Midterm 1 Flashcards
What are cells?
Small membrane enclosed units filled with concentrated aqueous solution of chemicals and capable of creating copies of themselves by growing and dividing into two.
What are the 4 properties of all cells?
Vary enormous in appearence an function
They posses the same molecular machinery
All cells evolved from the same ancestrall cell
Genes provide instructions for cell function, form and behavior.
Describe cell theory:
- Everything that id alive is made at least of one cell.
- All living organisms owe their structure and function to the fact that they are made of cells.
- All cell arise from pre-existing cells.
What are the two domains of prokaryotes?
Archea and bacteria.
What is the main characteristic of prokaryotes?
They don’t have a nucleus nor membrane-enclosed organelles.
How is the genome of prokaryotes?
It carries very little superfluous genetic package and it is relatively small.
What are the three different forms that prokaryotes can adopt?
- Spherical
- Rod like
- Corkshrew
What is the main characteristic of eukaryotes?
They are bigger and more elaborated, they have a nucleus and membrane enclosed organelles.
Describe nucleus:
Has a double membrane called nuclear envelope that contains nuclear pores.
Contains DNA molecules that become visible as chromosome in M-phase.
Describe mitochondria:
Have two separate membranes the internal is enfolded forming cristae.
Perform cellular respiration
Contain their own DNA and reproduce by dividing in two.
Describe chloroplasts:
They are present only in plants
They have two membranes plus internal stacks of membranes that contain chlorophyll.
Describe the Endoplasmic reticulum:
Irregular maze of interconnected space enclosed by a membrane. It creates cell membrane components and material destined for export.
Describe Golgi apparatus:
Stacks of flattened membrane enclosed sacs that modifies and package molecules coming from the ER.
How is the inside of the Golgi apparatus and of vesicles?
Is similar to the extracellular environment.
Describe lysosomes:
Small regularly shaped vesicles that make intracellular digestion and release nutrients.
Describe peroxisomes:
They provide a safe environment for reaction involving hydrogen peroxide.
Describe cytosol:
The largest cell component not contained within intracellular membranes and is the site of many chemical reactions.
What are the three components of the cytoskeleton?
- Actin filaments
- Intermediate filaments
- Microtubules
What are motor proteins:
They use energy stored in ATP to trundle along the cytoskeleton.
What are the 4 factors that make think that the eukaryotic cell originated as a predator?
1) Flexible cell membrane
2) Large size
3) Cytoskeleton to move and eat
4) Nuclear envelop to protect DNA
What is the function of enzyme?
Catalyze covalent bond formation and breakage.
What is the function of structural proteins?
Provide mechanical support to cells and tissues.
What is the function of storage protein?
Store amino acids and ions.
What is the function of receptor proteins?
Carry extracellular signals from cell to cell
What is the function of gene regulatory proteins?
To bind to DNA to switch gene expression on or off.
What is the side chain of a molecule?
The part of amino acid that is not involved in the formation of peptide bonds.
What are the four forces that constrain the free rotation of polypeptides?
1) Hydrogen bonds
2) Van der Waals forces
3) Electrostatic attraction
4) Hydrophobic interaction
What are the three types of interaction within a protein?
1) Backbone-backbone interaction
2) Backbone- side chain
3) Side chain- Side chain
What is conformation?
Final folded structure of a protein.
What is denaturation?
Nonfunctional configuration of a protein.
In which 2 ways do chaperone proteins assist protein folding?
1) Some of them binds to the folding proteins and help them folding to the most energetically favorable pathway
2) they forms isolation chambers in which each polypeptide can fold without the risk of forming aggregates.
Describe backbone model:
Show the overall organization of the polypeptide chain and provide a straightforward way of comparing the structure of related proteins.
Describe ribbon model:
show the polypeptide backbone in a way that emphasizes its various folds.
Describe the wire model:
Include the positions of all the amino acids side chain and this view is useful for predicting which amino acid will be involved in protein activity.
Describe space-filling model
provides a contour map of protein surface that reveals which amino acid are exposed on the surface.
Describe alpha helix:
Hydrogen bonds every 4 amino acids
Right handed helix
Backbone is hydrogen bonded to itself
Describe beta sheets:
Hydrogen bonds made between segments of various polypeptide lying side by side.
Can be parallel or antiparallel.
Describe primary structure:
Sequence and number of amino acid.
Describe secondary structure:
How segments of the sequence fold
Descrbie tertiary structure:
Three dimensional conformation of a protein.
Describe quaternary structure:
Complex structure of more polypeptide chains
What is a protein domain?
