Bio Exam 3 / Final Exam Review

Learning objectives and quizzes

What is bioinformatics?

Computational techniques for solving
biological problems

What is biotechnology?

the use of biological agents for technological advancement.

What are the fields of biotechnology?

Medicine, agriculture, fermentation, oil spill treatments, production of biofuels

What are proteomics

The study of entire set of proteins in a given organism

What is genomics?

the study of entire genomes

Why was the discovery of DNA so important?

understand DNA replication, allows scientists to find genetic diseases

Why clone DNA?

target genes and find cures

What type of diseases has technology led us to study? (cloning)

Pulmonary Fibrosis

How do you interpret a BLAST output?

Give info on all sequences that have been found and stored in NCBI; most (top to least)

What does the percent sequence identity mean?

How identical the two strands are across the nucleic and amino acid sequence

How are protein and gene sequences represented in Computational Biology?

Amino acids represented using strings of alphabets; DNA = ATCG

What is the plasma membrane?

phospholipid bilayer/fluid mosaic model; defines borders and keeps cells functional by being selectively permeable; allows some materials to enter

What are the principal components of plasma membrane?

Lipids, carbohydrates, proteins

Why is the cell surface important?

It provides protection by controlling what enters and leaves the cell like recognizing foreign cells (like facial features); glycoproteins and glycolipids found

What is active transport?

require the cell’s energy, low to high concentration, works against diffusion

What is passive transport?

does not require cell energy, high to low concentration, diffusion

What is endocytosis?

cell membrane engulfs external substances and brings them into the cell

What are the different types of endocytosis?

Phagocytosis (cell "eating" = large) and pinocytosis (cell "drinking" = small )

What is exocytosis?

vesicles containing substances fuse with the plasma membrane and the contents are released to the exterior of the cell

How many cells are in the human body?

37.2 trillion

What is the difference between integral and peripheral proteins?

Integral proteins integrate into membrane structure vs peripheral proteins found on the exterior and interior surfaces of the membrane (attach)

What are examples of integral proteins?

Transport proteins, channel proteins, carrier protein, aquaporins

What are examples of peripheral proteins?

Glycoproteins

What is cell signaling and why is it important?

- part of any communication process that governs basic activities of cells and coordinates all cell actions.
- Errors in signaling interactions and cellular info processing are responsible for diseases (cancer, diabetes, autoimmunity)
- Diseases treated more effectively and theoretically, artificial tissues maybe created

What is the process of cell signaling as it occurs in receptor tyrosine kinases?

- Signaling molecules bind to receptor
- Receptors dimerize
- Tyrosine resides are phosphorylated
- Triggers a downstream cellular response

What is phosphorylation?

addition of a phosphate group

What are second messengers?

molecule that helps activate something (specific termination)

What is phospholipase C?

an enzyme that facilitates the breakdown of PIP2 and DAG, which are both second messengers

What are some responses to cell signals?

Gene expression (transcription of RNA), increase in cellular metabolism (muscle cells), cell growth (cell divison ), cell death (apoptosis), termination of signal cascade

What is Respiration?

molecular process that breaks down glucose, produces waste products, and energy

What is ATP and how is it used by the cell as an energy source?

makes energy and provides fuel for the body

What is glycolysis?

breakdown of glucose by enzymes, releasing energy and pyruvic acid

What are the two phases of glycolysis?

Step 1: (energy required) uses two ATP molecules in the phosphorylation of glucose, which is then split into three-carbon molecules
Step 2: (energy releasing) involved phosphorylation without ATP investment and produces two NADH and four ATP molecules per glucose

What is the outcome of glycolysis?

4 new ATP molecules and 2 molecules of NADH

What is
a rate-limiting enzyme?

an enzyme that regulates the rate of a metabolic pathway

What are some examples of a rate-limiting enzyme?

phosphofructokinase, pyruvate kinase

What is the electron transport chain?

series of electron transported embedded in inner mitochondrial membrane that shuttles electrons from NADH and FADH2 to molecular oxygen

What is lactic fermentation?

method used by animals and certain bacteria like yogurt

What is metabolism?

All the chemical reactions that take place inside cells including those that use energy and release energy

What is a metabolic pathway?

Series of interconnected biochemical reactions that convert a substrate molecule(s), step-by-step, through series of metabolic intermediates, eventually yielding a final product(s)

What happens during the glycolysis cycle?

breakdown of glucose in order to obtain ATP

What happens during the oxidative phosphorylation cycle?

disposal of electrons released by glycolysis and citric acid cycle

What happens during the krebs cycle / citric acid cycle?

acetyl-CoA oxidation in order to obtain GTP and valuable intermediates

What is an enzyme?

substance that lowers the activation energy of a reaction, but does not change the free energy of the reaction

What is a coenzyme?

small organic molecule which enhances activity of an enzyme; ex: vitamins

What is a cofactor?

non-protein channel chemical compound / metallic ion that is required for an enzymes activity

What is a substrate?

chemical reactants to which an enzyme binds

What is energy coupling?

transfer of energy from catabolism to anabolism / transfer of energy from exergonic process to endergonic process

What is activation energy?

energy required for a reaction to proceed, and it's lower if reaction catalyzed

What is kinetic energy?

energy associated w/ objects in motion; ex: airplane in flight

What is potential energy?

potential to do work

What is chemical energy?

providing living cells w/ energy from food; the release of energy is brought by breaking molecular bonds w/in fuel molecules (stored)

What are some examples of kinetic energy?

