Eukaryotic Cells & Synthesis

• Genomes are more than just the genes themselves, which contain the information that influences characteristics (phenotype)
• Genes consist of DNA segments which produces proteins or functional RNA

From Atoms to Cells

• Order of size: atoms, molecules, organelles, then cells
• DNA synthesis or replication goes to RNA synthesis or transcription, which then goes to protein synthesis (translation) with ribosomes

Eukaryotic Cells

• The nucleus holds DNA and genetic information
• Endoplasmic reticulum and the Golgi apparatus are organelles that define eukaryotes
• Lysosomes, mitochondria, peroxisomes, and vesicles are organelles that are unique to eukaryotes
• Cytosol (cytoplasm) is the space where everything floats

Synthesis

• Process of 'making something'

Main Functions

• Membrane-enclosed organelles of eukaryotic cells serve various key functions
• Cytosol contains metabolic pathways, performs protein synthesis, and has a cytoskeleton
• Nucleus contains the main genome, DNA, and RNA
• Endoplasmic reticulum synthesizes the majority of lipids and proteins and distributes them among organelles and the plasma membrane

Endoplasmic Reticulum

• The ER is part of the endomembrane system, which are membrane-enclosed organelles that work together
• The two kinds of ER are Smooth and Rough
  • Smooth ER: Lipid formation (membrane lipids, steroids, etc.)
  • Rough ER: Makes proteins (ribosomes). Ribosomes reside in the cytoplasm and on the rough ER

Transport

• Lipids and proteins travel through vesicles to the Golgi apparatus/body
  • Golgi apparatus modifies lipids and proteins from the ER
  • Sends the lipids and proteins elsewhere

Endocytosis

• Endocytosis, "cell eating," is when the cell absorbs materials
• The plasma membrane bends around food and encircles it to bring it inside
  • Result is an endosome

Exocytosis

• Also known as ‘cell defecation’ or secretion

Mitochondria & Chloroplast

• Mitochondria synthesizes ATP through oxidative phosphorylation
  • Chloroplasts are about the same size
• Chloroplasts synthesize ATP and fix carbon through photosynthesis
• Peroxisomes break down molecules and do oxidative breakdown of toxic molecules
• Lysosomes participate in lysing fats/molecules and intracellular degradation

Cytoskeleton

• The cytoskeleton protects the cell, supports its structure, and allows movement but is not rigid
• Provides cells with structure and shape and is required for cell reproduction and movement and keeps organelles in place
• The three types of cytoskeletal pieces are:
  • Microtubules: tiny tubes made of proteins (mitotic spindle)
  • Actin filaments (microfilaments): drives cytokinesis, creation of two cells
  • Intermediate filaments: structure, flexibility, and nuclear lamina (only in some animals/cells)
• All completely made of proteins and in cytoplasm
  • They make long polymers of proteins
• Interphase

Mitochondria

• Powerhouse of the cell
• Makes most of the ATP

Nucleus

• Houses and protects genetic material

Model Organisms

• Studying some model organisms facilitates understanding of similar organisms and processes
• Species include Humans, Mice, Fruit flies, Plants, Roundworms, Yeast, and Bacteria

Biomolecules

• There are four categories
  • Carbohydrates: sugars (simple or complex)
  • Proteins: polymers of amino acids
  • Nucleic acids: polymers of nucleotides (DNA, RNA)
  • Lipids: polymer example such as lipids/oils/fats/waxes/steroids

Macromolecules

• A polymer is a larger organic molecule in a cell
• It is made from monomers or subunits

Polymers and Subunits

• Sugars become polysaccharides, glycogen, and starch in plants
• Fatty acids become fats and membrane lipids
• Amino acids become proteins
• Nucleotides become nucleic acids

Assembly

• Macromolecules assemble from monomers into polymers during dehydration (synthesis or condensation) reactions
• Bonds have different strengths
• Intermolecular forces hold atoms together

Covalent Bonds

• Strongest bond
• Represented as lines
• Water is a polar covalent bond

Noncovalent Bonds

• Weak individually, strong collectively
• Require a small amount of energy
• Multiple creates strong bonds
• Aka hydrogen bonds
• Atoms share electrons between atoms in covalent bonds

Covalent Bond Types

• Two types of covalent bonds affect whether molecules dissolve in water (cytoplasm)
  • Most molecules have both types of bonds
  • Depending on the structure and number of bonds, the molecule can be hydrophilic, hydrophobic, or amphipathic

Hydrophobic vs Hydrophilic

• Lipids: fats, waxes, and oils dissolve in oil:phobic, amphipathic lipids dissolve in both water and oil, and are in the cell membrane
• Amphipathic: membrane lipids contain polar and nonpolar regions
• Proteins: amino acids with hydrophobic and hydrophilic characteristics will determine the protein's folding

Covalent Bonds (cont.)

