BIOL 205 Lecture Notes - Lecture 1: Regulatory Sequence, Alternative Splicing, Dna Replication

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4 Dec 2016

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The hereditary information in cells is encoded in the linear order, known as a sequence, of the four different nucleotide subunits that make up dna. Proteins are the principal constituents of cells and determine not only cell structure but also cell function. The information contained in genes somehow directs the synthesis of proteins. Therefore, genetic instructions carried by dna must specify the amino acid sequences of a protein. Dna does not synthesize proteins itself, but acts as a manager, assigning tasks to a team of workers. When a certain protein is needed by the cell, the nucleotide sequence of the appropriate segment of a dna molecule is first copied into another type of nucleic acid known as ribonucleic acid (rna). That segment of dna is called a gene, and the resulting rna copies are then used to direct the synthesis of the protein.

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1. Use the following definitions and phrases to describe to which molecules of life and their subunits it belongs:

a. Energy-storing molecule, typically water soluble - b. Subunits are called monosaccharides â c. Used to speed chemical reactions - d. Subunits are joined to each other with peptide bonds - e. Most prevalent molecule in cell membranes - f. Some of them function as hormones - g. Used for storing, transmitting, and executing genetic information - h. Subunits are nucleotides

2. Weak hydrogen bonds between water molecules are responsible for the many properties of water. Acidity is expressed as pH. Buffers stabilize pH. a. What characteristics of water molecule makes it polar? Provide two examples why this property is important in microbiology. b. What is the role of buffers in living organisms, including microbes? c. What must be added to pure water to decrease OH- and/or H+ concentration, respectively

3. Carbohydrates serve as storage molecules and structural material. Lipids are hydrophobic molecules; phospholipids are main component of cell membranes. Protein has a complex structure based on identity and sequence of amino acids. Nucleic acids (DNA and RNA) are genetic station of storage information and for synthesis of proteins. ATP serve as the main energy source in the living cell. a. Name the subunits (building blocks) of carbs, simple lipids, proteins, and nucleic acids b. What level of protein structure is described as an alpha helix? c. If DNA is placed in boiling water, what and how the molecule would change?

QuestionGroup: #21 Gene expression 2

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The direct end result of gene expression is which of the following?

Amino acids

Translation

Proteins

Carbohydrates

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QuestionGroup: #22 Mutation

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Which of the following is the ways in which nucleotide mutations lead to altered proteins?

One nucleotide is substituted by another nucleotide, which can cause an early stop codon to be incorporated into the amino acid sequence resulting in a truncated protein.

One nucleotide is replaced by another nucleotide, which can change an amino acid in the protein sequence

Nucleotides are inserted into a nucleotide sequence causing a frameshift in the sequence.

All three choices may cause mutations.

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QuestionGroup: #23 Mutation 2

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Mutations are the result of which of the following?

Change in the normal nucleotide sequence in the DNA directly resulting in different carbohydrates

Change in the normal nucleotide sequence in the DNA directly resulting in different proteins

Change in the order of transfer RNA to messenger RNA so that the transfer RNA take over the role of Messenger RNA

Primarily an alteration in the sequence of nucleotides in the abnormal proteins

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QuestionGroup: #24 Cell division

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There are two major kinds of cell division. Which of the following plays a major role in promoting genetic diversity?

Meiosis since it causes the cells to make more daughter cells than mitosis

Mitosis since it causes the cells to duplicate and eventually have mutations

Meiosis since it causes the DNA sequences to be separated into new patterns in the daughter cells.

Mitosis since it essential for the ovaries in humans to separate and duplicate

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QuestionGroup: #25 Cancer

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Genes that slow down or stop the cell cycle are called...

Apoptotic genes

Oncogenes

Restriction genes

Tumor suppressor genes

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QuestionGroup: #26 Cancer2

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The common theme in the development of all cancers is...

Mutation

Evolution

Infection

Syncopation

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QuestionGroup: #27 Genetics

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Punnett's square is which of the following?

Example of all possible combinations of alleles

Example of all possible combinations of chromosomes

Example of only certain combination of alleles since some will not be expressed.

Example of all possible combinations of DNA

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QuestionGroup: #28 Embryo development

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Which of the following is the end of the cleavage phase?

A fetus

Formation of a blastocyst

Implantation to the lining of the uterus

Fewer number of cells

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QuestionGroup: #29 Development of organ system

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For organs to be differentiated, which of the following is the first step?

Stem cells trigger the development of differentiated cells

Tissues assemble into organ systems such as blood

Tissue specific genes in stem cells are triggered

Differentiated cells form tissues

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QuestionGroup: #30 Development and society

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A pregnant mother ingests a chemical which her mother said would be great for the baby. When the baby was born, it had a large head and flippers for arms. What caused this phenotype?

The chemicals were teratogens which influenced oxidative phosphorylation causing the changes in the phenotype.

The chemicals influenced the expression of different stem cells.

There is no way to assume the chemicals caused the phenotype since we have no data on other mothers who took this medicine. It could have been purely by chance.

The chemicals were teratogens which caused the baby to show early signs of evolution.

1. Look up the tyr and trp content and molecular masses ofbovine serum albumin and chicken

lysozyme in the ExPASy Protein Knowledgebase

ExPASy Protein knowledgebase: http://www.uniprot.org

Search the Protein Knowledgebase (UniProtKB) for ï¿½bovine serumalbuminï¿½. Select ALBU_BOVIN by clicking on accession P02769. Thensearch for ï¿½chick egg lysozymeï¿½ and select LYSC_CHICK by clickingon accession P00698. Scroll down each of these pages and you willcome to a section entitled "Sequence". This section gives thelength of the protein in amino acid residues, its molecular mass indaltons, and its sequence using one-letter abbreviations. Thesequence and molecular mass given for both BSA and chicken lysozymeare derived from the DNA sequence and therefore are of theunprocessed protein. This includes an N-terminal extension for bothproteins. To get the information about the processed protein,select ï¿½ProtParamï¿½ from the Tools function at the upper right ofthe protein sequence. Then click ï¿½GOï¿½. This will take you to a newwindow with a list of regions of the protein that can be analyzed.Click on the numbers to the right of ï¿½CHAINï¿½ (these numbers denotethe amino acid residues of the main chain. A new window will openthat shows only the amino acid sequence of the processed protein.Below the sequence you will find the molecular mass of theprocessed protein, listed as ï¿½molecular weightï¿½, and a tableshowing the amino acid composition of the protein. You will findthe number of tyrosine and tryptophan resides listed on thistable.

2. Calculate ?mol tyr + trp / mg protein

for BSA and lysozyme.

3. Answer the following questions:

Should a standard curve for a Lowry protein assay using a BSAstandard look identical to

a standard curve based on lysozyme? Why or why not? A comparisonof the amino acid composition of these two proteins that you justcalculated will help you answer this question. If you believe thatthe curves will look different, be specific about how they will bedifferent.
Why would it be poor lab procedure to use a standard curve froma previous assay and run an assay only on the new unknown sampleswith fresh reagents? Name specific sources of error that this wouldcreate.

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BIOL 205 Lecture Notes - Lecture 1: Regulatory Sequence, Alternative Splicing, Dna Replication

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