Bio Quiz 4

DNA transposons

- "cut and paste" remove themselves from one place in the genome and move to a new site

Barr body

- (dramatic example of heterochromatin) the inactive X chromosome in a female's body cell - The inactive X chromosome is tightly packed away - Females have two X chromosomes, but only one is active

"punctuation" codons

- 1 start codon = AUG - 3 stop codons = UAA, UAG, UGA - 4. Start and stop signals

Induced mutation

- A mutation intentionally brought on by a researcher

- Clone livestock that have desired traits

- Best milk production, best meat production, egg production, etc.

Frameshift mutation

- Caused by the insertion or deletion of a nucleotide in a DNA sequence - Almost always renders the resulting protein nonfunctional - Shifts the codon reading frame

- Pharmaceutical industry

- Clone animals for medical use (e.g. pigs as organ donors)

silencer

- DNA sequence that inhibits transcription

enhancer

- DNA sequence that stimulates transcription

2 DNA strands, antiparallel

- Each strand is the exact opposite sequence of the other (complementary base pairing)

Insert vector into bacteria for DNA replication

- Humulin gene will be copied every time a bacteria cell divides from one cell into two - billions/trillions of copies are produced over night - Low error rate (DNA polymerase 1/billion)

Point mutation

- Involving a change in a single DNA nucleotid - Can lead to change(s) in the amino acid(s) during translation - Changes one codon (or more) to a different codon(s) Types: silent, missense, nonsense, and frameshift

Point Mutation Effects on protein

- Nonfunctional - Reduced functionality Unaffected

Spliceosome

- RNA/protein hybrid machine responsible for removing introns and fusing exons

Spontaneous mutation

- Random chance in nucleotide sequence, occurs randomly caused by: - Chemical mutagens - Error by DNA polymerase during replication - Transposon insertion (occurs randomly)

- Restock populations of endangered animals

- Wild mouflon, banteng, gaur, and gray wolves

Recombinant DNA

- a DNA molecule carrying genes derived from two or more species

Silent mutation

- a change in a single DNA nucleotide that results in the same amino acid being incorporated - Would go unnoticed in the cell, no change in phenotype - Degeneracy of genetic code allows for this

Chromatin

- a complex of DNA and protein found in living cells - Functions to package DNA into a smaller volume to fit in the cell - Controls gene expression and DNA replication

Pandemic

- a global epidemic (ex. 1918 WWI)

Gel electrophoresis

- a method for sorting nucleic acids by their size and electrical charge - DNA has a net negative charge - DNA migrates toward the positive end, smaller fragments migrate fastest

STR analysis

- a method of DNA profiling that compares the lengths of STR sequences in the genome - Utilized in forensics to identify individuals

Virus

- a microscopic particle capable of infecting cells of living organisms and inserting its genetic material - very simple in structure - generally not considered to be alive "organisms at the edge of life" - require living cells to reproduce

Gene mutation

- a permanent change in the sequence of bases in a gene - Note that we aren't concerned about RNA mutations or amino acid mutations 1. No effect on protein activity 2. Complete inactivation of protein activity 3. New function

Polynucleotide strand (nucleic acid)

- a polymer made up of many nucleotides covalently bonded together

Gene

- a segment of DNA that encodes function, typically is a recipe for making a protein - Molecular unit of heredity in all living things

Vector

- a small ring of DNA (plasmid) that is used to move genes from one cell to another - Engineered by scientists, are very similar to prokaryotic plasmids - Are often put into bacterial cells for DNA cloning, cloning vector

Polymerase chain reaction

- a technique in molecular biology used to amplify a single copy of DNA to millions using a thermocycler instead of a living organism

Taq DNA polymerase

- a thermostable DNA polymerase able to withstand temperatures that will denature (split apart) the DNA double helix into single strands - Discovered in a bacterial cell named thermus aquaticus from Yellowstone

Universal

- all organisms use the code the same way - Same 20 amino acids are coded by the same 64 codons GFP (green fluorescent protein) gene from jellyfish works in all organisms

Genetically modified organism (GMO)

- also called a transgenic organism, is any organism whose genetic material has been altered using genetic engineering techniques

