Exam 3 Review

Exam 3 Review: Key Biological Concepts

Chromatin Structure

• Euchromatin:
    - Definition: Loose form of chromatin.
    - Implication: Associated with ACTIVE genes.

• Heterochromatin:
    - Definition: Tight form of chromatin.
    - Implication: Associated with INACTIVE genes.

Chromosome Basics

• Sister Chromatids:
    - Definition: Identical copies of a chromosome.

• Centromere:
    - Function: Holds sister chromatids together.

• Kinetochore:
    - Function: Point where spindle fibers attach during cell division.

• Telomeres:
    - Function: Protect the ends of DNA from degradation.

Gene Structure

• Promoter:
    - Definition: Region where transcription of a gene begins.

• Coding Region:
    - Definition: Part of the gene that is transcribed into RNA and ultimately translated into protein.

• RNA Processing:
    - Description: RNA is transformed from its initial transcribed form into a mature messenger RNA (mRNA) through several steps, such as capping, polyadenylation, and splicing.

Prokaryotic Genes

• Monocistronic:
    - Definition: Refers to mRNA that codes for a single protein (1 gene -> 1 protein).

• Polycistronic:
    - Definition: Refers to mRNA that codes for multiple proteins (1 RNA -> Multiple proteins).

• Operons:
    - Description: A cluster of genes transcribed together under the control of a single promoter. They often are involved in the same metabolic pathway or function.

DNA Methods

• PCR (Polymerase Chain Reaction):
    - Purpose: To amplify a specific DNA segment.
    - Steps:
      1. Denature: Separate the DNA strands by heating.
      2. Primer Binding: Short DNA primers bind to their complementary sequences on the single-stranded DNA.
      3. Extension: DNA polymerase synthesizes new DNA strands.
      4. Result: Exponential growth of the target DNA region.

• Sanger Sequencing:
    - Purpose: To determine the nucleotide sequence of DNA.
    - Description: Utilizes dideoxynucleotides (ddNTPs) to terminate DNA chain elongation; results in fragments of different lengths that are then read to derive the sequence.

• Crispr:
    - Purpose: To edit DNA within genomes.
    - Mechanism: Guide RNA directs the Cas9 enzyme to the target DNA sequence where it creates a double-strand break, facilitating either the knockout of a gene or the insertion of new genetic material.

• Gel Electrophoresis:
    - Description: A method used for separating DNA fragments based on their size.
    - Principle: DNA moves toward the positive charge (+) in the gel; smaller fragments migrate faster than larger ones.
  

• Plasmids:
    - Definition: Circular DNA molecules distinct from chromosomal DNA.
    - Use: Commonly used in genetic engineering to insert foreign genes.
    - Features: Contain an origin of replication and often carry genes for antibiotic resistance.

Carbohydrates

• General Formula:
    - CnH2nOn: Represents the chemical structure of carbohydrates.

• Primary Functions:
    - Energy Storage: Provides fuel for cellular processes.
    - Structural Components: Contributes to cellular structure (e.g., in plant cell walls).
    - Cell Signaling: Plays a role in cell communication and recognition.

Types of Sugars

• Aldose:
    - Definition: A sugar with an aldehyde group in its structure (e.g., glucose).

• Ketose:
    - Definition: A sugar containing a ketone group (e.g., fructose).

Identification of Sugars

• D vs. L Configuration:
    - Determination: Based on the orientation of the hydroxyl group (-OH) on the second to last carbon in the sugar molecule:
      - D: OH group on the right.
      - L: OH group on the left.
    - Notably, most biological sugars are in the D configuration.

• Enantiomers:
    - Definition: Mirror images of each other.

• Diastereomers:
    - Definition: Stereoisomers that are not mirror images; differ at one or more carbon.

• Epimers:
    - Definition: Stereoisomers that differ at exactly ONE carbon atom.
    - Note: All epimers are diastereomers.

Chemistry of Sugars

• Aldose:
    - Forms hemiacetal upon cyclization.

• Ketose:
    - Forms hemiketal upon cyclization.

• Anomeric Carbon:
    - Definition: The carbon atom in a sugar that becomes a new stereocenter upon cyclization.
    - Can represent α and β anomers depending on the orientation of the hydroxyl group.

Enzymes

• Definition: Catalysts that speed up chemical reactions.

• Function:
    - Lower the activation energy (E_a) needed for reactions to occur.
    - Enzymes do NOT change the overall energy of the reaction.
    - Mechanism: Stabilize the transition state to make the reaction more favorable.