Biology Final: Semester 1

Question 1

Know the 9 most common elements in living systems (SPONCHNa CaFé) and know a function/ role for each

Answer 1

Sulfer: Formation of some amino acids
Phosphorus: Formation of phospholipids/ nucleotides/ ATP/ nucleic acids
Sodium: Membrane function, osmoregulation, sending nerve impulses
Calcium: Enzyme co-factor, cellular messenger, formation of bones/ teeth, nerve transmission, muscle contraction Iron: In cytochromes and hemoglobin
Carbon: forms the foundation of ALL four classes of organic compounds, can form 4 covalent bonds
Hydrogen: structural component of ALL four classes of organic compounds; reducing agent in photosynthesis and cellular respiration
Oxygen: used in aerobic respiration in cells
Nitrogen: formation of amino acids, nucleotides, and ATP

Question 2

Know the four most common elements in living systems (CHON) and a function/ role for each

Answer 2

Carbon – forms the foundation of ALL four classes of organic compounds, can form 4 covalent bonds
Hydrogen – structural component of ALL four classes of organic compounds; reducing agent in photosynthesis and cellular respiration
Oxygen – used in aerobic respiration in cells (to make ATP = Adenosine Triphosphate, the cell’s “energy” molecule)
Nitrogen – formation of amino acids (which make up proteins), nucleotides (which make up nucleic acids (DNA/ RNA)), and ATP

Question 3

+++Explain and diagram the structure of water molecules (and how other water molecules interact with another)

Answer 3

A polar molecule: The opposite ends of the molecule have opposite charges (dipolarity)
Polar covalent bonds form WITHIN water molecules (between oxygen and hydrogen atoms)
Unequal sharing of electrons
Due to electronegativity of oxygen
Oxygen becomes slightly negatively charged, and hydrogen atoms become slightly positively charged
The polarity of water molecules allows them to form hydrogen bonds with other water molecules (up to 4 per molecule) and with other polar (charged) substances

Question 4

Thermal Properties of Water (Due to Hydrogen Bonds)

Answer 4

1. High Specific Heat (Water can absorb or give off A LOT of heat without changing its own temperature very much)
   Specific heat: the amount of heat that must be absorbed or lost for 1g of a substance to change its temperature by 1 degree Celcius. It is a measure of how well a substance resists changing its temperature when it absorbs or releases heat.
   The specific heat of water is 1 cal/g/ºC, which is extremely high
   Why so high?!?
   HYDROGEN BONDS! Hydrogen bonds absorb heat and break. Hydrogen bonds also release heat when they form.
   As water molecules absorb heat, the hydrogen bonds between these molecules break before the water molecules themselves can begin absorbing heat and moving faster. Therefore, water molecules can absorb much more heat before their total kinetic energy – due to motion – is impacted by the heat absorption, allowing bodies of water to gain large amounts of heat without changing its own temperature very much!
2. High Heat of Vaporization (Water molecules absorb A LOT of heat when they evaporate)
   Evaporation (or vaporization) is transformation of a substance from liquid to gas
   Heat of vaporization is the amount of heat a liquid must absorb for 1 g of it to be converted to gas
   Water has a HIGH heat of vaporization because of its… HYDROGEN BONDS!
   A great deal of heat must be absorbed by water in order to break the hydrogen bonds between the molecules before any individual molecules can absorb enough heat to “escape” and move into the air.
   Why is this important to life? Because it causes EVAPORATIVE COOLING: The “hottest” (fastest) molecules at the surface evaporate and take the absorbed heat (heat is absorbed from the body heat/ surface of the organism) with them, thus the new surface molecules that remain cool down (and cool the organism).
   Transpiration (in plants), panting/ sweating (animals)

Question 5

Adhesive Properties of water

Answer 5

Adhesion (the chemical attraction of one substance to a different substance) is also an important property of water
As it travels up the xylem (vascular tissue in plants), water forms hydrogen bonds with the cell walls (cellulose) of plants, helping to counter the effects of gravity (capillary action) as water molecules move up through a plant

Question 6

Proverties of water compared to methane

Answer 6

Water and methane differ in thermal properties despite having similar structures (comparable weight, size, valence structure)
The differences are due to the polarity of water and its capacity to form intermolecular hydrogen bonds
Formula: CH4 H2O
Polarity: Nonpolar Polar
Heat Capacity –1 –1 (J.g .oC ): 2.2 4.186
Boiling Point (oC): -161 100

Question 7

Solvent Properties of water

Answer 7

Water is a versatile solvent due to its POLARITY
“Like dissolves like” – Water dissolves:
The majority of all molecules found inside of and surrounding cells are polar (charged) – carbohydrates/ proteins/ nucleic acids/ enzymes
Inorganic charged particles (ions – ie: Na+, K+, Cl-)
Because water dissolves almost all of the molecules and particles needed for life, it is involved in almost all of chemical reactions in living organisms – it is the medium for metabolic reactions.

Question 8

Explain the properties of water that are significant to life (and be able to compare these properties to methane)

Answer 8

The Structure of Water Provides it with Four Properties Which are Extremely Important to ALL Life as We Know It!
1. Cohesive Properties
2. Adhesive Properties
3. Thermal Properties
4. Solvent Properties

Question 9

Cohesive Properties of water

Answer 9

Collectively, hydrogen bonds connect water molecules to other water molecules. The linkage of the same type of molecule by multiple hydrogen bonds is called cohesion, which:
1. Helps the transport of water against gravity in xylem of plants
Transpiration (evaporation of water from stomata) causes a “tug” on water molecules in the leaves, stems, and all the way down to the roots of plants, forming a water “column” through the vascular tissue (xylem) of plants
2. Causes spilled water to form into droplets
3. Allows water to have a high surface tension (certain organisms can live on
water surface)
4. Causes water to have a high boiling point (remains a liquid rather than a gas over global temp. range)