Sugar-phosphate backbone

- alternating chain of sugar and phosphate to which DNA and RNA nitrogenous bases are attached

Prions

- always localize in the brain - Build up in neuron cells causes a toxic effect and cells being to die - very similar to Alzheimer's , Parkinson's, and Huntington's - All cases are untreatable and fatal

Transgenic animals

- an animal that contains extra genes derived from another organism

DNA polymerase

- an enzyme that copies existing DNA by pairing free nucleotides to bases present on each strand of the original DNA molecule - Found in every living organism - Extremely accurate, fewer than 1 mistake in 1,000,000,000 base pairs - 50 nucleotides/sec

Restriction enzyme

- an enzyme that cuts DNA at one very specific nucleotide sequence Ex. EcoRI is a RE that cuts DNA only when it comes across the sequence: GAATTC

RNA polymerase

- an enzyme that produces an mRNA copy of a DNA gene - Responsible for finding and recognizing the promoter sequence - Unzips the double stranded DNA to read the gene -important in elongation - makes a copy of the gene (DNA) in mRNA - C pairs with G (just like in DNA), A now pairs with U (different from DNA) - Accuracy is 1 mistake in 10,000 base pairs

Prions

- an infectious mis-folded protein - Have the ability to self-propagate and be infectious - Unique in that they do not contain information (no DNA or RNA), just structure - Spread by causing normal versions of proteins to mis-fold

DNA profiling

- analyzing an individual's unique collection of genetic markers using PCR and gel electrophoresis - Can be used to determine whether 2 samples of genetic material were derived from the same individual

Transposable element

- any of several kinds of parasitic DNA sequences that are capable of moving themselves, or copying themselves, to other locations of the genome -can cause spontaneous mutations -known as "selfish genes"

Biotechnology

- any technological application that uses biological systems, living organisms (or their derivatives), to make/modify products or processes for specific use

Proofreads

- can back up, correct mistake, and then continue

Viral genome

- can be either DNA or RNA, single stranded OR double stranded - code for as few as 2 genes or as many as 2,500

Conservative

- changes amino acid to another with the same properties

Non-conservation

- changes amino acid to one with different properties

Unambiguous

- codon are exclusive - each codon specifies only 1 amino acid - e.g. UUU "spells" phenylalanine and only phenylalanine - it won't suddenly code for serine

Genome

- complete set of DNA within a single cell of an organism

Messenger (mRNA)

- copy of a gene, copy goes to ribosomes for production of proteins - made during transcription

Peptide bonds

- covalent bonds that form between amino acids to form chains known as proteins - Ribosomes catalyze these bonds

Alternative RNA splicing

- different mRNA molecules can be produced from a single gene by alternating intron removal by the splicesome - allows a single gene to code for multiple proteins - alternate patterns of intron removal lead to different proteins

Gene cloning

- directed DNA cloning that results in the production of many identical copies of the same gene - Necessary for DNA sequencing (requires millions of copies) and the creation of transgenic organisms

Genomics

- discipline of genetics that applies DNA sequencing methods to compile and then analyze the function and structure of genome

Semiconservative replication

- each strand of the original double helix (parental molecule) serves as a template for a new strand in a daughter molecule

- Complementary base pairing

- ensures that a purine is always bonded to a pyrimidine (A with T, G with C)

Mutagen

- environmental factors that alter the base composition of DNA - Include radiation and harmful chemicals

DNA ligase

- enzyme capable of joining two pieces of DNA together - "sticks" cut pieces together

Epidemic

- general outbreak of a disease (ex. Flus during flu season)

Meiotic drive elements

- genetic elements that bias gene transmission during meiosis so that they are preferentially passed on to the offspring

Elongation

- growth in length of polypeptide chain - Ribosome reads codon in mRNA - Allows only complementary tRNA to bond to mRNA

Vaccines

- harmless variant or derivative of a disease-causing virus or bacteria - Used to prevent infectious diseases - Provides blueprint to immune system for destroying actual virus/bacteria

Promoter

- is a specific sequence of DNA that designates the location of a gene - "start transcribing" signal - many promoters are universal (found in all species) - Many are identical - They act as address labels for genes - important in initiation

