BIO1A03 Test 1 real

What are the main differences between prokaryotes and eukaryotes

?

Prokaryotes are bacteria cells that do not contain a nucleus and lack membrane bound organelles. Eukaryotes are plant, animal, and fungi cells that contain a true nucleus and membrane bound organelles.

Microbiome

The populations of micro-biotic organisms within our bodies (Includes prokaryotic bacteria but also small eukaryotic organisms)

microorganism

Organisms that are not visible to the naked eye, but only visible under a microscope

Streptococcus salivarius

a normal inhabitant of the upper respiratory tract and oral cavity (contributes to formation of dental plaque)

Staphylococcus haemolyticus

Resides on skin where it is harmless but it can be pathogenic if it gets inside the body

Bacteroides thetaiotaomicron

Predominant intestinal bacteria that makes enzymes that are useful in the breakdown of plant materials that we ingest.

What is the cell membrane composed of, and how does this contribute to the function of the cell membrane?

The cell membrane is made up of phospholipids that have hydrophobic tails and hydrophilic heads that allow for the separation of the cell interior from the exterior.

What are phospholipids made of?

A phosphate head (with glycerol combined) and two fatty acid tails.

saturated fatty acid

A fatty acid that does not contain any double bonds

Unsaturated Fatty acid

Fatty acids that contain carbon-carbon double bonds

How do the kinks at each double bond in an unsaturated fatty acid affect fluidity of the membrane?

The kinks have the effect of pushing neighbouring phospholipids further apart to increase fluidity.

lipid micelles

ball of lipids with the head on the outside of the ball and the tails on the inside - Important for absorption of fat soluble vitamins and complex liquids in the body

How is fluidity of the cell membrane affected?

1. # of carbons in the hydrocarbon chain - Longer chains pack together more tightly than shorter chains, reducing fluidity

2. Double bonds/kinks in the chain: pushes neighbouring phospholipids further apart, increases fluidity

3. External environment Ex. Temp: Higher temp = fluidity and lower temp = decreases fluidity

4. Steroids: packs together, or separates phospholipids depending on the temperature

Lipid raft

Region of lower fluidity - it can hold macromolecules together in the membrane (found to gather proteins involved in same metabolic pathway)

How do small molecules, ions, and hydrophobic molecules cross the membrane?

Along a concentration gradient (High to low) through diffusion

fluid mosaic model

Membranes consist of proteins and carbohydrates embedded in a fluid phospholipid bilayer

transmembrane integral proteins

Proteins embedded within the cell that enable the transport of hydrophilic molecules across the membrane

passive/simple diffusion

Movement of molecules across bilayer from areas of high to low concentration (Involved lipid soluble molecules, gases, uncharged polar molecules, water)

facilitated diffusion

The movement of small molecules with the concentration gradient but involves proteins embedded in the CM -DOES NOT REQUIRE ENERGY

What is active transport and what are the two types?

Active transport is the movement of molecules against a concentration gradient

1. Primary active transport: The transmembrane protein is directly affected by the energy released from ATP and undergoes a conformational change to "pump" the substance across the gradient

2. Secondary Active transport: If neighbouring transmembrane transport proteins take advantage of electrochemical gradients established by the primary active transport pumps to move their own solutes against the gradient

Osmosis

Movement of water from a less concentrated solution (hypotonic) to a more concentrated solution (Hypertonic)

Aquaporins

transmembrane protein channels that allow rapid passage of water

- Alpha-helicases form a central pore

- do not undergo changes in shape when transporting water

isotonic environment

The concentration of a solution is the same inside and outside the cell (No net movement of water)

hypotonic environment (Swelling cell)

Extracellular fluid that has a lower solute concentration than the inside of the cell (Water into cell)

hypertonic environment (Shrivelled cell)

Higher solute concentration on the exterior of the cell relative to the interior (water moves out of cell)

sodium-potassium pump

Allows the cell to establish differences in concentration of sodium and potassium on either side of the cell - for every 3 sodium ions pumped out of the cell, 2 potassium ions are pumped from extracellular environment into cell. Generally more sodium on outside of cell and more potassium on inside of cell.

