Cell Bio Exam - Lectutres 1-10 (some stuff, not the pathways directly)

What is Cell Biology

How a particular biological task is performed with molecules and how organisms function

Basic Properties of cells

• Highly complex and organized

• Possess a genetic program and the means to use it

• Capable of producing more of themselves

• Acquire and utilize energy

• Carry out a variety of chemical reactions

• Engage in mechanical activities

• Able to respond to stimuli

• Capable of self-regulation

• Evolve

What kinds of cells are Prokaryotes?

• Archaea (Archaebacteria)

• Bacteria (Eubacteria)

What kind of cells are Eukaryotes?

• Protists

• Fungi

• Plants

• Animals

Similarities between Prokaryotes and Eukaryotes

• Have DNA as their genetic material

• Are membrane bound

• Have ribosomes (makes proteins)

• Similar basic metabolism

Prokaryotes Differences

• No structured nucleus (nucleoid)

• DNA is circular

• Lack complex membranous organelles (No mitochondria, chloroplasts, or endoplasmic reticulum)

• Cell walls contain peptidoglycans (mesh-like polymer of sugars and amino acids that contribute to the cell wall)

Eukaryotes Differences

• Nucleus is separated from cytoplasm by nuclear membrane

• Linear DNA that are arranged in chromosomes

• Complex membranous organelles

• Complex cytoskeletal system

• Cell walls contain cellulose plants

Nucleus Function

Contains DNA. Where transcription to mRNA occurs. Contains nucleoli where ribosomal RNA is produced. Where DNA replication occurs during cell division.

Rough endoplasmic Reticulum (Rough ER) Function

Translation of mRNA to make new proteins (at attached ribosomes), folding and modification of newly translated proteins.

Smooth Endoplasmic Reticulum (Smooth ER) Function

Lipid synthesis. Drug metabolism. Calcium homeostasis

Golgi Apparatus Function

Modification, packaging, and sorting of newly-made proteins

Mitochondria Function

Energy (ATP) production

Centrioles Function

Part of a compound structure called the Centrosome. Organization of the cytoskeleton; Particularly important during cell division.

Free Ribosomes Function

Translate proteins that will remain in the cytosol

Cytosol Function

The aqueous space in which organelles are suspended (not an organelle per se)

Plasma Membrane Function

Separates the interior and exterior of the cell. Controls which molecules enter or leave the cell.

Lysosomes Function

Breakdown of large molecules (like proteins and polysaccharides)

Peroxisomes

Use oxidation reactions to break down fatty acids

What do Eukaryotic plant cells have that animal cells do not have

• Chloroplasts

• Plastid

• Central vacuole

• Plasmodesma (allows transport through ridged cell wall)

• Cell wall

Differences in animal cells between plant cells

• Lack chloroplasts

• Lack large vacuoles

• Lack cell wall

• Have lysosomes and centrioles; also sometimes have pseudopods, flagella, and cilia

Modern Eukaryotic cells evolved from a symbiosis:

Mitochondria:

• Are about the size of bacteria

• Have their own genome in the form of circular DNA

• Have their own ribosomes

• have their own transfer RNAs

It is likely that it originated from aerobic bacterium that was engulfed by an archaeal anaerobic cell. They formed a symbiotic relationship.

What are the major macromolecules that are found in cells?

• Carbohydrates (polysaccharides)

• Lipids

• Proteins

• Nucleic Acids

What do monosaccharides make?

Polysaccharides

What do fatty acids make?

Lipids

What do amino acids make?

Proteins

What do nucleotides make

Nucleic acids

What do carbohydrates consist of

C, H, and O. Typically with an H:O ratio of 2:1 (H₂O).

What is the simplest form of carbohydrates?

Monosaccharides

What are carbohydrates called with 2 monosaccharides?

Disaccharides

What are carbohydrates called with 3 or more monosaccharides?

Polysaccharide

What are the primary roles of carbohydrates?

• Energy production

• Modify protein structure and function

• Contribute to the cell walls (in plant cells)

• Components of the extracellular matrix

What are the simple sugars of carbohydrates?

Monosaccharides

• Glucose

• Fructose

• Galactose

These are broken down as far as they can, not much energy to get out of them

What is between the simple and complex carbohydrates

Disaccharides

• Maltose

• Sucrose

• Lactose

What are the complex carbohydrates

Polysaccharides

• Starch

• Glycogen

• Cellulose

These break down from polysaccharides to monosaccharides and the energy comes from the bonds breaking.

What do lipids do?

They are a diverse group of molecules which are hydrophobic or amphiphilic (both hydrophobic and hydrophilic). They make up fats, waxes, sterols, several vitamins and phospholipids.

