Biology 101 - DNA and Proteins

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Three Purposes of Cell Division

1) Reproduction (reproducing new cells), 2) Growth and development of organism, 3) To repair damage of tissues

Simplest form of cell division (found in bacteria)

Binary fission

Four phases of cell cycle

G1 (First gap phase lasting 5-6hrs), S (Synthesis phase of DNA, lasting 10-12hrs,), G2 (Second gap phase, lasting 4-6 hrs) , M (Mitosis and Cytokinesis phase, lasting 1 hr)

Checkpoints and their purposes

G1 checkpoint: before S, makes sure cell is big enough to divide and has all the organelles and equipment required for division. G2 Checkpoint: At end of G2, checks for errors in DNA, proofreading, any chromosomes lost, indicator of genome stability, cell big enough to divide properly. M checkpoint: occurs halfway through M, ensures all chromosomes are aligned equally at the metaphase plate.

What is MPF and what does it do?

Maturation promoting factor (complex of two proteins: cyclin and CDK), Promotes mitosis by phosphorylating various proteins, MPF activity is regulated by high levels of cyclin

5 steps in mitosis

Prophase, prometaphase, metaphase, anaphase, telophase

Steps in prophase

DNA is already replicated, and the identical sister chromatids are paired up in the nucleus, chromosomes condense, centrosomes move away from each other. Mitotic spindle (microtubules) form in the cell.

Steps in prometaphase

Nuclear envelope begins disintegrating, microtubules invade nuclear space, some are kinetochore microtubules that attach to the centromere of the sister chromatid pair.

Steps in metaphase

Centrosomes are at opposite poles of the cell. Sister chromatids line up at the metaphase plate. Kinetochore microtubules ensue a "tug-of-war"

Steps in anaphase

(quickest phase), sister chromatids are pulled apart to opposite poles of the cell (as kinetochore microtubules shorten)

Telophase

Two nuclei are formed, cytokinesis occurs in which cytoplasm is divided between the two newly forming cells (as a cleavage furrow pinches the one cell into two cells). A nuclear envelope reforms around each of the two nuclei.

Name a cell that divides frequently, one that divides infrequently, and one that does not divide

Skin cells divide frequently, Liver cells divide infrequently, Nerve cells do not divide

Chromatin

Entire complex of DNA and proteins is called

Cohesins

Sister chromatids attach by protein complexes called

Aster

A short array of radial microtubules that extend from each centrosome

Separase

During anaphase, sister chromatid cohesins are cleaved by an enzyme called

Protein kinases

These molecules are important chemical signals during interphase

Cyclins (called cyclin-dependent kinases, CDK)

Protein kinases must be activated by

Platelet derived growth factor

Involved in wound healing after an injury (type of growth factor, inducing cells to divide)

Explain how PDGF helps heal wounds

Injury --> Platelet derived growth factor production triggered --> Bind to receptor --> Other signals produced --> Produce connective tissues (fibroblasts) --> signal cascade occurs --> cell division occurs

Six differences between cancer cells and normal healthy cells

1) Do not need growth factors, 2) Do not respond to regular cell signals, 3) Are not density dependent in their growth, 4) Believed to have their own set of internal regulators, 5) Can continue to grow for up to 50 years, 6) Genetic control of cell growth is lost

Three cancer treatments

Radiation, damages DNA which cannot be repaired. Chemotherapy, actively targets dividing cells. Taxol, inhibits spindle tubule formation in prometaphase, prevents cell division.

Amphipathic

Term used to describe the phospholipids that have a hydrophobic and a hydrophilic end

Oligosaccharides

Carbohydates in membrane that are mostly short-chain

Function of carbohydrates in cell membrane

Cell-to-cell recognition, determining cell features (eg. blood types A, B, AB, O)

Six functions of proteins in cell membrane

1) Transport of materials across membrane, 2) cell-to-cell recognition, 3) Intercellular joining, 4) Enzymatic activity, 5)Signal transduction, 6) Attachment to cytoskeleton and extracellular matrix

