Bio 105 Exam 2

First Law

Energy cannot be created or destroyed, but it can be changed from one form to another.

Second Law

Energy cannot be changed from one form to another without loss of usable energy.

When ________ _________________ occur, energy is neither created nor destroyed(1st Law) but there is always the loss of usable energy, usually as heat (2nd Law).

energy transformations

Concept of Potential Energy

- An object that is not in motion may still have energy.

- On a molecular level, the bonds that hold atoms and molecules together have potential energy.

Kinetic energy energy associated with objects in motion.

Energy is associated with objects in motion.

Concept of Kinetic Energy

A molecular level, the bonds that hold atoms and molecules together release kinetic energy when broken.

Bioenergetics use most life forms to get their energy from the sun, which is passed through the food web.

• Plants use photosynthesis to capture sunlight

• Herbivores eat the plants to obtain energy, carnivores eat the herbivores to obtain energy, etc.

• The eventual decomposition of plant and animal material contributes to the nutrient pool.

The sum of all chemical reactions that occur in a cell is referred to as the cell's ______________.

Metabolism

Cells require chemical energy to perpetuate life, so cells must:

1) import nutrients into the cell,

2) process those nutrient molecules,

3)synthesize novel (new) molecules (in some cases),

4) distribute the molecular-8es throughout the cell and to other cells in the organism

Activation energy

needed to get the reaction going. Reactant converted to Product in reactions and G = the change in chemical energy

Two types of metabolic processes (metabolism)

-Anabolic: build large molecules from small molecules (consumes energy)

-Catabolic: Breaks large molecules down into smaller particles(releases energy)

This does not happen without the assistance of a protein called an enzyme, which helps to facilitate the reaction.

Enzymes

• Molecules that catalyze (speed up or help) a reaction by lowering the activation energy of some reactions.

• Enzymes require a proper shape to do the intended job.

Enzymes bind to an area of the chemical reactants called the enzyme's ___________. The area in the enzyme where the substrate binds is the _______ ______. Products are the results of the substrate-enzyme interaction

substrates

active site

The small amount of energy input needed for any chemical reaction to occur is called _____________ __________. Enzymes lower the ___________ __________ of the reaction but do not change the energy exchange of the reaction.

activation energy

Metabolic Energy and Adenosine Triphosphate (ATP)

• A small molecule that contains potential energy available for cellular work.

• The primary energy currency of cells in the same way that money is the currency that people exchange for things they need.

• The basic structure includes two-ring adenine, five-carbon ribose, and three phosphate groups.

ATP and Adenosine Diphosphate (ADP)

The transfer of the 3rd phosphate group is key. It takes energy to add the 3rd phosphate to ADP to make ATPATP have the potential energy stored in that chemical bond. When the phosphate is removed, kinetic energy is released and provides energy for biochemical reactions. It is basic chemistry that explains how ATP works.

Autotrophs

Produce their own food via photosynthesis. Plants, algae, and a type of bacteria known as cyanobacteria all produce their own food.

Heterotrophs

unable to carry out photosynthesis and must obtain energy and carbon by consuming other organisms.

It is important to understand that all food consumed, whether animal products or plant products, can link back to ____________________ ___________.

photosynthetic vegetation

Stomata

small openings in a leaf that allow oxygen out and CO2 in.

Chloroplast

Organelle that contains structures for photosynthesis to occur.

Thylakoids

structures in the chloroplast that is the site for photosynthesis

Stroma

Area in chloroplast outside of the thylakoids.

Photosynthetic Pigments

molecules that are involved in the capture of solar energy(chlorophyll a)Leaf Structure

Light and Photosynthesis

Visible light is the form of light used in the process of photosynthesis. Photosynthetic pigments act to absorb light.

Chlorophyll a

appears green because it absorbs all wavelengths of visible light and reflects green

Chlorophyll b

absorbs blue and red-orange light. Having more than one type of pigment allows for a broader absorption spectrum.

