Bio 183 Exam 1

Properties of water

• High surface tension and adhesion (created by forming H bonds with itself and other compounds)

• High heat capacity and heat of vaporization

• Water is a small, polar molecule.

Polar vs nonpolar covalent bond

Polar bond- A bond where electrons are shared unequally due to a large EN difference between atoms of 2 different elements

Nonpolar- A bond between atoms where electrons are shared more equally

Why is carbon unique?

Each carbon only has 4 electrons in it’s outer shell, so it dorms up to 4 covalent bonds with other atoms to satisfy the octet rule

What are isomers?

molecules that have the same chemical formula, but differ in the arrangements of atoms.

Different types of isomers

Remember: Isomers are molecules that have the same chemical formula, but differ in the arrangements of atoms.

1. Structural isomers - have the same chemical formula, but differ in arrangement of atoms

2. Geometric isomers- have the same chemical formula, but have a different arrangement of atoms around a double bond.

3. Enantiomer isomers- have the same chemical formula, but differ in 3D placement

• Ex: Amino acids are an L isomer, Monosaccharides are a D isomer

What are macromolecules?

Larger molecules within cells created from small organic molecules

Which of the 4 classes of macromolecules are often not considered true polymers?

Lipids

What are the 4 classes of macromolecules?

Carbohydrates, lipids, proteins, and nucleic acids

What are monomers and their functions?

Monomers are small molecular units which link together with covalent bonds to create polymers.

They are the building blocks, but can also be used as signaling molecules

What joins together carbohydrates?

glycosidic bonds

What are the simplest carbohydrates?

Monosaccharides

which types of carbohydrates flip between linear and ring forms?

5 and 6 carbon monnosaccharies (glucose)

What determines if a 5/6 carbon monosaccharide is an alpha or beta glucose?

If the -OH group ends up, it is an beta glucose

if the -OH group points down, it is an alpha glucose

why does alpha or beta configuration matter?

Because it has a direct impact on the characteristics of the polysaccharide, because it creates major differences in their polymers, starch (ALPHA) and cellulose (BETA)

Polymer examples of carbohydrates

Starch and cellulose

Examples of polysaccharides

Starch (plants store glucose as this)

Cellulose (major component of plant cell wall)

Animals store extra glucose as glycogen

Chitin (in the exoskeleton of arthopods and in cell walls of fungi)

Dehydration synthesis vs Hydrolosis

Dehydration synthesis: reaction in which a water molecule is REMOVED so a covalent bond forms b/w two monomers to build a larger molecule (h2o is a PRODUCT)

Hydrolosis: reaction in which a water molecule is ADDED to a covalent bond to split a polymer into individual monomers

Major functions of lipids

Lipida= fats. major function is long term energy storage, but can also cushion vital organs and act as an insulator

What is a fat molecule called and what is it made up of and connected by?

Triglyceride - 1 glycerol linked to 3 fatty acids, joined by an ester bond

what bond links lipid monomers

Ester bonds

Are lipids hydrophobic or hydrophillic and why?

Lipids are hydrophobic because they mainly consist of hydrocarbons which form non-polar bonds

Saturated vs Unsaturated fatty acids and examples

Saturated acids: have NO carbon-carbon double bonds, and are saturated with hydrogens at every possible position

ex: most animal fats - butter, lard, milk

Unsaturated acids: Have at least 1 carbon-carbon double bonds, formed by the removal of hydrogen atoms from the carbon skeleton. has a bend in it’s chain due to the c=c bonds

ex: plant and fish oils

what are hydrogenated oils?

unsaturated fats that have been synthetically converted to saturated fats by adding hydrogen, heat, and a nickel catylast

What are steriods? How are different steriods made?

Lipids with a carbon skeleton consisting of 4 fused rings.

Diff steriods are made by varying functional groups attached to the rings

What steriod kind is the precursor for all other steriods

Cholesterol

Why is cholesterol special

It is a steriod that is a component in animal cell membranes, and is the precursor for all other steriods

What are phospholipids and their characteristics (what are they made of)?

