# Bioinformatics: Sequence Analysis

Save this PDF as:

Size: px
Start display at page:

## Transcription

1 1 Bioinformatics: Sequence Analysis COMP 571 Luay Nakhleh, Rice University Course Information 2 Instructor: Luay Nakhleh office hours by appointment (office: DH 3119) TA: Leo Elworth (DH 3121; office hours by appointment Meeting time and place: T&TH 9:25-10:40, HZ 210 Website: Grading 3 A set of homework assignments: 50% Midterm 1: 25%; in-class on 23 February 2017 Midterm 2: 25%; in-class on 20 April 2017

2 Course Textbooks Highly recommended, but not required Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids 4 Durbin et al., Cambridge University Press Algorithms on Strings, Trees, and Sequences Gusfield, Cambridge University Press Genome-scale Algorithm Design Makinen et al., Cambridge University Press A list of other recommended books is available on the course website Intended Audience 5 This is a computer science course! The course uses mathematics and algorithms, and homework assignments and exams will include these (and assume knowledge of programming). This is NOT a programming for biologists course! This is NOT a course about how to use bioinformatics tools or databases! Students are expected to have had (or are currently taking) an algorithms course, can program, and are not afraid of math. Tentative List of Topics 6 Pairwise sequence alignment Markov chains and HMMs Pairwise alignment using HMMs Profile HMMs for sequence families Multiple sequence alignment Phylogenetic tree inference Phylogenomics Suffix trees The Burrows-Wheeler transform Read alignment Genome compression Applications from genomics, transcriptomics, and metagenomics

3 7 I teach COMP 182 immediately after this class (10:50-12:05 on TR)! So, I need to leave the classroom by 10:40. Please talk to Leo (the TA) first. 8 Questions about administrivia? 9 Background

4 Life Through Evolution 10 All living organisms are related to each other through evolution This means: any pair of organisms, no matter how different, have a common ancestor sometime in the past, from which they evolved Evolution involves inheritance, variation, and selection Life Through Evolution 11 Inheritance: passing of characteristics from parents to offsprings* Variation: process that leads to differences between parent and offspring Selection: favoring certain individuals over others doe to phenotypic differences * this is challenged by horizontal gene transfer 12 I have called this principle, by which each slight variation, if useful, is preserved, by the term Natural Selection. The [neutral] theory does not deny the role of natural selection in determining the course of adaptive evolution, but it assumes that only a minute fraction of DNA changes in evolution are adaptive in nature, while the great majority of phenotypically silent molecular substitutions exert no significant influence on survival and reproduction and drift randomly through the species. Nothing in biology makes sense except in the light of evolution.

5 Evolution 13 The accumulation of change over time in a population Population genetics mainly focuses on evolutionary analysis of changes within populations, whereas phylogenetics is mostly aimed at inter-species relationships We will discuss later (under phylogenomics ) how these two disciplines are now coming together due to dense sampling of genomes. The Tree of Life 14 Prokaryotic vs. Eukaryotic Cell Structure 15 Source: Pearson Education, Inc. The Biology Place

6 Prokaryotic vs. Eukaryotic Cells 16 Prokaryotes Eukaryotes Size 1-10 ϻm in length ϻm in length Nucleus Intracellular organization does not exist no compartments exists, and separated from the cytoplasm compartments (nucleus, cytosol, mitochondria, etc.) Gene structure no introns introns and exons Cell division simple cell division mitosis or meiosis Ribosome consists of a large 50S subunit and a small 30S subunit consists of a large 60S subunit and a small 40S subunit Reproduction parasexual recombination sexual recombination Organization mostly single cellular mostly multicellular, and with cell differentiation Source: Systems Biology in Practice, Klipp et al. The Nucleic Acid World 17 The full diversity of life on this planet from the simplest bacterium to the largest mammal is captured in a linear code inside all living cells. DNA 18 Deoxyribonucleic Acid DNA molecules are linear polymers of just four different nucleotide building blocks. Genomic DNA molecules are immensely long, containing millions of bases each, and it is the order of these bases, the nucleotide sequence or base sequence of DNA, which encodes the information for making proteins.

7 19 RNA Ribonucleic Acid RNA molecules are also linear polymers, but are much smaller than genomic DNA. Most RNA molecules also contain just four different base types. Several classes of RNA molecules are known, some of which have a small proportion of other bases. The Building Blocks of DNA and RNA The Double Helix (DNA) Watson-Crick base-pairing: A T, C G Each strand of a DNA double helix has a base sequence that is complementary to the base sequence of its partner strand.