Cell Membranes are:

Self-healing, conductive to vesicle, and semi-permeable (small molecules and gases like H₂O, O₂ and CO₂ can get through, and small nonpolar molecules like ethanol and methane can get through. Large or charged molecules cannot get though by themselves)

What do proteins make

• Polypeptides - molecule made up of multiple amino acids

• Proteins - larger polypeptide with folded structures

Protein Functon

• Can act as an enzyme: a substance which catalyzes a chemical reaction

• Can bind with high specificity to other molecules

  • Act as a scaffold for other proteins

  • Regulate transport of molecules across membranes

  • Maintain cell or organelle structures (i.e cytoskeletal proteins)

  • Sense signals from the extracellular environment

  • Generate movement

Nucleic Acids are:

Biomolecule made of nucleotide monomers

• Nucleotide = sugar + phosphate group + base

  • DNA bases = A (adenine), T (thymine), C (cytosine ), G (guanine)

  • RNA bases = A (adenine), U (uracil), C (cytosine ), G (guanine)

• DNA is meant to last 1000s of years and RNA is meant to be destroyed once the message has been received and it is no longer needed.

What is the importance of DNA?

It contains hereditary information.

• Heredity: the phenomenon in which an organism specifies the characteristics of its offspring

It Instructs for the production or regulation of all other cellular components

What is a gene?

It is a region of DNA that instructs for the production of a protein or functional RNA

What are the building blocks of DNA

Sugar, phosphate and a base and it makes a nucleotide

What is the steps of making amino acids

• DNA synthesis/ Replication

• RNA synthesis/ Transcription

• Protein synthesis/ Translation

Why is yeast good for growing and testing single-celled organisms?

• Simple single-celled eukaryotic cell

• Reproduces rapidly (doubling in about 90 mins)

• Small genome; mutants available for every gene

• Excellent model for cell cycle

Why is Arabadopsis good for growing and testing plants

• Can be grown indoors

• Get large numbers

• Thousands can be produced in just 8-10 weeks

Why are C. Elegans good from reproducing and studying

Worms

• Small, harmless

• Cheap

• Short life cycle (a few days)

• can survive in a freezer

• Great for genetic studies

  • Exactly 959 body cells (does not vary)

• Cell division and cell death

Why are drosophila good for studying

• Insects

• Giant, banded chromosomes

• Small genome

• Change the DNA, change the banding sequence

• Reproduce rapidly

• Ultimately result in wrong parts in the wrong place

• Fast development

• Cheap

Why are xenopus good at studying

Advantages

• Amphibian

• Embryonic development studies

• Eggs are ig and easy to manipulate (fertilized outside of the animal)

Disadvantages

• Poorly suited for genetic/multional anaylsis

• Difficulty raising larvae to adulthood in lab

• Long time to reach sexual maturity (greater than about 10 months)

Why are zebrafish good at studying

• Fish

• Vertebrate

• Small genome (1/2 that of humans)

• Sexual maturity in 3 months (live 3-5 years)

• Transparent for the first 2 weeks of life (good for development studies)

Why are mice good at studying

• Mammal

• Sexual maturity at around 2 months; live around 2 years

• Small

• Hardy - easy to keep alive and resist infection

• Similar mutations in mouse result in similar phenotypes in humans

• Can make knock-out knock-in and other types of mutations to study the functions of proteins.

What do Proteins Do?

• They form channels in plasms membrane

• Carry messages from one cell to another

• Relay signals from membrane to nucleus

• Serve as machines with moving parts

• (control, detect eveything)

Aspartic Acid

• Asp

• D

• Acidic (negative charge)

Glutamic Acid

• Glu

• E

• Acidic (negative charge)

Arginine

• Arg

• R

• Basic (positive charge)

Lysine

• Lys

• K

• Basic (positive charge)

Histidine

• His

• H

• Basic (positive charge)

Asparagine

• Asn

• N

• Uncharged polar

Glutamine

• Gln

• Q

• Uncharged polar

Serine

• Ser

• S

• Uncharged polar

Threonine

• Thr

• T

• Uncharged polar

Tyrosine

• Tyr

• Y

• Uncharges polar

Alanine

• Ala

• A

• Nonpolar

Glycine

• Gly

• G

• Nonpolar

Valine

• Val

• V

• Nonpolar

Leucine

• Leu

• L

• Nonpolar

Isoleucine

• Ile

• I

• Nonpolar

Proline

• Pro

• P

• Nonpolar

Phenylalanine

• Phe

• F

• Nonpolar

Methionine

• Met

• M

• Nonpolar

Tryptophan

• Trp

• W

• Nonpolar

Cysteine

• Cys

• C

• Nonpolar

Basic features of Proteins

• Side chains project from alpha-Carbon

• Typical weight of one amino acid is 110 MW

• Most proteins are 135 to 635 AA

• Typical length of primary structure of AA is 1,000 to 5,000 A

• Folded 40 to 80 A

Proteins are also help together by 4 non-covalent attractions

• Van der Waals Attractions (London dispersion forces)