• phospholipids are a class of lipids similar to fats, but consist of 2 fatty acids attached to glycerol and a phosphate group

• They are amphipathic, as it is both hydrophobic and hydrophillic.

  • The fatty acid tails are hydrophobic

  • The phosphate groups and attachment form a hydrophillic head

How are phospholipids arranged?

As a bilayer, where the tails point to the interior and the head points to the exterior

what are phospholipids a crucial component of?

The cell membrane

What are the most structurally complex molecules known?

Proteins

what are the polymers of proteins?

Polypeptides

How many amino acid monomers are in a protein polymer/polypeptide

all polypeptides are made from the same 20 amino acid monomers.

What bond connects amino acid monomers?

A peptide bond

Monomers of proteins

amino acids

What components make up amino acids?

They have an asymmetric carbon atom at the center called the alpha carbon. attached to the alpha carbon is a hydrogen atom, a carboxyl group, an amino group, and a variable R group.

which monomer has an amphoteric nature, and what does this mean?

amino acids have an amphoteric nature, meaning they can act as an acid and a base because they contain a basic (amino) group and a acidic (carboxyl) group.

What determines the shape of a protein?

the order of amino acids.

What determines the function of proteins?

The specific conformation/structure of the protein made up from the amino acids

4 levels of structure in a protein

Primary: unique sequence of amino acids

secondary: polypeptide chains coiled or folded (alpha-helices or beta sheets)

tertiery: 3D shape of the polypeptide, determined by interactions among R groups

quaternary: when 2 or more polypeptides join to form a functional protein

What does denaturing do on a protein?

Changes the 3D shape of the protien, making it lose it’s function. this is often irreversible.

Function of nucleic acids:

to store genetic information

What are the monomers of nucleic acid and what are they joined by?

nucleotides are the monomers, which are joined by phosphodiester bond

2 types of nucleic acids and how they differ (important)

• Ribose, is in RNA, and contains an -OH group attached to it’s second carbon

• Deoxyribose, in DNA, is missing an oxygen at it’s second carbon, so it has an -H instead of an -OH group

• They are BOTH sugars but differ by 1 oxygen atom

3 parts of a nucleotide (nucleic acid monomers)

• a nitrogenous base (a,t , c,g in DNA, a,u , c,g in RNA)

• A pentose sugar

• a phosphate group

What elements make up a carbohydrate?

Carbon, Hydrogen, & oxygen

When two monosaccharides form to create a disaccharide, what is the bond called?

Glycosidic linkage

What is an ester bond?

The bond that creates lipids when formed between the carboxyl and hydroxyl groups

bond that links amino acids to form a polymer

Peptide bond

Alpha helix vs Beta Sheet

Alpha helix - A secondary structure (in proteins) where a segment of a polypeptide chain is coiled into a spiral shape

Beta Sheet- A secondary structure in proteins where a segment of the polypeptide chain is folded

The basic unit of all life is

cells!

What is cell theory

the theory that cells are the basic units of all life, all living organisms are made of cells, and all cells arise from pre-existing cells

Basic components/structure of both eukaryotic and prokaryotic cells

Plasma membrane - separates the cell’s interior from the environment

Cytoplasm - made of cytosol and fills the cell and holds components

DNA - genetic material of the cell

Ribosomes - synthesize proteins

Prokaryote characteristics and examples

Single-celled organisms with NO nucleus, and lack most internal structures. Believed to resemble the first cell. Contain 70s ribosomes (in the cytoplasm). small. Bacteria and Archea

Prokaryotes vs Eukaryotes

Prokaryotes - no nucleus, 70s ribosomes, very small, DNA is in a nucleiod. Bacteria & archea

Eukaryotes- have a nucleus. 80s ribosomes, larger, DNA is in nucleus. Organisms (plants, animals, fungi, protists)

Why are smaller cells more favorable to prokaryotes?

