molec cell final 2025

transcription

first step in gene expression

RNA polymerase

enzyme that catalyzes the synthesis of RNA from a DNA template

number of subunits in bacterial RNA polymerase

five

function of the σ subunit in bacterial RNA polymerase

identifies the correct sites for transcription initiation and binds first

promoter

gene sequence upstream of transcription start site to which RNA polymerase initially binds

promoter length in prokaryotes

6 nucleotides

prokaryote promoter locations

10 and 35 base pairs upstream of the transcription start site

bacterial RNA polymerase unwinds this many bases of DNA for transcription

12 - 14

the σ subunit is released after:

addition of ~10 nucleotides

function of the ß and ß’ subunits in bacterial RNA polymerase

form a claw-like structure that grips the DNA template

stop signal

terminates transcription in prokaryotic RNA synthesis

most common stop signal in E. coli

repeat of a GC-rich sequence followed by 7 A residues

result of transcribing the GC-rich repeat in E. coli

RNA forms a stable stem-loop structure

chromatin

location of transcription in eukaryotes

number of RNA polymerase in eukaryotes

3

RNA polymerase II

synthesizes mRNA

RNA polymerase III

synthesizes tRNA and rRNA 5S

RNA polymerase I

synthesizes rRNA 5.8S, rRNA 18S, and rRNA 28S

general transcription factors

proteins involved in transcription from polymerase II promoters

TATA box

promoter for RNA polymerase II that resembles the -10 sequence of bacterial promoters

5 general transcription factors that form the preinitiation complex

TFIID, TFIIB, TFIIF, TFIIE, TFIIH

TFIID

general transcription factor that initially binds the TATA box (or other promotor region)

mediator

protein complex of more than 20 subunits that interacts with both the general transcription factors and RNA polymerase II

process that starts gene transcription

phosphorylation of the polymerase CTD by the TFIIH protein kinase

process that stops gene transcription

RNA polymerase II reaches the terminal signal

process that follows transcription of the terminal signal

RNA endonuclease cleaves RNA polymerase II from the DNA

number of transcription factors that recruit RNA polymerase I

2

general ribosome structure

1 small subunit + 1 large subunit

size of the mammalian ribosome

80S

size of the large subunit in a mammalian ribosome

60S

size of the small subunit in a mammalian ribosome

40S

components of the large subunit

28S rRNA + 5.8S rRNA + 5S rRNA + 49 proteins

components of the small subunit

18S rRNA + 33 proteins

number of promoter types for polymerase III

3

1st step of pre-rRNA modification

cleavage of rRNA

2nd step of pre-rRNA modification

ribose methylation

3rd step of pre-rRNA modification

uridine isomerization to pseudouridine

snoRNA function

guides modification of pre-rRNA

snoRNP

RNA/protein complex formed with snoRNA to carry out modification

processing of the 5’ end of pre-tRNA

cleavage by the ribozyme RNase P

processing of the 3’ end of tRNA

addition of a CCA terminus

modified bases formed by modification of uridines in tRNA

dihydrouridine and ribothymidine

modified bases formed by modification of guanosines in tRNA

inosine and methylguanosine

when are pre-mRNAs extensively modified

before export from the nucleus

addition of a 7-methylguanosine cap

modification of the 5’ end on mRNA

polyadenylation (addition of a poly-A tail)

modification of the 3’ end on mRNA

G-U rich downstream sequence

signal for polyadenylation

hexanucleotide (AAUAAA)

signal for polyadenylation

number of adenines added by poly-A polymerase to form the poly-A tail

200

1st step of pre-mRNA splicing

cleavage at the 5’ splice site, loop forms by joining the 5’ end of the intron to an A within the intron (branch point)

2nd step of pre-mRNA splicing

cleavage at the 3’ splice site, simultaneous excision of the exons from the loop

spliceosomes

five types of snRNAs

5 types of spliceosomes

U1, U2, U4, U5, U6

snRNP structure

6 - 10 protein molecules complexed with a snRNA

this snRNA binds to the 5’ splice site of pre-mRNA by base pairing recognition

U1

this snRNA binds to the branch point of pre-mRNA

U2

these snRNAs act together to form the intron loop of pre-mRNA

U4, U5, U6

fate of apolipoprotein B when translated from unedited mRNA

synthesized in the liver

fate of apolipoprotein B when translated from edited mRNA

synthesized in the intestine

turnover rate of rRNA

stable (lasts a long time)

turnover rate of tRNA

stable (lasts a long time)

turnover rate of mRNA

very quick; degrades rapidly

short-lived mRNAs code for

regulatory proteins

mRNAs with long half-lives code for

structural proteins

shortening of the poly-A tail

initiates mRNA degradation

regulation of mRNA degradation

extracellular signals, siRNA, miRNA

introns

noncoding sequences

introns are removed at this step of mRNA

splicing

basal laminae

thin layers on which epithelial cells rest, surrounds muscle cells, adipose cells, peripheral nerves

major structural protein

collagen

collagen structure

triple helix consisting of a repeating glycine-X-Y sequence

typical amino acid in the X position for collagen

proline

typical amino acid in the Y position for collagen

hydroxyproline

hydroxyl groups

stabilize the triple helix in collagen by forming hydrogen bonds

most abundant form of collagen

Type 1 collagen

type 1 collagen function

forms collagen fibrils in which the triple helical molecules form regular staggered arrays

covalent cross-links

bonds between side chain residues that help strengthen the fibrils

importance of collagen covalent cross-links in medical science

forms and repairs tissues

type of collagen in brain tissue

type IV collagen

glycosaminoglycans (GAGs)

polysaccharides formed from repeating units of disaccharides; form extracellular matrix gels

fundamental unit of GAGs (except for hyaluronan)

dimers

GAG found in cartilage, brain tissue, and neural tissue

hyaluronan

GAGs found in dermis tissue

dermatan sulfate, keratan sulfate

GAGs found in many different tissues

chondroitin sulfate, heparan sulfate

charge on GAGs due to sulfate groups

highly negative charge

only GAG that is a single long polysaccharide chain

hyaluronan

proteoglycans

formed by GAGs linked to proteins

function of hyaluronan

interacts with proteoglycans to form large complexes in the extracellular matrix

main adhesion protein of connective tissues

fibronectin

molecules for which fibronectin has binding sites

collagen, GAGs, and integrin

adhesion proteins in basal laminae

laminins

laminin structure

3 polypeptide chains, each with rod-like domains interspersed with globular domains, and binding sites on the subunits

structure formed by multiple laminins

networks

adhesion protein that is tightly associated with laminins

nidogen

type of collagen that nidogen binds

type IV collagen

structure of integrin

dimer formed by an α subunit and a ß subunit

number of possible α subunits in integrin

18

number of possible ß subunits in integrin

8

number of different integrins

24

extracellular matrix molecules bound by integrin

collagen, fibronectin, laminin, cytoskeleton