Bio 112 UBC, Biol 112 (Midterm) Flashcards

What does the cell theory state?

1. all organisms are made up of cells

2. cells are the basic units of structure and function in organisms

3. cells come only from preexisting cells because cells are self-reproducing

All cells include what 4 things?

1. DNA

2. Cell membrane

3. Cytoplasm

4. Ribosomes

What is the central dogma?

It's the basic flow of information in a cell, it's the two step process of transcription and translation by which information in the genes flow into proteins.

What is the purpose of the cellular membrane?

To control the movement of materials into + out of the cell

What are the 3 domains of life?

Bacteria, Archaea = prokaryotes

Eukarya = Eukaryotic

What does metabolism mean?

The chemical reaction by which cells convert energy from one form to another

ATP allows cells to do what?

Growth, division + moving substances in and out of the cell

What are some traits of prokaryotic cells?

- Does not have a membrane bound nucleus (it has a nucleoid region)

- Much smaller then Eukaryotic cells

- No organelles

- Different promoter recognition

- DNA is a single circular chromosome

What are some traits of eukaryotic cells?

- Has a membrane bound nucleus

- Cholesterol is present in the cell membrane

- Much larger then Prokaryotic cells

- Contains organelles

- DNA is linear

What are some traits that Prokaroytic and Eukaryotic cells share?

- Contain protein, water and DNA

- Contain Ribosomes

- Has a cellular membrane

What are the 4 major categories of macromolecules in cells?

1. Protein

2. Nucleic Acid

3. Lipids

4. Carbohydrates

What is the monomer of Protein + what is its bond?

Monomer: Amino Acid

Bond: Peptide bond

What is the directionality of protein + the reason for it?

The amino group (of one amino acid) attaches to the carboxyl group of another amino acid

= "N" terminus (is how it starts) to "C" terminus (how it always finishes)

What is the monomer for Nucleic Acid + what is its bond?

Monomer: nucleotides

Bond: phosphodiester bond

What is the directionality of Nucleic Acids?

The phosphate group of one nucleotide covalently bonds to the sugar unit in another nucleotide

5' - 3'

(A 5' attaches to a 3')

What is the monomer for carbohydrates + what is its bond?

Monomer: monosaccharides

Bond: Glycosidic bond

What is the directionality for carbhydrates?

The 4' end is added to the 1' end of the 1st monosaccharide (the should be lined up spout - handle)

What is the monomer for Lipids + what is its bond?

Monomer: Fatty acids

Bond: Ester

What is the directionality of Lipids?

The fatty acid tail is added to the glycerol head (different fatty acids have a different number of tails)

Structure of a nucleotide?

Structure of a Protein?

Structure of a Carbohydrate?

Structure of a Lipid?

What is the difference between a Saturated and a Unsaturated Fat?

Saturated: Will be saturated in C atoms (it has double bonds) = this fat is good

Unsaturated: It is not saturated in C atoms (no double bonds) = this fat is bad

Arrange O,N,C,S,P,H from most - least electronegative.

1. O

2. N

3. C + S

4. P + H

What does it mean when an atom is nonpolar?

The two atoms share electrons equally = there electronegativity is less than 0.4

What does it mean when an atom is polar?

The electrons forming the bond are unequally shared between atoms = one end will have a -'ive charge and one end will have a +'ive charge, the elctronegativity is greater than 0.4

What does amphipathic mean?

having both hydrophilic and hydrophobic regions

When two nonpolar molecules react what kind of dipoles are formed?

ID-ID

When two polar molecules react what kind of dipoles are formed?

PD-PD

Hydrogen bonds are the same as what kind of dipoles?

PD-PD

What 3 molecules indicate polar bonds?

S,O,N

List the dipoles from strongest to weakest.

1. Ionic

2. Ion - PD

3. PD-PD/Hydrogen bonds

4. PD-ID

5. ID-ID

What kind of structures will form when lipids are mixed with water? (3 options)

1. Micelles = lipids with bulky heads + a single fatty acid tails = they are wedge shaped

2.Bilayer = less bulky heads + two hydrophobic tails (kind looks like a sandwich with the tails in the middle)

3. Liposomes = structure that surround a central space (donuts). They are usually formed in a lab and form when the pH of water is similar to that of a cell

How does Thermodynamics + the spontaneous formation of the lipid bilayer work?

The lipid bilayer will formed as long as the concentration of free phospholipids is high enough + the pH of the solution is similar to that of a cell

= This is driven by thermodynamics, towards a stabilizing system

What is entropy + enthalpy?

Entropy: Measure of disorder/randomness of a system

Enthalpy: Sum of the internal energy of a system + the product of the pressure and volume of the system

How does the structure of phospholipids dictate the structure of the lipid bilayer?