As cells grow larger, volume increases faster than surface area. B/c of this, the cell has a lower ability to interact with the environment through simple diffusion. Prokaryotes rely on diffusion, so it is more favorable for them to be smaller.

Plasma/cell membrane

In both pro + euk.

• Consists of a phospholipid bilayer, which keeps fluid inside separate from the outside environment.

• This bilayer has tunnels that let specific substances move through the membrane.

What are glycoproteins and glycolipids?

Molecules in the cell membrane that have sugar chains facing the outside of the cell that help cell signaling, recognition, and adhesion.

Nucleus

In eukaryotes only

• Usually 1 per cell

• Bigger than most prokaryotic cells

• Usually the largest organelle in animal cells

• houses DNA and is where transcription occurs

Nuclear envelope

Eukaryotes only

• A double membrane perforated with nuclear pores, to connect nucleoplasm and cytoplasm

• encloses the nucleus

• Separates DNA from cytoplasm

• Separates transcription from translation

Nucleolus

In eukaryotes only

• A region inside the nucleus where ribosomes are assembled from RNA and proteins

Ribosomes (what they do & what they are made of)

In prokaryotes and eukaryotes

• Assemble amino acids into proteins in the cytoplasm during translation

• Made of RNA and proteins

• Larger in eukaryotes (80s) compared to prokaryotes (70s)

Mitochondria

In eukaryotes only

• The site for the conversion of stored energy from macromolecules into a usable form, ATP

• has a folded inner membrane called cristae

• Has an innermost mitochondrial matrix

• has it’s own circular DNA and ribosomes

What is the folded inner membrane of the mitochondria called? What is it the site of?

cristae, the cite of electron transport chain of cellular respiration

mitochondrial matrix

The innermost space of the mitochondria, is the location of the krebs cycle and holds circular mitochondrial DNA

Peroxisomes

Eukaryotes only

• Small, rounded organelles enclosed by a single membrane that break down fatty acids and animo acids.

• Has a crystalline core composed of enzymes with a high concentration of the enzyme called catalase

Lysosomes

in eukaryotic ANIMAL cells ONLY

• Contain digestive enzymes that can fuse with vesicles to break down large biomolecules and worn-out organelles (autophagy)

What is autophagy?

The process by which a cell uses lysosomes to digest it’s worn-out organelles

Endomembrane system

Consists of internal membranes and organelles that modify, package, and transport lipids and proteins.

Includes: Golgi Apparatus, Plasma membrane, endoplasmic recticulum, lysosomes and vesciles, nuclear envelope

Endoplasmic recticulum (ER)

A network of interconnected membranous sacs (lumen) with two sections:

• Rough ER: synthesizes and modifies proteins and has attached ribosomes to the outer surface

• Smooth ER: Continous with the rough ER but does NOT have attached ribosomes. Synthesizes carbs and lipids and detoxifies poisons. (Has Cytochrome P450 enzymes which add a hydroxyl group to toxins, making them water-soluble for easy excretion)

What enzymes does the smooth ER have for easy excretion of toxins?

Cytochrome P450 enzymes which add a hydroxyl group to toxins to make them water-soluble

What is lumen?

The hollow portion of ER tubules

Golgi Apparatus

A series of flattened membranes called the cisternae where lipids and proteins in transport vesicles are sorted, packaged, and tagged.

Has a cis face (recieving) and a trans face (shipping)

Cis vs Trans face of the Golgi apparatus

Cis: recieves proteins and lipids from transport vesicles coming from the ER

Trans: Releases the modified proteins and lipids to be sent to another place.

What are centrosomes and centrioles?

ONLY Animal cells have centrosomes, microtubial organizing centers,

which are made up of two centrioles that lie at right angles to each other.

Each centriole is a cylinder made up of 9 sets of 3 microtubials.

structures that only plant cells have that animals do not

Cell wall, chloroplasts, plasmodesmata, and a large central vacuole.

Chloroplasts & their structure

In plant cells ONLY

• organelles in the green cells of land plants

• double-membraned organelles with their own 70s ribosomes and DNA

• has an internal structure of interconnected membranes called Thylakoids, where the light-dependent reactions of photosynthesis occur.

