Cell Bio Exam 1

Review from previous classes + new content.

What is cell theory?

All living things are formed by growth and division of cells. All cells come from other cells.

What is a cell?

An aqueous solution of chemicals enclosed by a membrane that can self replicate and perform functions of life.

What is cell biology?

The study of cells and their structure. functions, and behavior.

Why should we study cell biology?

1. Provide insight on the origins of life

2. Understand how diversity is achieved

3. Understand why cells colonize every environment

4. Understand how drugs interact with cells

What are 3 characteristics of all cells?

1. All cells are made of the same basic chemistry, following the central dogma and containing genes, therefor the ability to evolve.

2. All cells reproduce

3. Living cells all evolved from the same ancestral cell

What is the Central Dogma of biology?

Genetic information flows in one direction; DNA is transcribed to RNA, and RNA is translated to proteins.

What are the differences and similarities between eukaryotes and prokaryotes?

Eukaryotes contain membrane-bound organelles, while prokaryotes do not (ribosomes not membrane-bound). Eukaryotes have a nucleus that is bound by two membranes (true nucleus), while prokaryotes only have a nucleoid region. Eukaryotes have linear chromosomes while prokaryotes have a single circular chromosome. Eukaryotes have larger ribosomes (80S, 40 and 60S subunits) while prokaryotes have a smaller ribosome (70S, 30S and 50S subunits). Both cell types have a plasma membrane, ribosomes, cytoplasm, and DNA.

Nuclear envelope

2 concentric membranes with protein pores that surround the nucleus

Mitochondria

Enclosed in two membranes with the inner membrane formed into folds. Site of cellular respiration and creates ATP for energy. Contain their own DNA.

Chloroplasts

Enclosed by two membranes, containing thylakoid stacks that contain a green pigment called chlorophyll. Site of photosynthesis and produce ATP. Found in photosynthetic plants and protists. Contain their own DNA.

Endosymbiotic Theory

The theory that mitochondria and chloroplasts originated as mutualistic prokaryotes before becoming organelles in the eukaryotic cell. Supported by ribosomal subunits being 50 and 30S, size and shape, containing own DNA, and containing respiratory chain elements.

Endoplasmic reticulum

The organelle where most cell components are made, made up of stacks of interconnected spaces enclosed by a membrane.

Golgi apparatus

A membrane-bound cell organelle that modifies, sorts, and packages proteins and lipids for delivery to targeted destinations inside or outside the cel

Lysosomes

Organelles that provide intercellular digestion, releasing nutrients from food and breaking unwanted molecules

Lysozymes

Antibiotic enzymes that break down the cell walls of bacteria.

Peroxisomes

Inactivate toxic molecules

Cytosol

The water like gel in cytoplasm

Cytoplasm

Cytosol and all organelles suspended in it, but not their inner contents.

Cytoskeleton

A dynamic network of protein fibers and tubules in the cytoplasm of a cell that gives the cell its shape, support, and ability to move. contains three major protein filament components; 1. Actin filaments. 2. Intermediate filaments. 3. Microtubules. Allows for motor protein movement

Motor proteins

Use ATP to carry organelles and proteins along the cytoskeleton

Pinocytosis

a cellular process where a cell swallows extracellular fluids and dissolved small molecules

Phagocytosis

the cellular process where a cell engulfs and digests large solid particles

What bonds are strongest within the cell, and why?

Covalent bonds. They can withstand cellular conditions, as ions disassociate in water.

Hydrogen bonds

a special type of attractive force that happens when a hydrogen atom covalently bonded to a very electronegative atom (like nitrogen, oxygen, or fluorine) experiences electrostatic attraction to another electronegative atom with a lone pair of electrons

Van der Waal attraction

weak, distance-dependent forces of attraction between atoms or molecules that do not involve sharing or transferring electrons

Hydrophobic force

the natural tendency of nonpolar substances (like oils and fats) to aggregate together in water rather than dissolve

How can non-covalent interactions hold macromolecules together if they are weaker?