8 22 DNA Replication * Hydrogen bonds are noncovalent bonds: the t wo DNA strands can be easily separated. * There are a number of processes in which strand separation is required. * One such process is DNA replication, which is a necessary prelude to cell division. 23 RNA Structure Almost all RNA molecules in living systems are single stranded. As a result, RNA has much more structural flexibility than DNA, and some RNAs can even act as enzymes, catalyzing a particular chemical reaction. Secondary and Tertiary Structures of RNA 24 The Tetrahymena ribozyme

9 The Central Dogma 25 A single direction of flow of genetic information from the DNA (information store), through RNA, to proteins This scheme holds for all known forms of life, with variations in the details of the processes involved in different organisms Not all genetic information in the DNA encodes proteins RNA can also be the end product, and other regions of the genome have as yet no known function of product The genomic DNA encodes all molecules necessary for life, whether they are proteins or RNA or... Transcript ion 26 (A) One strand of the DNA is involved in the synthesis of an RNA strand complementary to the strand of the DNA (B) The enzyme RNA polymerase reads the DNA and recruits the correct building blocks of RNA to string them together based on the DNA code Te rminology 27 RNA transcribed from a protein-coding gene is called messenger RNA (mrna) When a gene is being transcribed into RNA, the gene is said to be expressed

10 Overlapping Genes 28 Although only one segment of the DNA strand is transcribed for any given gene, it is also possible for genes to overlap so that one or both strands at the same location (locus) encode parts of different proteins. This most commonly occurs in viruses as a means of packing as much information as possible into their very small genomes but it could also occur in mammals (the above figure shows overlapping genes in the human genome) Regulated Gene Expression 29 The genomic DNA sequence contains more information that just the protein sequences. The transcriptional apparatus has to locate the sites where gene transcription should begin, and when to transcribe a given gene. At any one time, a cell is only expressing a few thousand of the genes in its genome. To accomplish this regulated gene expression, the DNA contains control sequences in addition to coding regions (More on this in a few slides). Translat ion 30 mrna is translated into protein according to the genetic code, which is the set of rules governing the correspondence of the base sequences in DNA or RNA to the amino acid sequence of a protein. Each amino acid is encoded by a set of three consecutive bases (codon)

11 31 The Standard Genetic Code 32 Reading Frames Translation occurs in nonoverlapping sets of three bases. There are thus three possible ways to translate any nucleotide sequence, each of which is called a reading frame These three reading frames give three different protein sequences. In the actual translation process, the detailed control signals ensure that only the appropriate reading frame is translated into protein. 33 Reading Frames

12 Gene Structure and Control 34 The regulation of many processes that interpret the information contained in a DNA sequence relies on the presence of short signal sequences in the DNA. The general term for these signal sequences is regulatory elements. For example, the molecules involved in transcription and translation require signals to identify where they should start and stop. Gene structure and control differ between prokaryotes and eukaryotes Transcription Regulation 35 The control regions at which RNA polymerase binds to initiate transcription are called promoters. RNA polymerase binds more tightly to these regions than to the rest of the DNA and this triggers the start of transcription. Gene Structure in Prokaryotes 36 * Bacterial promoters typically occur immediately before the position of the transcription start site (TSS), and contain two characteristic short sequences, or motifs, that are almost the same in the promoters for different genes. * The termination of transcription is controlled by the terminator signal which in bacteria differs from the promoter is that it is active when transcribed to form the end of the mrna strand (forms a loop structure that prevents the transcription apparatus from continuing). * Single type of RNA polymerase transcribes all genes.

13 Gene Structure in Eukaryotes 37 * Regulatory elements in eukaryotes are more complex. * Three types of RNA polymerase transcribe genes: RNA polymerase II transcribes all protein coding genes, where other RNA polymerase tpyes transcribe genes for trnas, rrnas and other types of RNA Splicing of an Intron 38 * The existence of introns necessitates an extra step between transcription and translation, which is known as RNA splicing: (1) the complete gene is initially transcribed into RNA, and (2) the introns are then excised and the exons spliced together to provide a functional mrna that gives the correct protein sequence when translated. In most protein coding genes, this process is carried out by the spliceosome, which consists of small nuclear RNA (snrna) and proteins. Operon Structure 39 In bacteria, functionally related protein-coding sequences are often clustered together into operons. Each operon is transcribed as a single mrna transcript and the proteins are then separately translated from this one long molecule. This has the advantage that only one control region is required to activate the simultaneous expression of all genes in the operon. Not all bacterial genes are contained in operons; many are transcribed individually and have their own control regions.

