Micro 1

Central Dogma of Molecular Biology 3 ideas

1. Cells store Information, long-term, in DNA, in the form of nucleotide sequences.

2. mRNA is a copy of a DNA sequence of a gene, made during transcription

3. Proteins are synthesized during translation, based on the nucleotide sequence of a mRNA.

What information is stored In cells DNA

all information required for making proteins (stored long-term in genes)

What is DNA made of?

Made of long-term stored proteins in genes

What is a "nucleotide sequence?

Monomers create into polymers (DNA/RNA) made from a N base, sugar (riose/deoxyribose) and 1/2/3 P groups (RNA \= 1,000's long DNA \= Mil. Long)

What enzyme complex performs DNA synthesis?

DNA polymerase

When is mRNA made? What is it?

mRNA is a copy of a DNA sequence of a gene, made during transcription .

What enzyme complex performs transcription?

RNA polymerase

What does mRNA stand for?

messenger ribonucleic acid

What is a gene

segment of DNA that codes for a protein

The recipe for making one protein (mRNA \= short-term)

When are proteins synthesized?

Proteins are synthesized during translation, based on the nucleotide sequence of a mRNA.

What is a protein?

chain of amino acids

(~300 per) Enzymes that catalyze chem. Reactions. How cells control all their biochemical reactions, metabolism, and ability to make new molecules. Can be structural (hold things together) or regulators (make decisions/plans)

What enzyme complex performs translation?

Ribosome "reads" mRNA to know how to make correct protein

What are polymers?

DNA, RNA, and proteins are all polymers.

What is a polymer?

long chain of monomers

Essential macromolecules composed of repeating subunits (aa)

What are proteins? (Essential what? (Structures for what?)

Most essential cellular machines and many cellular structures are proteins.

Sequence of amino acids determine what about proteins?

The sequence of amino acids determines everything about a protein, including its function.

List three example functions of proteins, being careful to think about cell functions, instead of organ or system functions

Structure/cell shape, inner organization, waste cleanup, manufacture product, routine maintenance

Why is microscopy important?

Microscopy is necessary in microbiology because most cells on earth are too small for the human eye to see

Magnification

Magnification is the process of making an image larger. It is easy to do with lenses or with computers. It is a necessary part of microscopy.

Explain how to calculate the total magnification from a light microscope such as what we use in lab

Uses two lenses for magnification. Total magnification \= ocular lens x objective lens magnification (4x/10x/40x/100x) Use 1000x for bacteria

List the typical magnification powers found in our lab for ocular and objective lenses.

Ocular lens magnification \= 10X or 20X Objective lens magnification \= 4X, 10X, 40X, 100X

Resolution (aka resolving power) (is it easy to do with lenses/computers?)

Resolution (or resolving power) is the ability to visually separate details in an image. It is NOT easy to do with lenses or computers. Resolution is the limit for what a microscope can see.

limits of resolution

There are physical limits on resolution, such as the size of a lens (or of a telescope mirror) and the wavelength of light being observed.

When is powerful magnification useful/useless?

High (powerful) magnification is useless unless there is also very good resolution.

Describe the appearance of a bacterial cell under high magnification with bad resolution

The outline of the bacteria is able to be seen, but no greater details, just looks like small blobs

Why is contrast important?

Contrast is essential in microscopy because without it, there are no details to observe.

Do all microscopes generate contrast?

Some microscopes generate contrast, others do not.

How do light microscopes work?

Light microscopes magnify images using visible light.

How do electron microscopes work?

Electron microscopes magnify images using electrons.

Compare the electron microscope to a light microscope and explain why the difference matters, using terminology from this guide.

Electron beams have a shorter wavelength than light \= better resolution \= stronger, more detailed magnification (for bacteria, not blurry!)

Prokaryotes are Bacteria and Archaea are single or multi celled? Do they have nuclei or membrane bound organelles?

single cells that don't have nuclei or membrane-bound organelles

size of prokaryotes vs eukaryotes

Prokaryotes are smaller than eukaryotes

examples of eukaryotes

Eukaryotes include Fungi and Protists, as well as plants and animals.

Helminths are technically animals*

Do eukaryotes have membrane bound organelles or a nucleus?

All of these have nuclei and membrane-bound organelles

examples of membrane bound organelles

endoplasmic reticulum, golgi apparatus, lysosomes, peroxisomes, mitochondria/chloroplasts

What are ribosomes?

Ribosomes are the large enzymatic complexes that synthesize proteins.

Name the process of synthesizing proteins

Makes short-term copy of gene (mRNA) \= Transcription (performed by RNA polymerase), cell's ribosome reads mRNA and makes protein \= Translation

What are ribosomes made of?

Ribosomes are made of both numerous proteins and several RNA molecules.

What does rRNA do? What do they not do?

These ribosomal RNA molecules (rRNA) do NOT encode proteins; they just act as structures that hold ribosomes together.

What kind of RNA DOES encode proteins?

mRNA

16S rRNA

polynucleotide (~1500 bases)

functions as part of the small subunit of the ribosome of Bacteria and Archaea and from whose gene sequence evolutionary information can be obtained; its eukaryotic counterpart is 18S rRNA

-Does not encode a protein, so never translated, plays role in scaffold, holds catalytic proteins in right place within ribosome

What are the DNA molecules found in prokaryotes?

Chromosomes and plasmids are DNA molecules found in prokaryotes.

Do all cells have chromosomes? Plasmids?