There is “strength in numbers”, many interactions working together become strong enough to hold molecules together

What are the 4 main organic monomers?

Sugar, fatty acids, amino acids, and nucleotides

What are the polymers (macromolecules) for the 4 main organic monomers?

Polysaccharides, lipids/fats, proteins, and nucleic acids

What bonds link simple sugars to make polysaccharides?

Glycosidic bonds (covalent)

Carbohydrates

Includes simple (glucose, fructose, sucrose) and complex sugars (starch, cellulose, glycogen)

What is the molecular formula for monosaccharides?

(CH₂O)_n

Glycogen and starch

Used to store energy. Glycogen for animals, and starch for plants

Oligosaccharides

Carbohydrates made of 3-10 monosaccharides. Can be covalently linked to form glycoproteins. Found in all cell membranes where sugar side chains protect cell surfaces and help cells adhere to each other.

Fatty acids

Amphipatic molecules that contain a long hydrophobic (nonpolar) hydrocarbon chain and a hydrophilic (polar) carboxyl group (COOH-)

Amino acids

small molecules with an animo (NH₂) group and a carboxylic acid (COOH) group attached to an alpha-carbon atom; contains an R side chain that allows for different functions and behavior

What bond holds amino acids together?

Peptide bonds (covalent)

Where is the C- and N-terminus of a polypeptide?

C-terminus is at the COOH group end and the N-terminus is at the amino group end.

Nucelotides

A monomer that is an N containing ring linked to a 5-carbon sugar (ribose or deoxyribose) with one or more phosphate group (PO₄^-3)

Nitrogenous bases

One of the components of a nucleotide, pyrimidines are a 6 carbon ring (cytosine, thymine, and uracil) while purines have two connected rings (a 6 and 5 carbon ring) (adenine and guanine)

Nucleoside

A nitrogenous bade + sugar with NO phosphate group

What type of monomer is ATP and GTP?

Nucleosides

What bonds connect nucleotides to form nucleic acids?

Phosphodiester bonds (covalent)

How are polymers formed

Condensation reactions/dehydration synthesis

What is the order of organization for molecules?

Subunits/monomers are linked by covalent bonds to form macromolecules, which are connected via non covalent interactions to form macromolecular complexes (organelles)

Why are noncovalent interactions important in cells?

They allow macromolecules to adapt to unlimited shapes and conformations that are important for activity and functions

What are the functions/roles of RNA?

1. Make proteins (not by itself)

2. Regulate gene expression

3. Gene splicing and processing

4. Help with defense against viruses

How does transcription begin?

In the nucleus, RNA polymerase weakly binds to DNA until it reaches a promoter region (TATA box in eukaryotes, Pribnow box and -35 region in prok.), and binds to transcription factors (sigma factors in prokaryotes) to form the transcription apparatus (holoenzyme in prokaryotes) and begin unwinding DNA

What is the lifespan of mRNA?

Less than 10 minutes to 30 hours

What are the components needed for transcription?

Template DNA, machinery such as RNA polymerase, transcription factors, and nucleotides

How does mRNA leave the nucleus?

mRNA recognizing proteins (nuclear pores) bind to mRNA and transport it through the membranes

How do microRNAs regulate gene expression?

They interact with target mRNA post-transcription and induce degradation, resulting in translational suppression

How does translation occur?

Ribosomal subunits bind to mRNA and reads it, linking amino acids together in a sequence determined by the mRNA. tRNA has anticodons to mRNAs codons, and carries amino acids that correspond to the codon on mRNA.

Ribozymes

rRNA in ribosomes that catalyze translation. Millions exist in the cytosol. Ribosomes are 60% RNA and 40% proteins.

What is the function of rRNA in ribosomes?

rRNA physically binds and aligns messenger RNA (mRNA) and transfer RNA (tRNA) within the ribosome. This ensures the genetic code carried by mRNA is read accurately and translated into the correct sequence of amino acids. It also provides the catalytic component of ribosomes.

