Lecture 4 Cellular level of organization 2 .pdf

Cellular Level of Organization 2 Dr. Elita Partosoedarso Kaltura Recordings: Part A, Part B, Part C YouTube Recording 1  Cellular level of organization 2 overview Cellular le...

Cellular Level of Organization 2 Dr. Elita Partosoedarso Kaltura Recordings: Part A, Part B, Part C YouTube Recording 1  Cellular level of organization 2 overview Cellular level of organization 2 Structure DNA Replication Transcription and editing Protein synthesis Translation & formation of function protein Interphase and Mitotic phase Cell cycle Mitosis and cytokinesis Cell cycle control Types Stem cells Differentiation 2 DNA (deoxyribose nucleic acid) 1.1 Histone ○ set of proteins with DNA wrapped around 4 along the chromatin threads 1 2 2. Nucleosome ○ single, wrapped DNA-histone complex 3.3 Chromatin threads 3 ○ composed of DNA and associated proteins 2 4.4 Chromosome ○ composed of DNA and associated proteins ○ condensed form of chromatin Multiple nucleosomes along the entire molecule of DNA appear like a beaded necklace, in which the string is the DNA and the beads are the associated histones 3  DNA DNA replication nucleotide Definition: copying of DNA that occurs before cell division can occur. Cells reproduce themselves by diving to produce 2 new daughter cells. Some cells divide very quickly (epithelium) while others do not (nerve cells, skeletal muscle fibers, cardiac muscle cells) Structure of DNA molecule is made of Two strands of DNA nucleotides bound together with hydrogen bonds in a double helix similar to a long twisted ladder Two strands are complementary, not identical Backbone composed of alternating sugar and phosphate groups “Rungs” are formed from pairs of protruding bases Four DNA bases: adenine (A), thymine (T), cytosine (C), and guanine (G) Complementary base pairs: A with T, and C with G The complementary strand of a region with the sequence AGTGCCT is ______________ 4 This Photo by Unknown Author is licensed under CC BY-SA-NC  Process of DNA replication 2 Stage 1: Initiation 1 Helicase and other enzymes 2 DNA strands separate: untwist at the replication fork become template strands Stage 2: Elongation 2 1 DNA polymerase synthesizes The new strands complement 2 new strands base by base their template strands 2 DNA replication continues until the cell’s Stage 3: Termination entire genome is replicated. DNA replication is stopped when the 2 original strands are bound to their new complementary strands, forming 2 new identical DNA molecules Genome: full complement of an organism’s DNA Proteome: full complement of an organism’s proteins 5 Comparing DNA with RNA DNA RNA Each nucleotide contains a sugar, phosphate group and a nitrogenous base Similarities Backbone consists of alternating sugars and phosphate groups Length: _________________ Length: _________________ _________________ stranded _________________ strand Differences Sugar is _________________ Sugar is _________________ Bases are _________________ Bases are _________________ Spot the difference: one is a DNA nucleotide and the other is an RNA nucleotide. 6  Gene expression transforms the information coded in a gene (portion of DNA) to a final gene product (protein) Protein synthesis: basics Two step process 1. 1 Step 1 Transcription Location: nucleus Process: Section of DNA is used to synthesize mRNA strand that is complementary to the gene of interest. Once mRNA is edited, it is then exported to the rough ER in the cytoplasm 2. 2 Step 2 Translation Location: cytoplasm. Process: mRNA is translated by ribosomes into an amino acid sequence which forms the primary structure of a protein 1 1 2 2 7  Protein synthesis: basics A(n) _________ is a 3-base sequence of DNA that codes for a specific mRNA codon A(n) _________ is a 3-base sequence of mRNA (messenger RNA) that codes for anticodon A(n) _________ is a 3-base sequence of tRNA (transfer RNA) that codes for a specific amino acid A DNA triplet is complementary to its corresponding _________. A mRNA codon is complementary to its corresponding _________ Each tRNA anticodon can attach a _________ Adenine on DNA is complementary to _________ on RNA Thymine on DNA is complementary to _________ on RNA Guanine on DNA is complementary to _________ on RNA Ribosome Cytosine on DNA is complementary to _________ on RNA (large subunit) Amino acid tRNA