CELL FUNCTION FINAL

Fundamental units of life that have a wide variety of sizes, shapes, and functions that perform specialized functions

Cells

Describe the central dogma

1. DNA encodes our genes using nucleotides

2. DNA transcribes into RNA

3. RNA translates into a protein

Complete set of genetic information of an organism, only expresses a specific set of genes depending on their internal state and cues which define the cell type

Genome

Type of microscope used to visualize cells around 5-20 micro meters

Light microscope

Type of microscope to visualize the subcellular structures - like organelles

Electron microscope

Type of electron microscopy to look at the surface of the cell

Scanning

Type of electron microscopy to look at slices of the cell

Transmission

Dense material outside of cell membrane that provides structure, made of proteins and polysaccharides

Extracellular matrix

Stores genetic material

Nucleus

Transparent substance enclosed in the lipid membrane, houses organelles for function

Cytoplasm

• Possess membrane-bound nucleus and organelles

• Much larger than prokaryotes

Eurkaryotes

• No membrane bound nucleus or organelles

• Much smaller than eukaryotic cells

• Most diverse and numerous cells on Earth due to their wide range of habitats and functionally diverse energy production

Prokaryotes

Two domains of prokaryotes

Archea and bacteria

The most common type of prokaryotic cell on Earth

Bacteria

Other type of prokaryotic cell, most diverse habitats

Archea

• Double layer membrane surrounding nucleus

• Provides structural support

• Controls transport between the nucleus and cytoplasm via the nuclear pore complex

Nuclear envelope

• Production of ATP through cellular respiration

• Double membrane structure

• Contains their own DNA (which is separate from nucleus)

• Hypothesized to have been engulfed from bacteria (symbiotic relationship)

Mitochondria

• Helps plant cells produce energy through photosynthesis

• Double membrane structure containing thylakoids and own DNA

• Hypothesized to have been engulfed from bacteria (symbiotic relationship)

Chloroplasts

• Aids in protein and lipid synthesis

• Rough: makes proteins on ribosomes

• Smooth: makes lipids and steroids

Endoplasmic reticulum

• Modifies and packages proteins made in ER for transport

• Flattened, membrane enclosed sacs

• Sent back out by vesicles for transport

Golgi Apparatus

• Digestive system of the cell

• Uses enzymes for digestion of intracellular matrix and recycling of old material

• Small, irregularly shaped organelle

Lysosomes

• Removes toxic substances and other metabolites using hydrogen peroxide (typically found in liver)

• Morphologically similar to lysosomes

Peroxisome

• Allows for exchange between the ER, golgi, lysosomes, and outside the cell

• Transports via endocytosis and exocytosis

• Commonly transports hormones and neurotransmitters

Transport Vesicles

Taking in particles into cell

Endocytosis

Release particles outside of cell

Exocytosis

• Provides structural support, cell movement and division, transport of organelles and structures

• Includes actin, microtubules, and intermediate types of filaments

Cytoskeleton

Present in all eukaryotic cells, but are especially abundant in muscle cells

Actin

Distribute duplicated chromosomes to daughter cells

Microtubules

Strengthen the cell mechanically

Intermediate

Organism that is studied to better understand fundamental biological processes and promote human health

• reproduces rapidly, easily maintained, genetically manipulated, transparent

• E. Coli, yeast, arabidopsis, flies, worms, fish, mice

Model organisms

Monomers of carbohydrates

Sugars

Energy storage (starch for plants, glycogen in animals) and structural support are what kind of polymer

Polysaccharides (carbohydrates)

Explain what happens during carbo-loading

• Eating food high in carbs gets stored as energy in glycogen.

• When the energy is needed, these glycosidic bonds get broken and the energy can be used.

Reaction when two monomers bond together through the loss of a water molecule

Dehydration synthesis

Bond between monomers is broken by addition of a water molecule

Hydrolysis reaction

• Oligosaccharides covalently linked to proteins (sugar + protein)

• Found in cell membranes to protect cell surface and cell-cell adhesion

Glycoproteins

• Oligosaccharides covalently linked to lipids (sugar + lipid)

• Found in cell membranes to protect cell surface and cell-cell adhesion

Glycolipid

Monomers of lipids

Fatty acids

• Long hydrocarbon chain + carboxyl

• Site of covalent interactions

• Has hydrophilic head and hydrophobic tail

Fatty Acids

Type of fat made of single bonds and has a linear structure

Saturated

Type of fat with double bonds and kinked structure

Unsaturated

• 3 fatty acids covalently linked together to a glycerol molecule

• Stores energy and found in fats

Triglyceride

• Made of phospholipids (2 fatty acids, glycercol, phosphate group)

• Polar head and nonpolar tail

Bilayer

Nucleic acid monomer

Nucleotide

Two type of nucleic acids

DNA and RNA

Nucleotide make-up

• Phosphate group

• Sugar

• Nitrogenous base

How is a nucleic acid formed

• phosphate group covalently binds to hydroxyl group of sugar

• forms a phosphodiester bond via dehydration synthesis

Pyrimidines

Cytosine, uracil, thymine

Purines

Adenine, guanine

• Sugar and phosphate group make backbones

• Bases are on the inside of helix

• Nitrogenous bases form hydrogen bonds

DNA structure

• Storage of chemical energy (like ATP)