Organelles

Membrane bound structures inside the cell that are essential contributors to cell function (Ex. Chloroplast, mitochondria)

What are the main differences between chloroplasts and mitochondria?

Chloroplasts (Plant cells): Engage in photosynthesis and produce sugars that we consume. Double membrane around exterior

Mitochondria (Animal and plant cells): Chemical energy in the form of ATP is generated in the mitochondria through the breakdown of sugars

Photosynthesis

A process used in plant cells and other organisms to convert light energy into chemical energy

celluar respiration

A process used by plant and animal cells to release the chemical energy stored in the bonds of carbohydrate molecules and partially capture it in the form of ATP

Explain the endosymbiotic theory of the mitochondria and chloroplast.

It is likely that a mutually advantageous relationship developed with anaerobic eukaryotes likely engulfing aerobic bacterium. As a result of this, the bacterium could now supply energy to its host cell while the eukaryote supplied the bacterium with protection and a supply of carbon compounds. Over the course of evolution, invaginations of the cell membrane allowed these ancestral prokaryotes to compartmentalize the genetic information into a nucleus thus becoming the most ancestral eukaryotes. Ancestral eukaryotes became hosts to aerobic and photosynthetic eukaryotes and evolved into modern day mitochondria and chloroplast

endosymbiotic theory

States that the temporary relationships between organisms are permanent and heritable (Evidence: mitochondria and chloroplasts contain their own circular genome and analysis of the genes and proteins show significant similarity to those of bacteria.

Explain 2 reasons why organelles are important?

1. Allows for compartmentalization of different cellular functions

2. Incompatible processes such as synthesis and degradation can be kept separate and not interfere.

How do chloroplasts make chemical energy?

Light energy is transformed into chemical energy in the form of ATP and NADPH via the light reactions cycle of photosynthesis. It is then in the dark reactions/calvin cycle that NADPH and ATP are used to drive the reduction of atmospheric CO2 into carbohydrates.

Polysaccharides

Structures that form when many monosaccharides are linked together (Ex. Starch: Storage polysaccharide found in photosynthetic plants)

How is energy stored in plants?

Energy is stored in the form of starch in plants. There are 2 types of starch:

1. Unbranched amylose - linear structure (Alpha 1-4 linkages)

2. Branched amylopectin - Branched structure (1-6 glycosidic linkages)

How is energy stored in animals?

glycogen - a lot of branches (Stored in liver and muscles of humans)(1-4 and 1-6 linkages)

What is glycolysis?

the breakdown of glucose by enzymes, releasing energy and pyruvic acid. Occurs in cytoplasm (Anaerobic process)

Yield: 2x Pyruvate

2x ATP

2x NADH

What is pyruvate oxidation?

Pyruvate from glycolysis is processed to form acetyl CoA which can enter the mitochondrial matrix (Occurs in inner mitochondrial matrix)

Yield: 2x CO2

2x NADH

What is the Krebs cycle?

8 reactions. Acetyl group of acetyl CoA is completely oxidized to CO2 and chemical energy is transferred to ATP and to the reduced electron carriers

Yield: 2x ATP

6x NADH

2x FADH2

What is the electron transport chain?

Is a sequence of electron carrier molecules that shuttle electrons,

down a series of reactions that release energy; used to make ATP. The movement of electrons in the ETC produces a concentration gradient of protons which is a source of potential energy that is used to synthesize ATP. (Occurs in inner mitochondrial membrane)

Yield: 32x ATP from all the electron carriers created in the Citric acid cycle

What is the order of metabolization of macromolecules?

Carbohydrates are metabolized first, followed by fats and then proteins

How can energy be released by the hydrolysis of ATP?

ATP has a high potential energy. The 3 phosphate groups have 4 negative charges in close proximity so groups repel each-other resulting in a high potential energy. ATP can react with water which breaks the bond between its outermost phosphate group and its neighbour resulting in ADP and inorganic phosphate - RELEASES A LOT OF ENERGY. (ATP used for contracting a muscle, active transport, or building large molecules)

endomembrane system

A group of organelles in eukaryotic cells that performs most lipid and protein synthesis.

What functions do proteins serve?

