Gene Regulation + Biotechnology

(Unit 8 - Ch 18 and Ch 20) Campbell Biology Version 10 Textbook

Metabolic Control in Bacteria

1\. adjusting activity of present enzymes

2\. adjusting level of certain enzymes

Operator

the single “on-off switch” (segment of DNA) that controls a whole cluster of functionally related genes

→ within the promoter

→ controls access of RNA Polymerase to the genes

Operon =

operator + promoter + genes they control

Repressor

turns off an “always on“ operator by binding to that region

→ always specific to their operon

Regulatory Gene

genes expressed continuously at a slow rate

Allosteric Regulatory Protien

a protein activated by a ligand (aka an effector)

Corepressor

a small molecule that cooperates with a repressor or protein to switch an operon off

Repressible Operon

transcription is usually on but it can be “repressed“

ex: trp operon (in this case when tryptophan binds allosterically to a regulatory protein )

Inducible Operon

transcription is usually off but it can be “induced“

ex: lac operon (the presence of lactose will induce this, the lactose molecules will come and bind to the repressor on the operator and hence the repressor will get removed and the RNA Polymerase can start producing the lactase enzyme)

Inducer

deactivates the repressor (it gone now lol) allowing the gene to be turned on

Negative Feedback Loop

switch is flipped, either turned on or off

ex: trp operon, lac operon

Positive Feedback Loop

if the switch is on, it gets turned even more on

CAP

regulatory protein (catabolite activator protein)

→ is an activator

Activator

a protein that binds to DNA and stimulates transcription of a gene

Differential Gene Expression

expression of different genes by cells with the same genome

ex: muscle + nerve cells are highly differentiated

Euchromatin

refers to any DNA that has been turned on

Heterochromatin

refers to any DNA that is off

Histone Acetylation

promotes transcription by opening up the chromatin structure by the addition of a functional group

→ addition of acetyl group (-COCH3) = polar; good thing; stimulates more transcription

→ addition of methyl group = non-polar; bad; slows down transcription

DNA Methylation

when it binds directly to DNA, that DNA is turned off

Genomic Imprinting

where methylation permanently regulates gene expression (of the maternal or paternal alleles) at the start of development

Epigenetic Inheritance

inheritance of traits transmitted by mechanisms not involving the nucleotide sequence

eg. environmental factors

→ these can be passed down to offspring

Transcription Initiation Complex

cluster of proteins that assemble at the promoter

Control Elements

segments of non-coding DNA for regulatory proteins to bind to

→ proximal

→ distal

Proximal Control Elements

located close to the promoter region

Distal Control Elements

located distant from the promoter region

Enhancers

groups of distal control elements

General Transcription Factors

can turn on all genes, has a low rate of initiation and only produced few RNA

Specific Transcription Factors

can only turn on few specific genes, has a high rate of initiation and high production of RNA

Activator Proteins

bind to the distal control elements

Silencing

reduced transcription (happens when repressors recruit proteins that remove acetyl groups from histones)

Alternative RNA Splicing

Different mRNA molecules are produced from the same primary transcript depending on which segments are considered exons/introns

Non-Protein-Coding RNAs

ncRNA

→ when the central dogma (dna to rna to protein) doesn’t get to the protein stage and the RNA becomes used for other things

microRNAs = miRNAs

→ small and single stranded

→ capable of binding to complementary sequences in mRNAs

a gene expression regulator

small-interfering RNAs = siRNAs

→ similar in size + function to the miRNAs

a gene expression inhibitor

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RNAi = when siRNA block gene expression

RNA-interference = RNAi

the blocking of gene expression by siRNA’s

Differentiation

process through which cells become specialized in structure and function

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at the non-DNA level, the actual process of building a specific cell type once the instructions have been read

Determination

refers to the point at which an embryonic cell has irreversibly committed to a particular cell type

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at the DNA level, the instructions for becoming any cell type

Morphogenesis

the physical process that give an organism its shape

Cytoplasmic Determinents

maternal substances (chemicals) in the egg cell that influence the course of early development

Induction

when signals (such as contact with neighboring cells or growth factors secreted by neighboring cells) cause changes in the target cell

Pattern Formation

cytoplasmic determinants + inductive signals contributing to the development of organization in which the tissues + organs of an organism are all in their characteristic places

Positional Information

molecular cues that control pattern formation

Homeotic Genes

massive regulatory genes, control groups of genes hence also pattern formation in late embryo, larva, and adults

Oncogenes

cancer causing genes

Proto-oncogenes

normal version of oncogenes

3 Ways Proto-oncogenes → Oncogenes

1\. point mutation (eg. substitution mutation)

2\. gene amplification (genes are duplicated unnecessarily)

3\. translocation (when a piece of a chromosome leaves and attaches to another chromosome)

Epigenetic Inheritance Removal Methods

1\. meiosis (when the DNA is duplicated and re-read, many epigenetic influences are not passed on, __but some are__)

2\. chemicals

3\. wearing off by time

Biotechnology

the manipulation of organisms or their components to make useful products

nucleic Acid Hybridization

the base pairing of one strand of a nucleic acid to the complementary sequence on a strand from another nucleic acid molecule

Genetic Engineering

the direct manipulation of genes for practical purposes

DNA Sequencing

exploiting the principle of complementary base pairing to determine the complete nucleotide sequence of a DNA molecule

DNA Cloning

a method for preparing well-defined segments of DNA in multiple identical copies

Plasmids

small circular DNA found in bacteria

Recombinant DNA Plasmid

molecule containing DNA from two different sources, very often different species

Gene Cloning

the production of multiple copies of a single gene is a type of DNA cloning

Cloning Vector

a DNA molecule that can carry foreign DNA into a host cell and replicate there

ex: bacterial plasmids

Restriction Enzymes

enzymes that cut DNA molecules at a limited number of specific locations

ex: Hind111, EcoR1

Restriction Site

the short particular DNA sequence that the restriction enzyme recognizes

Restriction Fragments

restriction enzymes will make many cuts in a DNA molecule, yielding a set of restriction fragments

Sticky End

not a blunt end,

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Blunt End

not a stick end

look like that → |

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DNA Ligase

joins the sugar-phosphate backbone with covalent bonds

Gel Electrophoresis

a technique used to separate and visualize DNA fragments of different lengths

→ this technique uses a gel made of a polymer as a molecular sieve to separate out a mixture of nucleic acids (or proteins) on the basis of size, electrical charge, and other physical properties

Polymerase Chain Reaction (PCR)

a technique used to obtain many copies of one gene

Stem Cells

cells found in the embryo, are cells that have the most genes turned on as compared to other cells in the body

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analogy: library is fully open with all books accessible

Totipotent

cells that can become any other kind of cell in the body if they are in the correct environment

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analogy: can read any book you want

Pluripotent

cells that can become **almost** any other kind of cell in the body if they are in the correct environment

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analogy: can read any book you want but the “r-rated“

Multipotent

cells that can become **some other kinds of cells** in the body if they are in the correct environment

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analogy: can read any book you want but the “r-rated“ and “tv-14“

Unipotent

cells that can become **only that cell**

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analogy: can read any book you want but the “r-rated“, “tv-14“, and “pg-13“ so basically you can only read the “pg“

Germ Layers

groups of cells in the zygote (baby forming)

→ three types: endoderm (skin + nervous system), ectoderm (linings in digestive + liver), mesoderm (bone + muscle + tissue)

Induced Pluripotent Cell (IPC)

a cell that is already differentiated (skin or rbc) and is turned back into pluripotent