Anticodon The complementary mRNA strand of a region of DNA with the Codon sequence AGTGCCT is ______________ mRNA Ribosome 8 (small subunit)  Protein synthesis: process of transcription (from DNA to mRNA) Stage 1: Initiation 1 A promoter (DNA sequence) at the start of the gene triggers the start of transcription Stage 2: Elongation 2 2 RNA polymerase unwinds DNA segment containing the gene 1 and builds a strand of mRNA that is complementary to coding strand Stage 3: Termination RNA polymerase reaches a stop codon (UAA, UAG, or UGA) to end transcription and release the mRNA transcript 9  Editing of an mRNA transcript 1 Pre-mRNA transcript is produced from gene sequence 1 initial mRNA containing multiple introns and exons 2 Spliceosome removes/splices introns from pre-mRNA transcript 2 Remaining segments of mRNA (exons) are joined together 3 Final mRNA transcript is transported from nucleus into cytoplasm 3 Introns are long regions of mRNA that can be non-coding or contain transcripts that give rise to different variations of a protein, resulting in a larger variety of proteins with differences in structures and functions 10  Translation: From RNA to Protein Overview: process of synthesizing a polypeptide (chain of amino acids) from 1 codons on an mRNA strand. Stage 1: Initiation 1 mRNA attaches to small subunit of a Small subunit comes together with ribosome large subunit Stage 2 Elongation: polypeptide is built 2 Transfer RNA (tRNA) with a tRNA attaches a Peptide bonds complementary anticodon is 2corresponding amino connect adjacent matched to its mRNA codon acid. amino acid 3 Stage 3 Termination (Stop codon) is reached Translation process is ended and completed polypeptide is released 3 11  Polypeptide synthesis overview 1. Unzips DNA molecule to expose bases 2. RNA nucleotides attach themselves to exposed DNA bases using complementary base pairing principles Transcription 3. Messenger RNA (mRNA) forms along one gene sequence of a (nucleus) DNA molecule within the cell's nucleus 4. mRNA molecule separates from DNA molecule 5. mRNA molecule is edited: exons joined together Editing/splicing (nucleus) 6. mRNA molecule leaves nucleus through large nuclear pores Transport 7. Ribosome subunits attach to start of mRNA molecule and begin the process of translation 8. transfer RNA (tRNA) molecules bring specific amino acids into place at the ribosome site Translation 9. Amino acids are brought into the proper sequence (coded by (cytoplasm) mRNA) and joined together by peptide bonds 10. Peptides join together to form long strands called polypeptides. Several polypeptide chains may be needed to make a complete 12 protein molecule.  From polypeptides to proteins After translation, enzymes in cytosol, ER, and Golgi apparatus fold polypetides into their secondary, tertiary, and quaternary structures so that they become functional proteins Misfolded and unfolded proteins are normally broken down and recycled by proteasomes. If this does not occur, they can accumulate to form clumps called plaques (Alzheimer’s Disease or Parkinson’s disease) Proteome is defined as all proteins synthesized by a cell 13  Overview: sequence of events in the life of the cell from the moment it is created at the end of a previous cycle of cell division until it then divides itself, generating two new cells. 1. Interphase: synthesis of cellular components. Most cells are in this phase most of the time A. G0 phase: resting phase: cells stop dividing (temporary or permanent, eg nerve cells) Cell Cycle B. G1 (gap 1 or 1st growth) phase: cell grows and carries out all normal metabolic functions and processes. C. S (synthesis) phase: DNA replication doubles the DNA content. D. G2 (gap 2 or 2nd growth) phase: cell continues to grow and prepare for mitosis. 2. Mitotic (M) phase: division of cellular content into 2 new cells E. Mitosis: nuclear content are pulled apart and divided to form 2 new, fully functional nuclei. Prophase, metaphase, anaphase, and telophase F. Cytokinesis: cytoplasm is divided into two distinctive cells 14  Structures present during the M phase 1.1 Centrioles: points of origin for growth of new microtubules, pairs of tiny cylinders in centrosome involved with producing spindle fibers (microtubules) 2.2 Centrosome: pair of centrioles together. 3.3 Mitotic spindle: structure made of centrosomes and their emerging microtubules. 