Chapter 5

Chapter 5 Review!

Central Dogma

●Flow of genetic material (DNA is transcribed → RNA →
Translated → Protein)

●DNA- information storage

●RNA - temporary message

●Proteins - functional units

Multiple Choice

What process transforms DNA into RNA?

• translation

• transcription

• production

• mitosis

What is DNA made up of?

Nucleotide has 3 parts:
1. Sugar
2. Phosphate
- sugar-phosphate backbone covalently linked to base
3. Base
- AKA nitrogenous base
- Adenine
- Thymine
- Guanine
- Cytosine

●Nucleotides are linked together covalently → DNA strand produced

Nucleotides are covalently linked by phosphodiester linkage to form polynucleotide chains (DNA strands) repeating sugar-phosphate-sugar-phosphate

Multiple Choice

What links the two sugars together?

• Ionic bond

• Glycosidic bond

• Phosphodiester bond

• Phosphate bond

●Between A & T: 2 bonds

●Between G & C: 3 bond

●Having more bonds essentially means that it’s harder to pull apart C&G

​hydrogen bonding

Chromosomes Contain our Genes

●Genes contain info for our cell to read

●Functional units of hereditary

●Genes make proteins and those proteins interact w/ each other

●Responsible for specifying a single protein or RNA molecule

●Contains large regions of noncoding DNA - referred as junk DNA but not the
case

Organization of genes on a human chromosome

• - Regulatory DNA sequences are involved in turning the gene on and off. They contain the code to say when this gene should be transcribed and how much.

●Introns are removed during RNA processing.

●Exons contain the sequence for the gene.

Multiple Choice

Exons are removed from the mRNA transcript

• True

• False

Cell Cycle

1. G1 phase: cell grows in size

2. S phase: DNA replication

3. G2 phase: organelles and proteins needed for cell division are produced

4. M phase: prophase, metaphase, anaphase, telophase

Origins of Replication

• In S phase, when DNA is being replicated, DNA helicase unzips the double helix at origins of replication (rich in A-T)

Interphase

• Long, thin, tangled threads of DNA

• Less compact than mitotic chromosomes (allowing access for protein expression & replication)

• • all

Mitotic Chromosome

• - DNA is dense & compact

• - Easily visualized

• - Chromatids joined at center via centromere

• - Telomeres at ends of chromatid

  • all

Nucleosomes

• Chromatin: complex of DNA & protein

• DNA is wrapped around histones

• Nucleosome - Beadlike
  structural unit composed of
  a short length of DNA
  wrapped around a core of
  histone protein to form
  chromatin

  • Nucleosome - DNA wrapped
    around a protein core of 8
    histone molecules

Chromatin Remodeling Complex

Protein complex that uses energy of ATP hydrolysis to change position of DNA wrapped around nucleosomes to condense & de-condense DNA (alters DNA accessibility to proteins)
-Repeated cycles of ATP hydrolysis allow the chromatin remodeling complex to loosen the nucleosomal DNA by pushing it along the histone core, exposing DNA to DNA-
binding proteins
-Can also condense DNA

Heterochromatin

• Closed

• - mostly highly condensed form of interphase chromatin
  -10% of interphase chromosome
  -concentrated near centromere and in telomeres at ends of chromosome
  -most regions do not contain genes

Euchromatin

• Open

• - more extended state

Different set of “histone tail modifications” establish and maintain chromatin structures

• Covalent modifications
  • Acetyl
  • Methyl
  • Phosphate
  – Affect ability to recruit certain proteins
  – Affect access to DNA by condensing or
  decondensing chromatin

Combinations of acetylation, methylation, and phosphorylation of histones alter gene expression - Implications not only for transcription but also for DNA replication and repair and any other process requiring proteins access to DNA

DNA polymerase (Enzyme that does
Replication)

Adds nucleotides to template strand to create new daughter cell using parental strand as template

●Only synthesizes in the 5’ to 3’ direction

●Meaning it can only add nucleotides on 3’ end !!!!!

●DNA polymerase cannot add on to 5’ end

●Okazaki fragments- DNA will be added in short segments

●Leading strand= 3’ open end , continuously replicated

●Lagging strand will have okazaki fragments due to rna primer being put down

Multiple Select

What is the difference between the leading and lagging strand?

• 5' 3' directionality is in opposite directions

• Leading has fragments and lagging doesn't

• Lagging has Okazaki fragments and leading doesn't

• DNA ligase glues the fragments together on the lagging strand NOT the leading

In order to start replication (s phase of cell cycle) , initiator proteins pry apart DNA and
opens it so DNA helicase can UNZIP the DNA at BOTH REPLICATION FORKS at either
side of bubble. REQUIRES ATP TO UNZIP DNA

Multiple Choice

What kind of bonds is DNA helicase breaking?

• Phosphodiester

• Ionic

• Non-covalent

• Hydrogen

RNA primer synthesis by DNA primase 5’3
→ DNA Polymerase adds to new RNA
primer to start new okazaki fragment →
DNA polymerase finishes DNA fragment →
old RNA primer is replaced (RNA→DNA) → the nick is sealed by DNA ligase and joins new okazaki fragment to the growing chain

Multiple Choice

Why does DNA ligase need to glue together the fragments on the lagging strand?

• DNA polymerase makes mistakes and leaves gaps between the fragments so DNA ligase fills in the gaps

• Some bases can be missing and DNA ligase brings in the missing bases to fill in the gaps

• Okazaki fragments are made rather than a continuous strand because the lagging strand runs in the opposite direction so DNA polymerase can't continually add bases

• Okazaki fragments are produced in the leading direction. The lagging strand does not contain these fragments.

DNA Synthesis

Name

Description

Origins of replication/Replication origins/Ori’s

Site at which DNA is first opened and where DNA synthesis begins.
There are hundreds of these on every chromosome (eukaryotes).

Initiator proteins

Recognize specific DNA sequence at origins of replication. Break H
bonds to pry two strands apart. A-T rich region (WHY?).

Replication forks (Y-shaped junctions)

Move away in opposite directions from multiple origins of
replication in eukaryotic chromosomes.

Replisome

The replication machine! Big collection of proteins copying DNA.
Goes lightning fast (Ending with “ome” signifies its a big thing.)