Question 10

Know the cell theory (including evidence to support it and exceptions to refute it)

Answer 10

1. All organisms composed of one (or more) cells
2. Cells are the smallest units of life
3. ALL cells come from pre-existing cells

Evidence:
-Living cells can be visualized using microscopes (since the 1600’s)

-No living organisms identified (to date) that are not made up of at least one cell

-Experimentation

Question 11

Know the 7 basic functions of all life

Answer 11

Metabolism – chemical reaction that release energy for cellular use

Response – respond to internal/external stimuli

Homeostasis – maintain stable internal conditions

Growth – increase in cell size or cell number, grow/develop

Reproduction – produce more offspring/cells – sexually or asexually

Excretion – remove waste products

Nutrition – obtain energy/materials from environment

Question 12

Know how to calculate cell sizes

Answer 12

(Mag = Manification size/ Actual size)

Conversions:
m to mm : 1 to 1000
m to cm: 1 to 100
m to um: 1 to 1x10^6

Question 13

Explain the significance of surface area/ volume ratio to cells (and be able to explain what happens to this ratio as cell size increases/ decreases and identify this on a graph)

Answer 13

To Maintain a HIGH Surface Area to (low) Volume Ratio (SA/ V)
In general, as cell size increases, the surface area to volume ratio decreases (which is a bad thing) – WHY?
MORE surface area = more nutrients, oxygen etc. IN that the cell needs, and more wastes/ excess heat OUT that the cell does not need
So, cells “want” to maximize surface area (increased rate of material exchange)
The mass/ volume ratio of a cell determines the rate of heat and waste production and consumption of resources (metabolic reaction rate)
So, cells “want” to minimize volume (smaller volume = faster metabolic reaction rates)
Cells with more surface area PER unit of volume are able to move more wastes and heat out of the cell and more resources into the cell per unit of volume (making these cells more effective)
As a cell grows, its volume increases faster than its surface area, which decreases the SA/V ratio.
If metabolic rate is greater than exchange rate (nutrients/ wastes) the cell will eventually die
When cells become too large they divide (mitosis) to restore large SA/ V ratio to survive

Question 14

Know what stem cells are, what characteristics they have that are important to life/ medicine, and how they differentiate (in multicellular organisms)

Answer 14

Stem cells are undifferentiated/ unspecialized cells with 2 key characteristics:
1. They can differentiate (into specialized cells)
2. They can continuously divide/ replicate (self renewal)

All cells in an early developing embryo are stem cells and are termed “totipotent”/ pluripotent” (toti = all, potent = potential, pluri = more), meaning that they are able to divide and become any type of cell (an important function in a developing embryo)
After birth (or germination in plants), only certain populations of stem cells remain, but with limited abilities. Stem cells post-birth/post-germination are only able to differentiate into tissue-specific cells within an organism (they are multipotent; multi = many)
Some cells in multicellular organisms lose the ability (or have a diminished ability) to reproduce once they differentiate during development

Example: Stargardt’s Disease
An inherited form of juvenile macular degeneration that causes vision loss to the point of blindness
Caused by a gene mutation that causes photoreceptor cells (rods/ cones) in retina to degenerate
Treated by replacing dead cells in the retina with functioning ones derived from stem cells

Question 15

Be able to explain the process of therapeutic stem cell therapy

Answer 15

Stem cells can be used to replace damaged/ diseased tissues with healthy/ functioning cells
Therapeutic Stem Cell Therapy Process:
1. Expose stem cells to biochemical solutions in a lab to trigger their differentiation into the desired cell type
2. Surgically implant new cells into patient’s tissue
3. Suppress patient’s immune system to prevent rejection (if cells are from foreign source)
4. Monitor new cells for cancerous activity

Question 16

Be able to discuss (both sides) the ethics of stem cell research

Answer 16

Ethical issues depend on the source of stem cells:
Using adult tissues is effective, but limited in application
Stem cells from newborns must be stored (at cost) – only those with the means for this benefit from it (issues of access/ availability)
Embryos provide the greatest amount of pluripotent stem cells, but acquiring them destroys a potential life, so…
When does life begin?
Does using embryonic stem cells “end” a life?
Is it better for excess embryos to be donated to science or to be disposed of as biohazard waste?
Which life is more valuable – that of an embryo with all of its potential or that of a human being already living its potential?
Is the suffering of an individual less important than the loss of an embryo?
Is the suffering of an embryo less important than the loss of an individual?
Are a human embryo and an individual equally important forms of life?

Question 17

Know the characteristics of ALL cells

Answer 17

ALL cells (whether they are prokaryotic or eukaryotic):
Have a plasma (cell) membrane (phospholipid bilayer)
Contain a semifluid substance called cytoplasm/ cytosol (metabolic reactions)
Have one or more chromosomes (genes - DNA)
Have ribosomes (organelles that make proteins – NO membranes and made up of 2 subunits)

Question 18

Compare prokaryotic and eukaryotic cells (similarities and differences)

Answer 18

Differences:
Prokariotic: DNA is naked (no proteins)
DNA is circular
DNA in nucleoid
DNA does NOT contain introns
No membrane-bound organelles/ no mitochondria
70S ribosomes
Smaller (size less than 10um)

Eukaryotic: DNA associated with proteins (histones)
DNA is linear
DNA in nucleus
DNA contains many introns
Membrane-bound organelles/ mitochondria
80S ribosomes
Larger (size more than 10um)

Similarities:
Both have DNA
Both have a cell membrane
Both have cytoplasm/ carry out all functions of life
Both contain ribosomes

Question 19

Know which organelles are present in what cells and their functions (connect what organelles do to the difference processes that we have learned about this semester) also be able to answer questions about if an organelle is absent in a type of cell what will it be able to do and what will it not be able to do

Question 20

Compare animal and plant cells (similarities and differences)

Answer 20

Differences:
Animals:
No cell walls (flexible/ rounded shape)
Centrioles
No chloroplasts
Small (if any) vacuoles
Carbohydrates stored as glycogen
Cholesterol in cell membrane

Plants
Cell walls (fixed, angular shape)
No centrioles
Chloroplasts
Large, central vacuoles
Carbohydrates stored as starch
No cholesterol in cell membrane

Similarities:
Similarities:
Both have DNA
Both have a cell membrane
Both have cytoplasm/ carry out all functions of life
Both contain ribosomes

Question 21

Be able to draw/ identify prokaryotic cells, plant cells, animal cells, and their organelles.

