Biology !!!!

BSCI170 @ UMD

Structures in ALL living cells

Cell membrane, cytoplasm, DNA, ribosomes

Structures of the endomembrance system

Nuclear envelope, smooth and rough endoplasmic reticulum, vesicles, golgi apparatus

Structures that are defined as membrane bound organelles

Chloroplast, mitochondria, nucleus, endoplasmic reticulum, vacuoles, golgi.

Structures found in plant, not animal cells

Cell wall, chloroplast, central vacuoles.

O-N+

polar bond

N-H+ bond

polar

Water's emergent properties

• surface tension

• high specific heat

• evaporative cooling

• less dense as a solid

• “universal solvent”

• pH

• polarity ( slightly negative + positive)

Endosymbiotic theory

Complex cells evolved to inhabit larger cells (they have a double membrane, own DNA/RNA, replication, ribosomes)

Membrane bound organelles that support endosymbiotic theory

Mitchondria and chloroplast

Hydroxyl

-OH, adds polarity

Polarity

distinct or opposite properties, structures, or charges

3 Types of Chemical bonds

1. Covalent (non-polar)

2. Polar

3. Ionic

Nonpolar bonds

Equal sharing of electrons, no charges, equal/similar electronegativity; aka covalent

Polar bonds

Unequal sharing of electrons, partial charges, slight difference in electronegativity

Ionic bonds

Extreme difference in electronegativity, electrons are transferred (not shared), ions form

Carbonyl

C=O, affects energy reactions, gives a V-like structure

Carboxyl

COOH, adds negative charge

Amino

NH2, adds positive charge

Sulfhydryl

-SH, important for protein structure → disulfide bridges

Phosphate

PO4, adds energy to molecules

Methyl

CH3, temporarily changes identity of molecules

Four ways carbon backbones can be modified to create different organic molecules:

1. Length

2. Ring

3. Double Bond

4. Branching

Big ideas in Biology

1. Structure-Function Relationship

2. Emergent Properties

3. Energy Transformation

4. Regulation

5. Evolution

6. Cell Theory

Compartmentalization

The organization of a cell's interior into distinct, specialized regions surrounded by membranes

Cytoskeleton

Provides combination of support and flexibility needed for large cells to interact and move around

3 structures in the cytoskeleton

1. Microfilaments

2. Microtubules

3. Intermediate fibers

Cells can use membrane proteins to anchor to _____ in tissues.

extracellular matrix

Desmosomes

Tightly connects 2 cells together at their cell membranes; connects to the cytoskeleton via intermediate filaments

Gap Junctions

Spans the membranes of neighboring cells; allows free diffusion of molecules between cells

Tight Junctions

proteins that closely connect the membranes of neighboring cells; makes a waterproof seal that prevents movement of solute between cells

When are atoms most stable?

No unpaired electrons, full shell

Do electrons closer to the nucleus have higher or lower energy than electrons further away from the nucleus?

Lower. When you are closer to the nucleus, the lower the energy is.

Properties of water

1. Polar

2. Universal solvent

3. Cohesion/adhesion

4. High Specific Heat

5. Lower density as solid

6. pH

Why is water able to form multiple hydrogen bonds?

Water is a polar molecule, with opposite electrical charges on different ends

Esther Linkage

a covalent chemical bond formed between a carboxylic acid group and an alcohol group

Peptide Linkage

a chemical covalent bond that joins two amino acids together

Primary structure

amino acid sequence, the "sequence" of amino acids, the order in which they are assembled into a polymer, is the first step in determining what a protein will look like and what it can do.

Secondary structure

Hydrogen bonds along the backbone of the same polypeptide: they will interact with each other through hydrogen bonding between the amino and carboxyl groups along the protein backbone

• alpha helix

• Beta Sheet

Tertiary Structure

3D folding of sheets and helices of a single polypeptide

• Interactions between R-groups

  • Hydrogen bonds

  • Ionic bonds

  • Hydrophobic interactions

  • Disulfide bridges

Quaternary Structure

More than one polypeptide chain together in a single structure, the difference between tertiary and quaternary being interactions between different polypeptides instead of between amino acids in the same polypeptide

Big ideas in Biology: Evolution

• ALL organisms evolve from other organisms

• ALL organisms share a common ancestor

Big ideas in Biology: Cell Theory

• ALL cells come from other cells

• ALL life is made of cells

Big ideas in Biology: Regulatory Mechanisms

All processes are regulated

Big ideas in Biology: Energy Transformation

Energy is moved around (comes from somewhere and must go somewhere)

Big ideas in Biology: Emergent Properties

• Small parts combine → NEW form

• New form = new function

Big ideas in Biology: Structure-Function Relationships

“Form follows function”

Components → structure → Function (modify, recombine, to create new functions)

Phagocystosis

cell engulfs and digests large, solid particles like bacteria, dead cells, or debris

Properties of molecules

• determined by size, shape, elements

• react in water

Why are there different types of bonds?