1. Transport and signalling

2. Enzymes

3. Movement and structure: Myosin proteins interact with scaffold proteins to facilitate intracellular movement

4. Defense: Immune system produces proteins called antibodies that fight off infection

Ribosomes

site of protein synthesis - Structural components of ribosomes are made in nucleolus

Free Ribosomes

Able to remain in the cytoplasm - Destined to remain in cytosol or be targeted to various cell organelles (Have signals that determine their transport and location in cell)

bound ribosomes

attached to the endoplasmic reticulum

All the possible proteins are derived from how many core amino acids?

20 core amino acids

What is the basic structure of an amino acid?

Central carbon atom

Amino group

carboxyl group

hydrogen atom

variable side chain

What is a polypeptide/Polymer?

Amino acid monomers put together to make linear strands

What does the r-group variant determine?

Each amino acid's distinct set of properties

Where does translation occur?

inside the ribosome

How is the specific sequence of the amino acid polymer determined?

By translating the information in the messenger RNA through the cleft between the large and small subunits of the ribosome (30S and 50S)

How does tRNA assist in translation?

tRNA's match the sequence of nucleotides on the mRNA and carries the appropriate amino acid to the next position in the growing polypeptide chain

Peptide Bond

Bond between carboxyl group of one amino acid and amino group of another

Primary Structure (Proteins)

linear sequence of amino acids in the polypeptide chain

Primary structure will largely determine the manner in which it folds

Secondary structures (Proteins)

Alpha helix: Linear structure turned into a spiral or coil by the formation of noncovalent hydrogen bonds (Between carbonyl of carboxyl group, and amide of another amino acid 4 positions away)

Beta Pleated Sheets: Parallel protein strands with hydrogen bonds

- Hydrogen bonds allow for pleated like organization of structure

What interactions are responsible for the formation of secondary structures?

It is the interactions between components of a proteins backbone

Tertiary structure (Protein)

The three-dimensional conformation of a single polypeptide chain, usually made up of several secondary structure elements.

What interactions are responsible for the formation of tertiary structures?

Interactions between amino acid r-groups

Many proteins are complete and fully functional as a single polypeptide chain with a tertiary structure

Quaternary structure (Proteins)

Two or more polypeptide chains or subunits with a tertiary structure that come together

Polypeptide subunits may be either identical or different

What are the cellular mechanisms that assist protein folding?

Molecular chaperones: These proteins bind to hydrophobic regions of the folding protein and prevent incorrect folding just long enough for the correct structure to form

Use of chaperonins: Large molecular complexes that form isolation chambers

- inside the chamber, a single nascent protein is sequestered away from the other proteins so it can fold without interference and the formation of incorrect bonds

In an aqueous solution, how do globular proteins fold?

So that the hydrophobic amino acids cluster in the interior

How do signal sequences help mRNA to get to the endomembrane system?

mRNA's that encode proteins destined for the endomembrane system have a pecial signal seqwuence that once translate, causes the ribosomes to become bound to the ER

The polypeptide can then continue to be translated and can enter in the lumen of the ER (SIGNAL SEQUENCE REMOVED INSIDE LUMEN)

How do proteins get modified in the ER and transported to the golgi apparatus?

Proteins get modified in the ER through the addition of one or more carbohydrate chains - Glycosylation (Contributes to protein stability, folding, and cell-cell recognition.

Proteins are then transported to the golgi apparatus in vesicles that pinch off the ER (Vesicles fuse with golgi and deposit contents in lumen of golgi apparatus)

Each protein that comes out of the golgi apparatus contains what?

a TAG that allows for it to be packaged into a particular type of transport vesicle

What are microtubules?

Part of the cytoskeleton and they form roadways that allow for vesicles to be transported along

Where is DNA contained in prokaryotic cells

The nucleoid

Plasmids

Small circular DNA molecules (found in prokaryotes) which often carry only one or two genes

- They can replicate independently of core genome and can be transferred from one cell to another which allows for rapid spread of genes and contributes to ANTIBIOTIC RESISTANCE

Where is DNA contained in eukaryotic cells

nucleus

Chromosome

Describes organization of a double stranded DNA molecule in its association with proteins and RNA's

*Some organelles contain their own smaller chromosomes like the mitochondria*

What is the 'supercoiling of DNA' and what does it help the DNA molecule with?

