Cell Biology Exam 1

Central Dogma

DNA → RNA → Protein

DNA → RNA

Transcription

RNA → Protein

Translation

Qualities of a Living Cell

1. growth

2. Reproduction

3. Convert Energy

4. Metabolism

5. Respond/adapt

Cell Theory

All cells are from the division of pre-existing cells and inherited characteristics from them

Prokaryotes

Bacteria & Archea

Lack organelles & lack nucleus

Simple

Abundant

Reproduce Rapidly

Can be aerobic (oxygen) or anaerobic (no oxygen)

Archea

Extremophiles; can live in harsh conditions

Eukaryotes

Have Nucleus & Membrane bound organelles

More complex & larger

Can be single-cell or multicellular

Nucleus

Has two membranes which form the nuclear envelope

house DNA- main site for DNA replication & transcription

Mitochonrion

Eukaryotic Cells

Enclosed by 2 membranes (outer: smooth; inner: folds (cristae) which increase surface area)

Generate ATP

Primary site for aerobic respiration

O2 → CO2 + H2O

Chloroplasts

Capture sunlight energy in which chlorophyll converts into chemical energy which is stored in sugars

CO2 + H2O → Sugar + O2

The mitochondria used the sugar as fuel for cellular respiration which produces ATP

Rough ER

Protein Synthesis

Smooth ER

Lipid (fat) metabolism & synthesis, carb. metabolism

modifies proteins from rough ER

Sort, package & ship

Lysosomes

Cellular Digestion (break down sugar, fats & proteins)

Generate and release nutrients

Peroxisomes

Generate Hydrogen Peroxide (H2O2) as a by product

Detoxification of the cell

Fatty Acid Metabolism & Lipid Synthesis

Catalase: H2O2 → H2O + O2

Vesicles

Transport “containers” of the cell

Cytoplasm (cytosol)

Everything Expect the Nucleus

Metabolic Reactions

Cytoskeleton

Internal Framework

1. Action Filaments

2. Microtubules

3. Intermediate Filaments

Model Organisms

Simplest organism that can adequately model biological process of interest

1. Short Generation Time

2. Large Number of Offspring

3. Thrive under laboratory conditions

4. Inexpensive & easy to house

5. Well-characterized genetics

6. Experimental Manipulation

Amphipathic

Both hydrophobic & hydrophilic properties

Biomolecules

organic molecules that function in aqueous (water) environments

Macromolecules

Proteins

Nucleic acids

Lipids

Carbohydrates

Atoms

Smallest unit of an element

Elements

Composed of only ONE type of atom

Molecules

Two or more atoms chemically bonded together. The atoms may or may not be from the same element

Atom Nucleus

Protons and neutrons

Electrons

negatively charged, organized in “electron shells”

Isotope

Different number of neutrons

Cations

Positive; formed by loss of electrons

Anions

Negative; formed by gain of electrons

Octect Rule

8=filled electron shell and non-reaction; will not bond with any other atoms

Electron shell

2,8,8,18,18

Covalent Bonds

Sharing of unpaired electrons in outer most valance shell to make molecules. These are the strongest bonds

Some atoms can have multiple covalent bonds (double & triple bonds). Less freedom, bond stiffer, Increase electron density- shorter and stronger bonds

Noncovalent Bonds

anytime we aren’t sharing electrons

• ionic bonds

• hydrogen bonds

• electrostatic bonds

• van der Walls attractions

• hydrophobic forves

Ionic Bonds

When an atom donates an electron to another atom, resulting in one cation and one anion

Strongest form of electrostatic attraction

very attracted to polar water molecules (hydrophilic)

Much weaker than covalent bonds

Double Bond

Four total shared electrons. Double bonds are shorter, stronger and block free rotation of two atoms.