• Light- independent reactions occur in stroma.

Thylakoids

interconnected membranes inside chloroplasts where the light-dependent reactions of photosynthesis occur

Cell walls (& what they are made of)

In plant cells only

• a rigid semipermeable protective structure outside of the plasa membrane, made up of

• cellulose in plants

• chitin in fungi

• peptidoglycan in bacteria

Large central vacuole

A large central vacuole is present in plant cells

• occupies most of the area of the cell

• helps regulate water content under changing environmental conditions

• contributes to cell expansion and is an important structural component

Endosymbiotic theory

The hypothesis that mitochondria and chloroplasts originated as independent prokaryotic organisms engulfed by ancestral eukaryotes as they are similar in size (1um)

which structural features of mitochondria and cholorplasts support endosymbiotic theory?

Circular DNA, double membranes, and ribosomes

What structure increases the surface area of the mitochondria?

the cristae, inner folds

Which structure within chloroplasts contains chlorophyll?

the thykalloids

where is dna stored in prokaryotic cells?

The nucleiod, an open area of cytoplasm

What is the fluid, gel-like portion of the cytoplasm?

cytosol

What is cisternae?

membrane sacs of the golgi apparatus

Which polymer forms bacterial cell walls?

Peptidoglycan

What is the cytoskeleton and it’s functions?

A network of protein fibers

• maintains cell shape

• holds organelles in position

• enables movement of cytoplasm and vesicles within the cell

what are microfilaments?

The smallest part of the cytoskeleton (7nm)

• Made of 2 intertwined actin strands (f-actin, made from G-actin)

• abundant under the plasma membrane, they determine and stabilize cell shape

• involved in movement of the cell and muscle contraction

What are microtubials? What are they made of?

Hollow tubes (25nm) that are a part of the cytoskeleton, made up of a and b tubulin dimers

• forms rigid internal skeleton

• provides tracks/ a framework for motor proteins to move structures

• has dynamic instability- rapidly assembles and disassembles

What are intermediate filaments?

Several intertwined strands of fibrous proteins (keratin), that hold organelles in place and resist tension.

• 8-12 nm

Do not exist in plants.

Flagella & cilia and their similarities/differences

Flagella - used for cell movement, smaller in number (ex: sperm)

Cilia - Shorter and more numerous than flagella. Used to move substances along the cell’s surface

• are both motile cells made of microtubials

• consist of a 9+2 array of microtubials - 9 sets of 2 on the outside with 2 unfused in the center

What is the extracellular matrix

A network of proteins and carbs that surround, support, and give structure to cells

Cell junctions & their functions

multiprotein structures in ANIMAL cell membranes that connect cells to one another

• Tissue integrity (holds cells together, which helps tissues maintain structure)

• Can create barriers b/w cells

• allow cells to communicate

3 types of cell junctions and important examples of each (no need to describe)

1. Occluding junctions

• Tight junctions

2. Communicating Junctions

• Plasmodesmata

• Gap Junctions

3. Anchoring Junctions

• Desmosomes

Tight junctions & what they are made of

• A type of occluding junctions.

• Form watertight connections between epithelial animal cells

• Made from 2 proteins - claudins and occludins

Gap Junctions (& what they are formed from)

• A type of communicating junctions

• Protein lined- channel that allows water and small molecules to pass between animal cells

• form when 6 proteins (connexins) form a donut structure (connexon) in the plasma membrane

• closely resemble plasmodesmata

Plasmodesmata

• A type of communicating junction

• Channels that pass between cell wals in plants to connect cytoplasm, allowing materials and signaling molecules to pass through

• Viruses and bacteria can exploit it and cause disease

Desmosomes

• A type of anchoring junction

• Strong “spot weld” b/w animal cells in tissues that stretch (heart, lung, muscle)

• Created by the linkage of proteins called cadherins and intermediate filaments.

Which motor protein moves toward the plus end of microtubules?

kinesen