14 40 Proteins 41 Levels of Protein Structure 42 Side Chains of the Amino Acids

15 Organization of the DNA 43 The genome is an organism s complete set of DNA Genomes vary widely in size some bacteria have 600,000 base pairs humans have about 3 billion base pairs Except for mature red blood cells, all human cells contain a complete genome DNA in the human genome is arranged into 23 pairs of DNA molecules, called chromosomes (physically separate molecules, and vary widely in length) Each chromosome contains many genes 44 Gene, Locus, Allele A gene is a unit of heredity, and usually refers to a DNA sequence that encodes a protein or an RNA that has some function A locus is the specific location of a gene (or, more generally, a DNA sequence) in the genome Each of the different DNA sequences at a given locus is called an allele Available Data Databases in total (as classified at the NAR Molecular Biology Database Collection Website, 2006)

16 Acknowledgments 46 Understanding Bioinformatics, Zvelebil and Baum, Garland Science

### Protein Synthesis How Genes Become Constituent Molecules

Protein Synthesis Protein Synthesis How Genes Become Constituent Molecules Mendel and The Idea of Gene What is a Chromosome? A chromosome is a molecule of DNA 50% 50% 1. True 2. False True False Protein

### Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure 3.11 3.15 enzymes control cell chemistry ( metabolism )

Biology 1406 Exam 3 Notes Structure of DNA Ch. 10 Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure 3.11 3.15 enzymes control cell chemistry ( metabolism ) Proteins

### DNA Replication & Protein Synthesis. This isn t a baaaaaaaddd chapter!!!

DNA Replication & Protein Synthesis This isn t a baaaaaaaddd chapter!!! The Discovery of DNA s Structure Watson and Crick s discovery of DNA s structure was based on almost fifty years of research by other

### Name Class Date. Figure 13 1. 2. Which nucleotide in Figure 13 1 indicates the nucleic acid above is RNA? a. uracil c. cytosine b. guanine d.

13 Multiple Choice RNA and Protein Synthesis Chapter Test A Write the letter that best answers the question or completes the statement on the line provided. 1. Which of the following are found in both

### 1. Which of the following correctly organizes genetic material from the broadest category to the most specific category?

DNA and Genetics 1. Which of the following correctly organizes genetic material from the broadest category to the most specific category? A. genome chromosome gene DNA molecule B. genome chromosome DNA

### Translation Study Guide

Translation Study Guide This study guide is a written version of the material you have seen presented in the replication unit. In translation, the cell uses the genetic information contained in mrna to

### Structure and Function of DNA

Structure and Function of DNA DNA and RNA Structure DNA and RNA are nucleic acids. They consist of chemical units called nucleotides. The nucleotides are joined by a sugar-phosphate backbone. The four

### From DNA to Protein. Proteins. Chapter 13. Prokaryotes and Eukaryotes. The Path From Genes to Proteins. All proteins consist of polypeptide chains

Proteins From DNA to Protein Chapter 13 All proteins consist of polypeptide chains A linear sequence of amino acids Each chain corresponds to the nucleotide base sequence of a gene The Path From Genes

### Name Date Period. 2. When a molecule of double-stranded DNA undergoes replication, it results in

DNA, RNA, Protein Synthesis Keystone 1. During the process shown above, the two strands of one DNA molecule are unwound. Then, DNA polymerases add complementary nucleotides to each strand which results

### Transcription and Translation of DNA

Transcription and Translation of DNA Genotype our genetic constitution ( makeup) is determined (controlled) by the sequence of bases in its genes Phenotype determined by the proteins synthesised when genes

### Basic Concepts of DNA, Proteins, Genes and Genomes

Basic Concepts of DNA, Proteins, Genes and Genomes Kun-Mao Chao 1,2,3 1 Graduate Institute of Biomedical Electronics and Bioinformatics 2 Department of Computer Science and Information Engineering 3 Graduate

### Transcription Study Guide

Transcription Study Guide This study guide is a written version of the material you have seen presented in the transcription unit. The cell s DNA contains the instructions for carrying out the work of

### 1 Mutation and Genetic Change

CHAPTER 14 1 Mutation and Genetic Change SECTION Genes in Action KEY IDEAS As you read this section, keep these questions in mind: What is the origin of genetic differences among organisms? What kinds

### Lecture 1 MODULE 3 GENE EXPRESSION AND REGULATION OF GENE EXPRESSION. Professor Bharat Patel Office: Science 2, 2.36 Email: b.patel@griffith.edu.

