1.2 Cell biology

codon

3 nucleotides/1 amino acid

tRNA

anticodon + amino acid that fits

ribosome

fabric that reads mRNA and tRNA and puts them together

unity of biochemistry

all living organisms share the same chemical reactions

plasma membrane

cell vesicle of double phospholipide(bilayer)

amphiphilic

hydrophylic head + hydrophobic tail

Brownian ratchet

mechanism to steer molecules in cell (soort tandwiel)

orthologs

same genes in 2 different species through speciation

paralogs

genes in same species that are duplicated

tree of life domains

bacteria, archaea, eukaryotes(with nucleus + organelles)

rRNA

ribosomal RNA, used to compare species of life

horizontal gene transfer(HGT)

transfers DNA between organisms(vooral prokaryoten)

organotrophic organism

gets energy from organic material (animals)

phototrophic organism

gets energy from light (plants, algae)

lithotrophic organism

gets energy from anorganic material (only some bacteria, eg hydrothermal vent, they use the chemical reactions)

LUCA

last universal common ancestor of cellular life

bacteria and archaea sizes

spherical, rod-shaped, spiral and smallest cells

Asgard archaea

group archaea thats closely related to eukaryotes and provides clues

origin of hybrid genomes of eukaryotes

endosymbiosis aerobic proteobacteria(mitochondria) + endosymbiosis photosynthetic cyanobacteria(plasmids)

bacteriophage

virus that infects bacteria(important to study molecular)

needed for modelorganism(they all have strong genetics)

1. easy to culture/kweken

2. fast reproduction

3. genetic good research already done

4. processes that are similar to other organisms

yeast(modelorganism)

small genome, cheap, simple

cell cycle, genetics, DNA, cell division

worm(modelorganism)

easy, fast lifecycle, genetically known, easy neurosystem

neurosystem, cell development, cell death, genetics

plant(modelorganism)

small genome, cheap

plants

fly(modelorganism)

low duplication frequency, cheap, long history

genetic studies and development

frog(modelorganism)

big eggs, cell division without growth, outside mother

cell division

zebrafish(modelorganism)

transluscent

vertebrate development

mouse(modelorganism)

similar to human, long history

diseases, immune system, development

humans(modelorganism)

lots of data

disease and behaviour

polar

negative and positive side

noncovalent molecule interactions(in order of strength)

1. electrostatic attractions (ionic bonds)

2. hydrogen bonds

3. van der waals attractions

4. hydrophobic interactions

H+ concentration

more H+ = acid

less H+ = base

major elements in cell

C, H, O, N

4 major families of small organic molecules/ building blocks of cell chemistry

1. sugars

2. fatty acids(fats and membrane lipids)

3. amino acids

4. nucleotides

macromolecules in cells

1. proteins

2. nucleic acids(DNA and RNA)

3. polysacharrides

(making them costs energy, dissolving them gives energy)

cells metabolism

complete chemical reaction of a cell (organized by enzymes)

alpha helix

spiral, discovered in keratin (hydrogen bonds N-H and C=O)

beta sheet

folded, discovered in silk (hydrogen bonds N-H and C=O)

4 protein structures

1. primary - amino acid sequence

2. secondary - alpha helix and beta sheets

3. tertiary - overall 3D shape of one chain

4. quaternary - several protein chains together

protein domain

part of protein that folds independently and has own function

ligand

molecule that binds specifically to a protein (noncovalent)

chromatine

DNA+proteins in nu

linear chromosome must contain

1. centromere

2. 2 telomeres

3. replication origins

nucleoside

base+sugar

phosphodiester bond

nucleotide bond between 3’ and 5’ (phospor bonds with 2 sugars)

right-handed helix(how do you know left or right)

hold thumb down and rotate to the right

human genome length

3.1 × 10⁹ nucleotide pairs

number of genes coding for proteins

around 20.000

percentage of protein-coding DNA sequence(in exons)

1%

percentage of DNA transcribed(protein-coding and noncoding RNA genes)

45%

5’ DNA strand

carbon connected to phosphate group

3’ DNA strand

carbon has free OH group

semiconservative replication

DNA has 1 old strand and 1 new strand

leading strand

replicates continuously

lagging strand

replicates in small bits (okazaki fragments)

DNA polymerase

sees mistakes during replication and deletes them (can only ad nucleotides to the 3’ OH)

primase

makes RNA primer because DNA polymerase cant begin from scratch

DNA helicase

opens helix up

single strand DNA binding proteins (SSB)

keeps the helix open

sliding clamp

ringshaped protein that holds DNA polymerase to DNA

mismatch repair system

after replication it checks DNA and deletes mistakes

topoisomerase

prevents DNA from tangling during replication (cuts and pastes to prevent tension)

DNA ligase

joins okazaki fragments together (costs energy, ATP)

origins of replication

where replication begins

during synthesis/S phase

in humans around 40000

telomerase

extends the telomeres so they dont become too short

DNA can be damaged by

1. chemicals

2. radiation

3. normal chemical reactions in cell

base excision repair (BER)

repairs ONE base

nucleotide excision repair (NER)

repairs larger section

translesion polymerase

can get past damage but makes mistakes

Nonhomologous end joining (NHEJ)

brings 2 broken strands together and seals them(can make mistakes)

Homologous recombination (HR)

use a similar/identical DNA to repair the break

difference DNA and RNA

1. RNA=single stranded

2. RNA has 2’OH (ribose)

3. uracil instead of thymine

mRNA

messenger RNA, codes for proteins

tRNA

transfers RNA, adaptors between mRNA and amino acids(protein synthesis)

rRNA

ribosomal RNA, form basic structure of ribosome and catalyze proteins

RNA polymerase I

rRNA

RNA polymerase II

mostly mRNA and other RNA’s

RNA polymerase III

tRNA + 5SRNA(part of ribosome)

general transcription factors

factors that are needed for polymerase in eukaryotes

name the 3 most important general transcription factors

1. TFIID → recognizes TATA box and others near start point (INR,DPE)

2. TFIIB → recognizes BRE in promoters + positions RNA polymerase at the start

3. TFIIH → unwinds DNA at start + releases RNA polymerase from promoter

supercoiling

positive=extra twisting of DNA helix/overwound

negative=less twisting of DNA helix/underwound

histone

protein where DNA can attach around

nucleosome

DNA + histone

chromatin

DNA + histones + other proteins

transcription initiation needs

1. activators(stimulate transcription)

2. mediator(help activators communicate with RNA polymerase)

3. chromatin-modifying proteins(make DNA accessible)

4. general transcription factors

transcription in eukaryotes

DNA

pre mRNA(capping,slicing,processing,poly(A)tail)

mature mRNA

export from nucleus

cytoplasm

translation

transcription in prokaryotes

DNA

mRNA

protein(all in cytoplasm)