• Not all electron sharing is the same

• Elements differ in electronegativity

= “Ability to attract and keep electrons”

Electronegativity

a measure of an atom's tendency to attract shared electrons toward itself when forming a chemical bond

Dehydration synthesis

Process to build/create polymers

1. Remove H to free up a bond to expose an unpaired electron

2. Polymer and unlinked monomer can link together into a longer polymer

Hydrolysis

• Split the bond and cap off each side with an OH and H

• Adds a water molecule, breaking a bond

Four types of biological macromolecules:

1. Carbohydrates

2. Nucleic Acids

3. Lipids

4. Proteins

Triglycerides

• 1 Glycerol + 3 fatty acids

• Ester linkage

  • Made by dehydration synthesis

• Used to store fat in cells for later use

Fats

• Triglycerides with saturated fatty acids

• No double bonds in fatty acid chains

• Very dense, they are very straight

Oils

• Triglycerides with unsaturated fatty acids

• One or more double bonds in fatty acid chains

• Ditch a couple H’s

  • Liquidy/fluid

Phospholipid bilayer

• Head is hydrophilic

• Tails are hydrophobic

Protein Emergent Properties

• Proteins have complex shapes

• Proteins can change shape

• Enzymes

• Receptors

• Transport proteins

Integral Membrane Proteins

a type of integral membrane protein that is permanently embedded within the phospholipid bilayer of a cell membrane

Peripheral Membrane Proteins

temporarily attaches to the surface of a cell membrane or to other membrane proteins without entering the hydrophobic core of the lipid bilayer

Lipid bilayer

double layered sheet that gives the cell membrane a strong, flexible barrier

Selectively Permeable

select substances or structures can pass through and others cannot

Passive transport

cellular transport that does not use energy

Diffusion

Process by which particles move from high to low concentration until equilibrium is reached

Facilitated diffusion

Process through which molecules pass through special protein channels in the cell membrane without using energy

Osmosis

movement of water through a selectively permeable membrane

Aquaporin

protein channel in the cell membrane that allows water to pass through

Polymerization

linking together smaller molecules to create a bigger structure

About lipids:

• lipids are hydrophobic

Saturated fatty acids

Has no double bonds are straight

Unsaturated fatty acids

Has double bonds → bent or kinked because of it

Groups of saturated fatty acids are more….

Dense (viscous)

Groups of unsaturated fatty acids are more…

Fluid

Phospholipid bilayers are…

the basis for cell membranes

• Hydrophobic tails

• Hydrophilic head

• Amphipathic

What influences fluidity?

• Which molecules the cell chooses to put in its membranes

• Fatty acid saturation

  • Saturated fatty acids → more viscous, less fluid (straight, allows them to pack closer together)

  • Unsaturated fatty acids → more fluid, less viscous (bended, push further parat

• Length of fatty acid tails → tails of adjacent phospholipids can interact with each other through van der Waals interactions, reducing fluidity

Cholesterol is…

• four-ringed steroid molecule (lipid) that modulates membrane fluidity, preventing a bilayer from becoming either too fluid or too viscous

• Adding cholesterol to a viscous membrane makes it more fluid

• Adding cholesterol to a fluid membrane makes it more viscous

Proteins are ___ of amino acids.

polymers

Passes freely through the phospholipid bilayer/membrane

• Small non-polar molecules

  • oxygen gas (O2) or carbon dioxide

→ These are small enough to go between the phospholipid molecules and non-polar so that they do not interact with water in any meaningful, so they can freely move about.

Does not pass freely through the phospholipid bilayer/membrane

• Small polar molecules can't move freely

• can still pass between the phospholipids of the bilayer, although at a slower rate. This includes water itself!

Does not have a reason to leave water

• Larger polar molecules or ions

  • Securely suspended in the hydration shell

→ Even if they were to leave the water, they will not be able to move through the hydrophobic layer of the membrane. These will NOT pass through the membrane without assistance

“Solvent of life”

Water

Rules of diffusion or facilitated diffusion

• If there is a concentration difference across a membrane but no specific transport protein, there will be no diffusion.

• If there is a concentration difference across a membrane that has a specific transport protein for that solute, diffusion will occur.

• Unless something else acts upon the solute, diffusion will continue until equilibrium is reached (same concentration on both sides of the membrane).

Uniport proteins

Simply move one specific solute across the membrane

Coupled transport or co-transport proteins

Move two or even three solutes across the membrane at the same time

Symport proteins

• Move two solutes in the same direction

• Both going into a cell or both going out of a cell

Antiport proteins

• Move two solutes in opposite directions

• One solute will be going into the cell while the other solute is going out.

Two types of transport

1. Active transport (w/ energy)

2. Passive transport (w/o energy)

Facilitated diffusion

• Also called passive transport

• it does require energy expenditure by the cell to move solutes.

Channel proteins

• create a "hole" through which water can pass creating an aqueous pathway through the membrane

• Small solutes like ions (individual atoms) can readily pass through these channels without having to leave the water

Carrier proteins

• carry larger solutes that are too big to pass through a channel protein (more than a few atoms), like sugars or amino acids

• passive transport because the conformational change "just happens" because the energy in the system represented by constant molecular motion

Conformational change

• Anytime anything interacts with a protein that protein will change shape

• if a solute interacts with its specific carrier protein, that protein will change shape and physically carry or push the solute through the membrane