Partial Double Bond

Second pair of electrons to fluctuation between two pairs of atoms, Resonance, such as a PEPTIDE BOND

Triple bond

Six shared electrons (3 pairs)

ex. Nitrogen gas

Polar Covalent

When electrons are shared unequally

Electronegativity- pull electrons toward electronegative atom

Highly electronegative- Oxygen & Nitrogen

Low electronegativity- Hydrogen

Nonpolar Covalent

Electrons are shared equally

Hydrogen Bonds

Most important non-covalent bond

polar bonds of oxygen & hydrogen and/or nitrogen & hydrogen

H bonds hold water & water together

Hold DNA strands, protein together

Very weak

Hydrophilic

“water-loving”

charged

Hydrophobic

“water-hating”

lack charge; water has no way to interact with them

Van der Waals- Noncovalent

“induced Dipole (2) interactions”

a single van der waal interaction is weak, but collectively they are strong

Hydrophobic Forces- Noncovalent

Hydrophobic molecules clump together and shield away from water to achieve as much entropy as possible

It is the shunning of water and the universe striving to maximize chaos that drives hydrophobic molecules together

NO WATER PRESENT, NO HYDROPHOBIC FORCE

Electrostatic Attraction- Noncovalent Bonds

Large molecules can have a pattern of + and - charges across their surface due to polar covalent bonds. can promote strong and specific binding

Specificity- complementary interaction surfaces. H-bonding, ionic, van der waal and hydrophobic bonding potentials will match up and line up perfectly

Bond Lengths

1. Covalent- 10 nm (shortest & strongest)

2. H-bonds- 0.17 nm (2nd shortest & strongest)

3. Ionic bonds- 0.25 nm (3rd shortest & strongest)

4. Van der Waals- 0.35 nm (4th shortest & strongest)

Water

Polar

Perfect Balance of hydronium and hydroxyl ions

Acids

H+ donors

More hydronium ions than hydroxyl ions

bases

H+ acceptors

More hydroxyl ions that hydronium ions

Sugars (carbs)

energy source

subunits of polysaccharides & oligosaccharides

Fatty acids

chain components of cell membranes

Amino Acids

subunit of proteins

Nucleotides

Subunits of DNA & RNA

Anabolism

Monomers → Polymers

“build”

Catabolism

Polymers → Monomers

“break”

Sugars (CH2O)n

Monosaccharides ‘glucose’ serves as energy storage. Broken down to release energy for cell to do work

Isomers

Same Formula, Different Structure

ex. glucose, fructose, galactose

What do sugars build?

Oligo/polysaccharides

Condensation/Dehydration Reaction

build monomers into polymers

Hydrolysis

break polymers down into monomers

energetically favorable

Sugar/Carb bond

Glycosidic Bond

oligo/polysaccharide fuction

store energy (animals- glycogen; plants- starches)- polysaccharides

Mechanical Support- (plants- cellulose; arthropods- chitin)- polysaccharides

Oligosaccharides are linked to form proteins or lipids

Fatty Acids

Two chemically Distinct Regions

• long hydrocarbon (hydrophobic)

• -COOH (carboxyl)- extremely hydrophilic, so becomes ionized (-COO-)

Amphipathic- both hydrophilic & hydrophobic regions

some serve as food reserves

• triacylglycerol- glycerol & 3 fatty acid tails

some serve as membrane lipids

• hydrophilic head: polar group + phosphate + glycerol

• two fatty acid hydrophobic tails

Saturated fatty acids

“saturated” with hydrogens; can’t fit anymore

no double bonds present

solid at room temperature

Unsaturated fatty acids

Missing hydrogens

Double bonds present- kinks/bends in the chain

liquid at room temperature

Amino Acid Structure

Attached to a central carbon, all amino acids contain:

• -COOH (carboxylic acid group)

• -NH2 (amino group)

• 20 different types of side chains

Amino Acid Polymer

Protein

Bonds Between amino acids that make proteins

peptide bond; formed via condensation reactions. This forms a rigid polypeptide backbone

Acidic Side Chains- negatively charged (hydrophilic)