• Nonpolar covalent: equal sharing of electrons
  • Molecules with mostly nonpolar bonds are hydrophobic
• Polar covalent: unequal sharing of electrons
  • Found in water and much of biology

Oxygen

• Often involved in covalent bonds
• Leads to "H" bonds
• Both form when two atoms share electrons
• Both are very strong bonds
• Most molecules are a combination of both types

Polar Covalent Bonds

• Polarity is often dependent on oxygen
• Ability of atom to pull electrons towards itself.
• Water: oxygen is electronegative, hydrogen is electropositive

Surface Tension

• Water molecules hydrogen bond to each other
  • Weak single H bond, Strong multiple H bonds
• Hydrogen bonds are weak bonds between a slightly positive hydrogen atom and a slightly negative atom
  • Create special water properties like surface tension and the ability to dissolve molecules and hold heat
• Hydrogen bonds can also form between polar molecules of water and other materials
  • Hydrophilic molecules hydrogen bond with water
  • Carbohydrates have polar bonds and are hydrophilic
• Hydrophobic molecules repel water
• Hydrogen bonds link protein and DNA strands together
  • Hold double helixes together

Carbohydrates

• Structural molecules that store energy
• Cell walls of plants are cellulose
• Crab shells are chitin
• Bacterium is peptidoglycan
• Sugars provide energy storage and structure
• Their general formula is (CH2O)n, where n= 3, 4, 5, 6
• Glucose (C6H12O6) is a simple monomer sugar which can be arranged into polymers
  • Glycogen: individual glucose branched together
  • Complex sugars: polysaccharide

Lipids

• Primary function is long-term energy storage and insulation with triglycerides (fats and oils)
• Serve as structural components of phospholipid plasma membranes
• Provides protection
• Also includes waxes, skin oil, and hormones (signaling information)
• Steroids

Fatty Acids

• Lipids are made from fatty acids (carbon and hydrogen)
• Carbon hydrogen (C-H) tails are hydrophobic and non-polar
• Fatty acids are attached to polar heads and are hydrophilic
• Amphipathic molecules have one region that likes water and another that hates it, like amphibian fats Amphipathic lipids assemble into membranes C-H tails are hydrophobic, non-polar, and heads are polar
• Double covalent bond
• Unsaturated fatty acids: bend/kink (molecular level double covalent bond)
  • Liquid oil
• Saturated fatty acids: straight
  • Solids

Steroids

• Consist of a hydrocarbon tail from a fatty acid
• Cholesterol in all animal membranes, provides one oxygen on one side of long molecule -Is amphipathic
• Testosterone are molecules with two oxygen

Nucleic Acids

• Nucleic acids store genetic information and help make proteins
  • The order of nucleotides in DNA and RNA encode the instructions for building proteins
• Nucleotides are monomers of DNA and RNA, which are polymers
• The two major polymers are:
  • DNA (deoxyribonucleic acid)
    • "Deoxy" denotes difference between DNA and RNA
  • RNA (ribonucleic acid)
    • Sugars around duouble helix

Nucleotides

• Phosphate group (yellow circle), 5 carbon sugar (blue), nitrogenous base
• Nucleotide Structure

Nucleotide Composition

• Complementary base-pairing occurs in DNA
  • A=T (2 H bonds)
  • G=C (3 H bonds)
  • Purines pair with pyrimidines, 2 rings combine with 3 rings

Carbon Sugars

• Five carbon sugars are in DNA and RNA, but DNA has one fewer oxygen
  • @2 prime RNA= OH, DNA=H
• Pentose sugar of nucleotides

