Molecular cell biology test 1

Cells ___ but have similar ____

vary, basic chemistry

All cells have

-DNA

-Plasma Membrane

-RNA
-Ribosomes

True or False? Living cells are self-replicating collections of catalysts

True

All cells share a ______

Common ancestral cell

Problem with the modern system

DNA stores information, but proteins perform most catalysis

Evolutionary Chick-and-egg problem

RNA world hypothesis

-Solution to the problem w modern system

-RNA is able to do both:

1. store info

2. catalyze chemical reactions (through ribozyme)

Ribozyme

Type of RNA molecule that has enzymatic activity (Splicing, ligation, polymerization)

-Known for helping catalyze peptide bond formation btwn amino acids in the ribosomes. This action is known as peptidyl transferase activity

Eukaryotes vs Prokaryotes

Why would DNA eventually replace RNA for information storage

DNA is more chemically more stable than RNA

Three Domains of Life

Eukarya, Archaea, Bacteria

~ Eukaryotes

~ Prokaryotes

Prokaryotes

-Cell wall

-No nucleus

-No membrane-bound organelles

-SIngle chromosome +plasmids

-Capsule

Bacteria

-Most diverse group

-There bacteria known as photosynthetic bacteria that can perform photosynthesis and get energy from sun

Archaea

-Live in extreme environments

-More linke eukaryotes than bacteria

-Mysterious

-Have unique cell wall chemistry and membrane lipids

Nucleus

Distinguishing feature of eukaryotes.

-Contain most of the DNA in the cell, rest is spread btwn the mitochondria and the chloroplast

Mitochondria

Organelles found in eukaryotic cells.

-Generate most of cell’s supply of usable energy

-DNA containing

-Encolsed by a double membrane

Chloraplasts

-Organells found in plants and algae

-Harvest energy from sunlight by photosynthesis

-DNA containing

-Have a thylakoid membrane system that has chlorophyll

Where did chloroplasts and mitochondria said to have evolved from?

An ancestral host cell (eukaryote) engulfed a bacterium which lead to mitochondria.

…..then they engulfed a photsynthetic cyanobacterium which lead to chlorplast

Evidence for endosymbiosis

-Resemble prokaryote in size

-Have their own DNA

-DNA resembles prokaryote

-Can divide independently

-Are surrounded by double membranes

Endocytosis

Import meidated by the formation of endocytic vesicles

Exocytosis

Export secretary vesicles

What determines how atoms interact?

Outermost electrons

Covalent bond

Sharing of electron

Nonpolar covalent bond

Electron are shared equally

Polar Covalent

Electrons are shared unequally

Ionic bond

Gain or Loss of electrons

Four types of weak molecule interactions

• Van der Waals attraction

• Electrostatic attractions

• Hydrogen bonds

• Hydrophobic interaction

Organic Molecules

Molecules w C-H bonds

Sugars, Fatty acid chains , Nucleotides, Amino acids

Chain of order for each organic compound

Sugars ———> Polysaccharides ———> Carbohydrates

Fatty acids——> Lipids and fats ——→ Cell membrane

Amino Acid ——> Protein

Nucleic Acid —→ Nucletoide ——> DNA and RNA

Monosaacharide

simple sugar and subinit to build carbohydrates

Ex: Glucose, fructose.

Binded by glycosidic bonds to create polysaccharides

Two monosaccharides

Disaccharide

Condensation/Dehydration

-Forms polymers

-Water is released

-Energetically unfavorable

Hydrolysis

-Breaks down polymers.

-Water is used

-Energetically faovrable

Fatty acid

-composed of a carboxyl group and a hydrocarbon tail (length of tail and saturation can very)

-Stored as energy reserves

Hydrocarbon tail is _____

Hydrophobic

Carboxyl group is _____

Hydrophillic

Hydrophilic vs Hydrophobic

Hydrophilic: Polar, forms hydrogen bonds

Hydrophobic: Nonpolar, cannot form hydrogen bonds

Phospholipids

-Made of Hydrophillic head and Hydrophobic tails

-Naturally form a lipid bilayer

Degree of saturation determines?

The physical properties of the fat molecules

-Saturated are solids produced by animals

-Undersaturated are liquid produced by plants

Saturated

No double bonds.