Photosynthesis converts solar energy into the chemical energy of a carbohydrate

Solar energy + 6CO2 + 6H2O → C6H12O6 + 6O2

Light Dependent Reactions

'Photo-' Captures energy from the sun and produces high-energy molecules

3 MULTIPLE CHOICE OPTIONS

Light Independent Reactions

'-Synthesis'Produces carbohydrate using high energy molecules from light-dependent reactions

3 MULTIPLE CHOICE OPTIONS

Cellular respiration

-The step-wise release of energy from molecules (usually carbohydrates) is used to synthesize ATP molecules.

-This is an aerobic process that requires oxygen (O2) and gives off carbon dioxide (CO2) and involves the complete break down of glucose to carbon dioxide and water.

- C6H12O6 + 6O2 → 6CO2 + 6H2O + energy (ATP)

Glycolysis

First Step in Breaking Carbon (C) Bonds: 2 ATP are harvested the 6 C glucose is split in half with a P attached to each 3C molecule, and Energy and Pares are transferred to NADH and ATP resulting in 23 C Pyruvate molecules.

Citric Acid Cycle

1. Oxidation Reaction: Removes a C from Pyruvate adds a Coenzyme A to the molecule and produces an NADH.

2. Citric Acid Cycle: Transfer energy from the 2 C molecule to create NADH, FADH2, and ATP; releases both remaining Carbons

3. By the end of the citric acid cycle:

• All 6 carbons in the original glucose molecule have been released as CO2.

• Hi energy ATP, NADH, and FADH2 molecules have been energized using the potential energy in the glucose molecule

• We have not mentioned oxygen yet! C6H12O6 + 6O2 → 6CO2 + 6H2O + energy (ATP)

Electron Transport System

Hi-energy NADH and FADH2 molecules transfer their electrons (energy) to protein carriers in the electron transport system. They also release their H+ causing a strong H+ gradient. The majority of ATP is produced in this process! Oxygen is the final electron acceptor for the electron transport system!!!!

Accounting of Energy Yield per Glucose Molecule Breakdown

Most ATP is produced by the electron transport system.

Photosynthesis and the Energy Cycle

Photosynthesis is the inverse of the reaction for cellular respiration: plants consume carbon dioxide and produce oxygen, while animals consume oxygen and produce carbon dioxide. Aerobic respiration and photosynthesis function in a constant biological cycle.

Anaerobic Respiration

The final electron acceptor is an oxygen molecule.However, some organisms employ processes that use an organic or inorganic molecule as the final electron acceptor if oxygen is not present.These processes are known as anaerobic respiration and produce either lactic acid or ethanol

The NAD+ cycle

When NAD+ -> NADH it has gained energy.

When NADH -> NAD+ it loses energy

Every living organism uses DNA(your genes)

It's genetic material.- Each person's DNA is unique(with the exception of identical twins).- DNA analysis, can be used for identifying pathogens, vaccine development, cancer treatment, tracing genealogy, paternity testing, animal and plant breeding, forensics/crime solving, and more.

DNA analysis is also being used to construct __________ to better understand the evolutionary history of life on Earth.

phylogenies

Carbon Order Matters in Deoxyribose

By numbering the carbon in the sugar ring, we can orient the nucleotide by the5' (5 - prime) and 3' (3 - prime) end.5' C - connected to phosphate group3' C - connected to OH (hydroxide)

There are four types of nitrogenous bases in DNA.

⮚ Adenine (A) and Guanine (G) are double-ringed purines,⮚ Cytosine (C) and Thymine (T) are smaller, single-ringed pyrimidines

Nucleotides Differ by Nitrogenous Base

The name of the nucleotide is based on the type of nitrogenous base it has. Uracil only in RNA, Thymine only in DNA

One Pair of Bases

- Four Bases: Adenine, ThymineGuanine, Cytosine

- A always binds with T(the word at)G always binds with C

- DNA is a strand of nucleotides and can be called a polynucleotide

Structure of DNA: double helix

- When the DNA double helix untwists, it resembles a ladder: --- Sides = sugar+phosphateRungs = complementary paired bases.