They have a hydrophilic head and a hydrophobic tail. Their heads face the water where as their tails face inwards away from the water (creating a sandwich)

Explain membrane fluidity.

refers to the viscosity of the lipid bilayer of a cell membrane or a synthetic lipid membrane. Lipid packing can influence the fluidity of the membrane.

What factors influence fluidity?

1. Temperature (heat up the membrane) = the molecules gain more kinetic energy and thus move around more freely making they membrane more fluid

2. The composition of the membrane = lipids with shorter tails are less stiff and more susceptible to changes in kinetic energy

3. Cholesterol = it stabilizes the membrane and raises it's melting point.

What is the fluid mosaic model?

The idea that lipids + proteins coexist in the membrane and that both are able to move freely in the plane of the membrane.

Arrange the molecules by their permeability across the lipid bilayer (high to low)

1. Small, nonpolar molecules

2. Small, uncharged molecules

3. Large, uncharged molecules

4. Ions

What is selective permeability of biological membranes?

The plasma membrane maintains homeostasis by selective permeability. It lets some molecules in + out freely, other under certain conditions, and prevents some from passing through at all.

What structural features contribute to the selective permeability?

The combination of lipids + embedded proteins = the membrane is composed of a hydrophobic interior and that prevents ions and charged polar molecules from diffusing freely.

Compare and Contrast the transport proteins, carriers vs. channels.

Channel: Provides an opening between the inside and outside of the cell within which certain molecules can pass (some are gated and open in response to some sort of chemical or electrical signal)

Carrier: Binds to and transports specific molecules = it has two conformations.

1. Open to one side of the cell

2. Open to the other side of the cell

What is the difference between diffusion and osmosis?

Diffusion: Spontaneous movement of particles from an area of high concentration to an are of low concentration

Osmosis: Spontaneous movement of water across a semipermeable membrane (water moves from an area of low concentration of solute to high concentration of solute)

What are some strategies to deal with osmotic pressure?

Plants: Contract Vacuole = take up excess water from inside the cell and expel it into the environment

Eukaryotic: Cholesterol = stabilizes the membrane making it less permeable to water

Explain Simple diffusion.

- Passive transport

- Random movement of molecules

- Substances move from higher concentration to lower concentration

Explain facilitated diffusion.

- Move by diffusion through membrane proteins and by passes the lipid bilayer

- Random movement of molecules

- Needs a concentration difference

Explain Active transport.

- Move molecules from areas of lower concentration to areas of higher concentration (against the concentration gradient)

- Uses energy (ATP) since its moving "uphill"

What is an induce dipole?

ID are fleeting and only occur in non-polar molecules due to random unequal distribution of electrons (which is why hydrophobic molecules participate in ID-ID interactions)

What are permanent dipoles?

Polar molecules for PD, it is when there is a large difference in electronegativity. As one end with be slightly +'ive and the other slightly -'ive.

What kind of bond are hydrogen bonds the same as?

PD-PD

Why does increasing the length of a fatty acid chain increase its melting point?

There is more intermolecular interaction and it takes more energy to break the vanderwaal interactions.

List the bonds from strongest to weakest

1. Covalent

2. Ionic

3. Ion - PD

4. PD - PD/hydrogen bonds

5. PD - ID

6. ID - ID

Molecule that has a molecular group with a polar bond is overall considered?

Hydrophilic (polar bonds are hydrophilic because water is polar)

When two atoms are involved in a polar covalent bond, what is the charge on each?

One has a permanent partial +'ive and the other a permanent partial -'ive

When two atoms are involved in a nonpolar covalent bond what is the charge on each atom?

Both atoms fluctuate between partial +'ive and -'ive charge

Name the different ways that the cell can adapt to deal with osmotic pressure.

- Stay small

- Change shape (increase SA to Volume ratio)

- Compartmentalize

- Get things moving (cytoplasmic streaming)

Cell size adaptation - Dilution

- Compartmentalization in eukaryotic cells (membrane enclosed regions for specific functions)

Cell size adaptation - Surface area to Volume ratio

- Folding to increase surface area

Ex: Microvilli in intestines

Cell size adaptation - Diffusion

- Cytoplasmic streaming in plant cells (proteins move the cytoplasm)

- Vesicle trafficking in animal cells (microtubules)

What are 3 factors that control cell size?

1. Rate of diffusion

2. Dilution

3. Surface area to volume ratio

What is the hydrophobic effect?

The burying of non-polar groups away from water. (The entropy of water increases)

What is entropic stability?

Water is motionally free = in a stable system water is motionally free and the lipids are more restricted

What do you need to know for thermodynamic? (Comparing)

- More vs. Less stable

- Spontaneous vs. Non-Spontaneous

- ∆G negative vs. positive

- Strongly bonded vs. Less strongly bonded

- Motionally free vs. Motionally restricted (water)

How can molecules diffuses through the lipid membrane?

The lipids are not covanlently bonded together, they move (vibrate) and spaces can open up allowing certain molecules to pass through

At equilibrium has everything stopped moving?

