What is the role of an RNA primer in DNA replication?

It serves as a template for DNA polymerase.

It functions as a proofreading enzyme.

It stabilizes the DNA template during replication.

It initiates synthesis of a complementary strand of DNA.

What is the function of DNA polymerase in DNA replication?

To synthesize a complementary strand of DNA

What is the purpose of DNA polymerase during DNA replication?

To add nucleotides to the growing DNA strand

To proofread and correct errors in DNA replication

The RNA Primer. DNA polymerase cannot initiate synthesis of a complementary strand of DNA on a totally single stranded template. DNA polymerase requires an RNA primer, which is a short piece of RNA base-paired to the DNA template. The free hydroxyl group on the 3’-end of the RNA primer serves as the first acceptor of the first deoxynucleotide. The RNA Primer , Primase This is a specific RNA polymerase that synthesizes the short stretches of RNA (~10 bases long) that are complementary and antiparallel to the DNA template. Synthesized in a 5’ to 3’ direction. Prokaryotic and eukaryotic DNA polymerases elongate a new DNA strand by adding deoxynucleotides, one at a time, to the 3’-end of the growing chain .It Reads 3’ to 5’ and synthesizes 5’ to 3’ direction

RNA Primer Excision and Replacement by DNA polymerase I DNA polymerase III continues to synthesize DNA on the lagging strand until it is blocked by an RNA primer. DNA polymerase I excises the RNA primer in a 5’ to 3’ Exonuclease direction, and then fills the gap with a 5’ to 3’ Polymerase direction. It also proofreads the new chain using a 3’ to 5’ Exonuclease activity for DNA.3’-exonuclease is always for proofreading functions.DNA Ligase The Okazaki fragments are joined by DNA ligase, which forms the phosphodiester bond in the sugar phosphate backbone between the two nucleotides.The creation of the phosphodiester bond requires 2 high energy bonds.

Origin recognition ORC,MCM proteins helicase activity, ssDNA RPA, Primer synthesis polymers alpha/primase,Sliding clamp PCNA, primer removal RNase H, FEN1.Pol α/Primase synthesizes an RNA chain of 10 nucleotides followed by another 20 nucleotides of initiator DNA (iDNA). Because Pol α/Primase has no proofreading ability, this whole section of RNA/iDNA is removed. The exonucleases RNase H removes the RNA and Fen1 removed the iDNA. The gap is filled in by Pol δ and DNA ligase joins the 2 ends.Eukaryotic DNA Replication All have 5’ to 3’ Polymerase activity.

The Role of RNA

RNA translation. The genetic information in DNA is used to synthesize proteins through the processes of RNA Transcription and RNA Translation. The sequence of three-letter code words in the gene determines the sequence of amino acids in a polypeptide chain. RNA Transcription DNA serves as a template for the synthesis of RNA. There are 3 major types of RNA that participate in the process of proteins synthesis. 1.5% of the genome encodes for proteins via mRNA, but an unknown % of the genome codes for noncoding RNA (ncRNA)

The Promoter Region is a region of DNA upstream where transcription is initiated for control of gene transcription Promoters are solely important for gene expression Pribnow Box in Prokaryotes. CAAT and Hogness box (TATA) in Eukaryotes They control the binding of RNA polymerases and Transcription factors (if Eukaryotic) Now RNA polymerase can transcribe DNA to RNA to further achieve the goal to mRNA to eventual protein formation Prokaryotic promoter are recognized by RNA polymerase and sigma factor (Sigma Subunit) Eukaryotic promoter is recognized and bounded by General Transcription Factors (GTF’s) and RNA Polymerase II

