BMED 3600 Exam 1 Review: Cells and Genomes, Proteins, & DNA

How can you get rid of genes after they are produced?

Short interfering RNA

How do cells store hereditary information?

As double stranded DNA

How do cells move?

By making matrix metaloproteases

What expresses genes?

RNA

What is the general order to produce a protein ?

DNA > RNA > Protein

What is the result of gene expression?

Protein

What drives reactions?

Free energy

What is the currency of energy?

ATP

What is the outer layer of a cell?

The plasma membrane

What is the plasma membrane made of?

Lipids

What is the structure of a lipid?

Polar hydrophilic head and non-polar hydrophobic tail

Describe how phospholipid mono layers and bilayers are formed.

Phospholipid mono and bilayers are formed using the hydrophobic effect, where the polar hydrophilic heads touch the solution (usually water) and the non polar hydrophobic tails are not. In a bilayer, the hydrophobic tails aggregate together with a subsequent hydrophilic head on the inside , making a meicelle. In a monolayer the hydrophobic tails are still exposed but do not touch the solution.

What is one thing lipids are important for?

Breathing

What are the 3 domains of life?

Bacteria, archaea, and eukaryotes

Why would a vaccine fail in someone who is taking antibiotics?

Antibiotics reduce metabolite production so the microbiome has changed

How can you determine a microbiome?

Via stool sample (clinical isolate)

What are bacteria flagellum made of?

Motor proteins

What is horizontal gene transfer

The non-sexual transfer of genetic material, usually occurring between bacteria.

**Only happens between organisms of the same species

What is the rate limiting step of mammalian migration?

The ability of the nucleus to move through a space

What is phagocytosis?

The process in which a white blood cell engulfs and breaks down a bacteria

How does your body make an antibody?

The proteins from the broken down bacteria act as a memory for the white blood cell to recognize the same pathogen

What do white blood cells do?

They act as the key immune cells, fighting disease and forming antibodies

How do things enter and leave the cell?

They enter by endocytosis with the help of an endoscope and are expelled by the Golgi apparatus by exocytosis

What is a covalent bond?

sharing of electrons between atoms

What charge is DNA?

negative

Why is DNA negatively charged?

phosphate groups

Why doesn't medicine use covalent bonds?

They are the strongest bonds, making them difficult to break and the purpose of medicine is to release something

How many amino acids are there?

20

What is the order of chemical bonds from strongest to weakest?

covalent, ionic, hydrogen, van der waals

What are the 4 macromolecules?

Polysaccharides, lipids, nucleic acids, proteins

What makes up polysaccharides?

Sugar

What makes up nucleic acids?

nucleotides

What makes up proteins?

amino acids

What makes up lipids?

Fatty acids

What is a condensation reaction?

When two molecules bond through the loss of a water molecule.

What is a hydrolysis reaction?

a reaction in which a bond is broken by the addition of a water molecule

What is entropy?

a measure of the disorder of a system

Are all chemical reactions a cell needs spontaneous?

No, some reactions are unfavorable and not spontaneous, which is why there are enzymes

What are enzymes?

Proteins that speed up chemical reactions by lowering activation energy

Do enzymes change the equilibrium point of a reaction?

No

How do changes arise between organisms?

Through alteration of genetic information

What allows hydrogen bonds to form?

polarity

What are the different noncovalent interactions?

hydrogen bonding, ionic bonding, hydrophobic forces, and van der waals interactions

Is it more energy to build or break down a molecule?

Building

What are the Gibbs free energy reactions?

dG = dH - TdS or dG = dG_o - R*ln([x]/[y])

How do you find the Gibbs free energy for a catalyst?

dG_cat - dG_uncat

What are different kinds of proteins?

Enzymes, structural proteins, motility proteins, regulatory proteins, transport proteins, antibodies

What do structural proteins do?

provide physical support and shape

What do motility proteins do?

contraction and movement

What do regulatory proteins do?

control and coordinate cell function

What do transport proteins do?

move substances in and out of cells

What do antibodies do?

Antibodies destroy bacteria and viruses, thereby preventing them from entering host cells.

What is ionized at pH 7 on amino acids?