Answer 21

Use notes

Question 22

Explain the endosymbiotic theory (including the characteristics of mitochondria and chloroplasts that SUPPORT, not prove, it)

Answer 22

Theory States:
~2 billion years ago, a prokaryotic cell was engulfed (endocytosis) by primitive predatory/ heterotrophic cell
Symbiotic relationship formed (both benefited – mutualism), so both remained as ONE cell
- Euk. cells evolved from Prok. Cells!!!
MITOCHONDRIA and CHLOROPLASTS:
(These organelles ARE evidence for this theory!)
Have two membranes (original one and second one formed through endocytosis)
Have their own ribosomes (70S)
Divide by binary fission (independently of “host” cell)
Have their own DNA (circular/ naked)
About the same size as bacterial (prokaryotic) cells

Question 23

Be able to diagram the cell membrane (2D only)

Answer 23

Use notes

Question 24

Explain the properties of phospholipids that maintain the cell membrane

Question 25

Know the functions of membrane proteins (in general)

Question 26

Exocytosis (active)

Answer 26

Substances produced inside the cell (or its organelles) are processed and packaged in vesicles (surrounded by a phospholipid bilayer), which will fuse with the cell membrane and release their contents to the extracellular space (requires ATP)
In exocytosis: (hint: exo = “exit”)
Proteins produced by the rough endoplasmic reticulum are packaged in vesicles which “bud off” of the RER
Vesicles travel to the cis (same facing) side of the golgi apparatus and fuse with the membrane, “dumping” their contents into the golgi
Proteins move through the golgi and are processed/ modified. When they reach the trans (opposite) side of the golgi they are packaged into more vesicles which “bud off” the golgi
Vesicles move from the golgi to the cell membrane, fuse (phospholipid bilayer join) with membrane, and “dump”/ expel their contents out of the cell/ into the extracellular space (resulting in secretion of their contents from the cell and a slightly larger cell membrane)
Note: The fluidity of the cell membrane is essential to vesicle fusion (and subsequent secretion)
Examples of exocytosis: insulin (hormone) secreted from pancreatic cells; neurotransmitters secreted from neurons into synapse

Question 27

Endocytosis (active)

Answer 27

The fluidity of the membrane allows it to change shape so parts of it can be “pinched off” (an infolding of the cell membrane) to form vesicles (small, membrane-bound structures in cells) around larger molecules/ fluids/ structures to move them into the cell (endocytosis)
When a vesicle enters a cell, the ends of the membrane that are left (where the membrane was pinched off) reattach due to the presence of water and the properties (hydrophilic and hydrophobic) of the phospholipids (this makes the cell’s membrane slightly smaller)
Phagocytosis is intake of large particles/ molecules/ organisms (“cell eating”)
Pinocytosis is intake of fluids (“cell drinking”)

Question 28

Active Transport:

Answer 28

Active (against concentration gradient, ATP is required):
Substances move from areas of low concentration to areas of high concentration through protein pumps (against a concentration gradient)
Note: in active transport molecules are moved “against nature,” so energy – ATP – is required to make this happen
Examples: glucose reabsorption in kidney, glucose absorption in small intestine (ileum)

Question 29

Simple Diffusion (passive)

Answer 29

Substances move from areas of high concentration/ high osmolarity (hypertonic solution) to areas of low concentration (hypotonic solution) to balance them out = move toward equilibrium (isotonic) – DOWN a concentration gradient
Note: diffusion is either directly through the phospholipid bilayer or through non-specific protein channels only gases, hydrophobic molecules and small polar uncharged molecules can do this (polar molecules and charged molecules cannot do simple diffusion)

Question 30

Facilitated Diffusion

Answer 30

Diffusion of large molecules/ ions through highly specific protein carriers/ channels (proteins change shape to “facilitate” this – rate of transport levels off with saturation of proteins)

Question 31

Osmosis (passive)

Answer 31

Osmosis (H2Osmosis!): Diffusion of water across membrane (through special protein channels called aquaporins); often to balance out solute concentrations (water moves from areas of low (hypotonic) solute concentration (high water) to areas of high (hypertonic) solute concentration (low water) to balance the solutes out)

Question 32

Passive transport mechanisms
Include examples of each and be able to describe concentration gradients (hypertonic, isotonic, hypotonic).

Answer 32

Passive (along concentration gradient, no ATP expenditure):

concentration gradients:
Hypertonic: High solute concentration (gains water)
* Hypotonic: Low solute concentration (loses water) * Isotonic:Samesoluteconcentration(nonetflow)

Question 33

Be able to explain the Daveson-Danielli model of a membrane and the evidence that falsified it.

Answer 33

In 1930s, Davson & Danielli first proposed the the “lipo-protein” sandwich model – lipid layers in between proteins layers
Because protein appears dark and lipids appear light in electron micrographs
This was the model accepted most widely for 30 years

Question 34

Know why cells divide/ how cell division is important to life (and the overall result of mitosis)

Answer 34

4 main reasons cells divide:
Tissue Repair/ Replacement:
If tissues are damaged or infected by bacteria/ viruses etc. their cells can be replaced by healthy cells
Cells/ tissues do not “live” forever and must be replaced as they get old and worn out
Organism Growth: As organisms grow, they need new cells and more cells
Asexual Reproduction: binary fission in bacteria/ vegetative propagation (stem cuttings) in some plants
Development from a fertilized egg (embryonic development)

Other reasons cells divide:
Maintaining a large SA/V ratio (cells divide when this ratio becomes too small)

Cell division is part of the cell cycle, the life of a cell from formation to its own division (from one cell into 2 identical daughter cells)

Question 35

What occurs during interphase of the cell cycle?