Why is RNA associated with early life? (RNA World Hypothesis)

Because RNA is the only biological molecule that can store genetic information AND catalyze chemical reactions. Proteins do not store information, and DNA does not have catalytic capabilities. If you need one to make the other, how did they come to be? RNA could theoretically copy themselves. Over time, DNA “took over” genetic storage due to its stable double-helix structure, and proteins “took over” reactions due to their better catalytic capabilities.

What are the 5 categories of proteins with examples?

Structural (keratin), protective (immunoglobulin), regulatory (insulin), contractile (myosin and actin), and transporting (hemoglobin)

What are the optical isomer forms of proteins?

D- forms and L- forms (L only exist in proteins)

How do amino acid side chains give proteins their shape and function?

Amino acid side chains have different polarities, sizes, and compositions. These cause different noncovalent interactions between each other to give proteins unique shapes and functions.

How can proteins become unfolded?

Environmental conditions such as pH change, chemical treatments, or temperature. Genetic mutations can also cause misfolding.

Denaturation

When proteins lose their conformation

Chaperones

Proteins that assist in folding. Increase the rate at which a protein could spontaneously fold; creates an energetically favorable pathway. Can also help denatured proteins renature (if the result of environmental conditions, not genetic mutation).

Amyloid structures

Aggregates of proteins as a result of misfolding, can damage cells and tissues.

What is the primary structure of proteins?

Amino acid sequence

What is the secondary structure of proteins?

Twists (alpha helixes) or pleated folds (beta sheets) formed by hydrogen bonds between amino acids

What is the tertiary structure of proteins?

The complete three-dimensional folding pattern of a single protein chain. This shape is driven by interactions among amino acid side chains (R-groups), including hydrophobic interactions, ionic bonds, and disulfide bridges

What is the quaternary structure of proteins?

2 or more polypeptide chains bonded together

When do functions appear in protein structure?

tertiary (if single subunit) and quaternary

How are alpha helixes and beta sheets formed?

hydrogen bonding between NH and C=O groups in the polypeptide backbone

How are tertiary structures formed?

Hydrophobic interactions between alpha helixes and beta sheets

Protein domains

Segments of a polypeptide chain that can fold into a compact, stable structure

How are quaternary structures formed?

Enabled by many weak noncovalent bonds, interacting via binding sites. Each polypeptide is a subunit

Globular proteins

Water soluble

Fibrous proteins

Not water soluble

How are extracellular proteins stabilized?

Cross-linkages, such as disulphur bonds. Reinforce shape. Ex. antibodies

Induced fit

Proteins have great specificity when it comes to binding.

Ligand

Any substance bound to a protein. (Ex. substrates for enzymes)

Binding site

The region of the protein associated with the ligand

Active site

The binding site of substrates in enzymes.

What are the steps of an enzyme catalyzing a reaction?

Substrates bind to the active site and form the enzyme-substrate complex. Substrates change in shape slightly as they bind. Substrates then become products and form the enzyme-products complex, and products are released.

Michaelis-Menten Enzyme Kinetics

A way of graphing enzyme affinity by plotting substrate concentration with a form of rate.

K_m

The affinity constant, equal to the x-intercept of ½ of V_max

V_max

Max rate of enzyme activity

Enzyme affinity

How strongly an enzyme binds its substrate

Higher affinity enzymes are…

Better at finding substrates at low concentrations

Lower affinity enzymes…

Worse at finding substrates in lower concentrations; less efficient

What is an example of enzyme affinity in humans?

Fetal hemoglobin has a higher affinity than adult hemoglobin, as there is less oxygen availability in the placenta, so hemoglobin has to be good at finding oxygen in low concentrations, and bind strongly to it.

At high affinity, V_max and K_m are ____ and the reaction rate at low concentrations is _____

Lower, faster

Lysozymes

Antibiotic enzymes found in egg whites, saliva, and other bodily secretions that bind to polysaccharide chains (NAM and NAG) in bacterial cell walls, causing them to lyse.

How can enzymes be regulated?

By the addition or removal of a phosphate group. Kinase adds P, phosphotase removes P.