Biology : SACE : Stage 2 : DNA and Proteins

DNA profiling

A procedure that analyzes DNA fragments to determine whether they come from a specific individual.

DNA analysis

A scientific technique capable of;

- Identifying people through their distinctive gene patterns

- Determining genetic and evolutionary relationships between Organisms

- Identification of gene mutations, which lead to the development of genetic diseases

DNA profile

A distinctive pattern of DNA fragments that can be used to match a sample of biological matter to an individual (The bands are equally inherited from the Father and Mother)

DNA extraction

The process of separating DNA from an isolated cell;

1. The cell and the nucleus are broken open to release the DNA inside (mechanically or chemically)

2. DNA is separated from the cellular debris, through the use of sodium and alcohol

3. The separated DNA is then purified through further exposure to alcohol

Polymerase chain reaction (PCR)

A technique for amplifying DNA in vitro;

1. Heating DNA to 90˚C (Separating hydrogen bonds)

2. Introduction of DNA primers (Heat resistant) at 40-65˚C

3. Introduction of DNA polymerase (Bacterial) at 72˚C

4. Free floating DNA nucleotides bond to the DNA fragments

5. Repeated several times afterwards

Target DNA

Specific sequence of DNA that will be copied

Primers in PCR

RNA segments that specify a segment of DNA to be amplified.

Gel electrophoresis

Procedure used to separate and assist with analysis of DNA fragments;

1. Placing a mixture of DNA fragments at one end of a porous gel

2. Apply an electrical current to the substance, separating the fragments dependent on the size

STR analysis

A method of DNA profiling that involves the comparison of the lengths of short tandem repeat (STR) sequences selected from specific sites within the genome

Genetic engineering

The direct manipulation of gene sequences for practical purposes.

Restriction enzymes

An enzyme produced by certain bacteria, capable of separating DNA molecules at specific sequences of nucleotides on either strand

Macromolecules

A very large organic molecule composed of many smaller molecules

Nucleic acids

A type of organic macromolecule. Most common examples are DNA and RNA

Nitrogenous base

A molecule found in DNA and RNA that encodes genetic information in cells.

5 Nitrogenous bases located in DNA and RNA

Adenine, Thymine, Guanine, Cytosine, Uracil

Sugar-phosphate backbone

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

Hydrogen bonds in DNA

Bonds that form between the nitrogenous bases that form the "rungs" of the DNA ladder

DNA in eukaryotic cells

- Linear

- associated with proteins called histones forming chromatin

- multiple chromosomes

DNA in prokaryotic cells

- Coiled into a region called the nucleoid

- no membrane surrounds the DNA

RNA

A single-stranded nucleic acid that passes along and transcribes genetic messages. It also contains the nitrogenous bases Uracil, Adenine, Guanine, and Cytosine

Chromosomes

A compacted threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

DNA replication

The process in which DNA makes a duplicate copy of itself, through a semi conservative process

Helicase

An enzyme that untwists the double helix of DNA at the replication forks.

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

Gene

A segment of DNA on a chromosome that codes for a specific trait or protein

Exons

Coding segments of eukaryotic DNA.

Introns

A noncoding, intervening sequence within a eukaryotic gene.

Protein

A three dimensional polymer made of monomers of amino acids.

protein synthesis

Forming proteins based on information in DNA and carried out by RNA molecules

Transcription

Synthesis of an RNA molecule from a DNA template;

1. DNA strand is separated at specific region

2. Free floating nucleotides attach to the desired Gene, forming a pre-mRNA strand

3. Once passing through the Nucleus into the cytoplasm, introns are removed, therefore becoming a mature mRNA Strand.

Codons

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

Translation

the process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm;

