Lecture 13: Gene Expression Flashcards

Question

trp Operon genes

Answer 1

- five genes (trpA-E) needed for the synthesis of tryptophan by trp operon (where those 5 genes are coded for) - trp repressor encoded by trpR elsewhere in genome - Trp repressor synthesized in inactive form (default for trp repressor)

Answer 2

-default state is expression bc trp repressor in inactive *trp repressor is activated by presence of tryptophan* - trp operon is repressible operon (operon is turned off when tryptophan is available, because prokaryotes don't want to waste energy on making it if its readily available) - tryptophan is the corepressor- regulatory molecule that combines w/ repressor to activate it and shut off operon | expression of trp operon ctrlled by trp repressor

Answer 3

negative - opposite pathways LAC: repressor synthesized in active form, inducer is present and binds to repressor and inactivates it operon is then transcribed TRP:repressor is synthesized in inactive form, when corepressor is present it binds to the repressor and activates it, the active repressor blocks transcription of the operon

Answer 4

- Trp repressor is inactive (default, can't bind to initiator) in binding to the operator and transcription proceeds - RNA polymerase binds and transcribes operon = OPERON ON

Answer 5

- the amino acids binds to and activates the Trp repressor - The active repressor binds to the operator and blocks transcription *Tryptophan and Trp Repressor (active)* = bind and undergo conformation change - binding would prevent RNA polymerase from binding to operator = OPERON OFF

Answer 6

Gene Expression in eukaryotes has more regulatory points - more complex - no operon - genes are scattered (multiple linear chromosomes) - chromatin has histones (determines level of condensation on chromosomes) - different types of cells - nuclear envelope (separates chromosomes with genes from rest of cell)

Answer 7

transcription: in nucleus translation: cytoplasm

Answer 8

No transcription

Answer 9

1) during transcription: *MOST IMPORTANT* Transcription regulation (during transcription) - chromatin remodelling to make genes accessible for transcription - regulation of transcription initiation = determines which genes are translated 2) Post-transcriptional regulation (after transcription, during translation) - variations in pre-mRNA processing - removal of masking proteins - variations in rate of mRNA breakdown - RNA interference = determines type and availability of mRNA to ribosomes 3) Translational Regulation (during translation) - variations in rate of initiation of protein synthesis = determines rate at which proteins are made 4) Postttranslational regulation (after translation) - variations in rate of protein processing - removal of masking segments - variations in rate of protein breakdown = determines availability of finished proteins

Answer 10

1) initiation of transcription 2) methylation of DNA 3) chromatin structure

Answer 11

- PROMOTER *includes the TATA BOX that binds transcription factors (once they bind, RNA polymerase can bind to transcription factors to begin)* - PROMOTER PROXIMAL REGION =upstream of promoter *DNA-nucleotide sequences that regulate gene expression* - contains promoter proximal elements, (activator = proteins can bind to enhance transcription) - increases transcription rates - ENHANCER further upstream to determine maximum transcription rate

Answer 12

general transcription factors initiate transcription - bind to TATA box area - recruit RNA polymerase 2 - transcriptional initiation complex = low rate (basal level) ACTIVATORS- bind to promoter proximal elements and increase transcription rate

Answer 13

1) TATA Box- first general transcription factor *recognizes and binds to TATA box of a protein coding gene's promoter* 2) Additional general transcription factors and then RNA polymerase add to the complex - general transcription factor unwinds promoter DNA and then transcription begins (once all bound together) = TRANSCRIPTION COMPLEX = LOW LEVEL OF TRANSCRIPTION

Answer 14

- activators are protein with 2 distinct domains - 3D arrangement of proteins produces highly specialized regions called MOTIFS - DNA binding activators have 3 MOTIFS 1) helix-turn-helix 2) zinc finger 3) leucine zipper | 2 domains: DNA BINDING DOMAIN, ACTIVATON DOMAIN

Answer 15

1) Helix turn helix - part of a protein bound to DNA, one of the alpha-helixes bind to base pairs in groove of DNA, looped region of protein connects to a second alpha-helix that holds the first one in place 2) Zinc Finger - parts of proteins, bind to specific base pairs in grooves of DNA 3) Leucine zipper - proteins are monomers consisting alpha-helical segments hydrophobic interactions between leucine resides within the leucine zipper motif hold onto monomers together - other a-helices bind to DNA base pairs in major groove