• Combines with other groups to form coenzymes and used as a signaling molecule

Functions of nucleotides

1. Enzymes

2. Structure

3. Transport

4. Motion and movement

5. Stores amino acids

6. Signal and receptor

7. Transcription regulators

Functions of proteins

Monomers of proteins

Amino acids

Make-up of amino acids

• R-group

• Alpha carbon

• Carboxyl and amino groups

Linear sequences of amino acids formed by peptide bonds covalently

Polypeptides

Common noncovalent interactions between polypeptides

• Hydrogen bonding

• Ionic

• Van der Waals

• Hydrophobic interactions (nonpolar clusters in the middle, polar side chains)

Final folded 3D structure of the polypeptide determined by the amino acid sequence in the polypeptide to be most energetically favorable

Conformation

Loss of conformation, tertiary structure, typically by change in pH, temperature, ionic concentration and solvents

Denaturation

Restoration of conformation of protein when denaturant is removed

Renaturation

Helps proteins fold into correct conformation

Chaperone proteins

• Linear sequence of amino acids

• Held together by peptide bonds

Primary Structure

• Regions of protein stabilized by hydrogen bonds between atoms on the backbone

• Includes alpha helix and beta pleated sheets

Secondary structure

Polypeptide that twists around itself to form a right-handed spiral shape using hydrogen bonds

• forms every 4th amino acid, complete turn every 3.6 amino acids

Alpha helix

Transmembrane proteins and coiled coils are formed by what structure?

Alpha helices

• hydrophilic peptide backbone groups face inside of coil

• hydrophobic side chains face away from the coil

• this allows helix to embed into hydrophobic lipid membrane

Transmembrane proteins

• 2-3 alpha helices twist around each other

• hydrophobic residues form a stripe along each helix that interact with each other

Coiled coils

Polypeptide that creates a pleated, sheet-like structure using hydrogen bonds, can be parallel or anti parallel

Beta sheets

3D shape of single polypeptide from interactions between R groups

Tertiary structure

A segment of a polypeptide that can independently fold into a stable structure with domains that are associates with a discrete function

Protein domain

Short, unstructured segments that link domains and provides flexibility for loops in a protein and tethering adjacent proteins

Intrinsically disordered

• Association of 2 or more polypeptides from interactions between R groups

• Each polypeptide chain is called a subunit (ex. hemoglobin)

Quaternary structure

Keratin, collagen, elastin are what type of protein?

Quaternary structured proteins

Alpha helix polypeptides that form a coiled-coil

Keratin

3 long polypeptide chains that wind around each other to form a triple helix

Collagen

Loose unstructured mesh network held together by disulfide bonds

Elastin

Nucleotide make up

Phosphate group, sugar, nitrogenous base

Nucleoside make up

Sugar and nitrogenous base

Kinds of bonds along the sugar phosphate backbone

Phosphodiester bonds (covalent): 3’ hydroxyl group bonds via dehydration synthesis with the 5’ phosphate end

Bonds between nitrogenous bases

Hydrogen bonding

Whole set of genes present, but may or may not get expressed

Genome

Why does the double helix in DNA twist?

Because of the bond angles that form between the atoms that make up the nucleotide (sugar, phosphate group, and nitrogenous base)

T/F: Purines are bigger than pyrimidines

True

Difference in 2’ carbon in RNA and DNA

DNA contains a H, RNA has OH group

• Rod-shaped structure make of condensed double stranded DNA

• Allows for efficient packing and division of DNA during cell division 

• DNA bound proteins compact DNA into condensed structure

Chromosomes

Complex with DNA and protein

Chromatin

Set of one maternal and one paternal chromosomes that form a pair that have the same genes, but different alleles (versions of genes)

Homologous Chromosomes

Identical copies of the single chromosome

Sister chromatids

The only non homologous chromosome pair, XY for male and XX for female, along with variances

Sex chromosomes

How many chromosomes do humans have? 

23 pairs total (22 autosomal, 1 sex chromosomes) 

Ordered display of the full set of 46 human chromosomes

Human karyotype

The ordered series of events that take place when a cell divides into two daughter cells involving the chromosomes going through interphase (where they are duplicated) and mitosis (where they are distributed to two daughter cells)

Cell Cycle

During this phase in the cell cycle, chromosomes are long, thin, and tangled threads of non-condensed DNA; loosely occupies a particular region of the nucleus

Interphase 

Three specialized DNA sequences during interphase

Replication origin, telomeres, centromeres

Specific sequence that initiates DNA replication

Replication origin

Repeated nucleotide sequences at the chromosomes ends, necessary for replication by preventing DNA degredation

Telomeres

Specialized sequence where microtubles attach during cell division

Centromeres

During this phase of the cell cycle, the chromosomes are highly condensed DNA structures. Attaches to mitotic spindle and separate duplicated chromosomes to each daughter cell.

Mitosis/mitotic chromosome

Proteins that pack and organize DNA

Histones

DNA wrapped around a core of histone proteins 

Nucleosomes 

The study of changes in gene expression that occurs without changing the DNA sequence, chemically modified to increase or decrease packing of DNA, which changes gene expression

Epigenetics