Foundations Exam Part 1 Flashcards
What are some examples of lipids in the body?
Fatty acids, cholesterol, and other hydrophobic molecules
What is the most essential component of a cells membrane?
The phospholipid
What is the definition of an epimer?
Diastereomers whose configuration differs only at one asymmetric carbon
Aldoses and ketoses form ________
cyclic structures
Glucose cyclizes to form Two Pyranose Ring Structures
These are called _______-type diastereomers
Anomer-type Diasteromers
Alpha-anomer has -OH at C-1 on ________ side of ring from -CH2OH at chiral carbon atom that determines ____ or ____ configuration
Alpha-anomer has -OH at C-1 on OPPOSITE side of ring from -CH2OH at chiral carbon atom that determines D or L configuration
Beta-anomer has -OH on the ____ side of ring as the CH2OH at the chiral carbon atom
Beta-anomer has -OH on the SAME side of ring as the CH2OH at the chiral carbon atom
D-Fructose Cyclizes to a 5-membered ______ ring structure
Furanose
List the Purines
Adenine and Guanine
LIst the Pyrimidines
In DNA: Thymine and Cytosine
In RNA: Uracil and Cytosine
Definition: Base attached to a pentose sugar
Nucleoside
Definition: Monophosphate, diphosphate, and triphosphate of esters of nucleosides
Nucleotide
A-T base pairs form ______ hydrogen bonds
A-T base pairs form 2 hydrogen bonds
G-C base pairs form _____ hydrogen bonds
GC base pairs form three hydrogen bonds and are more stable than AT-rich regions
Proteins are ______ chains of _______ covalently linked amino acids
Proteins are linear chains of COVALENTLY linked amino acids
Polypeptide chains are directional and the chains are denoted from ____ to _____ end
Polypeptide chains are directional and conventionally chains are denoted from N to C end.
Secondary structures of proteins entail
alpha helixes (side chains are on the outside of the helix)
Beta strands align in parallel or antiparallel orientation to form Beta sheets
Hydrogen bonding rich in secondary structures
In tertiary structures of proteins, what is the folding driven by?
Folding is driven by the burial of hydrophobic residues from water
Where do proteins undergo post-translational modification?
In the ER and Golgi body proteins under post-translational modification
What is Glycosylation?
Glycosylation is a form of protein modification in the secretory pathway.
Secretory proteins have a signaling sequence at the beginning of them
What are Signal recognition particles and in what processes do we find them?
SRPs bind to signaling sequences in glycosylation. Glycosylation is a form of post-translational modification.
SRP binds to receptors on the endoplasmic reticulum and move protein through pores in the ER.
Where does glycosylation occur?
Glycosylation occurs in either the ER or the Golgi.
What are the roles of glycosylation?
-N linked on asparagine, O-linked on Serine
-Assists in protein folding to reach the correct shape
-Enhance protein solubility
-Stabilize the protein against denaturation
-protect the protein from proteolytic degradation
-target the protein to specific subcellular locations
-Serve as a recognition signal for carbohydrate-binding proteins (lectins) or provide special properties
Write out the answers to the following questions
write out
What are some of the main types of lipids found in the body?
- TRIACYLGLYCEROLS (aka triglycerides the most common lipid)
- Phospholipids
- Sterols
Be able to describe properties of glucose and fructose
Glucose and fructose are functional isomers of each other.
They have the same molecular formula C6H12O6
-But the have DIFFERENT functional groups in the chemical formula
-GLUCOSE HAS AN ALDEHYDE GROUP
FRUCTOSE HAS A KETONE AS A FUNCTIONAL GROUP
Give some examples of disaccharides and polysaccharides
Common disaccharide examples:
1. Sucrose (glucose-fructose)
2. Lactose (galactose-glucose)
3. Maltose (glucose-glucose)
Examples of polysaccharides:
Starch, cellulose, glycogen
Describe the structure of an amino acid
Amino acids are made up of a basic amino group (-NH2), and acidic carboxyl group (-COOH), and an organic R group that is unique to each amino acid
Describe the different types of amino acid side chains
There are 4 different classes of amino acid side chains
1. non polar and neutral
2. polar and neutral
3. acidic and polar
4. basic and polar
How do Enzymes catalyze reactions?
Sometimes reactions have too big of an activation energy to occur,
the enzyme reduces that thermodyanmic barrier so that a reaction can occur at a useful rate
For this happen, the enzyme and the substrates must bind together, form a transient complex where the reaction occurs, then releases the products
What is the protoplasm composed of?