Answer 35

• DNA is uncondensed (chromatin)
• DNA is replicated (S phase) to form
  genetically identical sister chromatids
• Cell grows in size and organelles are
  duplicated (G1 and G2)

Question 36

What occurs during metaphase of the cell cycle?

Answer 36

• Centrosomespindlefibresattachto the centromere of each chromosome
• Spindle fibres contract and move the chromosomes towards the cell centre
• Chromosomes form a line along the equator (middle) of the cell

Question 37

What occurs during anaphase of the cell cycle?

Answer 37

• Spindlefibrescontinuetocontract
• Sister chromatids separate and move
  to opposite sides of the cell
• Sister chromatids are now regarded as two separate chromosomes

Question 38

What occurs during cytokinesis of the cell cycle?

Answer 38

• Cytoplasmic division occurs to divide
  the cell into two daughter cells
• Each daughter cell contains one copy of each identical sister chromatid
• Daughter cells are genetically identical

Question 39

What occurs during telophase of the cell cycle?

Answer 39

• Chromosomes decondense (DNA forms chromatin)
• Nuclear membranes form around the two identical chromosome sets
• Cytokinesis occurs concurrently

Question 40

What occurs during prophase of the cell cycle?

Answer 40

During prophase the centrosome divides into two centrosomes
Each of the two centrosomes move to opposite ends of the cell as they make microtubules (the mitotic spindle), which will grow out of them
Chromatin (DNA and protein in the nucleus) condenses, forming visible chromosomes (made up of sister chromatids connected together at the centromere, as they have already been duplicated)
The nucleolus disappears and the nuclear membrane breaks down/ disappears

Question 41

Be able to outline the stages of the cell cycle (in order) and be able to describe what happens in each.

Answer 41

The cell cycle (whether being used for asexual reproduction or somatic (body) cell production) consists of two phases:
Interphase
Cells spend MOST of their “lives” in this phase
Growth, protein production, ATP production, and copying of chromosomes – DNA replication – in preparation for division
Mitotic (M) Phase (mitosis and cytokinesis)
Mitosis = division of the nucleus
Cytokinesis = division of the cytoplasm

Question 42

Be able to calculate the number of chromosomes/ chromatids in a haploid (gamete) or diploid (somatic) cell based on given information on number of chromosomes

Answer 42

Mitotic Index = Cells in mitosis*/ Total number of cells

Interphase, Prophase, metaphase: 2n
Anaphase: 2n -> 4n
Telophase, cytokinesis: 4n

Question 43

Describe controls of the cell cycle

Answer 43

A cell cycle contains numerous checkpoints that ensure the fidelity and viability of continued cell divisions
G1 checkpoint
* Monitors potential growth conditions (nutrients, etc.)
* Assesses level of DNA damage (from UV, etc.)
G2 checkpoint
* Monitors state of pre-mitotic cell (suitable size, etc.)
* Identifies and repairs any DNA replication errors
Metaphase checkpoint
* Ensures proper alignment (prevents aneuploidy)

How cyclins control cell cycle:
Cyclins (protein) bind to cyclin-dependent protein kinases (CDK’s) to activate them
CDK’s are enzymes (end in “-ase”) that control chemical reactions that allow a cell to move into the next phase
Cyclin/ CDK complexes bind to target proteins and activate them via phosphorylation to cause an “event” that moves the cell into the next phase of the cell cycle
Cyclins are degraded after “event” and CDK’s become inactive again
Different cyclins are produced at different times and bind to specific CDK’s to ensure cell cycle occurs in proper sequence/ at normal rate – cyclins are ONLY in high amounts when their target protein is needed for function/ progression in cell cycle (they are highly regulated)
Some cells “pause” after G1 and do NOT enter S-phase and enter G0 (non-growing/ amitotic) instead.
Damaged cells/ DNA
Muscle cells, nerve cells

Question 44

Cancer is uncontrolled cell division
Be able to identify what cancer can result in (continued uncontrolled cell division)

Answer 44

Cancer is uncontroled cell devision
Uncontrolled cell division → tumors result from uncontrolled cell divisions
Cancer cells do not respond to cell cycle regulators and divide uncontrollably (usually at a faster rate too)
Mutagens: something that changes genetic material (causes a mutation) → if it is known to lead to cancer, we refer to it as a carcinogen (see next slide)
Oncogenes: gene that has the potential to lead to cancer
Proto-oncogenes: make proteins that stimulate the cell cycle and promote cell growth and proliferation
Tumor suppressor genes: make proteins that represses cell growth progression and promote apoptosis (cell death) when activated
Benign tumor: if abnormal cells remain at the original site (primary tumor) and/ or they are contained within a membrane
Malignant tumor: if abnormal cell invade surrounding tissue they are a malignant tumor
If they reach blood vessels, abnormal cancer cells can move or metastasize to other parts of the body where they can form secondary tumors (brain tumor made up of breast cancer cells)

Question 45

In general, explain condensation and hydrolysis

Question 46

Be able to diagram a section of DNA (including labeling one nucleotide, 5’ and 3’ ends, and all of the bonds)

Answer 46

See Notes

Question 47

Know the function of DNA

Answer 47

DNA (deoxyribonucleic acid) is a molecule that carries genetic information for the development and functioning of an organism
DNA is the building block of life

Question 48

Know what a nucleosome is (and its structure) and understand that nucleosomes are the fundamental unit of DNA packaging in eukaryotic cells (also important in gene expression/ transcription regulation)