Supercoiling is the coiling that occurs in addition to the coil of the helical DNA structure.

This preserves the double helix structure and compacts DNA into a small space

Fred Neufeld

R strain streptococcus - harmless member of mouse microbiome

S Strain streptococcus - virulent form of same bacteria

What was Griffith's experiment?

Heated virulent S strain in order to reduce harmful bacteria and injected it into mice causing no result

He then killed the virulent strain and incubated the remains with living cells of the benign strain which resulted in the mouse dying

This indicated that the cells of the benign strain had acquired the information, or the ability to be virulent from the dead cells (DNA is hereditary material)

Transformation

A change in cell behaviour resulting from the incorporation of hereditary/genetic material from outside the cell (Bacteria cells can uptake DNA through membrane)

What is the structure of a nucleotide?

5-carbon deoxyribose sugar

Nitrogenous base

Phosphate group

What are purines and pyrimidines?

Adenine and guanine are purines (2 rings)

Cytosine and Thymine are pyrimidines (1 ring)

What reaction and bond is formed when synthesizing DNA nucleotides?

Condensation reaction releases a water molecule and forms a COVALENT bond called a phosphodiester bond

The sugar phosphate backbone has a _____________ polarity created by the linkages

5' to 3'

How many hydrogen bonds are involved in the bonding of

1: Guanine and Cytosine

2: Adenine thymine

Guanine-cytosine: 3 Bonds

Adenine-thymine: 2 bonds

Messenger RNA

RNA copy of genes coding for proteins

- single stranded molecules and serve as a template for protein synthesis

Transfer RNA

Functional RNA

- Never translated

- Folds into a 3-dimensional structure held by base pairing between ribonucleotides

- Carry amino acids into the ribosome and match the amino acid to the appropriate mRNA sequence

Ribosomal RNA

Functional RNA

- transcribed from the ribosomal genes of which there are many copies in the cell (Large proportion of total RNA in cell)

- multiple rRNA's and proteins form the functional ribosome complexes that perform translation of mRNA's into proteins

How is DNA arranged in a eukaryotic chromosome?

Linear molecules organized around proteins (histones) to form chromatin

Is the eukaryotic chromosome and genome smaller than that of prokaryotes?

The chromosome and genome of a eukaryote is much greater in size relative to prokaryotic genome

How do prokaryotic and eukaryotic genomes support the endosymbiotic theory?

Basic units of both genomes are the same despite differences in size and organization

Electron microscope

uses electrons in a chamber to blast cells

- can see down to nanometer resolution

flourescence microscopy

Labels proteins with fluorescent molecules

- allows us to understand what proteins the cell is releasing

brightfield microscope

Convenient to study cell types that move across the body that can be potentially harmful

Our microbiome is inherently dynamic, what does this mean?

Microbe population can change continuously

Staphylococcus aureus

Found in upper respiratory tract and on the skin

- can cause skin and lower respiratory tract infections (gastroenteritis)

- If it moves into lungs on its own, it is dangerous

Klebsiella Pneumoniae

Found in normal flora of mouth, skin, and intestines

- Can cause lung inflammation

Pseudomonas

Able to colonize many different environments

- Able to form polysaccharide biofilms

- resistant to most antibiotics

Escherichia coli

Can cause bloody diarrhea, stomach cramps, vomiting

- it must be balanced in intestines

MCR-1 gene

New gene that is resistant to antibiotics (Mobilized colistin resistance)

Pseudomembranous colitis

Inflammation of the colon caused by the bacteria Clostridium difficile. (Can cause diarrhea and antibiotic resistance)

C.difficile

Can be asymptomatic, but individuals may have outbreaks due to prolonged antibiotic treatment, weak immune system, advanced age, exposure to other people with C.difficile infection

What did Ben Eiseman do when faced with 4 cases of pseudomembranous colitis?

Eiseman used donor fecal enemas (Fecal transplants) which balanced out the microbes in the body which allowed good bacteria to multiply and patients were cured

How does the camel hump benefit a camel?

The hump is essentially a mound of fat (tristerarin) which allows the animal to survive a long time (2 weeks) with limited food.

The fat is also a source of water when metabolized, allowing camels to go long periods of time without drinking water as well.