Answer 16

- coactivators: bridge enhancers and promoters, come together to bind to activators in both regions = increase transcription to maximal rate using activators and repressor proteins - repressors oppose effect of activators = decrease transcription a) bind to specific site in DNA near activator and interact w/ it so it cant bind b) bind to same regulatory sequence as activators Transcription rate depends on balance between activation and repression signals (to determine amount of gene expression and transcription, we then create differences in cells w/ regards to regulation)

Answer 17

- form a transcriptional complex that facilitates RNA polymerase II recruitment and stabilization, leading to maximized transcription rates. -gene is looped to make a bridge which increases rates of transcription

Answer 18

- high gene regulation with low numbers of activators = used in different combos so we can have diff levels of regulation w/o needing many - therefore, a unique combo of activators ctrl gene A and B

Answer 19

- allows for genes with related functions to response to one signal HORMONES - signal molecules activate all cells with specific hormone receptors - all gene regulated by a specific hormone contain a steroid hormone response element =EFFICIENCY

Answer 20

- found in all genes regulated by the same steroid - increases transcription and therefore translation

Answer 21

a) add methyl groups to cytosine - gene silencing occurs when DNA methylation is located in promoters, meaning RNA polymerase can't attach=silence b) Genomic imprinting - permanent silencing of a maternal/paternal allele - inherited methylated allele is silenced - methylation maintained as DNA is replicated

Answer 22

Eukaryotic DNA + histones = nucleosomes - promoters inaccessible Chromatin Remodelling (relax vs highly coiled) 1) activators recruit remodelling complexes that displace nucleosomes 2) Activators recruit histone acetyltransferase enzyme (transfers acetyl group to histones) that acetylates and loosens histones association with DNA = Makes gene promoters more accessible (once they're loose)

Answer 23

- displaces histones - exposes genes promoter - promoter not accessible to proteins for transcription initiation (RNA polymerase can't get to promoter) SO... - use activator and remodelling complex which requires ATP and produces ADP + Pi AND... - loosening the bond, allows w/ RNA polymerase to bind + transcribe = we can now express those genes

Answer 24

- loosens up the charge - attractive forces between DNA and histones decrease, loosening up the DNA = acetylation by histone acetyltransferase - DNA (-q) allows us to form nucleosome complex (+q) = deacetylation by histone decetylase - removes acetyl groups from histones

Answer 25

- posttranscriptional regulation controls availability of mRNA to ribosomes = pre-mRNA processing changes which proteins are made - alternative splicing of introns and exons - regulatory proteins: ctrl abundance of mRNA

Answer 26

- controlled by regulatory proteins specific to each of these cells = ctrl whether we go smooth or striated muscle for example (diff groups of regulatory proteins for either muscle)

Answer 27

Masking proteins binds to mRNA to prevent translation - signal for mRNA activation removes masking proteins during development = you don't usually translate mRNA right away, we use masking proteins until we are ready for translation, this is common for eggs when they will translate once fertilization takes place to allow for organism to form - mRNA breakdown rates (degradation) are variable depends on 5' UTR nucleotide sequences (determine speed of breakdown)

Answer 28

(posstranscriptional regulation) - breakdown is slower during lactation and faster w/o lactation

Answer 29

mIRNA- cell made it itself, and it interferes with gene expression by blocking translation *coded by a non-coding gene* - regulates gene expression through RNA interference (RNAi) - miRNA binds to any complementary mRNA sequence and silences it - Small interfering RNA (siRNA)- form RNA encoded outside the cells genome - often used by viruses

Answer 30

- enzymes will clip off loop of 3' miRNA and bind to it - imperfect pairing=block translation miRNA-induced silencing complex: enzyme in protein complex degrades 1 strand of RNA and leaves the miRNA -miRNA in miRISC binds to target mRNAs that have a complementary or nearly complementary base sequence in 3'UTRs leading to imperfect/perfect pairing perfect: every nucleotide matches=blocks translation to destroy DNA imperfect: some nucleotides don't match (bulge) - miRNA will block translation but won't destroy mRNA

Answer 31

- controls rate at which mRNAs are used in protein synthesis (w/ translation regulatory proteins) - increasing length of poly(A) tail increases translation of mRNA