Lecture 1 MODULE 3 GENE EXPRESSION AND REGULATION OF GENE EXPRESSION Professor Bharat Patel Office: Science 2, 2.36 Email: b.patel@griffith.edu.au What is Gene Expression & Gene Regulation? 1. Gene Expression

### 13.2 Ribosomes & Protein Synthesis

13.2 Ribosomes & Protein Synthesis Introduction: *A specific sequence of bases in DNA carries the directions for forming a polypeptide, a chain of amino acids (there are 20 different types of amino acid).

### RNA & Protein Synthesis

RNA & Protein Synthesis Genes send messages to cellular machinery RNA Plays a major role in process Process has three phases (Genetic) Transcription (Genetic) Translation Protein Synthesis RNA Synthesis

### Algorithms in Computational Biology (236522) spring 2007 Lecture #1

Algorithms in Computational Biology (236522) spring 2007 Lecture #1 Lecturer: Shlomo Moran, Taub 639, tel 4363 Office hours: Tuesday 11:00-12:00/by appointment TA: Ilan Gronau, Taub 700, tel 4894 Office

### The vast majority of RNA functions are concerned with protein synthesis.

RNA Structure, Function, and Synthesis RNA RNA differs from DNA in both structural and functional respects. RNA has two major structural differences: each of the ribose rings contains a 2 -hydroxyl, and

### Molecular Genetics. RNA, Transcription, & Protein Synthesis

Molecular Genetics RNA, Transcription, & Protein Synthesis Section 1 RNA AND TRANSCRIPTION Objectives Describe the primary functions of RNA Identify how RNA differs from DNA Describe the structure and

### Basic Characteristics of Cells. Cell Structure and Function. Each Cell Has Three Primary Regions. Basic Characteristics of Cells. The Plasma Membrane

Basic Characteristics of Cells Cell Structure and Function Chapter 3 Smallest living subdivision of the human body Diverse in structure and function Small Basic Characteristics of Cells Each Cell Has Three

### Chapter 17: From Gene to Protein

Name Period This is going to be a very long journey, but it is crucial to your understanding of biology. Work on this chapter a single concept at a time, and expect to spend at least 6 hours to truly master

### II. DNA Deoxyribonucleic Acid Located in the nucleus of the cell Codes for your genes

HEREDITY = passing on of characteristics from parents to offspring How?...DNA! I. DNA, Chromosomes, Chromatin, and Genes DNA = blueprint of life (has the instructions for making an organism) Chromatin=

### Genetics Module B, Anchor 3

Genetics Module B, Anchor 3 Key Concepts: - An individual s characteristics are determines by factors that are passed from one parental generation to the next. - During gamete formation, the alleles for

### GENE REGULATION. Teacher Packet

AP * BIOLOGY GENE REGULATION Teacher Packet AP* is a trademark of the College Entrance Examination Board. The College Entrance Examination Board was not involved in the production of this material. Pictures

### CCR Biology - Chapter 8 Practice Test - Summer 2012

Name: Class: Date: CCR Biology - Chapter 8 Practice Test - Summer 2012 Multiple Choice Identify the choice that best completes the statement or answers the question. 1. What did Hershey and Chase know

### RNA and Protein Synthesis

Name lass Date RN and Protein Synthesis Information and Heredity Q: How does information fl ow from DN to RN to direct the synthesis of proteins? 13.1 What is RN? WHT I KNOW SMPLE NSWER: RN is a nucleic

### Protein Synthesis. Page 41 Page 44 Page 47 Page 42 Page 45 Page 48 Page 43 Page 46 Page 49. Page 41. DNA RNA Protein. Vocabulary

Protein Synthesis Vocabulary Transcription Translation Translocation Chromosomal mutation Deoxyribonucleic acid Frame shift mutation Gene expression Mutation Point mutation Page 41 Page 41 Page 44 Page

### Lecture 5 Mutation and Genetic Variation

1 Lecture 5 Mutation and Genetic Variation I. Review of DNA structure and function you should already know this. A. The Central Dogma DNA mrna Protein where the mistakes are made. 1. Some definitions based

### From Gene to Protein Transcription and Translation i

From Gene to Protein Transcription and Translation i How do the genes in our DNA influence our characteristics? For example, how can a gene determine whether a person is an albino with very pale skin and

