Biology 005A UCR Final

Electronegativity

The atoms strength on tug. Depends on distance between nucleus and valence shells (closer-stronger), and the configuration of valence shells (electron accepts=stronger). C and H have almost equal electronegativity.

Periodic Table (in terms of electronegativity)

Elements increase in electronegativity as they move to the right of the table and up the table.

Hydrogen Bonds

The attraction between 2+ hydrogen atoms (in a polar molecule) to nearby negative charge. Attraction between partial positive and partial negative charges.

Acids

Substance that increases hydrogen ion (H+) in concentration of a solution. Strong acids: HCL, H4So4, and HNO3—>H+ and Cl-, H+ and HSo4, H+ and NO3.

Bases

A substance that reduces the concentration of hydrogen ions in a solution. Or molecule that accepts a proton. Ex: NaOH—> Na+ and OH-.

pH scale

pH=negative log of the [H+]. The lower the pH, higher # of of hydrogen ions, higher pH, lower # of hydrogen ions.

Questions to ask to determine how a functional group will impact the molecular function

1. Is it Polar

2. Is it Non-Polar

3. Is it an acid or negatively charged?

4. Is it a base or positively charged?

Hydroxyl Group

1. Polar

2. Not nonpolar

3. Not negatively charged

4. Not positively charged, or base

Carbonyl Group

1. Polar

2. Not nonpolar

3. Not negatively charged or acid

4. not positively charged or a base

Carboxyl Group

1. Polar

2. Not nonpolar

3. Yes negatively charged or acid

4. Not positively charged or base

Amino Group

1. Polar

2. Not nonpolar

3. Not negatively charged or acid

4. Yes positively charged or base (base)

Methyl Group

1. Not polar

2. Nonpolar

3. Not acid or negatively charged

4. Not base or positively charged

Phosphate Group

1. Polar

2. Not nonpolar

3. Acid or negatively charged

4. Not base or positively charged.

Proteins

Important for functions of living things. Ex: Hemoglobin —> oyxgen around blood + transports it. Ex: Insulin—> regulates metabolism

Dehydration Synthesis

Combine amino acids and create a polypeptide by taking an h20 out.

Primary Structure (Proteins)

Primary protein structure-sequence of amino acids. Outcome: polypeptides. Bonds: Covalent.

Secondary Structure (Proteins)

Outcome: Alpha helix (local structures), beta pleated sheet. Bonds: hydrogen bonds between atoms in the backbones of polypeptides.

Tertiary Structure (Proteins)

Van der Waals hydrophobic interactions. Includes nonpolar side chains. Forces: Hydrophobic interactions, hydrogen bonds, disulfide bridges, ionic bonds. Outcome: 3d shape of protein.

Quaternary Structure (Proteins)

Outcome: Folded proteins w/multiple polypeptides. Forces: Hydrogen bonds, hydrophobic interaction, disulfide bridges, ionic bonds.

Denaturation

Process in which protein loses its 3d structure. Causes proteins to denature: Heat above 50 degrees C disturbs H-bonds. Alcohols form H bonds and disrupt the intramolecular bonds. Salts of heavy metals form strong bonds w/acid r-groups. Alkaloid Reagents combine with charged r-groups, disrupting ionic bonds.

Carbon numbering

The first carbon is the one connected to 2 oxygens, then the next numbers follow the ring clockwise.

Monosaccharides—> Disaccharides

Glucose undergoes dehydration synthesis to form a glycosidic linkage.

Polysaccharides

Used to store energy for later use, and for cellular structure. Function determined by: individual monosaccarides, how they are linked, # of carbons and what number carbons are being linked.

REDOX reactions

Reduction: gaining electrons. Oxidation: losing electrons. FADH2—> Reduced. FAD—>Oxidized.

Mitochondria

Cellular respiration occurs here. Includes membrane (outer, innermembrane), cristae (integral membrane proteins-ETC), Ribosomes and DNA.

Endosymbiosis Hypothesis

The theory is that mitochondria and chloroplasts originated from an ancestor of Alpha Proteobacteria. Evidence includes the double membrane, ribosomes, DNA, and binary fission.

Glycolysis

INPUTS: Glucose, 2 NAD+, 2 ATP

OUTPUTS: 2 ATP (net gain), 2 NADH, and 2 pyruvate

Citric Acid Cycle

INPUTS: Acetyl-CoA

OUTPUTS: carbon dioxide (CO2), NADH, FADH2, and ATP (or GTP)

Chloroplast Membranes

3 membranes: Outer membrane, inner membrane, thylakoid (ETC, ATP Synthase)

Stroma

Fluid that fills the internal space of the chloroplast

Cyanobacteria

Free-lining prokaryotic bacteria, pigments (Chlorophyll A, Careteroids), preform photosynthesis independently.