• Hydrogen bonds

• Electrostatic interactions (ionic bonds)

• Hydrophobic forces

Secondary Structures

• Alpha helix

• Beta structure/sheets

Secondary structures are maintained by HYDROGEN bonds

Alpha-helices

• Side chains (R) stick out of helix

• Preferred structure without other interactions

• Hydrogen bonds between NH and C=O

• 3.6 amino acids per turn

• Common in hydrophobic portions of membrane proteins

Beta-sheets

• Can be parallel or anti-parallel

• Beta-sheet propensity is also influence by van der waals forces

• Repeat distance is 7A

• Two segments of one chain or two chains

Tertiary Structures

• Folding of alpha helix and beta sheets

• Interactions:

  • Ionic bonds: salt bridges and cation-pi interactions

  • H+ bonds in amino acids side chains

  • Hydrophobic Clustering (most important)

  • Disulfide Bonds

  • Metal Ion coordination complexes

Protein Domain:

A substructure formed by any part of the polypeptide chain that can fold independently into a stable structure

Quaternary Structure of Proteins

Structure of a protein complex formed from the interaction of multiple, folded polypeptide chains

Ion complexes

• A domain which forms multiple helices separated by a loops that act as a sequence-specific DNA binding domain

• DNA-binding motif are found as part of transcription regulatory proteins

Fibrous Proteins

• Long and thin

• Mainly secondary structures

• Cell and tissue structure

• Collagen, elastin, and actin

Globular protein

• Short and interspersed runs of secondary structure

• Catalytic Proteins

• Require more complex structure

Molecular Motor

• A protein that moves in a machine like fashion

• Binds ATP or GTP

• Examples: kinesin, dynein, and dynamin

What is the start codon

AUG

What are the stop codons

• UAG

• UGA

• UAA

What are the building blocks of DNA

• 1 5-carbon sugar

• 1 phosphate

• 1 nitrogenous base (pyrimidines - T, C. Purines - G, A)

Transcription

• DNA sequence is transcribed into RNA sequence

• Transcription initiated when RNA polymerase binds to promoter binding site on DNA

  • Transcription of RNA moves along DNA strand and adds corresponding complementary RNA nucleotides

• RNA polymerase adds nucleotides in the 5’-3’ direction

What are the 3 phases of transcription

1. Initiation

2. Elongation

3. Termination

What is initation

Protein complexes assembles near a region called a promoter that signals the beginning of a gene, and RNA polymerase II prepares to synthesize a chain of RNA nucleotides from the DNA template

What is elongation

RNA polymerase II causes phosphodiester bonds to from, linking nucleotides in the growing RNA molecule together to form one long chain in the 5’-3’ direction

What is termination

This process is not extremely well understood in eukaryotes. The newly synthesized RNA transcript get cleaved from the DNA template strand and released from transcriptional machinery, and immediately beings undergoing modification to prepare it for translation

What is an exon?

A segment of DNA/RNA sequence that codes for a protein/polypeptide

What is an intron?

Segment of DNA/RNA sequence that does not code for protein/polypeptide

What is a promoter?

The gene segment that serves as the initiation site where RNA polymerase binds to and initiates the transcription of certain genes

What is the TATA box?

A DNA sequence (TATAAA) in the promoter region involved in binding RNA polymerase via a TATA binding region

What is an enhancer?

A short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes

During elongation, a series of modification to the growing transcript begins…

Almost as soon as it starts. These are commonly referred to as - Post Transcriptional Modifications

What is the splicesome

• It is an enormous complex (over 300 Proteins) that splices pre-mRNA

• In addition to distinct proteins, it is composed of 5 subunits known as snRNPs

  • snRNPs - small nuclear RNA and a set of proteins

tRNA:

• Small RNA molecules (about 80 nucleotides)

• Anticodon region of tRNA contains 3 nucleotides that are complementary to 3 nucleotides on mRNA

• The 3-nucleotide region of mRNA that tRNA binds is called a codon.

• Acts as a “shuttle” to transport the correct amino acids iin the polypeptide?

What are the 3 types of RNA in translation

• Ribosomal RNA (rRNA): the site of polypeptide assembly

• Messenger RNA (mRNA): directs which amino acids are assembled into polypeptides

• Transfer RNA (tRNA): transports and positions amino acids in the proper sequence within the polypeptide