### Lecture Series 7. From DNA to Protein. Genotype to Phenotype. Reading Assignments. A. Genes and the Synthesis of Polypeptides

Lecture Series 7 From DNA to Protein: Genotype to Phenotype Reading Assignments Read Chapter 7 From DNA to Protein A. Genes and the Synthesis of Polypeptides Genes are made up of DNA and are expressed

### 13.4 Gene Regulation and Expression

13.4 Gene Regulation and Expression Lesson Objectives Describe gene regulation in prokaryotes. Explain how most eukaryotic genes are regulated. Relate gene regulation to development in multicellular organisms.

### Coding sequence the sequence of nucleotide bases on the DNA that are transcribed into RNA which are in turn translated into protein

Assignment 3 Michele Owens Vocabulary Gene: A sequence of DNA that instructs a cell to produce a particular protein Promoter a control sequence near the start of a gene Coding sequence the sequence of

### a. Ribosomal RNA rrna a type ofrna that combines with proteins to form Ribosomes on which polypeptide chains of proteins are assembled

Biology 101 Chapter 14 Name: Fill-in-the-Blanks Which base follows the next in a strand of DNA is referred to. as the base (1) Sequence. The region of DNA that calls for the assembly of specific amino

### 2. The number of different kinds of nucleotides present in any DNA molecule is A) four B) six C) two D) three

Chem 121 Chapter 22. Nucleic Acids 1. Any given nucleotide in a nucleic acid contains A) two bases and a sugar. B) one sugar, two bases and one phosphate. C) two sugars and one phosphate. D) one sugar,

### Module 3 Questions. 7. Chemotaxis is an example of signal transduction. Explain, with the use of diagrams.

Module 3 Questions Section 1. Essay and Short Answers. Use diagrams wherever possible 1. With the use of a diagram, provide an overview of the general regulation strategies available to a bacterial cell.

### The Steps. 1. Transcription. 2. Transferal. 3. Translation

Protein Synthesis Protein synthesis is simply the "making of proteins." Although the term itself is easy to understand, the multiple steps that a cell in a plant or animal must go through are not. In order

### Lab #5: DNA, RNA & Protein Synthesis. Heredity & Human Affairs (Biology 1605) Spring 2012

Lab #5: DNA, RNA & Protein Synthesis Heredity & Human Affairs (Biology 1605) Spring 2012 DNA Stands for : Deoxyribonucleic Acid Double-stranded helix Made up of nucleotides Each nucleotide= 1. 5-carbon

### Sample Questions for Exam 3

Sample Questions for Exam 3 1. All of the following occur during prometaphase of mitosis in animal cells except a. the centrioles move toward opposite poles. b. the nucleolus can no longer be seen. c.

### Replication Study Guide

Replication Study Guide This study guide is a written version of the material you have seen presented in the replication unit. Self-reproduction is a function of life that human-engineered systems have

### Given these characteristics of life, which of the following objects is considered a living organism? W. X. Y. Z.

Cell Structure and Organization 1. All living things must possess certain characteristics. They are all composed of one or more cells. They can grow, reproduce, and pass their genes on to their offspring.

### From DNA to Protein

Nucleus Control center of the cell contains the genetic library encoded in the sequences of nucleotides in molecules of DNA code for the amino acid sequences of all proteins determines which specific proteins

### DNA, RNA, Protein synthesis, and Mutations. Chapters 12-13.3

DNA, RNA, Protein synthesis, and Mutations Chapters 12-13.3 1A)Identify the components of DNA and explain its role in heredity. DNA s Role in heredity: Contains the genetic information of a cell that can

### MCAS Biology. Review Packet

MCAS Biology Review Packet 1 Name Class Date 1. Define organic. THE CHEMISTRY OF LIFE 2. All living things are made up of 6 essential elements: SPONCH. Name the six elements of life. S N P C O H 3. Elements

### 2.1 Nucleic acids the molecules of life

1 2.1 Nucleic acids the molecules of life Nucleic acids information molecules of the cells form new cells stored in chromosomes in nucleus of the cell in the form of a code in DNA / parts of the code are

### To be able to describe polypeptide synthesis including transcription and splicing

Thursday 8th March COPY LO: To be able to describe polypeptide synthesis including transcription and splicing Starter Explain the difference between transcription and translation BATS Describe and explain