- DNA

- is double stranded - Genes lie either on one strand or the other

Nucleic acids

- large biomolecules that store information, provide instructions for building proteins, and can act like an enzyme - essential to every living organism

Euchromatin

- loosely packaged DNA - transcriptionally active (acetylated) i.e. genes are available for being transcribed into mRNA

Thermocycler

- machine capable of raising and lowering temperature with great accuracy

Retrotransposons

- make copies of themselves that integrate randomly into the genome, utilizes a reverse transcriptase - Results in duplication of the element - Found abundantly in eukaryotic genomes

Viroid

- naked, single-stranded RNA strands that replicate inside host cells - do not code for any proteins! - "living relics" most likely represent the crucial step in abiogenesis

Acetylation

- of DNA and histones causes nucleosomes to loosen and spread apart - Genes are accessible and are therefore able to be transcribed

Methylation

- of DNA and histones causes nucleosomes to pack tightly together - Genes become inaccessible and are therefore inactive

RNA-world hypothesis

- only the biomolecule RNA was needed to progress toward formation of the first cell(s) - RNA can act as an enzyme (ribosomes, rRNA) - RNA can store information (mRNA) - RNA can form structures (tRNA)

Transgenic plants

- plants used in agriculture that contain engineered DNA - Foreign genes are introduced into immature plant embryos

DNA replication

- process of producing two identical replicas from one original DNA molecule - Occurs in all living organisms, for every chromosome present - Occurs during S phase of interphase in preparation for cell division (mitosis and meiosis)

Cloning

- production of identical copies of DNA, cells, or organisms - Bacterial colony on a petri dish, all originate from division of same cell - Identical twins, single embryo separates

Reverse transcriptase

- protein enzyme capable of transcribing mRNA back into DNA

Capsid

- protein shell of a virus - encloses the genetic material, acts as barrier - take many shapes (e.g. icosahedral, helical, circular)

Histones

- proteins found in the cell nucleus that package and order DNA into structural units called nucleosomes

Chromatin remodeling complex

- push nucleosomes aside so RNA polymerase can read the genes

Ribosome

- rRNA/protein hybrid enzyme responsible for manufacturing proteins - Reads mRNA, starting with AUG - Links amino acids together in the order specified by the mRNA - Chain of amino acids = polypeptide chain = protein

Degenerate

- redundant, most amino acids have more than 1 codon - 64 codons for only 20 amino acids - e.g. there are 6 different ways to "spell" leucine

Human Genome Project (HGP)

- scientific research project with the goal of determining the nucleotide sequence of the human genome - Federally funded project started in 1990, completed in 2003 at the cost of $3 billion - Privately funded project (C. Venter) started in 1998, completed in 2001 at the cost of $300 million

Terminator

- sequence of DNA that marks the end of a gene

Genetic code

- set of rules by which information encoded within mRNA is translated into proteins

Short tandem repeat (STR)

- short DNA sequences repeated many times one after another - remember the other 98.5% of the genome?

Gene regulation

- the ability to turn genes "on or off" or to fine tune the expression of genes under certain conditions - Make proteins when they are needed - Respond to changes in the environment

Genetic engineering

- the direct manipulation of genes for practical purposes - Ex. engineering bacteria to produce vaccines

Double helix

- the form assumed by DNA in living cells, similar to a twisted ladder - Sugar-phosphate backbones make up the sides - Hydrogen-bonded bases make up the rungs

Nucleosome

- the fundamental subunit of chromatin - each unit is composed of 8 histones with DNA wrapped around them

Nucleotides

- the monomer unit of nucleic acids 1. Phosphate group 2. 5 carbon sugar 3. Nitrogenous base

RNA splicing

- the removal of introns and joining of exons in mRNA after transcription

Heterochromatin

- tightly packaged DNA - transcriptionally inactive (methylated) i.e. genes are packaged away and are thereby inaccessible for transcription

tRNA

- transfers appropriate amino acids to ribosomes for the production of proteins

Transfer (tRNA)

- transfers appropriate amino acids to ribosomes for the production of proteins - translation

The Progressive Hypothesis

- transposons gained the ability to exit one cell and enter another

Pre-transcriptional gene regulation

- turns transcription of genes on/off or up/down based on the needs of the cell/organism - modification of the mRNA transcript which then alters the protein being produced

