Rapid Learning Center Presents. Teach Yourself High School Biology in 24 Hours. and Functions

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1 Rapid Learning Center Chemistry :: Biology :: Physics :: Math Rapid Learning Center Presents Teach Yourself High School Biology in 24 Hours Gene e Structures and Functions High School Biology Rapid Learning Series Wayne Huang, PhD Andrew Graham, PhD Elizabeth James, PhD Casandra Rauser, PhD Jessica Habashi, PhD Sara Olson, PhD Jessica Barnes, PhD Rapid Learning Center Rapid Learning Inc. All rights reserved. Rapid Learning Inc. All rights reserved. :: 1

2 Learning Objectives By completing this tutorial, you will learn about: DNA: Chemical Composition and Structure Genes: the Genetic Code and the Central Dogma How genes are inherited Mutations and Genetic Disease Gene Therapy 3/52 Concept Map DNA Replication DNA Daughter cell rrna Transcription trna Transcription mrna Assembly Assembly Amino acids Translation Ribosomes Assembly Protein 4/52 Rapid Learning Inc. All rights reserved. :: 2

3 DNA Structure Chemical composition of DNA Physical structure of DNA DNA organization in cells Relationship between DNA and genes. 5/52 DNA and You Genes dictate your phenotype. Your weight Your face 6/52 Your height Disease susceptibility Rate of aging Rapid Learning Inc. All rights reserved. :: 3

4 DNA Basics Genes are considered as the unit of genetic inheritance. Chromosomes are made up of genes and are associated with proteins. They are located in the nucleus. DNA (deoxyribonucleic acid) is made up of genes. Genes code for the physical development and phenotype of an organism. 7/52 The Building Blocks of DNA Nitrogenous Bases Adenine Guanine Thymine BASE Glycosidic Bond Cytosine Deoxyribose Nucleoside 8/52 Nucleotide monophosphate Phosphate Base + Deoxyribose + Nitrogenous Base = Deoxyribonucleic Acid Rapid Learning Inc. All rights reserved. :: 4

5 Chemical Composition Four bases make up DNA: Adenine (A), guanine (G), cytosine (C) and thymine (T). A only pairs with T and G on pairs with C in DNA. DNA has a phosphate backbone. Backbone Bases A T G C C T G A C T T T G T G T A C G G A C T G A A A C A C Backbone 9/52 Putting the DNA Blocks Together Phosphate Nitrogenous Bases 5 Deoxyribose DNA Nucleotides are linked at their phosphate groups in a phosphodiester bond. 3 10/52 Notice the phosphate bonds are formed at the 5 and 3 positions. Rapid Learning Inc. All rights reserved. :: 5

6 Purine and Pyrimidine Nucleotides (Adenine A) (Guanine G) Deoxyadenosine 5'-phosphate (damp) Deoxyguannine 5'-phosphate (dgmp) (Cytosine C) (Thymine T) 11/52 Deoxycytosine 5'-phosphate (dcmp) Deoxythymine 5'-phosphate (dtmp) DNA Strands are Antiparallel The arrangement of the components of DNA 12/52 Rapid Learning Inc. All rights reserved. :: 6

7 RNA DNA Structure Comparison Major Differences between RNA and DNA: DNA RNA Base: A, T, G, C A, U, G, C Sugar: Deoxyribose Ribose 3D Structure: Long, Double Helix Various Conformations 13/52 Organization of DNA in the Cell DNA is highly organized into chromosome within cells. DNA strands Double Helix Nucleosome Chromatin Chromosome Chromosome (in cell nucleus) 14/52 Rapid Learning Inc. All rights reserved. :: 7

8 Gene Basics Genes are sections of the DNA that code for a protein. There are many genes within a DNA or chromosome molecule. This is chromosome 16. Notice the stripes which indicate genes. 15/52 90 million base pairs are contained in this chromosome and dozens of genes. Gene to Protein Gene translation and transcription. Genetic code for protein sequence. Central Gene Dogma Proteins, amino acids and basic structure. 16/52 Rapid Learning Inc. All rights reserved. :: 8

9 DNA to mrna to Protein mrna transcript is exported from the nucleus to the cytoplasm DNA mrna Protein Newly formed peptide chain mrna ribosome Amino acid added to growing protein chain. Amino acid trna trna binding to codon Completed protein Translation at the ribosome level Start of polypeptide chain Maturing protein Cytoplasm ribosomes 17/52 Transcription Translation mrna Different Types of RNA mrna carries the information for the amino acid sequence of a polypeptide (protein) chain. rrna are pieces of RNA that form complexes with ribosomes (protein) to facilitate the transfer of amino acid from trna to the polypeptide chain. trna carries amino acids to the ribosome and transfers them to the growing polypeptide chain. snornas small nuclear RNAs used to process and chemically modify 18/52 rrnas. snrna forms complexes with proteins used in eukaryotic RNA processing (e.g. exon splicing and intron removal). Rapid Learning Inc. All rights reserved. :: 9

