Biology 204 Midterm 1 Study Guide

Chapter 3

Chapter 3

RNA

-Single Stranded

-AU CG (form hydrogen bonds to create unique structures)

-Ribonucleic Acid (OH on 2’ Carbon)

DNA

-Double Stranded

-AT CG

-Deoxyribonucleic Acid (Only H on 2’ Carbon)

RNA Polymerization

-Nucleic acids polymerize from 5’ to 3’

-Begin at the 3’ end from the template

-New nucleotides are added onto the 3’ OH of the growing nucleic acid chain

-First phosphate of incoming nucleotides attaches to 3’ OH

-Removal of 2 phosphates provides energy for polymerization

-Forms a phosphodiester bond (covalent)

-Sequence determined by complementary base pairing

• Original RNA polymer serves as template for information of new RNA polymer

Nucleotide

-Sugar (Carbon sugar)

-Base (1’ nitrogenous base)

-3 Phosphates (5’ end)

-OH or H (3’ end - RNA is OH, DNA is H)

Spiegelman Experiment

Question: Can template-directed RNA polymerization produce enough variation for natural selection?

• Testing whether RNA polymerization leads to mutations

-Found that evolution can happen in RNA → Evolution requires variation: there must be changes during polymerization (mutations)

Components:

• Test Tube 1: Added 1 species of RNA (3300 nucleotides) + Replicase Enzyme + all 4 nucleotides

• Test Tube 2: 4 nucleotides + Replicase enzyme + transferred RNA

-Performed this 75 times

-3300 nt RNA decreased → 2000 nt increased then decreased → 1000 nt increased then decreased → 550 nt increased

Spiegelman Experiment Results

• RNA replicates in a test tube (outside of a cell); can replicate in primordial soup

  • Supports self-replicating RNA for origin of life

• Replication imperfect in sequence and size → Mutations: variation for evolution

• Most abundant species changed over time: Evolution of RNA species

• Replacement of 3,300 nucleotide sequence with progressively shorter sequences: Shorter RNA strands survive longer; they are “better” → shorter provides competitive advantage (polymerizes faster)

Replicase Enzyme

-Speeds up reactions by lowering activation energy; catalyst

-Lowers activation energy; amt of energy invested

-Made up of Proteins → Amino Acids

-Structure of Protein determines enzyme function

Ribozyme

-Made up of RNA → Nucleic Acid

-RNA molecule that catalyzes a chemical reaction

-Complementary base pairing/hydrogen bonding allows it to fold

-Structure of RNA detemines function of Ribozyme

• Mutations of RNA lead to different structures

-No known Replicase Ribozyme, only hypothesized

Ribozyme in Primordial Soup

-Believed that their presence was key to RNA replication

Complementary Base Pairing

Nucleotides can form hydrogen bonds with and recognize specific other bases

-A to U

-C to G

Antiparallel

Synthesis of RNA is antiparallel

-Synthesis runs 5’ to 3’ of replicated strand

-To form hydrogen bonds, one nucleotide must be upside down

Template Directed Polymerization

-Original RNA polymer serves as template for RNA polymerization by complementary base pairing

-Synthesis runs 5’ to 3’ on template strand, starts at 3’ end of template strand

-Antiparallel

-Energy produced by breaking off 2 phosphate groups

Template Directed Polymerization Steps

5’ to 3’ (New strand)

-Antiparallel

-First Nucleotide binds to 3’ end of template

-Breaking off phosphate groups gives off energy

-Makes complement strand →replicates again→ makes replica (same as original) strand

Undirected Polymerization

-Nucleic acids first synthesized by undirected polymerization

-Nucleic acids polymerize from 5’ to 3’

-New nucleotides add to 3’ OH of growing nucleic acid chain

-Lose 2 phosphates providing energy

-Forms covalent phosphodiester bonds

-Random, base does not matter

-Pro:

• Required formation of first RNA molecule due to RNA polymer forming from 5’ → 3’

-Con:

• Random process so no single RNA molecule can be duplicated regardless of function - odds are too low

• Molecules degrade and are lost

• Definition of life requires genetic material - cannot happen with undirected polymerization

Catalyst

Molecule that speeds up the rate of reaction without being used up or destroyed

-Decreases activation energy

Enzyme

Biological catalyst made up of proteins

-Catalyzes reactions by decreasing activation energy

-3D shape recognizes specific reactants and weakly interacts

-Holds in place long enough to change covalent bonds → lowering activation energy

-Substrate bind to enzyme

Activation Energy

Amount of energy required to allow a reaction to occur

-Catalyst decreases this

Substrate

Reactant that binds to the active site of an enzyme

Active Site

Part of enzyme where reactants/substrates bind

Protein Folding

-Peptides fold into proteins with backbone to R-group interactions

-Enzyme properties are determined by protein folding

-Structure determines function

Original Genome

RNA based

-Store information through base sequences

-Function as a catalyst

Evolution

Change in gene frequencies over time

-Rules:

