AP BIO UNIT 7 KOEHLER

UNIT 7: DNA, PROTEIN SYNTHESIS, AND BIOTECHNOLOGY

The Molecular Basis of Inheritance (Ch. 13)

• The structure of a DNA strand and components of nucleotides

• Each DNA nucleotide  monomer consists of a base with T,A,G,or C; deoxyribose sugar; and a phosphate group which is attached to the sugar of the next forming a backbone of alternate phosphates and sugars; has a 5’ and 3’ end

• Structure of DNA forms a double helix with the sugar and phosphate groups acting as a backbone, covalent bonds link the units of each strand and hydrogen bonds between the bases hold one strand to the other; the strands are also antiparallel

• A goes with T, C goes with G 

• The functions of DNA polymerase, DNA ligase, and nuclease in DNA replication

• DNA Polymerase: Binds to the primer and adds complementary bases in the 5’ to 3’ end; leading strand is made continuously from 5’-3’ while lagging strand is made up in Okazaki fragments from 3’-5’

• DNA Ligase: Seals up the fragments of DNA to form a continuous double strand

• Nuclease: A DNA cutting enzyme that removes damaged DNA strands

• The organization of chromosomes

• A chromosome consists of a DNA molecule packed together with protein

• Chromatin: DNA combined with protein that fits into the nucleus and makes up chromosomes

• The process: Proteins called histones are added to the double helix strand and form a nucleosome, which then packs together to form looped domains and eventually packs to form the chromosomes

• How restriction enzymes and ligases are used to make recombinant DNA

• Restriction enzymes cut the plasmid and human DNA at specific sequences

• Human and bacterial cell must be cut with same restriction enzyme

• Ligase joins the DNA molecules to form a new recombinant strand 

• The mechanisms and reasoning behind the semiconservative model

• DNA replication is semiconservative since every newly replicated DNA molecule has one old strand of DNA bound to one strand of replicated DNA

• The process of DNA replication with antiparallel elongation, including the different proteins involved 

• The 2 strands of DNA are antiparallel, so the 2 new strands that are formed must also end up antiparallel

• DNA polymerase can add nucleotides to the free 3’ end of a primer or growing DNA strand, neverto a 5’ end so DNA can elongate only in the 5’ to 3’ direction

• The leading strand is the strand that is made continuously by DNA polymerase continuously elongating the new DNA in the 5’ to 3’ direction

• The lagging strand is made in fragments called Okazaki fragments and is made away from the replication fork in the 5’ to 3’ direction

• After the Okazaki fragments are made, DNA ligase joins together the sugar phosphate backbones of the Okazaki fragments into a continuous DNA strand

• How restriction enzymes recognize and cut sites, and how those sites will travel on gel electrophoresis

• Restriction enzymes recognize a particular short DNA sequence called a restriction site and they cut both DNA strands at precise points within this restriction site

• Restriction enzymes can make many cuts in a DNA molecule and result in restriction fragments, and all copies of a particular DNA molecule result in the same restriction sites when exposed to the same restriction enzymes

• Gel electrophoresis is used to see restriction fragments by separating a mixture of nucleic acids by length 

Gene Expression: From Gene to Protein (Ch. 14)

• The overview of transcription and translation

• Transcription takes place in nucleus and translation takes place in ribosomes

• RNA: Usually single stranded sugar and phosphate group, has U instead of T

• 3 types of RNA: Messenger (mRNA), Ribosomal (rRNA), transfer (tRNA)

• Given a DNA sequence, the ability to transcribe to an RNA sequence, and then use a codon chart to assign an amino acid

• 3’-5’ DNA is template strand

• mRNA is the complementary strand of that but replace the T with U

• Every 3 letters codes for one amino acid

• The difference between introns and exons

• Introns: Noncoding segments of DNA/RNA, removed from pre mRNA

• Exons: Coding segments of DNA/RNA

• Pre mRNA- Complement of the 3’-5’ end of DNA with U instead of T

• Mature mRNA- remove the introns

• mRNA Codons: The base pairs grouped into 3

• How to assign a tRNA anticodon to an mRNA codon (based on sequences)

