College Biology - DNA Unit

Test 6

Nucleotide

• 1 sugar

• 1 phosphate

• 1 base

• HYDROGEN BOND

  • Anti-parallel

Nucleotide Diagram

How do nucleotides connect?

1. 3rd carbon connects with phosphate

2. Hydrogen bond between bases

Nitrogenous Bases

Adenine (2)

Thymine (1)

Guanine (2)

Cytosine (1)

Nitrogenous Bases Connections

Apple in the tree (A to T)

Car in the garage (C to G)

DNA Replication: Topoisomerase

Makes sure DNA doesn’t tangle

DNA Replication: Replication Fork

Half-way point between the helix and zipper

DNA Replication: Helicase

Unzips DNA at the origin of replication

DNA Replication: DNA Polymerase (III)

Makes new strands of DNA

• Adds nucleotides to the template

DNA Replication: Single Strand Binding Proteins

Keeps the two strands unzipped

• Expressed as little dots on zipper

DNA Replication: Primer

The start of replication (RNA)

DNA Replication: Leading Strand

DNA Polymerase (III) adds nucleotides from 5^I to 3^I continuously

DNA Replication: Lagging Strand

Nucleotides added in segments

DNA Replication: Primase (Lagging)

Lays down the RNA primer — start signal

DNA Replication: Okazaki Fragments (Lagging)

What the segments are called

DNA Replication: DNA Polymerase (I) (Lagging)

Changing primer from RNA to DNA

DNA Replication: Ligase (Lagging)

Bonds the okazaki fragments together

Summary of Leading Strand

Primer begins process

DNA Polymerase makes new strand

• Fast and Simple

Summary of Lagging Strand

Primase sets down the primer

Works downwards (5^I to 3^I)

Goes back a few and starts over

DNA Polymerase (I) changes primer RNA to DNA

Chunks of DNA (Okazaki Fragments) are connected by Ligase

Editing Mistakes

DNA Polymerase (II) is able to “backspace” and put in new, correct bases

All Proteins Listed in DNA Replication

1. Helicase

2. SSB Proteins

3. Topoisomerase

4. Primase

5. DNA Polymerase (I and III)

6. Ligase

Where does replication start?

At specific points called origins where helicase unwinds the double helix, creating a replication fork, and primase lays down its primers, providing a starting point for DNA polymerase

Semi-Conservative

DNA makes a copy of itself and the original unwinds

• 2 parents serve as a template

• Contains 1 old and 1 new strand

DNA Replications are needed when…

1. When a cell dies

2. To fix errors

3. Reproduction

DNA Replication Drawing

Compare Replication and Protein Synthesis

Both are DNA functions

Contrast Replication and Protein Synthesis

However, DNA Replication is a complete copy of DNA, and Protein Synthesis reads genes and makes proteins by transcription and translation

DNA Attributes

• Double Helix

• H-Bonds

• A, T, C, G

• Sugar: Deoxyribose

RNA Attributes

• Single Helix

• NO H-Bonds

• A, U, C, G

• Sugar: Ribose

mRNA

A piece of RNA that encodes info for protein synthesis and brings it to ribosomes

What does RNA Polymerase bind to at beginning of transcription?

It binds to the DNA at a promotor

TATA Box

Promotor DNA sequence that is recognized by RNA Polymerase

Transcription Factors

Helps with binding RNA polymerase to its promotor

How is mRNA made?

ALWAYS 5^I to 3^I

Elongation - DNA Transcription

RNA Polymerase moves along DNA and makes mRNA

• May include multiple, making many copies of the gene

Beyond the gene… what happens with transcription?

It continues transcribing

Polyadenylation Signal Sequence

AAUAAA

What happens after the AAUAAA signal?

• 10-30 nucleotides downstream

• RNA polymerase is set free

Where does DNA modification happen?