- The two DNA strands are anti-parallel – they run in opposite directions (notice 5’ and 3’ orientation.)

One More Look

Ribonucleic Acid (RNA)

• A second nucleic acid in all cells and is also a polymer of nucleotides.

• Each of the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group.

• RNA has Ribose, not deoxyribose (know the difference!)RNA DNA

Structure of RNA

RNA is a single-stranded nucleic acid.

In certain situations, A pairs with U (uracil) while G pairs with C.DNA=T-A; G-CRNA=U-A; G-C3 Types of RNA: Messenger RNA (mRNA), Transfer RNA (tRNA), Ribosomal RNA (rRNA)

DNA has ThymineRNA has Uracil

RNA Versus DNA

RNA• Single Stranded• Has Ribose for the sugar• Does NOT contain Thymine(replaced with Uracil)

DNA• Double stranded• Has Deoxyribose for the sugar• Does NOT contain Uracil(replaced with Thymine)

How DNA Is Arranged in Prokaryotes?

• In prokaryotes, the DNA is twisted beyond the double helix in what is known as supercoiling.

• Some proteins are involved in the supercoiling; other proteins and enzymes help in maintaining the supercoiled structure.

How DNA Is Arranged in Eukaryotes

• At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes.

• The nucleosomes, with their DNA coiled around them, stack compactly onto each other to form a 30-nm-wide fiber.

⮚ This fiber is further coiled into a thicker and more compact structure called a chromosome.

DNA Replication

• During DNA replication, each of the two strands that make up the double helix serves as a template for the new strand.

⮚ Each new double strand consists of one parental strand and one new daughter strand.

• This is known as semiconservative replication.• When two DNA copies are formed, they have an identical sequence of nucleotide bases and are divided equally into two daughter cells.

Overview of DNA replication

Hydrogen bonds between bases break and enzymes “unzip” the molecule. Each old strand of nucleotides serves as a template for each new strand.

The Details

• Helicase(Enzyme names end in -ase) opens the DNA at the origin spot• DNA Polymerase adds the new strand in the 5' to 3' direction

• One direction is continuous, the other broken into Okazaki fragments(lagging strands)

• RNA primers are laid down at the start of replication, then later removed as Okazaki fragments are joined

Ladder Configuration and DNA Replication

- New nucleotides move into complementary positions and are joined by DNA polymerase.

- The process is semiconservative. Each new double helix is composed of an old strand and a newly formed strand.

The Central Dogma:DNA Encodes RNA; RNA Encodes Protein

• The sequence of nucleotides in DNA corresponds to specific instructions (genes) for protein synthesis and needs to get to the ribosomes in the rough endoplasmic reticulum.

• Transcription: the process which a copy of DNA is made as RNA

• Translation: the process where the directions to build a protein are put into action by a ribosome.

The Genetic Code: Codon

• DNA specifies the synthesis of proteins because it contains a triplet code: every three bases stand for one amino acid.

• Each three-letter unit of an mRNA molecule is called a codon.

• The code is nearly universal among living organisms.

Messenger RNA codons

Anticodon GCU lines up with the Codon for Arg

123 = amino acid

AUA = isoleucine

CCG = proline

GAU = aspartate

GAC = aspartate

1 MULTIPLE CHOICE OPTION

Transcription: from DNA to mRNA

Transcription always proceeds from one of the two DNA strands, which is called the template strand. The enzyme RNA polymerase builds an RNA strand called messenger RNA (mRNA)The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the non-template strand, with the exception that RNA contains a uracil (U) in place of the thymine (T) found in DNA.

Endo-membrane Summary

mRNA from the Nucleus is sent to the Rough ER, where proteins are synthesized at the Ribosome by the process of translation, transported to the Smooth ER where it is packaged into a Vesicle and then sent to the Golgi Apparatus for reworking and more packaging and sent to its destination in a Vesicle!

Transfer RNA: Amino Acid Carrier

Each amino acid has its transfer RNA(tRNA) and associated anticodon. The anticodon is a 3 nucleotide sequence that can bind with the codon for that particular amino acid.

