bio 211 final - cell cycle, cancer, CR, and photosynthesis

ploidy

number of complete chromosomes sets (n)

• eg: humans have two complete sets of chromosomes

aneuploidy

irregular number of chromosomes in a set (± 1 chromosome)

haploid

one set of chromosomes (n)

diploid

two sets of chromosomes (2n)

homologous chromosome

have similar size and shape, code for same genes with different alleles

autosome

codes for body genes (not related to sex, general)

sex chromosome

codes for sex of an individual

gamete

sex cells (egg or sperm)

• when fertilized, they form a zygote

karyotype

chart showing all chromosomes isolated from metaphase

• used in diagnosis of chromosomal abnormalities

tetrad/bivalent

pair of homologous chromosomes that are joined during meiosis

chiasmata

structures that tie homologous chromosomes together, allowing for crossing over

crossing over

exchange of DNA between homologous chromosomes during prophase 1

allele

a version of a gene

homozygous

individual has the same alleles on both homologous chromosomes

heterozygous

individual has different alleles on homologous chromosomes

sexual reproduction

• progeny are not identical to parents

• high phenotypic variability between offspring

• high survivability and adaptability

• favored in variable conditions

• less reproducing adults (only females can bear young)

asexual reproduction

• progeny are genetically identical

• no phenotypic variation between offspring

• low survivability and adaptability

• favored in constant conditions

• faster and more efficient

prophase one

• chromosomes condense

• centrosomes begin moving to opposite ends of the cell

• nuclear envelope beings dissolving

• crossing over occurs

metaphase one

• kinetochores attach to centromeres

• tetrads line up along cell’s equator

anaphase one

• homologous chromosomes are separated and move to opposite ends of the cell (pulled to spindle fibers)

telophase one

• nuclear envelopes begin forming around chromosomes

cytokinesis (of mitosis and meiosis)

• cleavage furrow separates two cells in animals (actin and myosin OR cytoskeletal proteins contract to form it)

• in plants, vesicles build a cell plate between two cells, eventually forming a cell wall

• organelles and cytoplasm are divided

meiosis 2

same as mitosis, produce four genetically unique cells

phases of cell cycle

g1, s, g2, M

g1

cells produce proteins required for DNA synthesis, cell prepares for cell division, grows larger

g0

cells are living, but are not actively growing/cycling

s

chromosomes are replicated

m

mitosis or meiosis (division of chromosomes and nuclear contents) followed by cytokinesis

g2

cell increases in volume, some organelles are duplicated, proteins required for M phase are synthesized (centrioles)

prophase

chromosomes condense, spindle fibers begin forming

prometaphase

nuclear envelope begins dissolving, microtubules attach to kinetochores

metaphase

chromosomes line up along cell’s equator

anaphase

sister chromatids are pulled to opposite ends of the cell

telophase

nuclear envelope forms around chromosomes, chromosomes decondense

centriole

barrel-shaped structures made up of microtubules

• always perpendicular to each other

centrosome or the microtubule organizing center

structure made up of a pair of centrioles in PCM

kinetochore

protein complex that attaches to centromere during metaphase

• microtubules attach to kinetochores to pull chromosomes during metaphase and anaphase

proteins that regulate metaphase to anaphase checkpoint

cohesin - protein that holds sister chromatids together

separase - enzyme, catalyzes cleavage of cohesin

securin - protein, keeps separase inactive until spindle fibers attach to kinetechores

APC - protein, marks securing for destruction

steps for metaphase to anaphase checkpoint

1. SAC proteins signal that chromosomes aren’t attached

2. chromosomes are attached to microtubules

3. APC is activated

4. securin is degraded

5. separase cleaves cohesin

6. sister chromatids move to opposite ends of the cell

mitosis products

two identical cells

MPF (M phase promoting factor)

protein dimer made up of Cdk (protein kinase) and cyclin (regulatory molecule)

• cyclins increase in concentration as a new phase of the cell cycle approaches, triggering Cdk to phosphorylate proteins that are involved in the next phase of the cell cycle

G1-S checkpoint

makes sure the cell meets required size, nutrients, and that DNA isn’t damaged

• controlled by E2F, a transcription factor that increases expression of S phase genes, which is inhibited by retinoblastoma (Rb)

G1-S phase checkpoint steps

1. growth factors arrive and cause increase in cyclin and E2F levels

2. cyclin bind to Cdk and Cdk is phosphorylated (with one activating and one inactivating phosphate)