Answer 48

DNA (deoxyribonucleic acid) is a type of organic molecule called a nucleic acid
Nucleic acids are made up of subunits (monomers) called nucleotides

Each nucleotide is made up of three parts:
1. A phosphate group covalently (phosphodiester bond) bonded to
2. A sugar (pentose) molecule covalently bonded to
3. A nitrogenous (nitrogen-containing) base

Nucleotides are linked together to form macromolecules (polymers) called nucleic acids. The nucleic acids in living systems are:
1. DNA (Deoxyribonucleic Acid) – genetic information
2. RNA (Ribonucleic Acid) – genetic information
3. ATP (Adenosine Triphosphate) – energy

The first structure involved in DNA packaging/ coiling is the nucleosome
In a nucleosome:
8 histone proteins (+ charged) make a core
A DNA strand (- charged) wraps around the core twice
A 9th histone protein (H1) attaches to hold the
DNA in place around the core

Many nucleosomes form along a single molecule of DNA, and resemble “beads on a string”
Single “strings” of DNA between nucleosomes are called “linker DNA” (because they “link” one nucleosome to the next)

Question 49

Know that Rosalind Franklin’s x-ray diffraction images showed that DNA is a helical structure.

Answer 49

Final model built was influenced by the work of Rosalind Franklin
X-ray diffraction/ X-ray crystallography using crystallized DNA molecules
X-ray beams pass through crystallized DNA (for tens of hours) and diffract (spread) when they hit atoms (or other objects) and their scattering pattern is recorded on a special film
The scattering pattern produces an image
Helical shape could be deduced from it

Question 50

Be able to explain the Hershey-Chase experiments and results.

Answer 50

Viruses (T2 bacteriophage) were grown in one of two isotopic mediums in order to radioactively label a specific viral component
Viruses grown in radioactive sulfur (35S) had radiolabeled proteins (sulfur is present in proteins but not DNA) → this labeled the protein
Viruses grown in radioactive phosphorus (32P) had radiolabeled DNA (phosphorus is present in DNA but not proteins) → this labeled the DNA

The viruses (phages) were then allowed to infect a bacterium (E. coli)
Then the virus and bacteria were separated via centrifugation
The larger bacteria formed a solid pellet while the smaller viruses remained in the supernatant (liquid)
The bacterial pellet was found to be radioactive when infected by the 32P–viruses (DNA) but not the 35S–viruses (protein) → bacteria contained the radioactive DNA
This demonstrated that DNA, not protein, was the genetic material because DNA was transferred to the bacteria

Question 51

Compare the structure of DNA and RNA

Answer 51

DNA and RNA are both polymers of nucleotides, however they differ in a few key structural aspects
DNA:
Sugar is deoxyribose
Has thymine (T) (along with A, C and G)
Is double stranded (forms a double helix)
RNA:
Sugar is ribose
Has uracil (U) (along with A, C and G)
Is single stranded

Question 52

Know WHY cells replicate DNA

Answer 52

When cells in your body divide (during mitosis) your DNA must first be copied exactly so that each new cell has its own complete set of DNA too (S-phase of interphase)

Question 53

Know the steps of DNA replication (including the overall direction and the limitations of DNA polymerase)

Answer 53

DNA replication is semi-conservative and occurs in a 5’ to 3’ direction and each strand acts as a template for a new strand
Double helix structure is unwound (unzipped) by Helicase
Helicase separates the two strands of DNA by breaking the hydrogen bonds between the complementary bases
Once helicase has uncoiled the molecule, the area is known as the replication bubble (which is initiated at the origin of replication - characterized by certain sequence of nucleotides)
Gyrase/ topoisomerase and single-strand binding proteins (SSBs) binds to unwound portion of DNA to stabilize single strand (helps to relieve strain during uncoiling)
DNA primase adds RNA primer that is complementary to exposed DNA bases on each parent strand (adenine, uracil, cytosine, guanine) which creates an attachment point for DNA polymerase III
5. DNA polymerase III adds free nucleotides (dNTPs) to the 3’ end of the RNA primer, creating a new strand in a 5’ to 3’ direction following the complementary base pairing (adenine to thymine (uracil), cytosine to guanine)
Note: DNA polymerase cleaves the two excess phosphates of the dNTP and uses the energy released to link the nucleotide to the new strand
On the leading strand: DNA polymerase III moves towards to replication fork and builds a continuous strand
On the lagging strand: DNA polymerase III moves away from the replication fork and builds short chains of DNA called Okazaki fragments
6. DNA polymerase I removes the RNA primer and replaces it with DNA
7. On the lagging strand, Okazaki (DNA) fragments are joined together by DNA ligase
8. Proofread→ mistakes are likely because of the rate of replication (4000 nucleotides/ second) so DNA polymerase will proofread its work and remove and replace any bases that are in incorrect in the hopes of avoiding mutations
Replication bubbles elongate in both directions as the DNA is replicated and eventually fuse, forming two, new identical daughter molecules of DNA.

Question 54

Explain and know the significance of the Meselson-Stahl experiments (semiconservative replication)

Answer 54

The Meselson-Stahl experiment supported the theory that DNA replication occurred via a semi-conservative process
They incorporated radioactive nitrogen isotopes into DNA
* Templates were prepared with heavier 15N
* New sequences were replicated with lighter 14N
The DNA was then separated via centrifugation in order to determine its composition of radioisotopes
* 1st division: DNA had 15N and 14N (i.e. mixed)
* 2nd division: DNA is mixed or has 14N only
The results were consistent with a semi-conservative model

Question 55

Know and describe the central dogma of molecular biology (all the steps- from DNA all the way to protein)

Answer 55

Transcription – making mRNA (messenger RNA) from DNA
Translation – making a polypeptide chain – a protein - (putting amino acids together) from mRNA
Amino acids are put together using the genetic code – universal to ALL life (uses mRNA bases in sets of 3, called codons)!