Chloroplasts

Found within the cells of plants and algae, include chlorophyll A, Carotenoid, and Chlorophyll B. Preform photosynthesis on plant cells.

Electron Transport Chain

a series of protein complexes embedded in the inner mitochondrial membrane that facilitates the transfer of electrons from electron carriers (like NADH and FADH2) to oxygen, ultimately producing ATP through oxidative phosphorylation. Its located in the inner mitochondrial membrane.

Fermentation

Process used to remake NAD+ for glycolysis

Lactic Acid Fermentation

Occurs when there is not enough O2 present. Glucose turns into 2 pyruvate through glycolysis, then 2 lactate. Reverts back when oxygen is regained.

Photosynthesis

Light dependent reactions that create energy in light harvest. Leads to the calvin cycle.

Electromagnetic Spectrum

Visible light is 400 nm to 700 nm

Calvin Cycle

Light reactions. INPUTS: Light, H2O, NADP+, ADP

OUTPUTS: O2, NADPH, ATP.

Components of Nucleotides

Have 3 main components: phosphate group, nitrogenous base, and sugar connected at first ribose or dioxyribose).

Ribose

Dioxyribose

Pyrimidines

Include Cytosine, and Thymine. Both have single rings.

Purines

Adenine (A) and Guanine (G). Have two rings.

Nucleotide bonding rules

Adenine pairs to Thymine, and Cytosine pairs to Guanine. Are bonded through hydrogen bonds.

Gene

Sequence of Nucleotides that encodes an RNA.

Genome

All of the DNA of an individual.

Histones

Consist of 8 polypeptides, they compact DNA by having the dna wrap around 1.6x. Compacts DNA by 40,000x.

Transcription

Process by which an RNA leaves the nucleus and a copy is made of DNA.

In what direction is DNA “read” in?

Always the 3’-5’ direction

In what direction is RNA “read” in?

Always the 5’-3’ direction. RNA is antiparallel to DNA.

Regulatory Gene

Present in Prokaryotic genes, encodes for proteins that control expression of structural genes. Located in the first part of the DNA.

Operator

Present in Prokaryotic genes, and is a segment of DNA that a repressor (protein that regulates) can bind to. Located after the promoter.

Promoter

In Eukaryotic gene structure, and is a region of DNA where the RNA polymerase binds.

Enhancer

In Eukaryotic gene structure, and is a region of DNA that binds to transcription factors (protein). Increases the likelihood of RNA polymerase coming in (binding).

Silencer

In Eukaryotic gene structure, and is a region that can bind to transcription factors, decreasing the likelihood of RNA polymerase binding to the promoter.

5’ UTR

In Eukaryotic gene structure, located in the first part of what is made. It is the untranslated region, so no amino sequence is coded from it, it helps the RNA attach to the ribosomes and plays a role in the mRNA leaving the nucleus.

Exon

In Eukaryotic gene structure, and is the coding sequence, resulting the amino acid sequence of the polypeptide.

Intron

Removed before RNA leaves the nucleus.

3’ UTR

Untranslated region, stability of mRNA and addition of poly A tail. mRNA leaves the nucleus.

Chlorophyll A

The key light capturing pigment that participates directly in light reactions.

Carotenoids

Hydrocarbons that are various shades of yellow + orange because they absorb violet + blue-green light

What happens when chlorophyll comes in contact with light?

It becomes “excited” by the light. When a molecule absorbs photons of light. one of the molecules electrons is elevated to an orbital w/ more potential energy.

ETC in Photosynthesis

Photosystems

Photosystem I→ Chlorophyll A=P68- (actually the second photosystem to be discovered)

Photosystem II—> Chlorophyll B= P700 (the first photosystem discovered).

mRNA

Messenger-takes message from DNA and brings it to the ribosome. It contains a sequence that will tell ribosomes what amino acids should be in the polypeptide.

tRNA

Transfer- bring amino acids to the ribosome.

rRNA

Ribosomal-component of ribosomes.

Secondary Structure of RNA

Primary: Covalent bonds between nucleotides.

Secondary: Local structures/interactions (molecules are close).

Tertiary: Fully folded RNA- H bonded and Van Der Waals interactions.

RNA polymerase

An enzyme that is responsible for catalyzing bonds between strands of nucleotides of RNA, and breaks hydrogen bonds temporarily between strands of DNA (come back together due to partial charges).