Answer 32

- controls functional proteins - chemical modification alters activity of protein - processes inactive precursors to active proteins - rate of degredation=UBIQUITIN

Answer 33

1) addition of ubiquimtin to a protein (requires ATP) - signalling molecules bind to ubiquimtin are proteins that will tell proteasome that it needs to be degraded = creates lack of expression of a gene 2) proteasome recognizes ubiquimtin tagged protein and unfolds it, enzymes that are part of core digest protein to small peptides (requires ATP) 3) Released peptides are degraded to amino acids by cytosolic enzymes = PROTEASOME AND UBIQUINTIN ARE RECYCLED

Answer 34

Epigenetic gene regulation - persists through cell or organismal generation - doesn't result from chances in DNA nucleotide sequence (+inherits that expression later) Two Epigenetic Mechanism 1. Feedback Loops - self-sustaining regulatory loop (eg phage lambda, comes back to further regulate it) 2. Chromatic packaging - regulation of packaging of DNA and its associated proteins (e.g. List noncoding RNA) = gene makes protein and RNA to turn it off

Answer 35

Loss of regulatory controls Tumour: a mass of cells due to dedifferentation - opposite of differentiation, therefore take specialized cells and make them unspecialized 1. benign tumours single mass 2. malignant tumors cancer invade other tissue by metastasis=spread to other parts of the body - tumor repressor gene function lost (code for proteins cells turning into cancer)

Answer 36

branch of medicine for the study, treatment, and prevention of cancer

Answer 37

a) CARCINOMA- tumor in cells of epithelial origin (breast, prostate, lung, colon) b) SARCOMA- tumour in cells of connective tissue (bone, cartilage, fat) c) LEUKEMIA- tumour in cells of blood systems and cells (bone marrow) d) LYMPHOMA- cells of the immune system (white blood cells)

Answer 38

- tumour grade (1-3) resemblance of tumour to normal tissue * looking to see cellular organization of tumours= cells in tumour are unorganized * - tumour stage (1-4) degree of tumour invasion (how far the tumour has gone) ex. stage 4: full metastasis to secondary site, left its primary site - prognosis probability of survival 5 years after diagnosis (5 is standard, 10 is also common)

Answer 39

Male: Prostate Lung Colon Bladder Female: Breast Lung Colon Uterus

Answer 40

Male: Lung Colon Prostate Pancreas (organ that's hidden so symptoms are found later on (at this point the cancer is in stages 3-4)) Female: Lung Breast Colon Pancreas

Answer 41

- 3 main classes of genes are implicated in cancer 1. Proto-oncogenes = genes that can become oncogenic (cancer-causing genes) 2. Tumour Suppressor Genes = genes that prevent cancer from happening 3. miRNA genes = find and bind to mRNA

Answer 42

- originally normal genes - encode proteins that stimulate cell division NORMALLY - tell the cell to grow and divide, loss of ctrl = over expression, porto-oncogene can go out of ctrl and since it'll keep telling the cell to grow to divide w/o ctrl ONCOGENE - altered proto-oncogene that cause a cell to be cancerous = deregulation of the cell cycle

Answer 43

Several ways: - mutations in promoter or other control sequences (**may** lead to cancer, not definite) - Mutations in coding segment may produce abnormally active protein - altering a.a. sequence and can result in a protein that's ALWAYS ON, continuous growth and division - Segment of chromosome translocation gated to area near promoter or enhancer (chromosomes that shouldn't be recombining but they are: proto-oncogene is carried on - viral infection of gene that regulates cell cycle leads to alteration in protooncogene = loose ctrl of cell division and growth

Answer 44

- encode proteins that inhibit cell division (prevent cancer) - In cancer, tumour suppressor genes can be mutated, alteration in nucleotide sequence = a.a. sequence EX. p53- guardian of the genome = over 50% of cancers=mutations in p53 - mutation causes gene to not be transcribed/translated properly *Regulates cell cycle by:* - holding cells at G1-S checkpoint by inhibiting CDKs - initiate apoptosis PREVENTS GENE MUTATIONS -activation of DNA repair proteins (enzymes will be triggered to fix DNA)