Protoplasm= cytoplasm + karyoplasm
Who proposed the cell theory and when?
Robert Hooke in 1839
What are the five components of the Cell Theory?
- Organisms are composed of cells
- Each cell is composed of small mass of protoplasm containing cytoplasm in its inside and a plasma membrane with or without cell wall on outside
- New cell arise from pre-existing cells
- All cells are similar in physiology and chemistry
- The activities of all organisms are a result of interactions between the cells
What are the basic features of a eukaryotic cell?
- plasma membrane
- cytosol that contains organelles
- chromosomes that carry genes
What molecule primarily makes up the cell membrane?
- LIPIDS
Describe the phospholipid bilayer
Describe the membrane fluid mosaic model
- The membrane is fluid: most protein and phospholipid molecules can move laterally like the icebergs in a sea of lipid
- A membrane is mosaic: Proteins and other molecules are embedded in a framework of phospholipid bilayer
The sealed compartment formed by a phospholipid bilayer is the most ______________ conformation
It is the most energetically favorable conformation
What are the two proteins embedded in the lipid bilayer
- Integral proteins: span the membrane
- Peripheral proteins: attached to the polar end of the lipids
What are the types of membrane proteins?
- Cell-cell recognition proteins
- Integrins
- Intercellular junction proteins
- Enzymes
- Signal transduction proteins (receptor proteins)
- Transport proteins (Passive and active)
What is the function of a kinase?
It attaches a phosphate group to the -OH on the side chain of serine or tyrosine in proteins
What is the function of a phoshatase?
Removes a phosphate
What is a protease?
An enzyme which opens peptide bonds in proteins
What is an isomerase?
Converts one isomer of a small molecule into another
What is a transferase?
It transfers one chemical group from one molecule to another
Experimentally you can measure the velocity as a function of substrate concentration using what equation
The Michaelis-Menten Equation
Explain how Km and Vmax are effected in: Competitive inhibition
Increases Km but no effect on Vmax
Explain how Km and Vmax are effected in: Non-competitive inhibition
No effect on Km but reduces Vmax
Explain how Km and Vmax are effected in: Allosteric inhibition
This is an inhibitor which laters the conformation of the enzyme and could affect both Km and Vmax
Define Vmax
its the rate of the work being done by companies (enzymes)
Define Km
Km is like the amount of workers (substrate concentration) for the company to be working at a rate of 50% of their max
What does a high Km mean
A high Km is like needing more workers (more substrate) to get the job done at half max speed (vmax) because they are less efficient (low affinity)
What does low Km mean
A low Km is like having less workers (less substrate) for the companies (enzyme) to get the job done at half speed, because they are more efficient (high affinity)
What does it mean for something to be at equilibrium?
At equilibrium, the rate of forward and reverse reactions are not changing so the concentrations of products and reactants are not changing.
A reaction at equilibrium DOES/DOES NOT mean that products and reactants have the same concentration
A reaction at equilibrium does NOT mean that products and reactants have the same concentration, but it means that the concentrations are not changing.
Blood and other body fluids are usually close to pH ____
7.4
Buffers rely on the equilibrium between a ________ and its _________
Buffers rely on the equilibrium between a WEAK ACID (HA) and its conjugate base (A-)
If you add acid (H+) you will drive the equilibrium to the ______, and the pH increase is ______
If you add acid (H+) you will drive the equilibrium to the left, so the pH increase is reduced
What is a really important biological buffer found in the body and where?
Bicarbonate is a really important biological buffer found in body fluids including saliva and blood
A mole of a substance contains ________ molecules
6.022 x 10^23 molecules
Molarity is _______
Molarity is the amount of substance moles per volume
1 mole of a substance is equal to its _______
Molecular weight in grams
Memorize this picture
An odontoblast cell is an example of a eukaryotic cell
What is the structure and function of the glycocalyx?
It is a carbohydrate layer made up of glycoproteins and polysaccharides. They can function for protection, attachment, and molecular recognition
What component makes up about 70% of the cell volume?
The cytoplasm.
Within cytoplasmic structures, what are the nonliving and living structures called?
- Nonliving structures are called inclusions
- Living structures are membrane bound and are called organoids or organelles.
What are inclusions? Describe them and give some examples.