What are different mechanisms by which signaling molecules can lead to changes in cells?

Making proteins, activating enzymes, secretion of products, stimulating cell division

What is the role of cyclin and cyclin dependent kinases in cell division?

Cyclins activate cyclin dependent kinases which are enzymes that cause the cell to move foward in the cell cycle or repress movement through the cell cycle.

when would p53 be made? what is the mechanism by which P54 regulated the cell cycle?

P53 would be made in situations of cellular stress. P53 is a transcription factor that increases transcription of P21. P21 activates a cyclin-CDK complex which removes phosphate groups from RB allowing it to attach to the transcription factor E2F serving as a co-repressor of cell-cycle genes.

When would Myc be made? How does Myc affect the cell cycle?

MYC would be made when an organism experiences wounding or needs to grow. Myc causes transcription of genes required for DNA synthesis. transcription of genes required for DNA synthesis

What are major functions of the different types of cytoskeleton?

Microtubule: Separates sister chromatids during cell division
Microfilament (actin): cell structure, works with myosin for cell movement
Myosin: Contraction and movement within cells
Intermediate filament: assembly of nuclear envelope

how does the cytoskeletal structure of muscle and neuron cells facilitate their function?

Muscle cells: Contractile assemblies made of actin and myosin pull on intermediate
filament to lead to contraction of cells and tissues.
Neuron: Axons are stabilized by microtubule and intermediate filament. Export and
import of neurotransmitters is facilitated by actin.

What is the difference between cohesin and the synaptonemal complex?

Cohesin: attaches sister chromatids

Synaptonemal complex: Holds homologous chromosomes together during crossing over.

If you had a cell that did not have a functional copy of the SPO 11 gene, what would the outcome be?

No recombination of chromosomes

What is the difference between homologous chromosomes and sister chromatids? Where in Meiosis do homologous chromosomes separate? Where do sister chromatids separate?

Homologous chromosomes: different versions of chromosomes-separate during meiosis I
Sister chromatids: duplicated chromosomes-separate during meiosis II.

What is the function of the following proteins in DNA replication?

Helicase, Topoisomerase, Primase, and DNA polymerase

Helicase: breaks hydrogen bonds between DNA strands
Topoisomerase: Unwinds supercoiling of DNA
Primase: Make primer (usually RNA) that starts a new DNA strand replica7ng
DNA Polymerase: Add nucleo7des to the 3’ end of a growing DNA strand

SS Binding protein: Stabilizes single stranded DNA once helicase has broken H bonds between the strands.

Why is there a leading and lagging strand in DNA replication?

Because DNA polymerase can only add nucleotides the 3’ end of a DNA molecule one grows as helicase opens the strands (leading strand) but one strand copies away from helicase (lagging strand). Therefore, the lagging strand is built in pieces (Okazaki fragments).

How are duplicated chromatids attached to each other after DNA synthesis? When do they seperate?

Duplicated chromatids are attached by a protein called cohesin. They seperate after metaphase of mitosis.

What are two mechanisms by which double stranded DNA breaks can be repaired?

Non-homologous end joining and homology directed pair.

What are three potential functions of steroids?

Hormones, bile acids, membrane fluidity regulation

What are two ways that membrane fluidity is regulated? How do each of those regulatory mechanisms work?

Membrane phospholipid composition: more saturated fatty acids lead to more rigid
membrane and more unsaturated fatty acids lead to more fluid membrane. Cholesterol maintains intermediate membrane fluidity- the rings increase rigidity while the tail increases membrane fluidity.

What is the role of the following components of the nuclear pore?

Cytoplasmic filament: Interact with the cytoskeleton

Nucleoporins: Controls movement of substances in and out of the nucleus

Nuclear basket: mRNA export from the nucleus

For a protein that is made in the rough E.R, explain the process of translation.

In the cytoplasm: Translation complex assembles, translation begins with the first 15-30 amino acids. Signal polypeptide attaches to signal particle. Translation complex moves to the ER and attaches to the docking protein integral to the ER.

How are molecules targeted from the ER to the golgi

Molecules are packed into vesicles. On the surface of those vesciles is COPII proteins that target the vesciles from the ER to the golgi.

Explain the function of the following proteins in targeting vesciles from the golgi to their destination. Clathrin, V-Snare, T-Snare.

Clathrin: Protein that facillitates formation of vesciles off of the golgi.

V-Snare: Protein that is embedded in vesicles that targets the vesicles to its destination where its companion T-Snare is embedded in a membrane.

T-Snare” protein embedded in the membrane of the vesicle target location.