In the nucleus

5^I end capped with…

A modified Guanine

3^I end capped with…

A run of Adenines, called the Poly-A-Tail

What do the caps help with? (3 things)

1. Export into cytoplasm

2. Protects from enzymes

3. Helps ribosomes attach

Introns

Noncoding regions

Extrons

Coding regions

How do Introns and Extrons work in modification?

Introns are cut out and exons are spliced together to make the final mRNA that will leave the Nucleus

DNA Transcription Drawing

tRNA

(t = transfer)

• Transfer RNA

• Carries a specific amino acid on one end [head]

• Anticodon on the other [three legs]

Ribosomes

• Mixture of proteins and rRNA

  • 2 subunits (small and large)

  • 3 binding sites (E, P, A)

  • Made in the nucleolus

Initiation - DNA Translation

• Small subunit binds to the mRNA and RNA

• Scans until it reaches the start codon

• Large subunit attaches

  • tRNA is in the p-site

What is the start codon?

AUG

Elongation - DNA Translation

• Amino acids are added 1 by 1 to proceeding

• tRNA with anticodon enters the A-site

• Peptide bond formed between amino acids

• tRNA in the A-site to P-site

Termination - DNA Translation

• Stop codon is reached

• Protein release factor binds to the A-site

• Released the polypeptide

• Translation apparatus comes apart

Stop Codons

UAG

UAA

UGA

DNA Translation Drawing

What makes genes turn on/off?

• Epigenetics

• Mutations

• Operon

E. Coli

• Model system

• Lactose is the inducer

• Bacteria will synthesize enzymes only in the presence of their substrate

  • Lactase only in presence of lactose

Iac Operon

• 3 genes (Z, Y, A)

• Transcribed as a unit onto one mRNA

• Upstream is the promoter

Operator

• Sequence of DNA between the promoter and the gene

  • Found in one of two states

Attached to a Repressor - Operator

Blocks RNA polymerase

Free of a Repressor - Operator

RNA polymerase can bind

Repressor

• Protein coded for by a gene upstream (I gene)

  • 2 binding sites

When bound to lactose - Repressor

Does not fit operator

When lactose is not bound - Repressor

Binds to the operator and blocks RNA polymerase

Gene Regulation Drawing

DNA Replication (Review) - Purpose and Where

Purpose = to copy DNA strand

Where = nucleus

DNA Transcription (Review) - Purpose and Where

Purpose = create portable RNA copy of gene’s DNA sequence

Where = nucleus

DNA Translation (Review) - Purpose and Where

Purpose = Build proteins

Where = Cytoplasm (on ribosomes)

Genetic Code - Translation Steps

• Read codon (sequence of 3)

• Use codon chart

• Find amino acid

DNA Translation - Silent Mutation

Nucleotide change that DOES NOT change the amino acids

DNA Translation - Frameshift Mutation

Deletion / Insertion that changes the way it is read

DNA Translation - Nonsense Mutation

Shortened, stop codon instead of coding for another amino acid

DNA Translation - Missense Mutation

Single nucleotide change = different amino acid in the chain

Basic Review of Protein Synthesize

A = transcription

B = mRNA

C = translation

D = protein

G₁ Phase - Cell Cycle

Cellular contents duplicated

• Growth

G₂ Phase - Cell Cycle

Chromosomes are duplicated by the cell

• Growth

S Phase - Cell Cycle

Double checks errors and makes repairs

• Replication

Interphase - Cell Cycle

Cell grows and hangs out

• Longest (G₁, G_2, S)

Mitosis - Cell Cycle

Division of the nucleus

• Includes PMAT

Cytokinesis - Cell Cycle

Division of the cytoplasm

Does the cell cycle have checkpoints?

Yes!

Cell Cycle Simple Diagram

Prophase - Cell Phases

Chromosomes visible, spindle forms as centrioles move

Metaphase - Cell Phases

Chromosomes line up along equator

Anaphase - Cell Phases

Chromatids separate

Telophase - Cell Phases

Nuclear membrane forms, cytokinesis begins