Answer 45

- both are tumour suppressor genes - involved in DNA damage and repair (they trigger enzymes to do this) - mutated genes are risk factors for breast cancer - 60% of breast cancers have BRAC1/2 mutation - up to 85% if both are involved *NOT ONLY WOMEN!* a) SPORADIC - 2 independent mutations of BRAC1 tumour suppressor =60% b) FAMILIAL - individual has predisposition of breast cancer because of inherited mutated BRAC1 allele = 60%

Answer 46

* Encode for miRNAs * In cancer: 1) OVEREXPRESSION of miRNA genes that encodes miRNA that prevent translation of tumour suppressor mRNA 2) Inactivation of mi-RNA genes that encode mi-RNA that prevent translation of porto-oncogenes What we want vs Cancer We want: - oncogene mRNA to not be translated because it can cause cancer - tumour suppressor mRNA to be translated to prevent cancer = in cancer, it wants and does the opposite, silences tumour sup. and not oncogene

Answer 47

- multiple genes must be modified to develop cancer - Explains why carcinogens may cause cancer years later - age is the greatest risk factor (2 rzns) - Removal of carcinogen may halt multistep progression oncogene a) As you age, you undergo cell cycle so many times, cells can make mistakes that go unnoticed and passed on, which can accumualte=CANCER b) environment risk factors - greater potential of exposure to potential carcinogens

Answer 48

NORMAL COLON CELLS *Loss of APC tumour-suppressor gene and other DNA changes = reduced number of cancer preventing proteins* - SMALL ADENOMA (benign growth) = benign: non-cancerous tumour *ras oncogene activation; loss of DCC tumour suppressor gene PROTO-ONCOGENE=ONCOGENE* - LARGE ADENOMA (benign growth) *loss of TP53 tumour-suppressor, (can cause adenoma to become cancerous) gene and other mutations* - CARCINOMA (malignant tumour with metastasis)

Answer 49

- detect early - early treatment for prevention

Answer 50

recruited by cancer cells using signals that benefit the cancer cells - signal transduction

Answer 51

Tumour cells signal the formation of new blood vessels - you want this 1) as you grow 2) when you're have to help repair CANCER CELLS: 3) use it to provide blood supply to get it to be a fast growing tumour *tumours will need ATP, need a lot of glucose and O2 (final e- acceptor)* = they send signals to endothelial cells to grow and form towards tumours allowing for increased growth *The cells providing the signal=NORMAL* *The cells sending the signal=CANCEROUS*

Answer 52

Intravasation- cancer cells ENTER blood vessels *Transported to other parts of the body* Extravasation- cancer cells EXIT the blood vessels *Metastasis=secondary site*

Answer 53

a) Surgery-removal of tumour and lymph nodes - part of lymphatic system that cancer cells may be collected in b) Chemotherapy- chemical that are selective and non-selective to cancer cells - systemic: drugs go around whole body - killing all cells that grow fast - side effects of chemotherapy (hair loss, WBC loss=immunocompromised) c) Radiotherapy- radiation Tx of cancer - will kill all cells that grow quick but in only one part of the body - kills normal and cancer cells d) Targeted Therapy- specific to cancer cells - Tx will only affect cancer cells - less damage to normal cells *Need to know patients genetics beforehand to determine form of Tx that's best*

Answer 54

Her2/neu - tyrosine receptor kinase (membrane-bound) - epidermal growth factor receptor (adds PO4) - involved in signal transduction pathways leading to increased cell growth (signal molecule, epidermal growth factors, tells cell to grow and divides, PROTO-ONCOGENE) - encoded by proto-oncogenes - 15-20% of breast cancer HER2 is over expressed HERCEPTIN- drug targeted therapy against HER2, specifically binds HER2 receptor and stops cell division - blocks signals from binding to receptor=no cell growth and division *GROWTH FACTORS BIND TO HER2 RECEPTOR* - triggers immune system to destroy cell so its not passed on, role 1 of Herceptin - Herceptin binds to HER2 and blocks signalling=role 2 of hereceptin

Answer 55

1) Lactose present, glucose absent – Highest transcription because CAP binds with cAMP, enhancing RNA polymerase binding and initiating transcription. 2) Lactose present, glucose present – Medium transcription, CAP is not activated due to low cAMP, but lactose prevents the repressor from binding. 3) Lactose absent, glucose absent – Low transcription, as the repressor binds the operator and blocks transcription. 4) Lactose absent, glucose present – Lowest transcription because the repressor is bound and CAP is inactive due to high glucose (low cAMP).