Moving water from a waterfall, an airplane in flight, a speeding bullet, a walking person, rapids molecule movement in the air, and electromagnetic radiation

What are some examples of potential energy?

suspended wrecking ball, water behind a dam

What are some examples of chemical energy?

The molecules in gasoline

What are the primary functions of the respiratory system?

deliver oxygen to cells of the body's tissue and remove carbon dioxide, a cell waste product

What are the structural components of the respiratory system?

nasal cavity, the trachea, and lungs

Why is hemoglobin so important?

carries oxygen to cells and carbon dioxide to lungs

What is the role of circulation within the immune system?

carries immune cells to destinations

What are examples of obstructive lung diseases?

COPD, Asthma, Bronchiectasis

What are examples of restrictive lung diseases?

Intestinal lung disease, scoliosis, neuromuscular cause, marked obesity

What is the difference between obstructive and restrictive lung diseases?

obstruction is reduction in airflow vs restrictive is reduction in lung volume

What is the process of blood flow to the heart and to the body?

Blood is pushed through by pumping the heart.
First the aorta --> blood travels ---> arteries --> arterioles
--> capillary beds

What are the differences between arteries, veins, and capillaries?

Arteries take blood away from the heart.
Veins are blood vessels that bring blood black to the heart.
Capillaries connect veins and arteries and smallest.

Which organisms use diffusion as a means of obtaining oxygen?

Human circulatory system

What are the types of circulatory systems?

systemic, pulmonary, and coronary circuits

What are examples of organisms that have circulatory systems?

Fish, amphibians, reptiles, mammals/birds

All of the DNA within a genome encodes protein.

False

What major development in 1988 became the starting point for curating bioinformatic resources?

NCBI

For the purposes of Bioinformatics, a single strand of DNA can be thought of as a string of bases comprised of A, T, C, and P.

False

Cells build their protein from __ different amino acids.

20

Books and articles are considered important types of databases.

False

An organism's genome contains genes

True

Which of the following contains instructions for making proteins?

Genes

Which plasma membrane component can be either found on its surface or embedded in the membrane structure?

Protein

Which of the following is not an example of an energy transformation?

Turning on a light switch

Which transport mechanism can bring whole cells into a cell?

phagocytosis

What happens to the membrane of a vesicle after exocytosis?

It fuses with and becomes part of the plasma membrane.

Which of the following statements about the control of enzyme activity by phosphorylation is correct?

Phosphorylation of an enzyme results in a conformational change.

In what important way does receptor-mediated endocytosis differ from phagocytosis?

It brings in only a specifically targeted substance.

Which of the following enzyme catalyzes the first step of glycolysis?

Hexokinase

Which of the following is not true about enzymes:

They increase delta G of reactions.

Which of the following statements about the regulation of a metabolic pathway is correct?

Most metabolic pathways are regulated.

Which of the following statements about the control of enzyme activity by phosphorylation is correct?

Phosphorylation of an enzyme results in a conformational change.

Which type of metabolic fuel is utilized for generating glucose under conditions of severe starvation?

Amino Acids

Which of the following plasma membrane receptors activate signaling pathways usually by forming molecular dimers that result in protein phosphorylation reactions upon binding of their specific ligand?

Receptor tyrosine kinases

Enzymes lower the reaction's activation energy but do not change the reaction's free energy.

True

In the capillaries and veins, the blood pressure continues to decrease but velocity increases.

True

What condition was discussed in class as arising during prolonged exposure to high altitude such as in aviation?

hypoxia

Boyle's law states that pressure and ratio are inversely related.

False

Which of the following correctly lists the 3 circuits of the mammalian circulatory system?

systemic, pulmonary and coronary

Cilia move mucus and particles out of the bronchi and bronchioles back up to the throat where it is swallowed and eliminated via the esophagus.

True

Animals and Fungi have specialized connective tissues.

False

Arteries and capillaries consist of three layers, while veins consist of a single layer.

False

As we discussed in lecture and based on your understanding of the relationship between animal body size and activity level, which animal has the fastest metabolic rate?

Mouse

What is ATP?

Source of energy for use by cells

Pulmonary fibrosis is an obstructive disease.

False

Asthma is a restrictive disease.

False

Which of the following is not a feature common to most animals?

asexual reproduction

Which of the following animal has the simplest circulatory system?

Fish