BIO II Exam 2

Chapters 20, 21, 22, 23

biotechnology techniques

include DNA sequencing, gene cloning, PCR amplification, expressing genes, analyzing gene expression, and gene editing

biotechnology applications

include agriculture, medicine, environmental cleanup, ancestry, and forensics

DNA technology

are the main technologies for sequencing and manipulating DNA

DNA sequencing

is the laboratory process of determining the exact order of the four nucleotide bases (A,T,C,G) to identify variations, mutations, or complete genomes; Ex: Sanger sequencing and NGS (Next-Generation Sequencing).

Fredrick Sanger

operated the first automated procedure based on chain termination sequencing (dideoxy)

sequencing by synthesis

is the process when many DNA fragments are copied to produce an enormous number of identical fragments; Ex: “high-throughput” tech.

nanopore

a very small pore in a membrane

DNA cloning

work directly with specific genes; when scientists prepare well-defined DNA segments in multiple identical copies

plasmids

are small, circular DNA molecules that replicate separately from the bacterial chromosome(gene cloning); researchers insert DNA into this to produce a recombinant DNA molecule which contains DNA from two different sources (foreign DNA)

bacterial plasmids

are widely used as cloning vectors b/c they are readily obtained, easily manipulated, easily introduced into bacterial cells​, rapidly multiplied once in the bacteria, and Gene cloning is useful for amplifying genes to produce a protein product for research, medical, or other purposes​

restriction sites

is the specific DNA sequences

restriction enzyme

makes many cuts in a long DNA molecule yielding restriction fragments; they are useful in cutting DNA in a staggered way producing a sticky end which allows researchers to join two DNA fragments from different sources

gel electrophoresis

is a techniques used by a gel made out of polymer that has microscopic holes of different sizes

PCR/ the polymerase chain reaction

can produce many copies of a specific target segment of DNA; includes a three step procedure of heating (denaturing), cooling (annealing) and extension; this process uses primers (short single-stranded DNA molecules complementary to sequences to either side of the target sequence)

electroporation

is a method of introducing recombinant DNA into eukaryotic cells; this process applies a brief electrical pulse to create temporary holes in plasma membranes; natural genetic recombination

The CRISPR-Cas9 system can be used for which of the following?

C. both a. (disable a normal gene in an organism) and b. (repair an abnormal gene in an organism)

Which of the following tools and/or techniques would not be suitable as part of the molecular cloning of a particular gene?

C. CRISPR-Cas9

Place the steps in a cycle of PCR (polymerase chain reaction) in the correct order:

1. Annealing—Cool to allow primers to form hydrogen bonds with ends of target sequence.​

2. Extension—DNA polymerase adds nucleotides to the 3 end of each primer.​

3. Denaturation—Heat briefly to separate DNA strands.

A. 3, 1, 2

Which of the following is not a correct statement about third-generation sequencing?

D. DNA must be cut into fragments or amplified

Which is an incorrect statement about STRs (short tandem repeats)?

A. They are tandemly repeated units of 5’- to 10’ nucleotide sequences

genomics

is the study of whole sets of genes and their interactions

J. Craig Venter

is a biologist that set up an entire genome

genomics

is a rich source of new insights into questions about genome organization, regulation of gene expression, and embryonic development, and evolution

proteomics

is an approach to studying large sets of proteins and their properties

proteome

is the entire set of proteins expressed by a cell or group of cells

gene annotation

uses three lines of evidence to identify a gene

steps of gene annotation

1. computers search for patterns that indicate the presence of genes

2. search for clues about the identities and functions

3. is to use RNA-seq or some other method to show that the relevant RNA is actually expressed from the proposed gene

RNA-seq

are used to analyze gene expression patterns in patients with cancers or other diseases

relationship between genome size and phenotype-

does NOT correlate to each other

pseudogenes

are former genes that have accumulated mutations and are nonfunctional

repetitive DNA

present in multiple copies in the genome

noncoding DNA found between genes

pseudogenes and repetitive DNA

transposable elements

prokaryotes and eukaryote have stretches of DNA that can move from one location to another within the genome; provide sites for crossover between nonsister chromatids

Eukaryotic transposable elements are of two types:

transposons that move by means of a DNA intermediate and require a transposase enzyme and retrotransposons move by means of RNA intermediate using a reverse transcriptase

(STR) short tandem repeat

is a series of repeating units of 2’ to 5’ nucleotides

exon shuffling

are errors in meiotic recombination lead to some mixing and matching of exons, either within a gene or between two nonallelic genes

evolution

refers to the process by which species accumulate differences from their ancestors as they adapt to different environments over time

Lamarck use and disuse

a theory that states body parts used extensively become larger and stronger, unused parts deteriorate

adaptations

are inherited characteristics that enhance an organism’s survival and reproduction in specific movements

natural selection

is a process in which individuals with certain inherited traits tend to survive and reproduce at higher rates because of those traits

descent of modification by natural selection explains:

the unity of life, the diversity of life, and the ways organisms are suited to life in their environments

Darwin’s two observations

#1- members of a population often vary in their inherited traits

#2- all species can produce more offspring than the environment can support and many of these