Question 56

Know the steps of transcription (including the direction and difference between the sense/ antisense DNA strands)

Answer 56

Transcription (making mRNA from DNA) happens in a 5’ to 3’ direction, and it happens in three stages:
1. Initiation
2. Elongation
3. Termination

Transcription is the process of synthesizing mRNA identical to the coding (sense) strand of DNA
The antisense strand acts as the template strand
DNA will be unzipped, RNA nucleotides will be added → creating an mRNA strand
mRNA will be processed before moving to the ribosome for translation

Initiation:
RNA Polymerase binds to a gene in DNA at a region/ sequence called the promoter (“start here”)

Enlogation:
RNA Polymerase unwinds the DNA double helix (breaking hydrogen bonds between bases)
This exposes DNA bases for pairing with RNA nucleotides
RNA Polymerase reads the DNA sequence of the gene (on the antisense/ template strand)
Uses it to add free RNA nucleotides together (5’ to 3’) to make a molecule of mRNA (complementary to the antisense/template strand of DNA; adenine and uracil, cytosine and guanine)
Hydrogen bonds form between A&U and C&G
Note: Free RNA nucleotides exist as nucleoside triphosphates, and they temporarily base pair to DNA during transcription.

Termination:
RNA polymerase continues until it reads a terminator sequence
mRNA molecule detaches from DNA (and DNA winds back together)
RNA polymerase detaches from DNA
This happens right at the terminator sequence in prokaryotes, but in eukaryotes the RNA polymerase continues for 10-35 bases beyond the terminator before it stops and detaches
Note: Many RNA polymerases can follow each other to transcribe the same gene multiple times in a row
This will make many copies of the same mRNA molecule, which allows the cell to make large amounts of the same protein (when needed)

Question 57

Explain RNA processing in eukaryotic cells

Answer 57

one gene = many polypeptides
mRNA molecules made during transcription in eukaryotic cells are called “pre-mRNA” because they must be modified (by enzymes) before they can exit the nucleus and be used by ribosomes to make a protein
1. A 5’ cap (of modified guanine) is added
Protects mRNA from hydrolytic enzymes in the cytoplasm (that want to break it down)
Functions as an “attach here” signal for ribosomes (for translation)
2. A poly-A tail is added (to the 3’ end)
Protects mRNA from hydrolytic enzymes in cytoplasm
Facilitates export of mRNA from the nucleus and ribosome attachment

Question 58

Explain the epigenetic control of gene expression

Answer 58

Gene expression in a cell is affected by an organism’s epigenome:
Epi = above, genome = entire collection of DNA sequences (“above the genome”)
Epigenome = a collection of all the factors that modify/ impact the activity/ expression of genes without altering DNA sequences
Nucleosomes
More nucleosomes = DNA packaged more tightly together/ genes less accessible to RNA polymerase (less transcription/ less mRNA/ less protein from those genes, if any at all)
Methylation
Methyl groups (CH3) bind to DNA, causing it to wrap more tightly around histones
More methylation = less transcription/ less protein from those genes (if any)
Highly methylated genes are usually not expressed at all, and methylation of DNA is maintained through cell division and even from parent to offspring!
Proteins/ Hormones
Transcription factors – aid in RNA polymerase binding to DNA
Transcription activators/ transcription repressors
Hormones – turn certain genes on or off at different times/ stages of development
The Environment
Can change methylation patterns and/ or affect proteins involved in regulating gene expression/ mRNA splicing (wrong genes on or off, incorrectly spliced mRNA etc.)
Chemicals (cigarette smoke, preservatives, pollutants, topical medications/ creams etc.)
Infectious agents (bacteria, viruses, prions)

Question 59

Know the steps of translation (including the direction)

Answer 59

translation occurs (mRNA → Protein)
During translation, blocks of three nucleotides called codons/ triplets (mRNA), are decoded into a sequence of amino acids that are attached together by peptide bonds

Initiation:
Small subunit of ribosome binds to mRNA at start codon (AUG) at 5’ end of mRNA molecule
tRNA (with complementary anticodon UAC) binds to mRNA at start codon AUG (complementary base pairing - temporary)
tRNA carrying amino acid MET
Large subunit binds (with 1st tRNA in P site)
Requires energy of GTP (guanosine triphosphate- like ATP)

Enlogation:
2nd tRNA comes into A site (complementary base pairing with mRNA codon)
Ribosome facilitates formation of peptide bond between amino acids of two tRNA molecules
1st tRNA moves into E (exit) site and detaches/ leaves ribosome
2nd tRNA moves (translocates) into P (polypeptide) site
Ribosome moves along mRNA in 5’ to 3’ direction (one codon at a time)
3rd tRNA comes into A site
Peptide bond forms between amino acids of two tRNA molecules (one in P site and one in A site)
The three steps of elongation (A-P-E) continue, codon by codon, to add amino acids together until the polypeptide chain is completed.

Termination:
Stop codon (on mRNA) reached (A site)
“Release factor” binds to stop codon on mRNA
“Release factor” hydrolyzes bond between polypeptide chain and tRNA in P site
Polypeptide released from tRNA in P site
Ribosome disassembles

Question 60

Describe the genetic code (and be able to use it to determine amino acid sequences)

Answer 60

Translation occurs following the genetic code
mRNA molecules contain codons (series of 3 – triplet – bases)
Each codon specifies ONE amino acid (61 of 64)
Start codon (AUG) specifies amino amid: MET
Stop codons (3 of them -do not code for amino acids – end translation)

Question 61

Describe the structure of ribosomes

Answer 61

Made of protein and rRNA (ribosomal RNA) → most abundant type of RNA in cells (made in the nucleolus in eukaryotes)
Has a tertiary structure and globular shape
Two subunits
Small subunit (has mRNA binding site)
Large subunit (has tRNA binding sites (A site, P site, E site)
Small and large subunits only join together during translation
Two tRNA molecules can bind at the same time
Form polysomes (many ribosomes translating same mRNA at the same time)- to make lots of one type of protein
Ribosomes are 70S in prokaryotes and 80s in eukaryotes

