Gene Regulation

Question 1

production of enzymes is regulated by

Answer 1

feedback inhibition or gene regulation
ex. operon model in bacteria

Question 2

operator

Answer 2

segment of DNA in bacteria that can act as an on/off switch for a cluster of related genes

Question 3

operon

Answer 3

stretch of DNA including promoter, operator, and genes

Question 4

repressor

Answer 4

product of a regulatory gene which can bind operator and switch transcription off (repress it)
can be active or inactive, depending on corepressor

Question 5

repressible vs inducible operon

Answer 5

repressible - operon is usually on, binding of repressor turns transcription off
ex. trp operon

inducible - operon is usually off, binding of inducer inactivates repressor and switches transcription on
ex. lac operon

Question 6

positive control

Answer 6

uses stimulatory protein
can increase synthesis of a product that is already being synthesized

ex. CAP - catabolite activating protein
CAP activated by cAMP binds to promoter to increase RNA pol II binding and increase rate of synthesis

Question 7

differences in cell type result from

Answer 7

differential gene expression because all cells share same genome

Question 8

how histone modification affects gene expression

examples

Answer 8

genes with packed heterochromatin not usually expressed
modifications influence chromatin structure and expression

acetylation - to lysine residues, opens chromatin structure, promoting transcription initiation
methylation - causes condensing of chromatin
phosphorylation - next to methylated AA can loosen chromatin

Question 9

DNA methylation can cause

Answer 9

long term silencing of genes due to condensation of chromatin structure
genomic imprinting - methylation of either parent’s alleles of a gene can be passed down to future generations of cells
genomic imprinting is type of epigenetic inheritance

Question 10

high level of transcription in eukaryotes depends on

Answer 10

control element associated with genes and specific transcription factors interacting

Question 11

control elements function and types

Answer 11

segments of non-coding DNA where transcription factors bind

proximal control elements - located close to promoter
distal control elements/enhancers - far away or on intron
(whole region is enhancer, control elements are individual sequences of which there can be multiple)

Question 12

activator in eukaryotic transcription

Answer 12

binds to enhancer and stimulates transcription
domains: DNA-binding and transcription activating
can facilitate protein-protein interactions, or influence chromatin structure
some can be repressors instead

Question 13

co-expressed eukaryotic genes

Answer 13

have same combo of control elements even if they are scattered across separate chromosomes

particular combo of control elements with right activator proteins can activate transcription when appropriate

Depending on cell, and required proteins, TF factors present will be tailored to required proteins to be transcribed

Question 14

is chromatin static in the nucleus?

Answer 14

no, it can move towards “hot spots” with higher transcription material availabilities
chromatin produces loops towards hot spots for transcriptions

Question 15

types of post-transcriptional regulation

Answer 15

1. alternative splicing
2. blockage of translation initiation by regulatory proteins binding to 5’ end of mRNA
3. Nucleotide sequences in 3’ UTR which dictate lifespan in cytosol

Question 16

which mRNA (eukaryotic vs prokaryotic) is longer lived?

Answer 16

eukaryotic mRNA

Question 17

Noncoding RNA regulate gene expression at the level of

Answer 17

mRNA translation and chromatin configuration

Question 18

miRNAs

Answer 18

bind to specific mRNA and block translation or signal its degradation
half human genes regulated by miRNAs

Question 19

siRNAs

Answer 19

mediate RNAi
formed by different RNA precursors from miRNA but processed by similar enzymes
used in lab to disable genes for study
shown to play role in heterochromatin formation at the centromere in yeast

Question 20

snRNA
snoRNA

Answer 20

snRNA: small nuclear RNA
splicing of pre-mRNA

snoRNA: help process and chemically modify rRNA

Question 21

piRNA

Answer 21

Piwi-interacting RNA: bind piwi proteins, protect germ line from transposable elements (jumping from one part of genome to another)

Question 22

marking proteins for degradation

Answer 22

marking with ubiquitin
ubiquitin is recognized by proteasomes which are large protein complexes that degrade protein

Question 23

stages of embryonic development

Answer 23

cell division, cell differentiation and morphogenesis

Question 24

cytoplasmic determinants

Answer 24

RNA, protein and other things unevenly distributed in unfertilized egg, influences early development
determination is irreversible, followed by differentiation
results in differential expression of genes

Question 25

Inductive signals

Answer 25

signals from embryonic cells target nearby cells and cause transcriptional changes inducing differentiation of specialized cell types

Question 26

pattern formation in embryonic development

Answer 26

development of spatial organization of tissues and organs along the major axes
maternal effect genes encode cytoplasmic determinants, or egg-polarity genes developing segmentation in flies

Question 27

bicoid gene example

Answer 27

type of maternal effect gene
affects front half of body, no bicoid gene, a fly ends up with 2 back ends

Question 28

morphogens

Answer 28

gradient of molecules that determine polarity and position in an embryo in early development, controlled by maternal effect genes

Question 29

homeotic genes

Answer 29

control pattern formation in late embryo, larvae and adult stages
mutation causes misplacement of structures

Question 30

proto-oncogenes vs oncogenes

Answer 30

cellular genes responsible for normal cell growth and division
mutated proto-oncogenes which are cancer-causing (abnormal stimulation of cell cycle)

Question 31

conversion of proto-oncogene to oncogene can be from:

Answer 31

1) translocation closer to promoter
2) amplification of proto-oncogene
3) point mutations of gene or control elements leading to increase in gene expression

Question 32

Ras

Answer 32

proto-oncogene, leads to hyperactive Ras which leads to increased cell division (MAPK pathway)
common in human cancers

Question 33

tumor-suppressor proteins

Answer 33

1) repair damaged DNA
2) control cell adhesion
3) cell signaling to inhibit cell cycle (ex. in case of damaged DNA)

decreases in these genes can lead to cancer onset

Question 34

p53

Answer 34

mutations in p53 tumor suppressor gene are common in human cancers
prevents transcription of faulty DNA

Question 35

a cancerous cell usually contains

Answer 35

at least one active oncogene and a few inactive tumor suppressor genes
requires accumulation of cancerous mutations to develop cancer

Question 36

common gene mutation in colorectal cancer

Answer 36

mutation of tumor-suppressor gene adenomatous polyposis coli (APC)

Question 37

types of breast cancer
additional mutation found in most types

Answer 37

luminal A/B, HER2, basal like
BRCA1/BRCA2 mutation

Question 38

Luminal A and B breast cancer

Answer 38

over-expressed estrogen receptors (A more than B) and progesterone receptors
lacks expression of HER2
can be treated with Tamoxifen
A type best prognosis and most common, B less so

Question 39

HER2 breast cancer

Answer 39

over expression of HER2, no hormone receptors expressed
can be treated with Herceptin
similar frequency and prognosis to luminal B type

Question 40

Basal-like breast cancer

Answer 40

no receptors expressed
aggressive, poorer prognosis, less frequent