### Central Dogma. Lecture 10. Discussing DNA replication. DNA Replication. DNA mutation and repair. Transcription

Central Dogma transcription translation DNA RNA Protein replication Discussing DNA replication (Nucleus of eukaryote, cytoplasm of prokaryote) Recall Replication is semi-conservative and bidirectional

### Alison Stewart 11/12/06 Prokaryotic Cells, Eukaryotic cells and HIV: Structures, Transcription and Transport Section Handout Discussion Week #7

Alison Stewart 11/12/06 Prokaryotic Cells, Eukaryotic cells and HIV: Structures, Transcription and Transport Section Handout Discussion Week #7 Compare and contrast the organization of eukaryotic, prokaryotic

### The sequence of bases on the mrna is a code that determines the sequence of amino acids in the polypeptide being synthesized:

Module 3F Protein Synthesis So far in this unit, we have examined: How genes are transmitted from one generation to the next Where genes are located What genes are made of How genes are replicated How

### ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes

ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes Page 1 of 22 Introduction Indiana students enrolled in Biology I participated in the ISTEP+: Biology I Graduation Examination

### Bob Jesberg. Boston, MA April 3, 2014

DNA, Replication and Transcription Bob Jesberg NSTA Conference Boston, MA April 3, 2014 1 Workshop Agenda Looking at DNA and Forensics The DNA, Replication i and Transcription i Set DNA Ladder The Double

### RNA Structure and folding

RNA Structure and folding Overview: The main functional biomolecules in cells are polymers DNA, RNA and proteins For RNA and Proteins, the specific sequence of the polymer dictates its final structure

### DNA is a double helix with two sugar phosphate backbones and nucleotide bases bridging the two chains.

BENG 100 Frontiers of Biomedical Engineering Professor Mark Saltzman Chapter 3 SUMMARY Nucleic acids are linear polymers made up of monomer units called nucleotides. Each nucleotide is composed of a pentose

### Nucleotides and Nucleic Acids

Nucleotides and Nucleic Acids Brief History 1 1869 - Miescher Isolated nuclein from soiled bandages 1902 - Garrod Studied rare genetic disorder: Alkaptonuria; concluded that specific gene is associated

### AP BIOLOGY 2010 SCORING GUIDELINES (Form B)

AP BIOLOGY 2010 SCORING GUIDELINES (Form B) Question 2 Certain human genetic conditions, such as sickle cell anemia, result from single base-pair mutations in DNA. (a) Explain how a single base-pair mutation

### PRACTICE TEST QUESTIONS

PART A: MULTIPLE CHOICE QUESTIONS PRACTICE TEST QUESTIONS DNA & PROTEIN SYNTHESIS B 1. One of the functions of DNA is to A. secrete vacuoles. B. make copies of itself. C. join amino acids to each other.

### 12.1 The Role of DNA in Heredity

12.1 The Role of DNA in Heredity Only in the last 50 years have scientists understood the role of DNA in heredity. That understanding began with the discovery of DNA s structure. In 1952, Rosalind Franklin

### BioBoot Camp Genetics

BioBoot Camp Genetics BIO.B.1.2.1 Describe how the process of DNA replication results in the transmission and/or conservation of genetic information DNA Replication is the process of DNA being copied before

### somatic cell egg genotype gamete polar body phenotype homologous chromosome trait dominant autosome genetics recessive

CHAPTER 6 MEIOSIS AND MENDEL Vocabulary Practice somatic cell egg genotype gamete polar body phenotype homologous chromosome trait dominant autosome genetics recessive CHAPTER 6 Meiosis and Mendel sex

### Prep Time: 15 minutes. Class Time: 30 minutes

ACTIVITY OVERVIEW Abstract: Students navigate the Basics and Beyond module to complete a web quest to learn about how proteins are made using the instructions contained in genes. Module: Basics and Beyond

### AP BIOLOGY 2009 SCORING GUIDELINES

AP BIOLOGY 2009 SCORING GUIDELINES Question 4 The flow of genetic information from DNA to protein in eukaryotic cells is called the central dogma of biology. (a) Explain the role of each of the following

### DNA & Protein Synthesis Exam

DNA & Protein Synthesis Exam DO NOT WRITE ON EXAM EXAM # VER. B Multiple choice Directions: Answer the following questions based on the following diagram. (1pt. each) 5. The above nucleotide is purine

### Provincial Exam Questions. 9. Give one role of each of the following nucleic acids in the production of an enzyme.

Provincial Exam Questions Unit: Cell Biology: Protein Synthesis (B7 & B8) 2010 Jan 3. Describe the process of translation. (4 marks) 2009 Sample 8. What is the role of ribosomes in protein synthesis? A.

### Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources

1 of 8 11/7/2004 11:00 AM National Center for Biotechnology Information About NCBI NCBI at a Glance A Science Primer Human Genome Resources Model Organisms Guide Outreach and Education Databases and Tools

### Forensic DNA Testing Terminology

Forensic DNA Testing Terminology ABI 310 Genetic Analyzer a capillary electrophoresis instrument used by forensic DNA laboratories to separate short tandem repeat (STR) loci on the basis of their size.

### Answer: 2. Uracil. Answer: 2. hydrogen bonds. Adenine, Cytosine and Guanine are found in both RNA and DNA.

Answer: 2. Uracil Adenine, Cytosine and Guanine are found in both RNA and DNA. Thymine is found only in DNA; Uracil takes its (Thymine) place in RNA molecules. Answer: 2. hydrogen bonds The complementary

### Keystone Biology Exam Information: Module A: Cell and Cell Processes

Keystone Biology Exam Information: Module A: Cell and Cell Processes Basic Biological Principles- Day 1 Describe the characteristics of life shared by prokaryotic and eukaryotic organisms. Compare cellular

### Specific problems. The genetic code. The genetic code. Adaptor molecules match amino acids to mrna codons

Tutorial II Gene expression: mrna translation and protein synthesis Piergiorgio Percipalle, PhD Program Control of gene transcription and RNA processing mrna translation and protein synthesis KAROLINSKA

### Ms. Campbell Protein Synthesis Practice Questions Regents L.E.

Name Student # Ms. Campbell Protein Synthesis Practice Questions Regents L.E. 1. A sequence of three nitrogenous bases in a messenger-rna molecule is known as a 1) codon 2) gene 3) polypeptide 4) nucleotide

### Biotechnology Test Test

Log In Sign Up Biotechnology Test Test 15 Matching Questions Regenerate Test 1. Plasmid 2. PCR Process 3. humulin 4. pluripotent 5. polymerase chain reaction (PCR) a b Is much smaller than the human genome,

### Translation. Translation: Assembly of polypeptides on a ribosome

Translation Translation: Assembly of polypeptides on a ribosome Living cells devote more energy to the synthesis of proteins than to any other aspect of metabolism. About a third of the dry mass of a cell

### The Nucleus: DNA, Chromatin And Chromosomes

The Nucleus: DNA, Chromatin And Chromosomes Professor Alfred Cuschieri Department of Anatomy, University of Malta. Objectives By the end of this unit the student should be able to: 1. List the major structural

### Common Course Topics Biology 1406: Cell and Molecular Biology

Common Course Topics Biology 1406: Cell and Molecular Biology 1. Introduction to biology --the scientific study of organisms --properties of life --assumptions, methods and limitations of science --underlying

### Thymine = orange Adenine = dark green Guanine = purple Cytosine = yellow Uracil = brown

1 DNA Coloring - Transcription & Translation Transcription RNA, Ribonucleic Acid is very similar to DNA. RNA normally exists as a single strand (and not the double stranded double helix of DNA). It contains

### BCOR 011, Exam 3. Multiple Choice: Select the best possible answer. Name KEY Section

BCOR 011, Exam 3 Name KEY Section Multiple Choice: Select the best possible answer. 1. A parent cell divides to form two genetically identical daughter cells in the nuclear process of mitosis. For mitosis

### Control of Gene Expression

Home Gene Regulation Is Necessary? Control of Gene Expression By switching genes off when they are not needed, cells can prevent resources from being wasted. There should be natural selection favoring

### Chapter 6 DNA Replication

Chapter 6 DNA Replication Each strand of the DNA double helix contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand. Each strand can therefore

### The world of non-coding RNA. Espen Enerly

The world of non-coding RNA Espen Enerly ncrna in general Different groups Small RNAs Outline mirnas and sirnas Speculations Common for all ncrna Per def.: never translated Not spurious transcripts Always/often

### AP Biology Learning Objective Cards

1.1 The student is able to convert a data set from a table of numbers that reflect a change in the genetic makeup of a population over time and to apply mathematical methods and conceptual understandings

### Lecture 26: Overview of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) structure

Lecture 26: Overview of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) structure Nucleic acids play an important role in the storage and expression of genetic information. They are divided into