Most of the functions of a eukaryotic cell are controlled by the nucleus, shown in Figure 4-12. The nucleus is filled with a jellylike liquid called the nucleoplasm, which holds the contents of the nucleus and is similar in function to a cell’s cytoplasm. The nucleus houses and protects the cell’s genetic information. The hereditary information that contains the instructions for the structure and function of the organism is coded in the organism’s DNA, which is contained in the nucleus. When a cell is not dividing, the DNA is in the form of a threadlike material called chromatin. When a cell is about to divide, the chromatin condenses to form chromosomes. Chromosomes are structures in the nucleus made of DNA and protein. The nucleus is the site where DNA is transcribed into ribonucleic acid (RNA). RNA moves through nuclear pores to the cytoplasm, where, depending on the type of RNA, it carries out its function. Nuclear Envelope The nucleus is surrounded by a double membrane called the nuclear envelope. The nuclear envelope is made up of two phos- pholipid bilayers. Covering the surface of the nuclear envelope are tiny, protein-lined holes, which are called nuclear pores. The nuclear pores provide passageways for RNA and other materials to enter and leave the nucleus. Nucleolus Most nuclei contain at least one denser area, called the nucleolus (noo-KLEE-uh-luhs). The nucleolus (plural, nucleoli) is the site where DNA is concentrated when it is in the process of making ribosomal RNA. Ribosomes (RIE-buh-SOHMZ) are organelles made of protein and RNA that direct protein synthesis in the cytoplasm. The nucleus of a cell is surrounded by a double membrane called the nuclear envelope. The nucleus stores the cell’s DNA. FIGURE 4-12 Nuclear envelope Nucleolus Nuclear pores DNA (chromatin) Copyright © by Holt, Rinehart and Winston. All rights reserved. 80 CHAPTER 4 MITOCHONDRIA Mitochondria (MIET-oh-KAHN-dree-uh) (singular, mitochondrion) are tiny organelles that transfer energy from organic molecules to adenosine triphosphate (ATP). ATP ultimately powers most of the cell’s chemical reactions. Highly active cells, such as muscle cells, can have hundreds of mitochondria. Cells that are not very active, such as fat-storage cells, have few mitochondria. Like a nucleus, a mitochondrion has an inner and an outer phos- pholipid membrane, as shown in Figure 4-13. The outer membrane separates the mitochondrion from the cytosol. The inner membrane has many folds, called cristae (KRIS-tee). Cristae contain proteins that carry out energy-harvesting chemical reactions. Mitochondrial DNA Mitochondria have their own DNA and can reproduce only by the division of preexisting mitochondria. Scientists think that mito- chondria originated from prokaryotic cells that were incorporated into ancient eukaryotic cells. This symbiotic relationship provided the prokaryotic invaders with a protected place to live and pro- vided the eukaryotic cell with an increased supply of ATP. RIBOSOMES Ribosomes are small, roughly spherical organelles that are respon- sible for building protein. Ribosomes do not have a membrane. They are made of protein and RNA molecules. Ribosome assembly begins in the nucleolus and is completed in the cytoplasm. One large and one small subunit come together to make a functioning ribosome, shown in Figure 4-14. Some ribosomes are free within the cytosol. Others are attached to the rough endoplasmic reticulum.

SB2. Obtain, evaluate, and communicate information to analyze how genetic information is expressed in cells. a. Construct an explanation of how the structures of DNA and RNA lead to the expression of information within the cell via the processes of replication, transcription, and translation. Learning Targets _______Identify the structural components of DNA and RNA Success Criteria _______Can accurately identify the key structural components of DNA (deoxyribose sugar, phosphate group, nitrogenous bases: adenine, thymine, cytosine, guanine). _______Can identify the key structural components of RNA (ribose sugar, phosphate group, nitrogenous bases: adenine, uracil, cytosine, guanine). _______Can describe the differences in the sugar backbone of DNA and RNA (deoxyribose vs. ribose). _______Can identify the double-stranded structure of DNA and the single-stranded structure of RNA. _______Identify the parts of protein synthesis and the location of each process Success Criteria _______Can identify and describe the two main processes of protein synthesis: transcription and translation. _______Can correctly explain that transcription occurs in the nucleus where DNA is transcribed into mRNA. _______Can explain that translation occurs in the cytoplasm at ribosomes where mRNA is translated into amino acid sequences to form proteins. _______Compare and Contrast DNA to RNA Success Criteria _______Can clearly identify similarities between DNA and RNA, such as both being nucleic acids and containing nucleotide structures. _______Can explain differences in DNA and RNA, including sugar types (deoxyribose vs. ribose), strand number (double-stranded DNA vs. single-stranded RNA), and nitrogenous base usage (thymine in DNA vs. uracil in RNA). _______Can describe the function of DNA as genetic storage and the function of RNA in protein synthesis (mRNA, tRNA, rRNA). _______Analyze the reasoning for enzymes usage in both DNA replication and protein synthesis. Success Criteria _______Can identify key enzymes involved in DNA replication (e.g., helicase, DNA polymerase, ligase) and explain their functions (e.g., helicase-unwinding DNA, DNA polymerase-synthesizing new DNA strands, ligase-sealing nicks in the DNA backbone). _______Can identify enzymes involved in protein synthesis (e.g., RNA polymerase) and explain their role in transcribing DNA into mRNA. _______Can analyze why enzymes are essential for speeding up chemical reactions…(ensuring accuracy, and catalyzing steps in replication and protein synthesis) _______Can provide specific examples of how enzyme malfunction can impact genetic replication or protein synthesis. _______Perform the steps of DNA replication and protein synthesis in order to demonstrate their understanding of how the structure of DNA supports the genetic expression in successive generations. Success Criteria _______Can demonstrate a step-by-step understanding of DNA replication, including unwinding, complementary base pairing, and proofreading. _______Can demonstrate the steps of transcription (formation of mRNA from DNA) and translation (conversion of mRNA into a polypeptide). _______Can show how DNA's structure (double helix, base pairing) ensures accurate replication for passing genetic information to offspring. _______Can illustrate how changes in DNA sequence can lead to changes in protein structure and function, thus affecting traits in successive generations.

The Structures of DNA and RNA

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