Ribosomal RNA

Ribosomal RNA (rRNA) combines with proteins to build a ribosome. Consists of a large subunit and a small subunit.

The Protein Synthesis Machinery

• The process of translation, or protein synthesis, involves decoding an mRNA message into a polypeptide product.

• Amino acids are covalently strung together in lengths ranging from approximately 50 amino acids to more than 1,000.

• In addition to the mRNA template, many other molecules contribute to the process of translation.

Translation: Linking the Amino Acids

1. The first tRNA lines up on the mRNA and small subunit

2. The large subunit then allows the next tRNA to line up on the appropriate codon

3. The amino acid from the first tRNA bonds to the 2nd amino acid

4. The 1st tRNA leaves and the mRNA shifts down to allow the third tRNA to align with its codon

5. The 3rd amino acid bonds with the second amino acid to build the protein

6. This process continues until the end of the mRNA is reached.

How Genes are Regulated

• If a 'gene' is actively being transcribed into mRNA and that mRNA is being translated into a protein, that gene is said to be turned on

• If a 'gene' is NOT actively being transcribed into mRNA or that mRNA is being prevented from being translated into a protein, that gene is said to be turned off

• The process of turning on a gene to produce RNA and protein is called gene expression

• Every cell has 100% of the genes, but not all genes need to be turned on in every cell or all of the time

• Gene expression can be controlled by multiple mechanisms, including external signals

Cell membranes are characterized by the presence of

phospholipids

Which movement is a passive process?

diffusion

Which cellular components main function is to make lipids, enzymes, and package substance?

endomembrane system

If free phospholipids were swirled into water, they would ____.

form aa lipid bilayer sheet with the hydrophobic tails in the center

The packaging of secretory proteins usually occurs in association with this structure

Golgi Bodies

This organelle is involved in lipid production and protein transport.

endoplasmic reticulum

DNA synthesis occurs in the nucleus. Its breakdown can occur in this organelle

lysosomes

These are the structures upon which proteins are assembled

ribosomes

The cellular digestion and disposal of biological molecules occurs inside this organelle

lysosomes

Ribosomes are often found on the surface of this organelle.

endoplasmic reticulum

Aerobic respiration occurs in this organelle

mitochondria

Sugar metabolism occurs in association with this organelle

mitochondria

What is a passive process that requires a protein for the movement of a solute across a membrane?

facilitated diffusion

What is a "building block" of carbohydrates?

monosaccharides

Which of the following organelles are not directly involved in lipid production

mitochondria

Which of the following is not a characteristic of the plasma membrane?

hydrophilic tails

Introduction to Mitosis (Cell Reproduction)

• For organisms that begin life as a fertilized egg (zygote), that original single cell becomes the ancestor of every other cell in the body

• That original cell goes through a series of cell reproductions (mitosis) that lead to a fully developed adult.

• Cell reproduction is also used to repair or regenerate tissues (new blood and skin cells are constantly produced).

genome

is the total DNA content of a given cell and controls the development of the single original cell to the fully formed final organism

Chromosomes

• Remember how we discussed DNA was coiled and packed into structures called chromosomes?

• Each eukaryote has a set number of chromosomes located in the nucleus of the cell.

Humans have 46, fruit flies have 8, spinach has 12, crawfish have over 200, and so on.

Chromosome Type and Copies

• A fertilized egg has its set of chromosomes plus the set of chromosomes delivered by the sperm

.• So, each cell has two sets of chromosomes: one from the mother and one from the father

Therefore, there are two copies of each type of chromosome

Haploid Versus Diploid

• The number of kinds of chromosomes in a cell is the haploid (n)number

• The total number of chromosomes in a cell is the diploid (2n)number (two chromosomes of each kind).

• Humans have 23 types (haploid) of chromosomes, so we have a total of 46 chromosomes (diploid).