1. mRNA template attaches to the Ribosomal unit

2. Codons on the mRNA strand attract complimentary anti-codons on the tRNA molecule

3. Once bonded, the tRNA molecule transfers the corresponding amino acid to the proceeding tRNA

4. This transferring of the amino acid chain continues until the ribosome reaches a termination codon on the mRNA

5. After the termination of the mRNA template, a specific polypeptide chain is synthesised from the sequence of amnio acids

Anticodon

Group of three bases on a tRNA molecule that are complementary to a mRNA codon

rRNA (ribosomal RNA)

Type of RNA that makes up the major part of ribosomes

tRNA (transfer RNA)

Type of RNA molecule that transfers amino acids to ribosomes during protein synthesis

mRNA (messenger RNA)

A single-stranded RNA molecule that is a template of a Gene, which encodes the genetic information to make a protein

Amino acids

An organic compound which when repeated in specific sequences constitutes the basic structure of proteins

Primary structure (Protein)

The amino acid sequence of the polypeptide chain

Secondary structure (Protein)

Protein structure is formed by folding and twisting of amino acid chain (hydrogen bonding between peptide groups) - a-helix, b-sheet

Tertiary structure (Protein)

Defined by the Unique interactions between R groups of amino acid chains (Active sites are created); Hydrophobic and Hydrophilic, Covalent bonding, Hydrogen Bonding

Quaternary structure (Protein)

Results when a protein consists of multiple polypeptide chains

Enzymes

Biological Catalysts for chemical reactions in living things

Intracelluar enzymes

Enzymes that catalyse reaction inside cell

Extracellular enzymes

Enzymes that act outside of the cell in which they are produced

Induced fit model

Change in the shape of an enzyme's active site that enhances the fit between the active site and its substrate(s)

Chemical inhibitors

Binds to enzymes and slows reaction rates

Non-competitive inhibitor

A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate.

Competitive inhibitor

A substance, other than the substrate, which binds to the active site of an enzyme

Exergonic reaction

A spontaneous chemical reaction in which there is a net release of free energy.

Endergonic reaction

A non-spontaneous chemical reaction in which free energy is absorbed from the surroundings.

Activation energy

The minimum amount of energy required to start a chemical reaction

Enzymes lower the activation energy of a reaction

1. Correct orientation of reactants

2. Placing strain on the chemical bonds

3. Breaks down the reaction into multiple stages

Gene expression

A process by which a gene produces its product and the product carries out a specific function

Promotor region

A portion of a gene which signals for RNA polymerase to begin transcription

Regulators of Transcription (Transcription factor)

Bind to DNA in the vicinity of a promoter and affect transcription of one or more nearby genes

Activators and Repressors

A protein which binds close to the promoter on a DNA Strand and either activates or represses the activity of RNA polymerase (transcription)

Phenotype

An organism's physical expression of it's gene or visible traits.

Cell differentiation

The process by which a stem cell becomes specialized for a specific structure or function.

Stem cells

Unspecialized cells that are able to renew themselves for long periods of time by cell division

Pluripotent stem cells

Stem cells that can become almost all types of tissues and cells in the body.

Multipotent stem cells

Stem cells that can become a limited number of types of tissues and cells in the body

Methylation of DNA

The process by which the methyl groups are added to certain nucleotides in genomic DNA, blocks the function of RNA polymerase (cytosine)

Cancer

Any malignant growth or tumor caused by abnormal and uncontrolled cell division

Tumour suppressor genes

These keep the activity of proto-oncogenes in check in normal healthy cells.

Protooncogenes

Normal cellular genes that regulate cell proliferation and differentiation that can become oncogenes.

Epigenetics

The study of environmental influences on gene expression that occur without a specific change in DNA sequence

Promotor region

Portion of a gene that signals for RNA polymerase to start transcription

CCDIAL

Communication and Collaboration
Development
Influence
Application and Limitation

Nucleotide

A monomer of nucleic acids consisting of a 5-carbon sugar, a phosphate group, and a nitrogenous base

Ribosomes

Site of protein synthesis in the cell (Facilitate translation)

Factors affecting enzyme activity

- Temperature

- pH levels

- Enzyme concentration

- Substrate concentration

- Presence of Chemical Inhibitors

Mutation

Change in a DNA sequence that affects genetic information

Point mutation

A mutation affecting only one or very few nucleotides in a gene sequence.