All cells have one or more chromosomes, but not all cells have plasmids.

Chromosomes ("size", what they do, why they are needed)

Chromosomes tend to be large (in other words, very very long DNA molecules) that encode thousands of proteins. A cell typically needs its chromosomes because they encode its most essential proteins, such as the ones that make up ribosomes.

Name two other essential protein complexes from the central dogma.

mRNA and RNA polymerase

Explain again what DNA is made of and why it is part of the central dogma

Made of nucleotides in a sequence (Mil. Long), contain information needed to make all our proteins

Plasmids

Plasmids are relatively shorter DNA molecules. They typically encode proteins that are useful only under special conditions.

Name two of the special conditions related to plasmids

can exist autonomously and can replicate independently of the bacterial chromosome

Structure and function of bacterial cell membranes vs humans cell membrane

The bacterial cell membrane has the same basic structure and function as a human cell's plasma membrane:

Cell membranes (plasma membrane) (made of what?)

It is a structure made of phospholipids that are arranged so that their hydrophilic "heads" are external and their hydrophobic "tails" are internal.

Phospholipid

a lipid that contains phosphorus and that is a structural component in cell membranes

*Lipid containing a P group in its molecule

Hydrophobic

Water fearing

Hydrophilic

water loving

What is a phospholipid membrane made of? How many layers

A phospholipid membrane is made of two leaflets, or layers of phospholipids

What layer is in contact with the cytosol? What layer is in contact with the external environment?

the deeper or inner leaflet that is in contact with the cytosol

outer or superficial leaflet in contact with the external environment

what is the difference between cytosol and cytoplasm?

Cytosol is part of the cell that includes fluids but not organelles and nucleus

Cytoplasm is a region of the cell that contains fluid cytoskeleton and all organelles except the nucleus

(Fluid in cells cytoplasm, surrounds organelles in E. cells, cytoplasm is part of the cell which is contained within the entire cell membrane)

Is the phospholipid membrane fluid? What can't move across it?

The phospholipids are not chemically bonded together, so the membrane is very fluid and molecules can move along it in two dimensions. Most molecules cannot freely cross the membrane

List functions of a cell membrane

Providing a waterproof barrier, keeping things in cell, unwanted substances out, allows transport (channels) for wastes and needed materials

(Regulates materials entering and leaving the cell (selective permeability). Also gives cells their shape.)

What is embedded in the phospholipid bilayer? On what sides?

There are many proteins embedded in the membrane. Some cross it, some are only on the external side, and some are only on the internal side.

Give some examples of membrane proteins in the phospholipid bilayer from human physiology.

Aquaporins, protein channels, peripheral and integral proteins

phospholipid bilayer permeability

membrane is waterproof and selectively permeable

Review the basic idea behind selective permeability and think of some relevant situations from human physiology.

Differentiate between types of molecules, allowing some in, and blocking others. Ex. Lipid-soluble in E. cells \= hydrocarbons, O2

Do human cells have a cell wall? Do bacterial cells have a cell wall? What is it made of?

Unlike human cells, most bacterial cells have a cell wall. This is made of the polymer peptidoglycan

Define polymer and explain how it differs from a bunch of phospholipids that make up a cell membrane

A long molecule consisting of many similar or identical monomers linked together.

Essential macromolecules composed of repeating subunits (aa). A phospholipid that makes up the cell membrane is composed of P groups in one molecule, polymers are made of aa. groups

What does the cell wall provide for the cell? What about the cell membrane?

While the cell membrane provides waterproofing and selective permeability, the cell wall provides physical strength.

Among common bacteria, there are two very common types

Gram positive and gram negative

Gram (+) CELL MEMBRANE:

Waterproof cell mem., superficial to that is a thick peptidoglycan cell wall, Techoic acids (diverse group of polymers embedded in the peptidoglycan, anchor the peptidoglycan to cell mem.)

Gram (-) INNER MEMBRANE:

Waterproof cell mem., superficial to the membrane a periplasmic space (periplasm), within the periplasm is a thin peptidoglycan layer, superficial to the periplasm is an "outer mem.", Lipopolysaccharide (makes up part of outer mem.)

Lipopolysaccharide (LPS)

molecule that makes up part of the outer (superficial) leaflet of the Gram negative outer membrane.

LPS combines a lipid (on its deeper end) and a carbohydrate (polysaccharide) on its superficial end.

The lipid end is embedded in the outer membrane, and the carbohydrate sticks out into the extracellular space

Extracellular

outside the cell

Lipopolysaccharide (LPS) AKA what? Why?

LPS is also known as endotoxin, because cells from the human immune system can detect it and rapidly respond by triggering fever and inflammation.

Even dead Gram negative cells, if injected into a person's blood or lymph, can thus cause dangerous high fever and excessive inflammation.

Flagella

Flagella are corkscrew-like protein appendages that bacteria can use to push themselves through water. A single one is called a flagellum. Bacterial movement is called motility.

What ways can flagella move?

Bacteria with flagella cannot turn left or right. They can only go forward, or randomly tumble by spinning the flagellum backwards.

Can bacteria move through chemical gradients? How?

Some bacteria can detect chemical gradients, and move towards an area of higher or lower concentration. They do this by regulating how often they go forward vs. how often they tumble.

Chemotaxis

Cell movement that occurs in response to chemical stimulus

This movement toward or away from a chemical is called chemotaxis.

Phototaxis

movement in response to light

Other bacteria can move toward or away from light. This is called phototaxis.