Question 62

Describe the structure of tRNA, its role in translation, and how it becomes “activated”

Answer 62

Structure and function:
tRNA facilitates translation
tRNA molecules are transcribed from DNA template in nucleus
20 different tRNA molecules (one for each amino acid)
All contain anticodons (3 bases – complementary to codons on mRNA – will base pair/ hydrogen bond to mRNA during translation)
Each made up of one chain of RNA nucleotides (single-stranded) that loops/ folds/ hydrogen bonds to itself to form a 3D clover leaf shape
Each tRNA binds with its amino acid at the 3’ end of the molecule (at the sequence CCA)

Role in translation:
Enzymes join each tRNA molecule to the correct amino acid (aminoacyl-tRNA synthetases/ tRNA activating enzymes)
20 different synthetases (20 different amino acids)
Each has active sites for only a specific tRNA and amino acid combination.
The synthetase catalyzes a covalent bond between tRNA and amino acid (utilizing ATP to do so).

Activation:Once tRNA molecules reach the cytoplasm, each tRNA is used repeatedly to:
1. Pick up its specific amino acid (which binds to the 3’ end of the molecule at a sequence of bases – CCA). Once attached to its amino acid, the tRNA is “activated”
2. Bring/ deposit the amino acid at the ribosome
3. Return to the cytoplasm to pick up another copy of its amino acid

Question 63

Compare protein synthesis in prokaryotes and eukaryotes

Answer 63

RNA polymerases are different
Eukaryotic cells require transcription factors
Transcription is terminated differently.
Their ribosomes are different (70S/ 80S).
Their chromosomes are different
Prokaryotes can transcribe and translate the same gene simultaneously.
Nucleus separates transcription from translation in eukaryotes
Extensive RNA processing occurs after transcription and before translation in eukaryotic cells

Question 64

Be able to explain the significance of complementary base pairing

Answer 64

To prevent mutations

Question 65

Be able to diagram the general structure of an amino acid and dipeptide

Answer 65

See notes

Question 66

Know the differences between polar and nonpolar amino acids

Answer 66

Polar vs nonpolar amino acids
Determined by the R group (side chains)
Position/ order of polar/ nonpolar amino acids determines a protein’s shape (which determines its function/ location)
Polar amino acids
Hydrophilic= water soluble → have stable interactions in water
R group is charged
Help to keep protein in position in the membrane
Form hydrophilic linings of protein channels in cell membrane (to allow polar/ hydrophilic/ charge molecules in)
Integral proteins have polar amino acids on the side of the membrane
Nonpolar amino acids
Hydrophobic= water insoluble → have stable interactions in lipid bilayer
R group is not charged
Form portion of protein channels in cell membranes that are in contact with nonpolar, fatty acid tails of the phospholipid bilayer

Question 67

Explain the significance of polar and nonpolar amino acids in membrane proteins

Answer 67

Position/ order of polar/ nonpolar amino acids determines a protein’s shape (which determines its function/ location)

Question 68

Primary level of protein structure

Answer 68

A protein’s primary structure is the sequence of amino acids bonded together via peptide bonds
The order that amino acids are put together is determined by the 3 nucleotide sequence on the mRNA called a codon (more on this later)
The primary structure in a protein determines all other levels of protein structure and therefore a protein’s shape!
Changing one amino acid (out of thousands) can completely change the shape (structure) and function of the protein

Question 69

Tertiary level of protein structure

Answer 69

The tertiary structure creates the 3D shape of the protein (a polypeptide chain bends and folds over itself)
Caused by interactions between R groups of amino acids
Disulfide bridges (between sulfur atoms)
Hydrogen bonds (between polar R groups)
Ionic bonds (between positively and negatively charged R groups)
Important in enzyme function and in the formation of globular proteins

Question 70

Quaternary Structure of protein structure

Answer 70

Involves linking several polypeptide chains to form one protein
Not always present → many only consist of one polypeptide chain
All types of bond from previous structure are present here
Example:
Haemoglobin
Transports oxygen in your blood
Has 4 polypeptide chains linked together
Each polypeptide chain contains a linkage to a non-polypeptide group called haem

Question 71

Secondary level of protein structure

Answer 71

The secondary structure is built by the amino acid sequence folding/ coiling on itself
Caused by hydrogen bonds → between carboxyl group (C=O) on one amino acid and the amine group (N-H) in another
2 types
βeta (β)-pleated sheets (repeated folds)
αlpha (α)-helix (repeated coils)
Secondary organization stabilizes the structure of the polypeptide

Question 72

Know what sickle cell anemia is and what causes it (be specific)

Answer 72

Sickle cell anemia is caused by a mutation (in the DNA) for haemoglobin
This mutation causes red blood cells to have a crescent like (sickle) shape
Impacts red blood cells ability to carry oxygen, can obstruct vessels, and can increase blood pressure
There is one base misplaced on the DNA strand (point mutation)
When DNA goes through transcription, this mistake is copied to the mRNA and then coded for in translation
The codon sequence is changed because of this mutation and causes a different amino acid to be added to the polypeptide
The polypeptide chain (and primary structure) now contains an incorrect amino acid (valine instead of glutamic acid)
This change causes the protein to fold differently, ultimately creating the sickle shape instead of the round shape that we want
People who are heterozygous for sickle cell have malaria resistance → so mutations do not always result in something horrible!