### Essential Vocabulary for Biology STAAR

Essential Vocabulary for Biology STAAR 1. Science 2. Hypothesis 3. Theory Use of evidence to construct testable explanations and predictions of natural phenomena, as well as the knowledge generated through

### Basic Principles of Transcription and Translation

The Flow of Genetic Information The information content of DNA is in the form of specific sequences of nucleotides The DNA inherited by an organism leads to specific traits by dictating the synthesis of

### Gene Models & Bed format: What they represent.

GeneModels&Bedformat:Whattheyrepresent. Gene models are hypotheses about the structure of transcripts produced by a gene. Like all models, they may be correct, partly correct, or entirely wrong. Typically,

### STANDARD 2 Students will demonstrate appropriate safety procedures and equipment use in the laboratory.

BIOTECHNOLOGY Levels: 11-12 Units of Credit: 1.0 CIP Code: 51.1201 Prerequisite: Biology or Chemistry Skill Certificates: #708 COURSE DESCRIPTION is an exploratory course designed to create an awareness

### Control of Gene Expression

Control of Gene Expression What is Gene Expression? Gene expression is the process by which informa9on from a gene is used in the synthesis of a func9onal gene product. What is Gene Expression? Figure

### Prep Time: 1 hour. Class Time: 45 minutes

ACTIVITY OVERVIEW Abstract: Students use edible models of the DNA molecule to transcribe an mrna sequence, then translate it into a protein. Module: The Basics and Beyond Prior Knowledge Needed: A basic

### the nature and importance of biomacromolecules in the chemistry of the cell: synthesis of biomacromolecules through the condensation reaction lipids

the nature and importance of biomacromolecules in the chemistry of the cell: synthesis of biomacromolecules through the condensation reaction lipids and their sub-units; the role of lipids in the plasma

### Introduction. What is Ecological Genetics?

1 Introduction What is Ecological enetics? Ecological genetics is at the interface of ecology, evolution, and genetics, and thus includes important elements from each of these fields. We can use two closely

### Chapter 17: From Gene to Protein

AP Biology Reading Guide Fred and Theresa Holtzclaw Julia Keller 12d Chapter 17: From Gene to Protein 1. What is gene expression? Gene expression is the process by which DNA directs the synthesis of proteins

### Biology Final Exam Study Guide: Semester 2

Biology Final Exam Study Guide: Semester 2 Questions 1. Scientific method: What does each of these entail? Investigation and Experimentation Problem Hypothesis Methods Results/Data Discussion/Conclusion

### The Molecules of Cells

The Molecules of Cells I. Introduction A. Most of the world s population cannot digest milk-based foods. 1. These people are lactose intolerant because they lack the enzyme lactase. 2. This illustrates

### Genetics Lecture Notes 7.03 2005. Lectures 1 2

Genetics Lecture Notes 7.03 2005 Lectures 1 2 Lecture 1 We will begin this course with the question: What is a gene? This question will take us four lectures to answer because there are actually several

### A disaccharide is formed when a dehydration reaction joins two monosaccharides. This covalent bond is called a glycosidic linkage.

CH 5 Structure & Function of Large Molecules: Macromolecules Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic

### 4.1 Cell Division and Genetic Material pg The Cell Theory is a central idea to Biology and it evolved in the 1800 s. The Cell Theory States:

4.1 Cell Division and Genetic Material pg. 160 The Cell Theory is a central idea to Biology and it evolved in the 1800 s. The Cell Theory States: 1. All living things are composed of one or more cells.

### Modeling DNA Replication and Protein Synthesis

Skills Practice Lab Modeling DNA Replication and Protein Synthesis OBJECTIVES Construct and analyze a model of DNA. Use a model to simulate the process of replication. Use a model to simulate the process

### 2006 7.012 Problem Set 3 KEY

2006 7.012 Problem Set 3 KEY Due before 5 PM on FRIDAY, October 13, 2006. Turn answers in to the box outside of 68-120. PLEASE WRITE YOUR ANSWERS ON THIS PRINTOUT. 1. Which reaction is catalyzed by each

### Chapter 4 Cellular Metabolism

Chapter 4 Cellular Metabolism Metabolic processes all chemical reactions that occur in the body Two types of metabolic reactions Anabolism larger molecules are made requires energy Catabolism larger molecules

### GenBank, Entrez, & FASTA

GenBank, Entrez, & FASTA Nucleotide Sequence Databases First generation GenBank is a representative example started as sort of a museum to preserve knowledge of a sequence from first discovery great repositories,