No, the molecules are still moving back and forth but at the same rate.

List the molecules from most to least likely to diffuse.

1. Small non-polar molecules

2. Small uncharged polar molecules

3. Large uncharged polar molecules

4. Ions

If Ions are small why can they not diffuse easily through the lipid bilayer?

They are charged and they have a hydration shell the surrounds Ions making them bigger + bulkier

Which one of the following amino acids is capable of forming a disulfide linkage with itself?

tyrosine

cysteine

arginine

methionine

isoleucine

Cysteine

What is the directionality of nucleic acids?

5' to 3'

What is the directionality of proteins?

N-terminus to C-terminus

What is the directionality of carbohydrates?

4' to 1'

What are the various roles of proteins in cellular activities?

Structural support, enzymatic activity, transportation, communication with the outside world.

What are the R groups of amino acids that are hydrophobic?

- Alanine

- Valine

-Leucine

- Isoleucine

- Methionine

- Phenyalanine

- Trytophan

- Tyrosine

What are the R groups of amino acids that are hydrophilic?

- Asparagine

- Glutamine

- Serine

- Threonine

- Lysine

- Arginine

- Histidine

- Aspartic Acid

Glutamic acid

What are the traits of the primary protein structure?

The unique order in which the amino acids are linked together to form a protein (a "straight" line)

What are the traits of the secondary protein structure?

The chains coils or folds, either an alpha helix or a beta pleated sheet

What are the traits of the tertiary protein structure?

The comprehensive 3-D shape, which is determined by the interactions between the amino acid and the R group (also different bonds effect it like ionic, hydrogen and van der Waal forces)

Predict the locations of different types of amino acids within a protein's folded structure based on their R-group features

The amino acids whose R-groups from bonds with each other may be far apart in the polypepetide chain, but can end up near eachother in the folded protien.

What is denaturation and what effect does it have on the protein structure?

Is a process that causes a protein to lose its shape (often caused by heat, chemical treatment and heavy metals). It disrupts the bonds holding the tertiary structure together and they lose their functional activity.

How to enzymes increase reaction rates?

They reduce the activation energy requires to start the chemical reaction.

What are allosteric enzymes?

They are regulated by molecules that bind at sites other than their active site (They are also a KEY function in metabolic pathways)

What are competitive inhibitors?

Molecules that bind to the active site of an enzyme and inhibit the ability of the substrate to bind.

What are noncompetitive inhibitors?

bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

How do enzyme inhibitors regulate enzyme activity?

When there is too much product the inhibitors are "turned on" to prevent the molecule from creating an excess of product. They help maintain homeostasis

Cell Theory

Summary:

Describes cells as the fundamental unit of life.

Critical Components:

1. Cells are the basic unit of life.

2. All living organisms are composed of cells.

3.Cells arise from pre-existing cells.

Characteristics of Cells

Definition:

Cells as the smallest unit of life.

Key Characteristics:

Metabolism

Reproduction

Genetic material

Evolutionary adaptation

Response to stimuli

Homeostasis

Cellular organization

Comparison: Bacterial vs. Eukaryotic Cells (structure)

Structural Properties:

Bacterial Cells: Lack membrane-bound organelles, circular DNA.

Eukaryotic Cells: Have membrane-bound organelles, linear DNA in nucleus.

Comparison: Bacterial vs. Eukaryotic Cells (chromosomal structure)

Bacterial Cells: Single circular chromosome.

Eukaryotic Cells: Multiple linear chromosomes within the nucleus/

Endosymbiotic Theory

Suggests that eukaryotic organelles like mitochondria and chloroplasts originated as independent prokaryotic organisms that were engulfed by ancestral eukaryotic cells.

Compare and Contrast population growth phases in terms of division rate and cell survival.

Lag Phase:

Division Rate: Slow or negligible.

Cell Survival: High, cells adapt to new environment.

Exponential (Log) Phase:

Division Rate: Rapid, cells divide at maximum rate.

Cell Survival: High, optimal conditions support growth.

Stationary Phase:

Division Rate: Equilibrium, birth rate equals death rate.

Cell Survival: Stable, limited nutrients and waste accumulation.

Death Phase:

Division Rate: Declining, death rate exceeds birth rate.

Cell Survival: Decreasing, conditions become inhospitable.

Lag Phase

"flat" period of adjustment, enlargement; little growth

exponential phase

Cells in this phase are typically in the healthiest state

Stationary Phase

period of equilibrium; microbial deaths balance production of new cells

Death Phase

as limiting factors intensify, cells die exponentially

Population Growth Curve

a graph that shows the change in population size over time

Growth in Prokaryotic Organisms

Means getting bigger and making more copies of itself.

Individual Cell Growth

Each cell gets bigger and duplicates its parts.

Division of Individual Cells:

One cell splits into two new cells.