Materials that enter the cell

Water, oxygen, Na+, Ca2+, Cl-, K+, sugars, amino acids

Materials that exit cell

Waste, water, carbon dioxide

Three types of passive transport

Diffusion (movement of particles across membrane from high to low concentration), Osmosis (movement of water from a hypotonic to a hypertonic environment), Facilitated diffusion (specific molecules for transport, water uses aquaporins (water channels which are proteins), and carrier and channel proteins)

Three types of active transport

Sodium potassium pump (moves molecules against the concentration gradient with use of cell energy ATP), Proton pump (electrogenic pump, H+ ions leave cell, a negative charge forms inside, from -50 to -200 millivolts, and this draws ions into cell), Co-transport (solute transport is accompanied by the protein pump)

Two types of bulk transport (neither active or passive)

Exocytosis and endocytosis (which transports large molecules, such as carbs and protein)

Three types of endocytosis

Phagocytosis (cell eating, large molecules are packaged into vesicles and these vesicles fuse with lysosomes which has digestive enzymes that break down these particles), Pinocytosis (cell drinking, liquids are brought into cell by vesicles), Receptor mediated endocytosis (receptors bind to specific molecules and transport them, eg, cholesterol movement)

Why is stem cell research so important?

Generation of cells that cannot otherwise regenerate, treatment of heart disease and organ cloning, understanding and treatment of cancer.

Watson and Crick

Discovered structure of DNA molecule

Origins of replication

Specific DNA sequences, proteins attach, causes strands to separate)

What are Okazaki fragments

Segments of nucleotides that attach to the lagging strand during DNA replication, they are joined together by DNA ligase

Which nitrogen bases bind together, and which are the purines and pyrimidines

Adenine binds with thymine (30% each) and cytosine bonds with guanine (20% each) Adenine and guanine are purines (two organic rings) and Cytosine and Thymine are pyrimidines (one organic ring)

Cause damage in DNA cells

X-rays, UV rays, chemicals such as pesticides and carcinogens in smoke

What are telomeres and what are their function

Short repeated nucleotides (TTAGGG repeated 100-1000 times), they are non-coding, provide protection to chromosome end, telomerase adds nucleotides and is active in babies and gametes. Telomeres shorten with age. Telomeres are even longer in cancer cells so the cells can divide longer.

Two diseases caused by a recessive allele in humans

Sickle cell anemia and cystic fibrosis (defective transport protein, defective in Cl- transport)

Polymerase Chain Reaction

Amplifies DNA from very small amounts, needs primers, nucleotides, DNA polymerase

DNA fingerprinting

Extracts DNA and cuts it up with enzymes such as Restriction Fragment Length Polymorphism, recognizes a specific sequence of DNA and cuts it. Then gel electrophoresis separates the DNA pieces based on size.

Gene cloning and recombinant DNA

Isolate gene of interest, transfer gene to another organism, express a unique protein based on this inserted gene (eg. Insulin growth hormones)

Genetic Engineering

Process that gives rise to GMOs, which involve inserting and expressing a new (foreign) gene into an organism

Cloning of an organism

Easy to do in plants, can produce a whole plant from a single gene. Animals need to create an embryo from a somatic cell.

Gene therapy

Replace a non-functional gene with a functional one. Has had limited success.

Genetic Testing

To determine whether specific genes that produce disease is present in a human. In adults they can test for inheritance, in children can test for disease, in fetus test for down's syndrome, can screen for most ideal embryo with in vitro fertilization.

List the different enzymes involved in DNA replication

Helicase, Topoisomerase, Single-stranded binding protein, Primases, DNA polymerase III, DNA polymerase I, DNA ligase

Helicase function

Opens up DNA strand in replication fork

Topoisomerase function

Unwinds DNA ahead of DNA fork

Single-stranded binding protein

Binds on and stabilizes single strand of DNA

Primases

Synthesizes an RNA primer at the 5' end of each Okazaki fragment.

DNA polymerase III function

Synthesizes new DNA strand from parental DNA.

DNA polymerase I

removes RNA primer and replaces it with DNA nucleotides

DNA ligase

Joins Okazaki fragments

What is a primer molecule and what does it do?

RNA chains synthesized by primase, complementary to the template strand. Initiates elongation, recognized and attached by DNA polymerase III. Replication occurs from primer in both leading and lagging strand.