-Straight glycerol

-Make membrane less fluid bc they can tightly pack together

Unsaturated

Has double bond

-Kink causes a bend in the glycerol

-Makes membrane less rigid/ more fluidity bc they can’t pack as tightly

Triacylglycerols

Fats and oils:

3 fatty acids + 1 Gylycerol connected through ester linkages

-Hydrophobic

Steriods is a type of ____

lipid

Amphipatchic

Molecule containing both a hydrphilc and hydrophobic region.

Amino acids

-Building block of proteins

Made up of four things, amino group, Carboxyl grouo, Hydrogen, and a R group

-Different R group gives different amino acid which ultimately gives us dif protein functions

What bond connects amino acids toghether?

Peptide bonds

Polypeptide chain

Amino acid linked together by petide bonds

Amino terminus and Carboxyl termins

Amino end= N terminus

Carboxyl end= C-terminus

Different R group effect

Different R group will determine the aminocide sequence which effects the way protein fold. The way protein fold gives them their shape which directly affects their function

Nucleotides

-Subunits of DNA and RNA

-# of phosphates varies from 1-3

-Linear arrangments of nucleotides store genetic info

Besides being building blocks of DNA and RNA, what other functions do nucleotides have?

Carry energy (ATP), act in intracellular signaling (Cyclic AMP [cAMP], and are component of coenzymes

1-3 phosphate

1-AMP

2-ADP

3-ATP

Nucleiotides are linkef through what covalents bonds?

Phosphodiester bonds

How are phosphodiester bonds linked

Linking the 5’ P of incoming nucleotide with 3’OH of the previous nucleotide

The incoming nucleotide is usualy in the ________ during polymerization

Triphosphate form

What type of bond connect the phopshate groups of atp

phosphoanhydride bonds

ATP——> ADP

Hydrolysis reaction that release energy.

-Water used to break ATP down

Macromolecule

-Is very large complex molecule

-Has a particular primary structure due to the sequence of monomers used to produce the polymer

-Various combination of monomers produces various 3-D shapes in molecules

How do macromolecules interact with on another

Through multiple noncovalent interactions btwn surfaces

Aldoses

Ex:Glcuose

Ketoses

Ex: Fructose

Functions of proteins

-transport

-Singal

-Receptors

-Structural

-Motor

-Storage

-Enzymes

-Transcription

The shape of a protein is specified by its

amino acid sequence.

-This is bc the sequence determines which R groups occurs and where thyey occur on the polypetide

-Interactions btwn R groups is what cause the polypetide to fold.

Folding in proteins

Due to non-covalent, weak interactions (Ex: Hydrophobic force) within the polypeptide chain

-Fold into comformation of lowest energy

-Assisted by chaperone proteins

-Some proteins can spontaneously refold into their proper shape

Chaperone proteins

What assist proteins to fold properly

Primary Structure of protein

-Amino acid sequence

-Connected by peptide bonds

Ex: Gly—Ala—Ser—Val—Leu

Secondary structure of protein

-Local folding of the polypetide backbone

-Stabilize by hygrogen bonds

-α helices and β sheets.

Tertiary Structure of protein

Forms when R groups btwn secondary structures interact

-Overall 3D folding of one polypeptide

Quaterny protein structure

Large protein molecule that contains more than one polypeptide chains.

-Each polypeptide in the large protein molcule is called a subunit

-Subunits can be the same or different

What is a protein domain?

Regions of a polypetide that has a particular structure and function is performs.

-Different domains can be across multiple proteins

-Most proteins ocntain multiple domains.

Families

Protein are organized into families based on homologous domains

Ex:THe serine protease in the pic carry the same job but on dif subtrates

How are collagen polypetides organized?

-Organized as triple coiled coil

Collagen’s triple structure resists pulling forces

Elastin

-Composed of multiple polypeptide cross-linked to each other

-Polypetides cross linked via di-sulfide bonds that form btwn cystine residues

Permits stretching

α helices

-Are often found as transmembrane region of proteins

-α helical regions are used to interact w other polypeptides

Transmembrane region

Hydrophobic region of protein that is exposed

β sheets

-Can form rigid structures at the core of many proteins

-Structures can be parallel or anti-parallel

-Structures can form large pores called β barrels

β sheets can stack to form damaging _______

Amyloid structures

Prions

Cause normal proteins to misfold and produce amyloid structures