Question 73

Know the function of a named protein

Answer 73

Protein General Function Specific function:
Spider silk : Structure : Fiber spun by spiders and used to make webs
Collagen :Structure :Supports structure of connective in skin/ ligaments/ tendons
Insulin: Hormones : Produced by pancreas, causes cells to take up glucose in the blood (lowers blood sugar)
Immunoglobulins/ antibodies: Immunity :Fight bacteria and viruses
Haemoglobin : Transport : Found in red blood cells- carries oxygen in blood
Rhodopsin : Sensation: Pigment in photoreceptor cells of the retina that detect light
Actin and Myosin : Movement: Filament responsible for muscle contraction
Rubisco: Enzyme: Enzyme involved in light independent stage of photosynthesis

Question 74

Compare fibrous and globular proteins (with a named example of each)

Answer 74

There are two main classes of protein tertiary structure:
Fibrous proteins are generally composed of long and narrow strands and have a structural role
Globular proteins generally have a more compact and rounded shape and have functional roles

Question 75

Know and be able to explain why denaturation is, the result of it, and how it occurs

Answer 75

Denaturation is a structural change in protein that can lead to permanent loss of biological properties (or FUNCTIONS)
The way a protein folds determines its function so a change in the tertiary structure will impact its functional abilities
Changes in the chemical environment can change in shape

Question 76

Know what enzymes are and explain how they catalyze biological reactions

Answer 76

Complex, globular proteins that act as biological catalysts cause biological reactions to happen at a faster rate than they normally would on their own
Determined by an organism’s genetic makeup
Note: In an enzyme-catalyzed reaction the enzyme itself is not a reactant or product and is not “used up”
HOW?
Enzymes LOWER the level of energy that is needed to start a reaction– this energy is used to destabilize bonds in reactant(s)
Enzymes do NOT change overall proportion of reactants and products

Question 77

Explain enzyme specificity and the induced fit model of enzyme activity

Answer 77

Each enzyme acts on a specific molecule (or molecules) called a substrate (reactant)
Each enzyme has a unique 3-D shape that is highly specific to its substrate – the 3-D shape of the enzyme and the shape of the substrate are complementary - fit together like a “hand and a glove”
Note: Enzymes can distinguish even the slightest difference in shape and will ONLY bind to their specific substrate
The part of an enzyme where the substrate(s) bind is called the enzyme’s active site– the active site has the shape that gives each enzyme its specificity for its substrate (holds substrate in optimum position to make/ break bonds and carry out the reaction)
When an enzyme is bound to its substrate(s) is called an enzyme-substrate complex

Induced fit: As substrate(s) enters the active site and binds it causes (induces) a slight change in shape of the active site (in the R groups) so that it fits the substrate better/ more snugly (like a clasping handshake/ snuggly hug!)

Question 78

Know the effect of temperature, substrate concentration, and pH on enzyme-catalyzed reactions (graphs – with labeled axes – are good to know here too)

Answer 78

Temperature:
The same information about proteins applies here
Enzymes have an optimal temp
Increase the temperature will increase the speed and motion of enzyme and substrate = higher enzyme activity
Higher kinetic energy= more frequent collisions between enzyme and substrate
At higher temperatures, enzyme can denature- losing its function and rate of reaction will decline

Substrate concentration:
If enzyme concentration is constant:
adding more substrate increases the rate of reaction (more collisions between enzyme and substrate – more product is formed more quickly)
Increasing substrate concentration will increase the rate of reaction (increased competition for active site of enzymes)
A maximum rate of reaction (Vmax) is eventually reached (reaction rate will plateau), where adding more substrate will not increase the rate any further – this is because all of the enzymes present are saturated (they are all working on as much substrate as quickly as they possibly can and cannot go any faster)

PH level:
A change in the pH will change the charge of the enzyme and its overall shape and solubility
A change in shape or active site can result in problems with substrate binding and rate of reaction
Enzymes have optimal pH (can differ between enzymes)

See notes for graphs

Question 79

Know what metabolism is and the types of chemical reactions in living systems (anabolic, catabolic, exergonic, endergonic). Be able to identify these reactions with and without enzymes in graphs.

Answer 79

The sum of all of the chemical reactions that occur in a living organism are its metabolism
Metabolic reactions are either:
Anabolic (“building” of complex molecules, endergonic – more energy IN to build bonds, often involves condensation)
Example: photosynthesis
Catabolic (“breaking down” of complex molecules, exergonic – more energy released as chemical bonds are broken, often involves hydrolysis, degradative/ digestive)
Example: cellular respiration
Almost all metabolic reactions in living organisms are catalyzed by enzymes! Without enzymes, biological reactions would not happen fast enough for us to survive!!!

Question 80

Explain competitive and non-competitive inhibition of enzymes

Answer 80

Molecules that affect the active site of an enzyme in some way are called inhibitors
Inhibitors are either competitive or non-competitive:

Competitive inhibitors
“Compete” with the substrate for the active site!
Bind directly to the active site of an enzyme, preventing the normal substrate from binding to it

Noncompetitive inhibitors bind to a part of the enzyme other than the active site. This binding causes a change in the 3-D shape of the enzyme’s active site, making it non-functional.

Question 81

Explain the control of metabolic pathways (end-product/ allosteric inhibition)

Question 82

Explain how lactase is used to create lactose-free milk

Answer 82

Lactase: the enzyme that breaks down the disaccharide milk sugar lactose
Most humans lose the ability to produce lactase as they age, causing undigested lactose to be fermented by microbes in the small intestine rather than being broken down into monosaccharides
Because of this, the enzyme lactase can be used to treat/ pre-digest milk and milk products before consumption, alleviating this problem
Also makes milk more sweet! → reduces need to add extra sugar to flavored milks
Expensive to keep extracting and purifying lactase though, so we need to be able to reuse enzymes over and over again
Problem: enzymes in solution get “washed away” because difficult to separate them out once they are dissolved/ being used
Solution: IMMOBILIZE THEM! “Trap” the enzymes in tiny pores of calcium alginate beads, then wash milk over them – can then recover beads, which recovers enzymes