4.4 Cleavage furrow: contractile band of microfilaments that forms during cytokinesis around midline of cell. The band contracts until the 2 cells are separated. 5. During prophase, the two centrosomes begin to move towards different sides of the cell and microtubules start to grow towards each other. Prophase Prometaphase Cytokinesis Centrosome Centriole Mitotic spindle Cleavage furrow 3 4 2 1 15  Chromosomes and chromatids 1 Normally each human cell contains 46 chromosomes (23 homologous pairs of chromosomes) 4 After the S phase, cells contain 92 chromatids (46 × 2), ie 2 copies of each chromosome. 3 1.1 Homologous chromosome pairs: one inherited from each parent 2 2. 2 Sister chromatids (chromatid pairs): 1 chromosome and its exact copy produced during S phase. Kinetochore 3.3 Kinetochore: protein complex that attaches microtubules of the mitotic 4 spindle and is associated with the centromere during cell division. 4.4 Centromere: connects the pair of identical chromosomes to each other Prometaphase 16  Mitosis and Cytokinesis Prophase Chromosomes condense and Centromeres produce spindle fibers Nuclear envelop and become visible and move towards opposite poles nucleolus disappear Prometaphase Chromosomes continue to Kinetochores appear at the Mitotic spindle microtubules condense centromeres attach to kinetochores Metaphase Chromosomes are lined up at the metaphase Each sister chromatid is attached to a spindle plate fiber originating from opposite poles Anaphase Centromeres Sister chromatids (now called chromosomes) Certain spindle fibers begin to split in two are pulled toward opposite poles elongate the cell Telophase Chromosomes arrive at Nuclear envelop material Mitotic spindle Spindle fibers opposite poles and begin to surrounds each set of breaks down continue to push decondense chromosomes poles apart Cytokinesis A cleavage furrow appears: daughter cells are separated 17 M phase of the cell cycle: Mitosis and Cytokinesis 18  Cell Cycle Control The movement of the cell from one phase of the cell cycle to the next is heavily controlled in order to maintain homeostasis and to prevent cancer occurring. The control system uses intracellular molecules and external triggers to provide checkpoints, a “stop” and “advance” signal. Precise regulation of the cell cycle is critical for maintaining the health of an organism, and loss of cell cycle control can lead to cancer. 1. Checkpoint: point in the cell cycle at which the cycle can be signaled to provide the stop or go signals ○ G1 checkpoint: cells needs to be ready for DNA synthesis to progress to S phase ○ G2 checkpoint: cell must be fully prepared for mitosis. ○ Metaphase checkpoint: sister chromatids are properly attached to microtubules and lined up at metaphase plate 2. Cyclins and Cyclin-dependent kinases (CDK): activating enzymes that drive the cell through the phases of its life cycle to determine progression past checkpoints 19  1 Stem cells are unspecialized cell that can divide without limit as needed to form new stem cells or can differentiate into more specialized cells. 2 Types of stem cells 1.1 Totipotent stem cell Stem Cells ○ Can differentiate into any cell needed to enable an 3 organism to grow and develop 2.2 Pluripotent stem cell ○ Can differentiate into any type of human tissue but cannot support the full development of an organism 3.3 Multipotent stem cell 3 ○ Can differentiate into different types of cells within a 4 4 given cell lineage or small number of lineages 4.4 Oligopotent stem cell ○ limited to becoming one of a few different cell types 5. Unipotent cell ○ fully specialized and can only reproduce to generate more of its own specific cell type 20  Differentiation (specialization of a cell) 1. Differentiation (when a cell becomes more specialized) can cause changes to cell size, shape, metabolic activity, and overall function. 2. Issue: if all cells in a body contain the same full set of DNA, how does differentiation occur? How does any cell know what it should differentiate into? Answer: __________________________________________________________________ _______________________________________________________________________________________ _________________________________________________________________ _________________ proteins that bind to specific genes on DNA to promote or inhibit transcription 21