Topics  Nucleic Acids: structure and function  DNA  RNA  Organization of the genome  Protein Synthesis (genetic expression)  Transcription  Translation  Mutations  Post-transcriptional modification  epigenetics

DNA: Structure and Function

DNA Function  genetic information  how to build, operate, and repair cell  Specifically how and when to make proteins  passed from one cell generation to the next;  from parent to child (gametes/sex cells)  From one cell to the next within an individual

DNA Structure  long chains of nucleotides  Nucleotide = sugar + phosphate + nitrogenous base  Sugar = deoxyribose (5C)  4 Different Bases: A, T, G, C  Bases = pyrimidines (1 ring) or purines (2 rings)

5’ 3’ DNA Structure Cont.: Double Helix  double stranded  sugar-phosphate backbone=covalent  base-base=hydrogen  Twisted=helix 5’ 3’ covalent bond hydrogen bond ‘f’-five; ‘f’ phosphate; 5’ end

DNA Structure Cont.: Complementary Base Pairing  4 different bases  Complementary pairing  C—G  A—T

Functional Characteristics of DNA: IMPORTANT!!  Information = order of the bases/base sequence  ATTGCGCA  ATTGCGGA  Complementary base pairing  Allows DNA to be copied over and over and the information stays the same. Different sequences  different meaning/info (proteins)

Importance of base-pairing ATTCGCGATATTCGCGAT ATTCGCGATATTCGCGAT TAAGCGCTATAAGCGCTA ATTCGCGATATTCGCGAT TAAGCGCTATAAGCGCTA

ATTCGCGATATTCGCGAT TAAGCGCTATAAGCGCTA TAAGCGCTATAAGCGCTA Importance of base-pairing continued ATTCGCGATATTCGCGAT TAAGCGCTATAAGCGCTA TAAGCGCTATAAGCGCTA ATTCGCGATATTCGCGAT

DNA Organization  DNA molecule = genes + regulatory DNA + “other”  gene =protein instructions  20-25k estimated genes (but >100,000 estimated proteins….problem…..)  regulatory = when to activate gene/make a protein  e.g., transcription factors such as hormones can bind regulatory DNA and signal a gene to be used non-coding: ~97% of DNA ~3% of DNA “chromosome” Protein building instructions (gene) Regulates when protein is made (gene activated)

DNA Organization  DNA is wrapped around histone (a protein)  DNA + Histone = Chromatin Chromatin 3-31 histone

DNA Organization: Histone and access to genes  Histone is important in making genes accessible (usable) or inaccesible (non-usable)  If DNA can’t be accesses  gene can’t be used (no protein)  If DNA can be accessed  gene can be used when needed  Histone can control which/if genes can be used=Epigenetics  acetylation allows access  deacetylation shuts off/prevents access  methylation prevents access/shuts off  demethylation allows access/shuts off  and others……….

Chromatin continued 3-33 and methylation acetylation and demethylation deacetylation and methylation Condensed chromatin: transcription factors can’t get to regulatory DNA to activate gene use Open/loose structure allows transcription factors to access DNA and initiate gene use Condensed chromatin: inaccessible

REPLICATION: duplication of DNA as part of cell division

DNA Replication  Happens as part of cell cycle  In preparation for cell division  Duplicates all the DNA: 1 copy  2 copies  One copy for each cell  Semiconservative  Errors in replication  mutations (i.e. a change in genetic information/DNA sequence) GCGATGCGAT CGCTACGCTA GCGATGCGAT CGCTACGCTA GCGATGCGAT CGCTACGCTA

1 copy of all DNA 2 copy of All DNA Replication of DNA 1 copy of DNA Mitosis divides/separate the two copies of identical chromosomes Cytokinesis divides up the cytoplasm contents Parent/mother cell daughter cells: each one identical copy of all the DNA: genetically identical to the mother cell

DNA Replication  DNA helicase “unzips” the DNA  New nucleotides are added/paired with the existing strands  DNA polymerase binds the new nucleotides together creating the P-S backbone  Result is two identical DNA molecules (i.e., the base sequence is the same)

Genetic Expression Proteins Synthesis: how dna is used to make functional proteins

Genetic Expression: from DNA to cell function/structure DNA  mRNA  Proteins  cell function/structure structure transport contraction receptors cell ID hormones/signaling