Substitution (mutation)

A type of point mutation in which a single nucleotide is substituted with (or exchanged for) a different nucleotide that may result in an altered sequence of amino acid during translation, which may render the newly synthesized protein ineffective.

Inversion (mutation)

A genetic mutation in which the order of a segment of genetic material is reversed. This type of mutation can involve a small number of nucleotides as well as larger sections of a chromosome containing more than one gene

Deletion (mutation)

A change in the base sequence of a gene that results from the loss of one or more nucleotide base pairs in the DNA

Insertion (mutation)

The addition of one or more nucleotide base pairs into a DNA sequence

Mutagen

Chemical or physical agents in the environment that interact with DNA and may cause a mutation

Ionising radiation

Type of radiation such as UV, X ray or gamma rays that can cause mutations in DNA, by breaking the bonds between DNA molecules

Non-ionising radiation

Radiation with photons that do not have enough energy to ionise molecules, and can cause chemical bonds to form between adjacent thymine bases

Mutagenic chemicals

Substances which interact with the structure of a DNA molecule and facilitate the occurrence of a point mutation

Virus (mutation)

Certain Viruses can initiate un-controlled cell division, through inserting oncogenes into the genome

Aneuploidy

The presence of an abnormal number of chromosomes in a cell, e.g. a human cell having 47 chromosomes instead of the usual 46

Polyploidy

A condition in which an organism has extra sets of chromosomes

(Mutations) Spontaneous

Occurs Naturally - a sudden random change in the DNA structure

(Mutations) Induced

Caused by mutagenic factors in the external environment

Somatic cells

Any cell of a living organism other than the reproductive cells.

Germ cells

Reproductive cells that give rise to sperm and ovum

Somatic mutation

A mutation that occurs in cells of the body other than gametes

Germ-line mutation

A mutation occurring in gametes; passed on to offspring

DNA/RNA probes

A stretched single strand of DNA/RNA, used to detect the presence of a complimentary nucleotide sequence (target sequences)

CRISPR

Clustered Regulatory Interspaced Short Palindromic Repeats; A collection of DNA fragments which tell Cas9 where to cut

Antibody Method (Gene location)

1. A protein, generated by the specific gene of interest, is injected into an multicellular organism.

2. The organism then creates antibodies which bind to the protein

3. The antibodies are collated and labelled (Radioactively or Chemically)

4. All DNA from the cell is separated into fragments, and incorporated into a large of number of bacteria, through recombinant DNA technology

5. Each bacterial cell absorbs 1-2 of the fragments

6. Each bacterial cell is incubated into colonies, which will use the new DNA fragment to produce proteins

7. All colonies are exposed to the labelled antibodies, but will only bind to the colony producing the original protein

Gene Cloning (Bacterial Plasmids)

A process through which a specified segment of DNA is inserted into a bacterial cell through the use of plasmids, which allows for the gene to be copied during binary fission

Transgenesis

The process during which foreign DNA is incorporated into higher order multicellular organisms

Ti plasmid

A plasmid of a tumor-inducing bacterium (Agrobacterium) which integrates a segment of its DNA into the host chromosome of a plant; frequently used as a carrier for genetic engineering in plants.

Viral vectors

Use of a virus as a delivery system (called a vector) to carry a gene into the nuclei of target cells to alter protein synthesis.

Microinjection

The introduction of DNA into the nucleus of an embryo or other cell by injection through a very fine needle.

Factors of gene expression

- Methylation or the addition of methyl groups to DNA (cytosine)

- Coiling of DNA around the Histones

- Transcription Factors

- The "Switching on/off" of specific genes during cellular differentiation