10 Types of RNA mrna encodes the amino acid sequence of a polypeptide and is copied from DNA. trna: transfer RNA, transports amino acids to the ribosomes during translation. rrna: ribosomal RNA forms complexes with ribosomal proteins and is essential for the translation of the mrna sequence. snrna: small nuclear RNA forms complexes with proteins used in eukaryotic RNA processing, e.g. exon splicing, intron removal. 19/52 snornas: small nucleolar RNAs guide chemical modification of rrnas and other RNA genes (trnas, snrnas). They are classed as snrna. Three Steps to RNA Synthesis Termination Elongation Initiation Termination, elongation and initiation of RNA synthesis occurs in prokaryotes and eukaryotes. Elongation is the same in prokaryotes and eukaryotes but initiation and termination differ. 20/52 Rapid Learning Inc. All rights reserved. :: 10

11 DNA is Transcribed to mrna DNA transcription begins with the unwinding and opening of the DNA double helix. Ultimately the mrna is exported from the nucleus to the cytoplasm for translation into a protein. A mrna molecule complementary to the DNA sequence is made. 21/52 Transcription RNA copies information from DNA template through baseparing mechanism, UA/AT or CG/GC. DNA Template (one strand) A TGCC T G A C A T T GTG Transcription Transcription RNA product U A C G G A C U G U A A C A C 22/52 Rapid Learning Inc. All rights reserved. :: 11

12 RNA Synthesis Process RNA synthesis is regulated by gene regulatory elements within each gene. RNA polymerase unwinds the DNA and RNA is transcribed 5 to 3 from the DNA template (3 to 5 ). RNA synthesis is similar to DNA synthesis with these exceptions: NTPs not dntps are used and there is no primer. Uracil instead of thymine is used. 23/52 And an RNA polymerase is used instead of a DNA polymerase. Processing of mrna In post transcriptional modification precursor mrna from eukaryotes are converted into mature mrna (this is not post translational modification) cap occurs while the RNA molecule is being transcribed after about 30 nucleotides have been added. The three main modifications are 5 capping, 3 polyadenylation and RNA splicing. 3. RNA splicing: introns (regions of RNA that do not code for protein) are removed from the premrna leaving exons connected. The splicing is catalyzed by a large protein complex called the spliceosome. There are many ways to splice a mrna allowing for a large variety of proteins from a limited amount of DNA. 24/52 2. Cleavage of the 3 end is followed by adding polyadenosine (poly-a) tail. Rapid Learning Inc. All rights reserved. :: 12

13 Transcription Termination Eukaryote transcription termination is not completely defined but seems to involve the cleavage of the nascent transcript, followed by template-independent addition of A s at the new 3 end. This is called Polyadenylation. Prokaryotes and Eukaryotes have different mechanisms to stop transcription. Bacteria use two kinds of RNA transcription ti termination ti strategy: t Rho independent type stops transcription when the RNA molecule forms a hairpin loop structure followed by a whole bunch of uracil bases. 25/52 Protein Basics There are 20 amino acid residues. The amino acids are joined together by a peptide bond. The amino acid sequence of a protein is determined by the DNA sequence of the gene. 26/52 Typically one gene encodes for one protein. This is called the one gene one protein hypothesis. Rapid Learning Inc. All rights reserved. :: 13

14 Introduction to Amino Acids Yes, an α amino acid has a central carbon atom, called an α carbon. Do you know what an amino acid is? Amino acids also have an amino and carboxylic acid group. And an H and R group 27/52 Protein Basics The protein sequence is determined by the DNA sequence of the gene. The sequence of amino acids is called the primary structure of a protein. Gene Protein (Gene Product) 28/52 Rapid Learning Inc. All rights reserved. :: 14

15 The Central Dogma How are genes converted into its final functional product? DNA DNA replication mrna Transcription Protein Translation trna, rrna, non-coding RNA 29/52 The Genetic Code DNA is made up of: Adenine, Guanine, Cytosine and Thymine. A codon is a three nucleotide sequence that codes for an amino acid. There are three codons that signal stop transcription. Codons Amin o Acid 30/52 Rapid Learning Inc. All rights reserved. :: 15

16 Protein Biosynthesis Three Phases There are three phases in protein biosynthesis. Who knows what they are? 31/52 The Genetic Code mrna is read in a sequential manner starting from a fixed point (initiation codon, AUG) and stopping at stop codons. Every three bases on mrna determine one amino acid (triplet code). Each of 64 combinations (4 3 ) of triplet bases encodes an amino acid or a stop codon. One amino acid may be encoded by multiple codons. The amino acid sequence is said to be degenerative because there are 64 codons for 20 amino acids. 32/52 Rapid Learning Inc. All rights reserved. :: 16

17 Protein Biosynthesis - Elongation Elongation: Incorporation of an Amino Acid Into a Protein Peptidyl trna attached to C-terminal of the growing Polypeptide chain 33/52 DNA Replication 34/52 Rapid Learning Inc. All rights reserved. :: 17

18 3-Step Replication Process Initiation Elongation Termination 35/52 Transmission of Genes Cell division and DNA Replication A new cell derives its DNA from an older cell An older cell prepares an extra set of DNA copies to give to its daughter cells (DNA replication) The duplicated DNA is separated evenly into two daughter cells, with each cell containing one complete set of DNA 36/52 Rapid Learning Inc. All rights reserved. :: 18