Aspartic Acid

glutamic acid

Basic Side chains- positively charged (hydrophilic)

lysine

arginine

histidine

Uncharged Nonpolar Side Chains (hydrophobic)

alanine

valine

leucine

isoleucine

proline

phenylalanine

methionine

tryptophan

glycine

cysteine

Uncharged Polar Side Chains (hydrophilic)

asparagine

glutamine

serine

threonine

tyrosine

Nucleotides

makes DNA & RNA (polymers of nucleotides)

nitrogen-containing ring, linked to five carbon sugar, and one phosphate group

Activated carriers- di and tri phosphates are the basis of chemical energy in the call

• can help perform unfavorable reactions by storing energy in their bonds

  • hydrolysis breaks off the phosphate, which is then used to power the reaction

DNA Bases

A-T; G-C

RNA bases

A-U; G-C

pyrimidine

1 ring

CUT

Purine

2 rings

Pure as AG (gold)

Nucleoside

Base + sugar

Nucleotide

Base + sugar + phosphate

Nucleotide bond name

Phosphodiester bond links the bases to create DNA and RNA

creates structural polarity/directionality

• 5’ → 3’

proteins- structure=function

complicated structure will lead to complicated function

there are many different size and shapes

Ribosomes

Make proteins

Structure of a protein

determined by the sequence of amino acids

structure determines fuction

Configuration of the R-Side chains

Side chains project away from the backbone in a trans configuration (up/down)

Peptide bonds join amino and carboxyl group in the polypetide chain

Peptide Chain Directionality

Start with N-(amino)-terminus and ending with the C-(carboxyl)-terminus

peptide bonds cannot rotate freely

Primary Structure

Sequence of amino acids

amino acid chains are very flexible

Secondary Structure

Non-covalent bonds

Proteins fold into most stable conformation

a-helix & B-pleated sheet form by hydrogen-bonding between N-H and C=O groups in the polypeptide chain

R groups do not participate in secondary structure

First three-dimensional structure

a-helix

H-bond is formed between the carboxyl group of one amino acid and the amino group 4 down in the sequence

generates a right-handed helix

common in membrane proteins where hydrophobic side interacts with the fatty acids of the phospholipid ad anchors the protein in place

2+ helices can wrap around one another to create a structural fiber called a coiled coil

• ex. keratin & collagen

B sheets

‘runs’ of amino acids side by side

• parallel: N & C are parallel

• Antiparallel: alignments run in opposite direction (N→C and then C→N)

stackable, good for storage proteins, channel, etc

Tertiary Structure of Proteins

“R” Group interactions- how the side chains interact with one another and with water

• Hydrophobic interactions: Nonpolar R groups cluster in center of protein, away from water

• Hydrogen bonds: Polar R groups form links with water or other polar side chains

• Ionic bonds: oppositely charged R groups attract to form salt bridges

• Disulfide Bridge: Covalent links between cysteine sulfur atoms lock parts of the chain together

Noncovalent bonds

Three noncovalent bonds that help proteins fold and stabilize them

electrostatic interactions

hydrogen bonds

van der waal interactions

Shape/structure

will form as most stable conformation (native conformation)

• releases the most free energy (negative delta G)

• forms the MOST non-colvalent bonds

Chaperones

Type of protein that aids in the folding of protein; can also have isolation chambers

Denatured proteins

protein becomes unfolded and thus looses its fucntion

• high concentration of Urea

• chemicals

• heat

• pH

Is denaturation reversible?

YES

BUT if a chaperon protein is denatured, denaturation cannot be reversed

How do extracellular proteins stay stable in the harsh environment of the extracellular space and avoid denaturation?

Covalent bonds between different amino acids (between disulfide bridges)

• if between a single polypeptide- contribute to tertiary structure

• if between more than one polypeptide- contribute to quaternary structure

Quaternary Structure

Multiple polypeptide interactions

hold together by noncovalent bonds

form a subunit

Domain

Segment of a protein that can fold into a tertiary shape independently and carry out a specific function

• Do things such as hydrolyze ATP, bind to DNA, etc.

If we cut out these domains from one polypeptide and insert it into another, it will retain its function

Protein Families

Similar structure & shape, but the subtle differences affect what substrate (location) they work on; similar function but different location