Chemical Bonds

• Carbon atoms meet where lines meet
  • H: 1 bond
  • O: 2 bonds
  • C: 4 bonds
  • N: 3 bonds
• For life, molecules need to physically interact with each other
  • Covalent bonds hold atoms into molecules
• Molecules with oxygen have polar covalent bonds
  • Polar covalent bonds yield hydrogen bonding
• Hydrogen impacts solubility AND interaction ATP, or adenosine triphosphate, is a key nucleotide that provides energy to cells

ATP

• Energy source to the cells (currency), consists of adenine, ribose, and 3 phosphates
• Is high energy molecule (last 2 unstable bonds)

Proteins

• Vital for metabolism, structure, and transport function
• Proteins are polymers of amino acid monomers
• They defend, regulate (protein hormones - insulin), and drive motion (muscle proteins)
• General formula of an amino acid
• Multiple protein copies

Common Amino Acids

• There are approximately 20 common amino acids

Protein Organization

• There are multiple levels:
  • Primary: Sequence of a chain of amino acids
  • Secondary: Local folding of polypeptide chain into helices or sheets
  • Tertiary: Three-dimensional folding pattern of protein due to side chain interactions
  • Quaternary: Protein consisting of more than one amino acid chain
• ATP Transfers energy from molecule to molecule

ATP Transfer

• ATP carries and transfers energy from molecule to molecule and is the most energized form
  • ADP contains less energy
• Organisms use energy to build ordered cells and bodies. Reactions are often coupled to transfer energy from one molecule to another
  • An activated carrier molecule temporarily holds the energy and transports it in the cell

ATP Power

• Drives a chemical reaction
• Proteins fold into their lowest energy conformation, which can be changed by interactions that denature the protein
• Protein shape must be correct for function
• Shape determined amino acid sequence and R-groups
  • Non-polar/hydrophobic or polar/hydrophilic R-groups
  • Primary (linear strand) structure determines both structure and function
• Proteins of different sequences have different shapes
• Hydrophobic forces push nonpolar regions away from cytoplasm, resulting in bending
• Peptide bonds and backbone bonds are rigid
• R group to alpha C bond rotates
• Hydrogen bonds are flexible
• Covalent peptide bonds between amino acids build polypeptide chains, facilitated by ribosomes

Amino Acids

• Side chain properties depend on how the protein will fold
• Protein is capitalized letters strung together
• Some are polar, some are not

Polar Amino Acids

• Oxygen is electronegative
• Examples: Serine (ser, or S), Threonine (thr or T), Tyrosine (Tyr or Y)
• Secondary structure: beta sheet
  • Rigid, pleated structure
  • Core of many proteins
• Helix or sheet
  • Alpha helix, coil
    • Every 3.6 amino acids
    • Backbone amino acid
    • ~ 20 Amino Acids required

G Protein

• G protein coupled receptor kinase
  • 7 helices across it
  • Coiled coil domains are alpha helices wrapped around eachother
    • Very strong, stable, flexible
    • Non-polar R groups repel water and attract eachother
    • Many elongated proteins (keratin)- hair
  • Structure: entire polypeptide folded into 3-D
    • Contains alpha-helices and beta sheets
    • "Domain"= functional units within proteins
  • The alpha helices and beta sheets and coiled coils create a 3D structure and become functional

Quaternary Structures

• Quaternary Structures form when one protein forms complex molecules from one protein
  • two subunits=dimer
  • Four subunits= tetramer
  • Or many
  • Homotetramer= 4 subunits same
  • Heterotetramer= 4 different subunits
  • Hydrogen bonds hold proteins into complexes
  • Multiple tertiary structures together
• Combining different polypeptides (proteins)
• For example, hemoglobin= heterotetrammer
  • Carries oxygen
  • Contains 2 alpha globin and 2 beta globin polypeptides, and 4 heme groups
  • Encoded by 2 different genes

Multi-Mers

• Multimers use non-covalent bonds (held together)
  • cytoskeleton → actin helix
• Disulfide bonds help stabilize protein structure
• Extracellular proteins need covalent bonds (cross-linkages) to help stabilize and maintain 3D structures
  • Cysteine: AA R-group needed to stabilize
  • Disulfide bond= covalent, strong bond

Protein Shapes

• Proteins interact with other molecules and slightly change shape
• Binding sites on proteins use non-covalent bonds to hold ligands