Both the amino (+) and carboxyl groups (-)

How are amino acids connected?

peptide bonds

What are peptide bonds?

covalent bonds between amino acids (C-N) with no rotation, partial double bonds

What type of interactions help proteins fold?

Non-covalent interactions

What determines a proteins charge?

pH, assembly, and type

What would result in an incomplete protein-protein interaction?

If specific points are not bound properly

What does interluekin-1 do?

cause inflammation

What determines whether or not something is very contagious?

How strongly and quickly it binds to a receptor

How does mutation benefit viruses?

It allows it to change to increase binding affinity and more efficiently infect a host

What is one example of viral mutation?

The COVID spike protein mutated over time to bind to the ACE-2 receptor, which is readily inside people and cats

How is the alpha helix formed?

hydrogen bonding between carbonyl Os and amide Hs of peptide backbone

- amino acid R- groups point outwards away from the central axis of the helix

How frequent are turns along the alpha helix?

1 turn every 3.6 amino acids

What parts of the alpha helix come together?

The hydrophobic parts (nonpolar interacts) interact with each other on the inside of the helix

Can all amino acids be accommodated into an alpha-helix?

No, due to sterics some amino acids will destabilize the alpha helix and as a result will be less likely to be found in an alpha helix.

(Glycine, Proline, valine, threonine, isoleucine)

How are beta sheets formed?

Hydrogen bonding between the side chains of the amino acids

What are alpha helices and beta sheets examples of?

Secondary structures

What is the tertiary structure of a protein?

3D folded structure, where each domain has its own function

What is the quaternary structure of a protein?

Occurs when a protein is made up of two or more polypeptides that for a stable complex with a single specific purpose

What is an example of a quaternary structure?

Hemoglobin

How does hemoglobin work?

It has 4 hemes that binds oxygen and changes conformation with each bonding of an oxygen molecule, it then carries and releases oxygen throughout the body. It also removes carbon dioxide from the body in a similar process.

Define cell signalling

A cascade of enzymatic reactions

How are proteins activated?

Phosphorylation

Define surface sampling

The process by which cells feel out their surroundings to determine cell differentiation

What does the gut lining do?

Prevents bacteria from entering the body and blood stream

What are metalloproteases?

Proteases that use specifically coordinated metal ions to do the same mechanism as serine proteases in place of the catalytic triad, they break down the extracellular matrix

What amino acids have thiols (S-H)?

Cysteine

What happens if you break down disulfide bonds?

The protein can change conformation (denature) and have unknown interactions

How big are typical eukaryotic cells?

10-100 um

Why are amyloid plaques bad?

They block neuron activity and result in immune response

What happens when the tau protein becomes hyper-phosphorylated?

Activity and signaling increasing, resulting in neuron death due to the system being overwhelmed

How do proteins work?

Selective binding with non-covalent interactions

What is the antibody naming convention?

Anti-"protein name"

What part of the antibody structure is made specifically for each virus?

The V_H domain

What cell makes antibodies?

B-cell

How do B-cells make a variety of V_H domains?

They undergo rapid division and mutations to create antibody molecules, survival of the fittest model

What happens when there are too many antibodies?

Lymphoma and lupus

How do antibodies function?

The bind to the proteins they are against to prevent it from binding

Define antigen

A protein, part of a pathogen or diseased cell

(Ex. Spike protein)

Why does your immune system not kill cancer cells?

They are your own cells

Define negative regulation

A side product inhibits the very pathway that initiates its production

Define Km

substrate concentration when V = 1/2 Vmax

Define Vmax

Maximum rate of reaction

What is the Michaelis-Menten equation?

V = (Vmax [S])/(Km + [S])

V = Rate

Vmax = Theoretical max rate

[S] = Substrate conc

Km = Michaelis constant

How does competitive advantage work with enzymes?

Hate bed has a higher affinity will bind to the substrate

Define binding affinity

the degree of chemical attraction between a ligand and a receptor

Define competitive inhibition

When an inhibitor has to compete with a substrate to bind to an enzyme. This is because there is only one active site for the inhibitor to bind to.

Define non-competitive inhibition

When an inhibitor binds to an allosteric site instead of an active so it does not compete with a substrate. The inhibitor's binding to the active site distorts the shape of the active site. Therefore, the substrate cannot bind to the active site anymore.

What does a kinase do?

adds phosphate