Bio Lab Exam 2

common features of a primary literature article

manuscripts must be critically evaluated by experienced scientists. Manuscripts judged as unacceptable are rejected and not published

what is found sections of a scientific journal article

(IMRD) Introduction; Materials and Methods, Results, and Discussion

the difference between a primary and secondary source in science.

Primary sources include articles that describe original research. Secondary sources interpret or analyze those primary sources.

Be able to identify a literature review from an original research article

simply gathering, reading, and subsequently summarizing information is a literature survey, not research. Original research includes several other elements of which interpretation is key

genetic transformation

change caused by genes," and involves the insertion ofa gene into an organism in order to change the organism's trait.

Describe and explain the purpose of the steps in the transformation process

manufacture - the physical creation of products

transport - the movement of materials

supply - change in ownership of goods

service - the treatment of customers or the storage of materials

plasmids

small circular DNA molecules that replicate separately from the bacterial chromosome

the purpose of the ampicillin resistance on the plasmid

to transfer the resistance gene into a susceptible strain of the bacteria.

what does arabinose do

the inductive operon turns on and the E. coli glows

How does arabinose regulate the GFP gene

transcription of the GFP gene into messenger RNA (mRNA), followed by the translation of this mRNA into GFP

transformation efficiency

A measure of how well cells are transformed to a new phenotype

How can transformation efficiency be calculated

Total number of colonies growing on the agar plate /

Amount of DNA spread on the agar plate (in μg)

the importance of model organisms

other scientists are able to compare their work amongst each other, teaches you how to use certain techniques, and is able to understand organisms better.

What makes Drosophila a good model system

they are easy and inexpensive to culture in laboratory conditions, have a much shorter life cycle, they produce large numbers of externally laid embryos and they can be genetically modified in numerous ways

What are Drosophila limitations

Humans have 24000 genes while fruit flies have 14000 genes, short life span, are a fly,

What kind of information can you look up in FlyBase

anatomy term reports, FlyBase controlled vocabulary term reports, development term reports, GO term reports and SO term reports

What kind of information can you look up in HPA

general gene information (eg. gene name or chromosome location) as well as data from all different sections of the HPA (eg tissue expression or prognostic cancer association)

What is an ortholog and why is it important

Ortholog is when different organisms have common genes. The model organisms can be used to studydiseases.

the difference between the genome and the transcriptome

Genome combines all distinct genes present in an organism, whereas transcriptome is all transcribed RNAs present in the organism.

the main steps involved in RNA-seq

RNA extraction, RNA fragmentation, cDNA generation, library amplification, and sequencing

bioinformatics and why is it important

Bioinformatics is when scientists use computer science to mostly answer questions about macromolecules.

the two columns in the HT-seq files

The two columns in an HT-seq file are Gene IDs and Read Counts. The Gene IDs shows which gene it is and Read Counts represents the amount of genes there are

What do the "reads" represent

readCount is the data frame while GeneID is gene.

Differential Expression Analysis

taking the normalised read count data and performing statistical analysis to discover quantitative changes in expression levels between experimental groups

the steps of DNA amplification by PCR

(1) denaturation of the template into single strands;

(2) annealing of primers to each original strand for new strand synthesis;

(3) extension of the new DNA strands from the primers

What is taq and why is it used

the most common enzyme used for PCR amplification. This enzyme is extremely heat resistant with a half-life of 40 minutes at 95°C

Alu sequence

This is a DNA sequence about 300 base pairs long that is repeated almost 500,000 times throughout the human genome

What does it mean to be +/+, +/- or -/-

+/+: 941 bp fragments

+/-: individuals with 941 and 641 bp fragments

-/-: individuals with 641 bp fragments

Explain the process of gel electrophoresis and how it can be used to visualize DNA and determine its size

Negatively charged DNA/RNA migrates through the pores of an agarose gel towards the positively charged end of the gel when an electrical current is applied, with smaller fragments migrating faster. The resulting bands can then be visualized using ultraviolet (UV) light.

denaturation

loss of normal shape of a protein due to heat or other factor

annealing

Binding of primers in PCR

primer

A short segment of DNA that acts as the starting point for a new strand

template

containing the intact sequence of DNA to be amplified which in this case is genomic DNA that will be extracted from your cheek cells

allele

Different forms of a gene

heterozygous

An organism that has two different alleles for a trait

homozygous

An organism that has two identical alleles for a trait

the purpose/function of Mitosis in the human life cycle

produces cells that are genetically identical to the parent cell for growth or to replace damaged or dead cells.

the purpose/function of Meiosis in the human life cycle

the production of gametes—sex cells, or sperm and eggs

What happens during interphase

The cell grows, copies its DNA, and prepares for cell division.

When is DNA replicated

S phase of interphase

what is happening during the steps of Mitosis

anaphase: sister chromatids are pulled toward opposite poles

telophase: chromosomes arrive at opposite poles, and nuclear envelope material surrounds each set of chromosomes

cytokenesis: the two daughter cells are separated

what is happening during the steps of Meiosis

begin with a cell with double the normal amount of DNA, and end up with 4 non-identical haploid daughter gametes after two divisions

When do sister chromatids separate in Mitosis

Anaphase I

When do sister chromatids separate in Meiosis

anaphase II

What are the big difference between Mitosis and Meiosis

Mitosis produces two genetically identical "daughter" cells from a single "parent" cell, whereas meiosis produces cells that are genetically unique from the parent and contain only half as much DNA

How do Mitosis and Meiosis relate to their function

two kinds of cell division

how evolutionary changes occur in a population over time

natural selection, which is a process that increases the frequency of advantageous alleles in a population. Natural selection results in organisms that are more likely to survive and reproduce.

What are the conditions of Hardy-Weinberg equilibrium

No mutations

No migration or emigration

No selective pressure for or against genotype

Large Sample Size

Random Mating

Calculate allele, genotype and phenotype frequencies using the Hardy-Weinberg equation.

p² + 2pq + q² = 1

p

dominant allele

q

recessive allele