Reproductive cloning

- using a body cell from one organism to make one or more genetically identical individuals - Requires the transfer of the nucleus of the body cell into an egg cell

Emerging viruses

- viruses that appear suddenly or are new to medical scientists - ebola

Bacteriophage

- viruses that specifically attack bacteria - Most abundant form of biological entity in aquatic environments - a teaspoon of seawater contains about 1,000,000 bacteriophages

translation

-The RNA copy, in turn, leaves the nucleus to find a ribosome that will build the protein from the blueprints =

transcription

-To make a specific protein, the cell first makes a copy of the gene (blueprint) out of RNA

Missense mutation

-a change in a single DNA nucleotide in which a single nucleotide change results in a codon that codes for a different amino acid. It is a type of nonsynonymous substitution.

Nonsense mutation

-a change in a single DNA nucleotide that results in a STOP codon - Prematurely ends the growing polypeptide chain

Ribosomal (rRNA)

-makes up ribosomes (w/ proteins), which read the message in mRNA - translation

DNA/genes

-specify information NOT form or function -is only a recipe/blueprint, it does not form structures or carry out chemical functions itself -acts as the master blueprint for the organism

Codon

1 unit of genetic code, specifies 1 amino acid - 3 nucleotides long (U, A, C, G) = triplet code

Transcription

1. A segment of DNA (gene) serves as a template for making an mRNA molecule 2. The DNA double helix is unzipped and the bases are exposed 3. RNA nucleotides bind to the exposed unpaired bases 4. When the entire gene is transcribed into mRNA, the result is an mRNA transcript of the gene - The base sequence of the mRNA is complementary to the base sequence of the DNA

two methods of gene coding

1. Bacterial vectors 2. PCR thermocycler

Transcription

1. Initiation - find the gene 2. Elongation - transcribe the gene 3. Termination - stop transcribing

what do viruses and living things have in common?

1. Living things are organized - viruses have structures and information 2. Living things respond to stimuli (behavior) 3. Living things reproduce and develop - viruses replicate but require cell to do so 4. Living things have adaptations - viruses mutate and evolve

Chargaff's Rule

1. The amounts of A, T, G, and C in DNA are constant among members of the same species & vary from species to species 2. In each species, the amount of A = T & G = C

Process of bacterial DNA cloning:

1. Use restriction enzymes to cut DNA 2. Ligate gene and vector 3. Insert vector into bacteria for DNA replication

3 parts to RNA nucleotides:

1. ribose sugar 2. phosphate group 3. nitrogenous base: uracil (U), adenine (A), cytosine (C), guanine (G) -Uracil replaces thymine (T) of DNA

Central Dogma of Molecular Biology

DNA-->transcribed-->RNA-->translated-->PROTEIN

1. 46 2. 3 billion

Humans have _______ chromosomes which contain ____________ nucleotide base pairs

-are constant among members of the same species -vary from species to species

The amounts of A, T, G, and C in DNA:

Germ cell mutations - (germ = sex cells; sperm, egg)

are mutations that can be passed from one generation to the next - passed from parent to offspring (meiosis) Ex. - down syndrome

Translation

initiates at the start codon - codon = AUG - codes for the amino acid Methionine - therefore, all proteins begin with the amino acid Met

Humulin (human insulin) gene

is inserted into bacteria for mass production for people with diabetes - Bacteria are grown in large vats called bioreactors - Insulin is harvested and purified for human consumption

RNA

is single stranded and often forms 3-D structures, much like proteins

Somatic cell mutations - (somatic = body cells; skin, etc.)

may only affect a single cell or a small # of cells in a tissue - may lead to cell death or cancer - not passed on to offspring in sexually reproducing organisms but passed on to daughter somatic cells (mitosis)

R strain:

not virulent (injected mice lived); has no capsule

1.5%

only _______ of the human genome is genes

Nucleosomes

regulate accessibility to DNA - Must move in order for RNA polymerase to access DNA and transcribe genes

Uracil

replaces thymine (T) of DNA

S strain:

virulent (injected mice died); has a smooth capsule