cells - cells arise from pre-existing cells: the ability to reproduce is characteristic of living matter, which must be able to duplicate DNA, create proteins, etc

Question 46

two main types of cell

Answer 46

eukaryotic and prokaryotic cells

Question 47

prokaryotic

Answer 47

- no nuclei - single celled (but communities may exist) - bacteria and archaea (domains)

Question 48

eukaryotic

Answer 48

- nuclei with membrane - single-celled (eg algae) or multicellular - plants, fungi, animals, humans, protozoans

Question 49

describe and draw a prokaryotic cell

Answer 49

- no membrane-bound organelles; localised DNA may be in nucleoid or not localised at all - smaller size than eukaryotes (~1micrometer) - less DNA than eukaryotes

Question 50

draw and describe a eukaryotic cell (plant)

Answer 50

- nucleus - several membrane-bound organelles - larger size and more complex (~5micrometers)

Question 51

draw and label a eukaryotic cell (animals)

Question 52

describe cytoskeletons in eukaryotic cells

Answer 52

- simple diffusion is not enough to guide transport - cytoskeleton includes microtubules and actin filaments