Protein Synthesis: making proteins from DNA 1. Transcription= DNA  mRNA (in nucleus) 2. Translation = mRNA  Protein (in ribosome)

Nucleic Acids - RNA  Single stranded chains of nucleotides  Sugar = ribose  Bases and Pairing  G, C, A, U replaces T  G-C  T-A or A (dna) –U (rna)  types of RNA (made from DNA):  Messenger RNA – mRNA  Transfer RNA – tRNA  Ribosomal RNA – rRNA  others (siRNA, miRNA, RNA based enzymes, etc) 2-59

Transcription: from DNA  mRNA  Transcription Begins:  When Transcription factors (e.g., hormones) bind DNA transcripition starts/is initiated  RNA polymerase binds to a “start” sequence/codon & unzips DNA  promoter = how much transcription  RNA Polymerase moves down template strand  complimentary RNA bases bind DNA  RNA nucleotides bind together (via RNA poly)  at end of gene mRNA detaches and RNA poly detaches  DNA zips up when transcription is done  Post-transcriptional modification 3-35

Transcription 3-36 Template strand Coding strand

Transcription

mRNA: a copy of the information on a gene  Created by transcription  Single strand of nucleotides  Phosphate, ribose sugar, bases  U instead of T  Codons = 3-base groups  One codon is a “start” codon  Three codons are “stop codons”  Each of the remaining 60 codons corresponds to an amino acid

tRNA  Single stranded piece of RNA  tRNA carries and delivers amino acids to mRNA/ribosome  tRNA anticodon binds to mRNA codon  complementary  Each tRNA carries a specific amino acid that corresponds to its anticodon 3-44

3-43 DNA template strand Protein Synthesis and the Genetic Code

Mutations, DNA, and Protiens  Mutation = change in DNA base sequence  change in protien  change in structure and/or function

Basic Types of Mutations  Point mutations  substitution  insertion  deletion frame-shift mutations

Point Mutations  Substitution:  ATT GCG AGT TAT CCG  ATT GCG AGT TAG CCG  Insertion:  ATT GCG AGT TAT CCG  ATT GCG TAG TTA TCC G  Deletion  ATT GCG AGT TAT CCG  ATT GCG GTT ATC CG A frameshifts

Base Sequences and Human Variation  SNP’s (single nucleotide polymorphisms)  single nucleotide differences in the DNA between different individuals  responsible for most differences in appearance and physiology  ATT GCG ATC CGA TAT TTT AAC CCC ATA CGG TAT TTT TCG  ATT GCG TTC CGA TAT TTT AAC CCC ATA CGG TAT TTT TCG  ATT GCG ATC CGA TAT TTG AAC CCC ATA CGG TAT TTT TCG  ATT GCC ATC CGA TAT TTT AAC CCC ATA CGG TAA TTT TCG  ATT GCC ATC CGA TAT TTT CAC CCC ATA CGG TAT TTT TCG  ATT GCG ATC CGA TAT TTT CAC CCC ATA CGG TAA TTT TCG

RNA Synthesis & Post-transciptional Modification  Human genome has <25,000 genes  Yet produces >100,000 different proteins  1 gene codes for an average of 3 different proteins  Accomplished by alternative splicing of exons  This allows a given gene to produce several different mRNAs 3-39

Post-transcriptional Modifcation  non-coding introns removed from mRNA  Coding exons spliced together to make the mRNA that will be used in translation  multiple splicing patterns for each “pre-mRNA”  1 gene  multiple mRNA/proteins 3-38

Alternative Splicing of mRNA: one gene  two proteins introns exons From one gene Two types of protein

Alternative Splicing of mRNA: one gene  3 proteins From one gene Three types of protein

Epigenetics  Changes in genetic expression that do not involve changes in base sequences (gene and regulatory DNA has not been altered)  Changes in expression are due to changes in histone.  Genes can be “turned off” or “allowed to be accessed”  Gene silencing (i.e., preventing gene use by making them inaccessible) can be cause by (but is not limited to):  Acetylation/deacetylation  Methylation/demethylation  These changes can be copied and transferred/inherited from generation to generation  Can contribute to diseases such as cancer, fragile X syndrome, and lupus  Identical twins can have differences in gene expression  --because of epigenetic changes in response to differences in their environments 3-74

acetyl, methyl, ubiquitin, phosphate, S.U.M.O

DNA (genetics)  characteristics/physiology DNA + environment = phenotype (characteristics)