Secretory substances found in the cytoplasm that are nonliving. Some examples are oil drops, tri-glycerols, glycogen, glycogen granules, and starch granules.
List membrane bound organelles:
- Mitochondria
- Golgi
- ER
4.Secretory granules (vesicles) - Lysosomes
- Microbodies (peroxisomes)
List the non membranous organelles
- ribosomes
- cytoskeletal structure
- centrioles
- cilia & flagella filaments
Cells are classified based on _________ or ____________
Cells are classified on the tissue they form or the specialized and unique function they carry out.
What molecules can pass through the cell membrane directly?
FATS AND OILS can pass directly through
The rate of diffusion of a molecules depends on lots of things but the main factor is its solubility in oil.
_______ , ________ molecules readily dissolve in lipid bilayers and therefore diffuse rapidly across the lipid bilayer.
Small nonpolar molecules readily dissolve in lipid bilayers and there diffuse rapidly across them.
The lipid bilayer is highly impermeable to _______ molecules
the lipid bilayer is highly impermeable to CHARGED molecules, no matter how small the charge
Facilitated diffusion is ______ dependent but requires the presence of __________.
Facilitated diffusion is concentration dependent but requires presence of protein carrying molecules to which molecules bind specifically but the binding is REVERSIBLE.
What is active transport and give an example.
Active transport is independent of a concentration gradient. An example is the sodium potassium pump. 3NA in and 2K out.
What is an important membrane adaptation for active transport?
The presence of a specific carrier proteins or pumps to facilitate movement.
What are the three types of proteins/transporters found in active transport?
- Uniporter: carries one specific ion or molecule.
- Symporter: carries two different ions or molecules, both in the same direction.
- Antiporter: Also carries two different ions or molecules, but in different directions.
These three types of transporters can also transport small, uncharged inorganic molecules like glucose. These three types of carrier proteins are also found in facilitated diffusion, but they do not require ATP to work in that process
Define: Endocytosis, phagocytosis, pinocytosis
Endocytosis: Transport of large molecules or small particles into the cells
Phagocytosis: (cell eating) ingestion of particulate matter, including bacteria and other cells
Pinocytosis: (cell drinking) ingestion of bulk fluid. Extracellular fluids such as hormones and enzymes by the body cells.
Describe the two forms of Pinocytosis
- Smooth pinocytic vesicles (fluid phase pinocytosis)
- Coated vesicles (receptor mediated endocytosis)
Explain how smooth pinocytic vesicles function and where they are found?
The plasma membrane invaginates to form small pits or caveolae that project into the cell.
-The opening of the pit constricts into a narrow neck, and further constriction results in the separation of a vesicle from the membrane.
*NUMEROUS IN THE ENDOTHELIUM OF BLOOD VESSELS AND UNDER THE PLASMA MEMBRANE OF SMOOTH MUSCLE CELLS)
When is receptor mediated endocytosis primarily used?
Mainly used when you want to transport a ligand into the cell. Ligands seen in the ECM will bind to specific receptors on the cell surface or cell membrane.
Whats the difference between
1. Constitutive pathway
2. Regulated secretory pathway
- Constitutive pathway: This process is continuous, proteins that leave the cell are secreted immediately after their synthesis and exit from the golgi app.
- Regulated secretory pathway: Proteins that are concentrated and stored in secretory granules pass along the regulated secretory pathway. A regulatory event must be activated for secretion to occur.
What three components are present in the cytoskleteon of the cell?
- Microfilaments
- Intermediate filaments
- Microtubules
- What is the main component in microfilaments?
- What is a distinct feature they have
- What growth occurs in microfilaments
- Main component is actin filament
2, Distinct structural polarity - Actin growth occurs in both ends (the barbed end (+) end, and the pointed end (-) end)
What are the four types of proteins involved in actin polymerization?
- Actin polymerization is ATP dependent and involves a mechanism called treadmilling.
- Proteins involved: thymosin, profilin, cofilin, and gelsolin.
What do microtubules consist of?
Alpha and beta tubulin dimers. These polymerize in the presence of GTP.
What are the 3 types of microtubules
- Astral
2, Kinetochore - Polar (or interpolar)
What do intermediate filaments consist of?
Monomers consisting of alpha helical rod flanked by head and tail domain
What is the most stable amongst microfilaments, intermediate filaments, and microtubules
Intermediate filaments are the most stable
How does DNA differ than RNA