3. Rb bind to E2F, inactivating it

4. Cyclin-Cdk phosphorylates Rb with the inactivating phosphate, causing conformational change

5. E2F is released and produces S phase proteins

Benign tumor

• non-cancerous

• surrounded by sheath

• doesn’t spread

• cannot metastasize

malignant tumor

• cancerous

• no sheath, allowing them to spread into nearby tissues

• can metastasize via blood and lymph vessels

carcinogenesis steps

initiation: cell acquires mutations (3-10 driver) that give cells a growth advantage

promotion: cell begins to divide uncontrollably

• best stage to catch cancer

• tumors may contain multiple cells with different types of growth advantages

progression: surrounding tissues are invaded

• metastasis begins (blood and lymph vessels are recruited and tumor can steal nutrients from nearby cells)

genes typically mutated in cancers

protooncogenes, tumor suppressor genes, repair genes

protooncogenes

encode proteins that stimulate cell growth

• accelerator, get a gain of function mutation

• called oncogenes when mutated

tumor suppressor genes

encode proteins that inhibit cell growth

• brake

• loss of function mutation in both genes results in loss of brakes in humans

repair genes

encode proteins that repair DNA damage

• aka the mechanic

• accumulation of mutations in DNA increases the chances of developing cancer

sister chromatid cohesion

shugoshin ( a phosphatase) holds sister chromatids together by preventing cohesion from being phosphorylated during meiosis one

• also recruits DP2A

• detaches during M2, allowing for cohesion to be phosphorylated and cleaved by separase at centromeres

meiosis one vs mitosis/meiosis two

• during metaphase one, tetrads line up along the cell’s equator instead of sister chromatids

• during anaphase one, tetrads are separated instead of sister chromatids

homologous recombination

occurs during prophase one

• aka crossing over

independent assortment

occurs during metaphase one

• homologous chromosomes line up along equator of cell randomly

random fertilization

increases diversity because each gamete is unique

gene

a section of DNA that codes for a protein or RNA product

locus

fixed position of a chromosome within a gene

dominant allele

produces a phenotype whenever present

• can be heterozygous of homozygous

• produce more protein OR have a more active protein OR express themselves irregularly (in irregular areas)

recessive allele

produces a phenotype in homozygous form only

• produce broken/mutated proteins that are inactive, OR are not efficient OR that don’t express themselves well

• eg: nonsense mutations

phenotype

an observable trait

genotype

a specific allele that cods for a phenotype

monohybrid

a cross between two homozygotes, producing heterozygotes

dihybrid cross

a cross for two traits between two individuals that are heterozygous for both traits

true breeding

homozgous individuals produced via self-fertilization

pedigree

chart showing inheritance patterns

Gregory Mendel

• took true bred plants and crossed them, forming F1 generations using paint brushes for cross pollination

• analyzed for seven trains with complete dominance to understand inheritance patterns

• used pea plants because they’re cheap, have a short generation time, produce a large number of progenies, can fertilize two ways

law of segregation

pairs of alleles in parents are separated during meiosis one

• cause by separation of tetrads during anaphase one

• means that there’s an equal chance of alleles in a parent being passed on, explaining why traits can disappear and reappear

law of independent assortment

states that genes on separate chromosomes separate independently during meiosis

• explained by random alignment of chromosomes along cell’s equator during meiosis

diseases caused by dominant alleles

• Polydactyly

• achondroplasia

• Huntington’s disease

• hypercholesterolemia

diseases caused by recessive alleles

• albinism

• color blindness

• sickle cell anemia

• DMD

• Tay-Sachs disease

codominance

occurs when allele products are expressed in equal numbers

eg: type AB blood, produce by IAIB

incomplete dominance

occurs when heterozygotes exhibit an intermediate phenotype

• typically seen in pigmentation

• eg: 4 o’clock produce white, bright pink, an light pink flowers

complete dominance

phenotype of heterozygotes matches phenotype of homozygous dominant individuals

polygenic inheritance

inheritance of traits that are affected by multiple genes (more genes means more traits possible)

• eg: skin color, height, eye color, hair color

epistasis

interactions between genes in a pathway

• occurs when the protein/enzyme coded for at one locus has an effect on the expression of other alleles at another locus

• typically because the product of one locus is a precursor to the expression of the secondary product

• eg; E locus controls fur of labradors

how the environment affects phenotypes

eg: skin color varies because of time spent in the sun

• this is in the addition to the variation that exists because of genetics

• — can also give individuals the opportunity to outcompete others

heritability

the proportion of the total phenotypic variation in a population that is due to genetic difference v. environmental differences