• Variation of traits in population

• Traits must be heritable

• Fit individuals have traits allowing them to survive longer and/or leave more offspring

• Subsequent generations have increased number of offspring from fit parents

• Most favorable traits accumulate in the population and less favorable traits diminish

Evolution of RNA

-Template directed replication cannot evolve due to lack of variation

-RNA is prone to mutation → leads to evolution in RNA

RNA Mutations

-Addition: AUCG → AUUCG

-Deletion: AUCG → AUG
-Substitution: AUCG → AUGG

-Duplication: AUCG → AUAUCG

Replicase Enzyme in the Primordial Soup

It was NOT in the primordial soup

-Had amino acids and short peptides

-No large proteins like replicase

-Ribozymes WERE present (catalysts in the primordial soup)

RNA can fold in on itself

Can fold due to single strand structure

-Hydrogen bonds fold in on itself

RNA Ribozyme Replicase Theory

-RNA Ribozyme catalyzes its own replication

-Scientists hypothesize that ribozyme replicase existed that was able to catalyze RNA replication

• Nucleotides would bind in pocket to lower activation energy → template directed polymerization was catalyzed

-Scientists are not sure of how it would have worked due to lack of discovery

Chapter 4

Chapter 4

Diffusion

The spontaneous, random spreading of molecules from a place of higher concentration to a place of lower concentration

-Molecules move from high to low concentration (down the concentration gradient)

-When molecules reach equilibrium, there is still movement but no net movement

-Occurs because molecules are constantly moving

-Movement is random

-It is not an all or nothing → It is about the rate and efficiency

Concentration Gradient

Molecules move down their respective concentration gradients

-Each solute diffuses across its own concentration gradient

Molarity

Measurement of the concentration of molecules

-Higher molarity = higher concentration

-Molarity = moles/L

Ribozyme Concentration

-Higher ribozyme concentration → more RNA replication + evolution

Process: Original RNA → Folds into Ribozyme → Ribozyme enhances replication → More RNA & increases catalyst concentration → Mutations occur → Limited nucleotides lead to competition → Some species (“better”) survive and some become extinct

(Process of natural selection occurs)

RNA in the Primordial Soup was at

Low Concentrations

RNA Replicase Ribozyme Issue in Primordial Soup

-Diffusion prevents RNA replicase from accumulating

-Concentration of RNA replicase is only slightly higher at site of replication than in surroundings

• May not be high enough to increase replication

-Needed method to concentrate RNA template near the ribozyme

Solution: First cell membrane created

-RNA cannot diffuse as far → higher concentration → increased rate of replication

-Nucleotide monomers could enter but replicase ribozyme could not

First Cell Membrane “Liposome”

-Very leaky → let nucleotide monomers pass through

-Liposome: “bubble" of membrane consisting of two layers of amphipathic molecules

• Made up of fatty acids (less amphipathic → very nonpolar → leaky)

• Hydrophilic head + Hydrophobic tails

-Water inside & outside of liposome (polar)

-”Bubble” structure entrap large solutes

Amphipathic Molecule

-Molecule with both polar and nonpolar ends

Ex:

-Phospholipid (modern cell membrane)

-Fatty acids (less amphipathic → very nonpolar)

Liposomes in the lab vs in the primordial soup

Lab: Created by adding fatty acid + sonication

Primordial Soup: Fatty acids in pool of replicating RNA + RNA template & nucleotides dissolved in H2O → Lightning strikes (energy) → RNA, template, free nucleotides in H2O trapped in liposomes

Protocells

-First Cells

-Formed when liposome surrounded RNA and other material in primordial soup

-Efficient replication = trapped RNA→ high RNA concentration → better replication

-Led to increases in types of RNAs with mutations

Natural Selection at Cell Level: RNA increases survival or division → Leads to more cells with that RNA

-Natural Selection at RNA level: RNA replicates faster → More RNA

Modern Cell Membrane

-Phospholipid Bilayer

-Selectively Permeable: Only certain molecules can pass through membrane of a cell

• Small, hydrophobic, uncharged molecules can pass: O2, CO2, N2

• Large, charged, hydrophilic molecules cannot pass: Sucrose, peptide, Na+, Cl-, CH3OH

Osmosis

-Diffusion of water from low to high solute concentration across a semi-permeable membrane

-H2O is the only polar molecule that can diffuse across a cell membrane

-Water diffuses through aquaporins (protein channels)

Hypertonic Solution

Animal Cell: Shrivels up

-Higher concentration of solute outside of cell

Isotonic Solution

Animal Cell: Normal

-Equal concentration inside and outside of cell

Hypotonic Solution

Animal Cell: Lyses or Swells

-Lower concentration of solute outside of cell