Karyotype

Homologous chromosomes are chromosome of the same type and can be paired up

The Cell Cycle: Interphase

1. Growth phase one

2. Synthesis (replication of DNA)

3. Growth phase two (ATP released, proteins made)

Most of the cell cycle is spent in interphase, a period of growth and DNA synthesis

Following interphase, the mitotic stage of cell division occurs

The Cell Cycle: Mitotic Phase

Prophase -> metaphase -> anaphase -> telophase -> cytokinesis

Mitosis is a nuclear division during which duplicated chromosomes are segregated and distributed into daughter nuclei.The cell will divide after mitosis in a process called cytokinesis in which the cytoplasm is divided and two daughter cells are formed

DNA replication

Takes place during the S phase of interphase before nuclear division (mitosis) occurs

Centrioles

Organelles that organize microtubules(cytoskeleton) in the cell. It creates a spindle fiber network that attaches to the chromosomes with the kinetochore during mitosis

Stages of Mitosis (Nuclear Division)

1. Prophase involves the breakdown of the nuclear envelope, condensing of chromosomes, the emergence of spindle fibers from the centrosomes, and migration of centrosomes to the "poles" of the cell.

2. Promet a phase is characterized by the appearance of kinetochores at the centromeres and the attachment of spindle microtubules to those kinetochores.

3. Metaphase involves the arrangement of chromosomes along the metaphase plate and the attachment of spindle fibers (from each "pole") to each sister chromatid.

4. Anaphase is the step where the centromeres split and the resulting sister chromatids are pulled toward each pole. Also, certain spindle fibers begin to elongate.

5. Telophase is the last step before the official division of the cell and involves the surrounding of the chromosomes (formerly sister chromatids) by a nuclear envelope at each pole. Additionally, the mitotic spindle breaks down and the spindle fibers push the poles further apart

Cytokinesis

division of the cytoplasm to form two separate daughter cells

Prokaryotic Cell Division: Binary Fission

• Mitosis is unnecessary because there is no nucleus or multiple chromosomes. This type of cell division is called binary fission.

• Replication of the circular piece of DNA in prokaryotes begins at an origin and proceeds in both directions.

• From there, the cell elongates and the duplicated chromosomes move to each pole of the cell.

• Fts Z proteins form a septum in the middle of the cell that will eventually divide the cell into two identical cells

Cell Cycle Checkpoints: G1v

The cell cycle is controlled at three checkpoints to ensure it is OK to replicate.

Before moving to the S phase of inter phase, the following things are checked:

• Integrity of the DNA

• Adequate reserves

• Cell SizeIf requirements are not met, then the cell does not enter the S phase

Cell Cycle Checkpoints: G2

Before moving to mitosis, the following things are checked:

• All chromosomes have been replicated

• Replicated DNA is not damaged, if requirements are not met, then repairs are made or the cell doesn't enter mitosis

Cell Cycle Checkpoints: M

Before moving past the metaphase stage of mitosis, the following thing is checked:

• All the sister chromatids are correctly attached to the spindle microtubules

The cycle will not proceed until the kinetochores of each pair of sister chromatids are firmly anchored to spindle fibers

Apoptosis

Programmed cell death. Some cells are programmed to die (think about the space between your fingers)

Mutations

• Even with the three checkpoints, uncorrected mistakes do happen

• Mistakes in the S phase (DNA replication) can lead to the insertion of an incorrect nucleotide into DNA (this is a mutation).

- Mutations lead to incorrectly formed proteins, which means their function will be altered.

- Mutations remain in the genome and can be passed down generations.

Proto-oncogenes

Genes that make proteins that initiate cell division- They receive a signal to get turned on

- Cdk is a protein that stimulates cell division and is normally made if the checkpoint says it is OK

• When a Proto-oncogene mutates, it becomes an oncogene(Oncology is the study of cancer)

- If the Proto-oncogene that makes Cdk is mutated to an Oncogene, then Cdk may be made when it is not supposed to be made, forcing the cell to divide and ignoring the checkpoints

• p53 protein is a tumor suppressor and halts cell replication

- Mutation to the p53 gene can stop the cells' ability to halt cell replication