Any segment of the polypeptide chain that can fold independently into a compact stable structure.
What are the two functions of intrinsically disordered regions:
- They provide flexibility
- They facilitate the encounter between domains.
Proteins can assemble into:
- Filaments
- Sheets
- Spheres
Proteins can be either:
Globular
Fibrous
Hollow tube
How are extracellular proteins often stabilized?
By covalent cross-linkages that help maintain their structure either linking together two amino acids on the same polypeptide chain or join different proteins in a large complex.
What is specificity?
Each protein can bind with a few or just one molecule.
Specificity is due to:
- Weak non covalent forces.
- Favorable hydrophobic forces.
What is a binding site?
The region of a protein that associate with the ligand.
What are antibodies?
Immunoglobulin proteins produced by the organism in response to foreign molecule
What is an antigen?
The substrate of an antibody.
How do cell control proteins?
1) The amount of proteins a cell contains is controlled.
2) Control the rate at which proteins are degraded.
3) Confining sets of enzymes to enclosed subcellular compartments.
How are catalytic activities of enzymes regulated?
Binding at the regulatory site alter the rate at which the enzyme converts substrate into products.
Define feedback inhibition:
An enzyme acting early in the reaction pathway is inhibited by a late product of that pathway.
What are the two way of regulation of an enzyme?
- Negative: prevent an enzyme from acting
- Positive: enzyme activity is stimulated.
Define allosteric enzyme:
It can adopt two or more slightly different conformation and their activity can be regulated through the shift from one to another.
Define phosphorylation:
Attaching covalently a phosphate group to one or more amino acid.
How do GTP binding proteins act as switches?
They are in active conformation when GTP is bound but they can hydrolyze this GTP to GDP releasing a phosphate and becoming inactive.
How are the two strands of DNA held together?
By hydrogen bonds between the base portion of the nucleotides.
What are the three components of a nucleotide?
1) A nitrogen containing base
2) A five carbon sugar
3) A phosphate group attached to the 5 carbone sugar
What are the two ends of a DNA strand?
a 3’ end (containing an hydroxyil group)
a 5’ end (containing a phosphate group)
What is the consequence of complementary base pairing?
Each strand contains a sequence of nucleotides complementary to the sequence on the other strand.
How is hereditary information encoded in the DNA?
Is encoded in the sequence of nucleotides along each strand of DNA.
What is chromatin:
A complex of DNA and protein
What are homologous chromosome?
Chromosomes identical to each other, one inherited from the mother and one from the father.
What are the ony nonhomologous chromosomes in humans?
The sex chromosomes of males.
What is a karyotype?
An ordered display of the full set of 46 human chromosomes.
What is the most important function of chromosomes?
To carry genes.
What is a gene?
A segment of DNA that contains the instructions for making a particular potein or RNA molecule.
What is a genome?
The total genetic information carried by all proteins.
What are the three specialized DNA sequences of an eukaryotic chromosome?
Replication origin
Telomere
Centrosome
Describe replication origin:
Where replication of DNA ensures that DNA are replicated rapidly.
Describe telomeres:
Contain nucleotide sequences required for the end of chromosome to be replicated.
Describe centromere:
Allow replicated chromosome to be separated during M phase.
What are the three ways in which interphase chromosomes are organized in the nucleus?
1) each chromosome occupy a particular region
2) some chromosome are attached to the nuclear envelope or the nuclear lamin
3) Some are in the nucleolus
What does the nucleolus contains?
It is where the chromosome that posses the genes that encode for rRNA are clustered.
Why are chromosome structures dynamic?
Because chromosomes condense and decondense during cell phase.
What are the two classes of proteins tat bind to DNA to form chromosomes?
1) Histones forms nucleosome
2) Other nonhistones chromosomal proteins.
What are the two components of nucleosom?
1) an octamer of histones
2) a stretch of 147 pairs long DNA sequence wound arund the octamer.
What are core histones?
Small proteins with high proportions of positivley charged amino acids that bind to the negative sugar-phosphate backbone.
How is the additional packing into chromatin fibers achieved?
Due to histone H1 that pull together adjacent nucleosomes.
What are the two ways of readjusting the structure of DNA?
1) Use chromatin remodelling complexes
2) reversible chemical modifications of histones.
Describe chromatin remodelling complexes:
Protein machines that hydrolyse ATP to get energy to change the position of DNA wrapped around the nucleus.
What are the two types of interphase chromatin?
1) Heterochromatin: highly condensed form and doesn’t contain genes or doesn’t allow their expression
2) Euchromatin: less condensed form.