How does the cell ensure that any errors are corrected?

DNA is proofread during replication, DNA polymerases read the strand and correct any mistakes.

How does cell repair damaged DNA

1) enzymes detect damaged DNA, 2) Nuclease cuts damaged DNA, 3) DNA polymerase replaces nucleotides, 4) DNA ligase joins the fragmented DNA

What useful information has the human genome provided us

Similarities and differences between humans and other animals, comparisons of genes also. Human evolution and culture. Causes and risks of human diseases (and prevention of disease)

What is meant by RFLP

Restriction Fragment Length Polymorphism - enzyme cut up DNA at specific restriction sites, fragments DNA at different lengths, useful in DNA fingerprinting, forms a pattern of DNA sequence specific to the person (requires gel electrophoresis)

Steps of transcription

Promoter region (called TATA box), transcription factors and RNA bind to this area. DNA unwinds and nucleotides are added using RNA polymerase II. A complementary strand is produced. The polyadenylation site (AAUAAA) releases signal and the polymerase detaches. This concludes the formation of the pre-mRNA.

Steps of RNA processing

A 5' cap (a modified guanine nucleotide) is added to the 5' end of the pre-mRNA, and a Poly-adenylation tail (which is the polyadenylation site of AAUAAA plus about 10-35 Adenine nucleotides) is added to the 3' end of the pre-mRNA. It is now called an mRNA molecule and it moves out of the nucleus to the ribosomes in preparation for translation. The 5' cap protects the mRNA from degradation, and signals ribosomes to attach. The 3' cap assists the mRNA out of the nucleus.

RNA Splicing

There are regions in the mRNA that are expressed (exons) and regions of nucleotides that are not expressed (introns). Spliceosomes are a complex of RNA and protein subunits that remove these introns.

Promoter

DNA sequence where RNA polymerase attaches and begins transcription.

3 properties of RNA that allow it to function as an enzyme

It is single stranded so it can base-pair with itself to allow for the 3D structure that an enzyme would have. Some of the functional groups on the nucleotides may have enzymatic properties. 3rd, the ability of RNA to hydrogen bond to other nucleic acid molecules adds specificity to its enzymatic activities.

Initiation stage of Translation

The tRNA reads the mRNA sequence and brings with it the appropriate amino acid. The amino acid is attached to one end of the tRNA molecule by the enzyme amino-acyl tRNA synthetase. The initiation stage brings together the mRNA, the two subunits of the ribosome, and the tRNA bearing the first amino acid (methionine). Once the mRNA, small ribosomal subunit, and initiator tRNA are brought together, the large ribosomal subunit attaches, and this concludes the initiation stage. (Initiation factors bring all of these components together).

Elongation stage of Translation

The tRNA carrying the next amino acid to be joined to the polypeptide at the P-site is brought to the A site, and the tRNA molecule that has attached its amino acid to the polypeptide chain at the P site exits at the E site. This elongation process continues until a stop codon is reached at the A site.

Termination stage of Translation

When a stop codon (codons are UGA, UAA, UAG) is reached on the mRNA molecule, the tRNA carries a release factor which binds to the stop codon directly on the A site, and a water molecule is added to the end of the polypeptide chain which causes the protein to break free of the ribosomal complex.

Cells use energy for

DNA replication, protein synthesis, membrane transport.

ATP breakdown releases how much energy?

7.3kcal per mole

Muscle cells require how many ATP per second when active?

10 million

Cell respiration reaction and energy released

Cellulose + O2 --> CO2

What does NAD+ stand for?

Nicotinamide adenine dinucleotide

Four characteristics of Enzymes

Substrate specific, affected by environment (pH and Temperature), requires cofactors and coenzymes, affected by chemical activity

Three types of enzyme regulation

Allosteric sites held open by allosteric activator molecule, or closed by an allosteric inhibitor molecule. Feedback inhibition, accumulation of product causes enzyme to switch off. Cooperativity (one active site causes others to remain open, increasing productivity)

What does NAD+ do?

binds with H ions, which contain energy in the form of electrons, and carries H+ to different parts of the cell.

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