19 DNA Replication - Definition The process of making an identical copy of a section of duplex (double-stranded) DNA, using existing DNA as a template for the synthesis of new DNA strands. 37/52 Semi-Conservative DNA Replication A parent DNA molecule is replicated. Original Parent Molecule One parent strand is in each of the two new molecules. 38/52 First-generation daughter molecules Rapid Learning Inc. All rights reserved. :: 19

20 DNA Replication Process The parent double helix opens and a complementary daughter strand synthesized. Newly Synthesized Strands 39/52 The product of semi conservative replication is two double helices each having one new strand and one parent strand. Initiation of Replication DNA strands separate at the origin and replication proceeds in opposite directions along the DNA. At the origins of replication a replication fork emerges opening the double helix. DNA replication is bidirectional. 40/52 The strands are primed and replication proceeds from, the 5 to 3 direction. Rapid Learning Inc. All rights reserved. :: 20

21 Lagging Strand Replication In DNA replication the lagging strand is the strand opposite of the replication fork of the leading strands. Replication is in the 3 to 5 direction. 41/52 1. On the lagging strand primase reads the DNA and adds RNA sequences to act as a primer for POL III DNA polymerase. Multiple RNA primers needed. 2. Pol III lengthens the primers forming Okazaki fragments. 3. Pol I then removes the RNA and adds its nucleotides. 4. DNA ligase joins the fragments. Leading Strand Replication The leading strand is done in a single unit not fragments as it is in the lagging strand. Replication is in the 5 to 3 direction. Helicases are enzymes that move directionally along a nucleic acid phosphodiester backbone separating two annealed nucleic acid strands. 42/52 1. On the leading strand Pol II reads the DNA and adds nucleotides continuously. 2. On the leading strand DNA polymerase III is able to synthesize DNA using free 3 OH group donated by a single RNA primer. 3. Continuous synthesis occurs in the direction the replication fork is moving. Rapid Learning Inc. All rights reserved. :: 21

22 Fidelity of DNA Replication Mutations Genetic Diseases Gene Therapy 43/52 DNA Mutations & Heredity A gene mutation is a permanent change in the DNA sequence that makes up a gene. Gene mutations occur in two ways: they can be inherited from a parent acquired during a person s lifetime. Acquired (or somatic) mutations occur in the DNA of individual cells at some time during a person s life due to environmental factors. Acquired mutations in somatic cells cannot be passed on to off spring. Mutations that are passed from parent to child are hereditary mutations or germline mutations. Mutations that are only in egg or sperm or those that happen immediately after fertilization are de novo mutations. DNA Mutant Gene and Inheritance 44/52 Rapid Learning Inc. All rights reserved. :: 22

23 5 Basic Types of Mutations These are the five basic DNA mutations. Deletion Mutation Duplication Mutation Inversion 45/52 Insertion Translocation Causes of Mutations X Incorrect nucleotide inserted. X Errors during DNA replication DNA damage caused by radiation, UV exposure or mutagenic chemicals. Chromosome translocation, deletion, duplication and inversion 46/52 There are many other causes of DNA mutations, including environmental and genetic instability. Rapid Learning Inc. All rights reserved. :: 23

24 Results of Mutations Silent mutations have a DNA base change but this change does not result in a different amino acid in the protein. Missense mutation is a DNA base change resulting in the insertion of a different amino acid in the protein. Nonsense mutations code for a stop where one should not be. This results in a truncated protein. 47/52 Gene Therapy Gene therapy may be used to fix a damaged gene or insert a new one. First a piece of DNA having the normal or new gene is isolated. The gene is inserted into a vector. A vector can carry the new gene to the target cell. 48/52 Vector-DNA complex infects target tissue. Replication of new gene begins and protein is synthesized. Rapid Learning Inc. All rights reserved. :: 24

25 Question: Review Phosphate base + deoxyribose DNA + nitrogenous base = Purine bases include and. Adenine, guanine Segments of DNA that code for a protein are called. DNA replication is. Genes Semi-conservative 49/52 Gene mutations happen in two ways. What are these ways? Inherited or acquired Learning Summary DNA mrna Protein DNA is transcribed to mrna. mrna is translated to protein. DNA Bases A:T adenine always pairs with thymine G:C guanine pairs with cytosine. 50/52 Result of DNA mutations include: 1. Silent mutation. 2. Missense. 3. Nonsense. 5 Types of Mutations 1. Deletion 2. Duplication 3. Inversion 4. Insertion 5. Translocation Rapid Learning Inc. All rights reserved. :: 25

26 Congratulations You have successfully completed the core tutorial Gene Structures and Functions Rapid Learning Center 51/52 Rapid Learning Center Chemistry :: Biology :: Physics :: Math What s Next Step 1: Concepts Core Tutorial (Just Completed) Step 2: Practice Interactive Problem Drill Step 3: Recap Super Review Cheat Sheet Go for it! 52/52 Rapid Learning Inc. All rights reserved. :: 26