• measured by placing an identical pop in different environments OR by placing different individuals in the same environment

• in humans, this is done with adoptive parents and twin

factors the limit heritability

• individuals don’t have —

• — doesn’t mean that the environment cannot affect how a trait is expressed

penetrance

the fraction of a population with a genotype that shows the expected phenotype

• eg: people with the dominant allele for polydactyly may have a normal amount of finger and toes (incomplete —)

expressivity

the degree/intensity a genotype is expressed in a phenotype

• eg: Beagles spotting

• eg: skin tags-fully formed extra digits in polydactyly

sex-linked traits

typically found on the X-chromosome

• affect males more often

nondisjunction

occurs when sister chromatids OR homologs fail to separate during anaphase, resulting in an aneuploidy

eg: down syndrome - trisomy 21

eg: Klinefelter syndrome - XXY

• development of testes and breast tissue

Turner’s syndrome - XO

catabolic reaction

complex to simple compounds

• releases energy

• eg: oxidize, hydrolyze, digest

anabolic reaction

simple to complex compounds

• require energy input

activated carriers

capture energy released from catabolic reactions and transfer it to anabolic reactions

eg: ATP, NADH, FADH2, NADPH

enzymes

proteins that catalyze biological reactions by lowering the required amount of activation energy

• bring substrates close together so they can interact in the correct orientation

• supply energy to move electrons and rearrange chemical bonds

• stabilize transition state

factors affecting enzyme reaction rates

• temperature, pH, salt concentration

• cofactors, coenzymes, prosthetic groups

• substrate concentration (more substrate means more enzyme activity)

• substrate affinity (aka how tightly the site constricts around the substrate)

substrate-level phosphorylation

ATP is formed by breaking a high energy phosphate bond

• the energy released is sued to phosphorylate ADP to ATP

oxidative phosphorylation

energy released from an electrochemical gradient (moving through ATP synthase) is used to phosphorylated ADP to ATP

cellular respiration stages

glycolysis, pyruvate oxidation, TCA cycle, ETC

glycolysis

breaks glucose into two pyruvate

• occurs in cytoplasm

• input is one glucoes, 2 ATP, 2 NAD+

• output is two pyruvate, 2 NADH, 4 ATP (2 ATP net)

pyruvate oxidation

pyruvate is converted into acetyl CoA for the TCA cycle

• occurs in the mitochondrial matrix

• input is two pyruvate 2, coenzyme A, and 2 NAD+

• output is 2 carbon dioxide, 2 acetyl CoA, 2 NADH

TCA cycle

oxidizes acetyl CoA and generates ATP and electron carriers

• occurs in mitochondrial matric

• input is two acetyl CoA, 2 oxaloacetate

• output is 4 carbon dioxide, 6 NADH, 2 FADH2, 2 GTP/ATP

• must turn twice for these outputs

ETC

forms electrochemical gradient and makes ATP

• occurs in inner mitochondria membrane

• input is 10 NADH, 2 FADH2, oxygen

• output is 24-25 ATP, water

energy investment of glycolysis

ATP is used to break glucose into G3P and DHAP

steps:

1. phosphorylation

2. isomerization

3. phosphorylation

4. cleavage

5. isomerization

energy payoff phase of glycolysis

2 NADH and 2 pyruvate are formed, plus two net ATP

steps:

6. redo6x

7. phosphorylation

8. isomerization

9. dehydration

10. phosphorylation

glycolysis regulation

PFK (an enzyme) catalyzes a committed step (step 3)

• PFK has an active and allosteric site

• when ATP is at a high concentration in the cell, it binds to the allosteric site, inhibiting — and glucose is converted into glycogen for storage

electron donors and acceptors for ETC

NADH and FADH2

O2 for aerobic

carbon dioxide, So4, NO3 for anaerobic

path of electrons through ETC

1. NADH is oxidized at complex one and electrons are handed of to ubiquinone. 4 protons are pumped into the intermembrane space

2. FADH2 is oxidized at complex two and electrons are passed to ubiquinone

3. electrons are passed from Q to complex 3

4. electrons are passed to Cyt C and four protons are pumped into the intermembrane space

5. Cyt C passes electrons to complex four, which passes electrons to oxygen and pumps 2 protons

reactions used to form ATP

redox reactions as electrons move down the ETC

• produce energy used to pump protons from matrix to intermembrane space

• power addition of P to ADP to form ATP