• A tRNA anticodon is the complementary of each mRNA codon

• Amino acids are found from the tRNA anticodon

• How to identify point mutations, substitutions, insertions, and deletions

• Mutations occur when DNA or RNA polymerase make a mistake

• Insertion: Frameshift mutation in which a base is added in the sequences and shifts everything to the right of it

• Deletion: Frameshift mutation in which a base is removed

• Substitution Mutations: When one base is substituted for another

  • Missense: When it results in a new amino acid

  • Nonsense: When it results in a stop codon

  • Silent: When the amino acid does not change

• The modifications of RNA in eukaryotic cells, such as splicing and alterations

• Splicing: Removal of large portions of the RNA molecule that was initially synthesized and introns are removed

• Introns: Non Coding segments of nucleic acid 

• Exons: Sections of nucleic acid that are expressed and translated and code for amino acids 

• The interactions between tRNAs and ribosomal binding sides in translation

• mRNA messages are translated into proteins using tRNAS

• After being bound to a specific amino acid by aminoacyl-tRNA synthetase, a tRNA lines up through its anticodon at the complementary codon on mRNA

• A ribosome facilitates this coupling with binding sites for mRNA and tRNA

• How to identify silent, missense, nonsense substitutions as well as hypothesize reasons mutations would occur, as well as their effects

• If the amino acid stays the same after the mutation, it's a silent

• If the amino acid turns into another one, it's a missense

• If the amino acid turns into a stop codon, it's a nonsense

• Mutations occur when DNA or RNA polymerase make a mistake

Regulation of Gene Expression (Ch. 15.1, 15.2, 16.1)

• Functions of: operator, repressor, corepressor, inducer, and activator. 

• Operator: a DNA sequence where the repressor binds to and blocks RNA polymerase

• Repressor: A protein that when binded to the operator can block RNA polymerase

• Corepressor: A small molecule that activates the repressor to turn the operon off 

• Inducer: Inactivates the repressor 

• Promoter: The place RNA Polymerase binds to move along the DNA strand

• Activator: A protein that binds to a DNA sequence near the promoter to enhance RNA Polymerase’s ability to bind to the promoter and start transcription

• Effects of acetylation and methylation

• Acetylation: Unwinds DNA from the histones making it easier for transcription

• Methylation: When a molecule called a methyl group attaches to a DNA and can turn the gene off

• Given background information, the ability to construct both repressible and inducible operons under various conditions, such as active or inactive representatives. 

• Repressible Operon: Usually on but can be repressed when the corepressor is present and activates the repressor

• Inducible Operon: Usually off but can be induced when the inducer is present and inactivates the repressor

• Explain the roles of items such as epigenetic inheritance, transcription factors, and enhancers in differential gene expression

• Epigenetic Inheritance: Your behaviors or environment can turn your genes on or off, and those genes can pass down to your offspring (ex: Mice who lick their children more raise children that also lick their children more)

• Transcription Factors: Play a crucial role in gene expression by binding to specific DNA sequences and regulate the transcription of genes into mRNA which is the first step in making proteins (basically like molecular switches that control when,where, and how much a gene is expressed)

• Genetic Enhancement: Activator proteins bind to enhancer DNA sequences which cause DNA to bend and transcription to start

• How cytoplasmic determinants and inductive signals work together in development 

• Cytoplasmic Determinants: Randomly distributed molecules in cytoplasm that cause cells to be unique from each other, control development in the early stages

• Induction: Cell communication

• Cytoplasmic Determinants provide the initial basis for what the cells function will be, and inductive signals build on that and adapt on it in response to cues from other cells

• How genes such as homeotic genes work in pattern formation

• Homeotic Genes: Genes that control pattern formation

• Pattern Formation: Basically the order in which your body parts are